Stop the war!Остановите войну!
for scientists:
default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDSearch dblp for Publications
export results for "biological data"
more than 1000 matches, exporting first 1000 hits only!
download as .bib file
@phdthesis{DBLP:phd/basesearch/Mandwal24,
author = {Ayush Kumar Mandwal},
title = {Modeling and data analysis of emergent properties in different biological
systems},
school = {University of Calgary, Alberta, Canada},
year = {2024}
}
@article{DBLP:journals/air/NssibiMCMK24,
author = {Maha Nssibi and
Ghaith Manita and
Amit Chhabra and
Seyedali Mirjalili and
Ouajdi Korbaa},
title = {Gene selection for high dimensional biological datasets using hybrid
island binary artificial bee colony with chaos game optimization},
journal = {Artif. Intell. Rev.},
volume = {57},
number = {3},
pages = {51},
year = {2024}
}
@article{DBLP:journals/cbm/AragonesPSCBSHC24,
author = {David G. Aragones and
Miguel Palomino{-}Segura and
Jon Sicilia and
Georgiana Crainiciuc and
Iv{\'{a}}n Ballesteros and
F{\'{a}}tima S{\'{a}}nchez{-}Cabo and
Andr{\'{e}}s Hidalgo and
Gabriel Fern{\'{a}}ndez Calvo},
title = {Variable selection for nonlinear dimensionality reduction of biological
datasets through bootstrapping of correlation networks},
journal = {Comput. Biol. Medicine},
volume = {168},
pages = {107827},
year = {2024}
}
@article{DBLP:journals/cce/Oh24,
author = {Tae Hoon Oh},
title = {Quantitative comparison of reinforcement learning and data-driven
model predictive control for chemical and biological processes},
journal = {Comput. Chem. Eng.},
volume = {181},
pages = {108558},
year = {2024}
}
@article{DBLP:journals/jcisd/SealSHGSBC24,
author = {Srijit Seal and
Ola Spjuth and
Layla Hosseini{-}Gerami and
Miguel Garc{\'{\i}}a{-}Orteg{\'{o}}n and
Shantanu Singh and
Andreas Bender and
Anne E. Carpenter},
title = {Insights into Drug Cardiotoxicity from Biological and Chemical Data:
The First Public Classifiers for {FDA} Drug-Induced Cardiotoxicity
Rank},
journal = {J. Chem. Inf. Model.},
volume = {64},
number = {4},
pages = {1172--1186},
year = {2024}
}
@article{DBLP:journals/kais/ChaudhariPJPS24,
author = {Jyoti Kant Chaudhari and
Shubham Pant and
Richa Jha and
Rajesh Kumar Pathak and
Dev Bukhsh Singh},
title = {Biological big-data sources, problems of storage, computational issues,
and applications: a comprehensive review},
journal = {Knowl. Inf. Syst.},
volume = {66},
number = {6},
pages = {3159--3209},
year = {2024}
}
@article{DBLP:journals/netmahib/OikonomouKGVGT24,
author = {Emmanouil D. Oikonomou and
Petros S. Karvelis and
Nikolaos Giannakeas and
Aristidis Vrahatis and
Evripidis Glavas and
Alexandros T. Tzallas},
title = {How natural language processing derived techniques are used on biological
data: a systematic review},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {13},
number = {1},
pages = {23},
year = {2024}
}
@inproceedings{DBLP:conf/wacv/WenVFEAW24,
author = {Junhan Wen and
Camiel R. Verschoor and
Chengming Feng and
Irina{-}Mona Epure and
Thomas Abeel and
Mathijs de Weerdt},
title = {The Growing Strawberries Dataset: Tracking Multiple Objects with Biological
Development over an Extended Period},
booktitle = {{WACV}},
pages = {7089--7099},
publisher = {{IEEE}},
year = {2024}
}
@article{DBLP:journals/corr/abs-2401-16664,
author = {Aleksandar Poleksic},
title = {Fast Dual-Regularized Autoencoder for Sparse Biological Data},
journal = {CoRR},
volume = {abs/2401.16664},
year = {2024}
}
@article{DBLP:journals/corr/abs-2402-00293,
author = {Takuma Yagi and
Misaki Ohashi and
Yifei Huang and
Ryosuke Furuta and
Shungo Adachi and
Toutai Mitsuyama and
Yoichi Sato},
title = {FineBio: {A} Fine-Grained Video Dataset of Biological Experiments
with Hierarchical Annotation},
journal = {CoRR},
volume = {abs/2402.00293},
year = {2024}
}
@article{DBLP:journals/corr/abs-2402-03319,
author = {Ivan S. Maksymov},
title = {Physical Reservoir Computing Enabled by Solitary Waves and Biologically-Inspired
Nonlinear Transformation of Input Data},
journal = {CoRR},
volume = {abs/2402.03319},
year = {2024}
}
@article{DBLP:journals/corr/abs-2402-04912,
author = {Dingfan Chen and
Marie Oestreich and
Tejumade Afonja and
Raouf Kerkouche and
Matthias Becker and
Mario Fritz},
title = {Towards Biologically Plausible and Private Gene Expression Data Generation},
journal = {CoRR},
volume = {abs/2402.04912},
year = {2024}
}
@article{DBLP:journals/corr/abs-2402-17572,
author = {Michiel Stock and
Dimitri Boeckaerts and
Pieter Dewulf and
Steff Taelman and
Maxime Van Haeverbeke and
Wim Van Criekinge and
Bernard De Baets},
title = {Hyperdimensional computing: a fast, robust and interpretable paradigm
for biological data},
journal = {CoRR},
volume = {abs/2402.17572},
year = {2024}
}
@article{DBLP:journals/corr/abs-2404-14169,
author = {Mattia Corti},
title = {Exploring tau protein and amyloid-beta propagation: a sensitivity
analysis of mathematical models based on biological data},
journal = {CoRR},
volume = {abs/2404.14169},
year = {2024}
}
@phdthesis{DBLP:phd/basesearch/Mubeen23,
author = {Sarah Mubeen},
title = {Contextualizing and interpreting biological data with pathway knowledge
and network algorithms},
school = {University of Bonn, Germany},
year = {2023}
}
@phdthesis{DBLP:phd/basesearch/Ranek23,
author = {Jolene Ranek},
title = {Resolving Biological Trajectories in Single-cell Data using Feature
Selection and Multi-modal Integration},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2023}
}
@phdthesis{DBLP:phd/hal/Simon23,
author = {Franck Simon},
title = {D{\'{e}}couverte causale sur des jeux de donn{\'{e}}es classiques
et temporels. Application {\`{a}} des mod{\`{e}}les biologiques. (Causal
discovery on classical and temporal datasets. Application to biological
models)},
school = {Sorbonne University, Paris, France},
year = {2023}
}
@phdthesis{DBLP:phd/tr/Guvenilir23,
author = {Heval Atas G{\"{u}}venilir},
title = {Integration and analysis of biological data for computational drug
discovery ({\.{I}}{\c{s}}lemsel ila{\c{c}} ke{\c{s}}fi i{\c{c}}in
biyolojik verinin entegrasyonu ve analizi)},
school = {Middle East Technical University, Turkey},
year = {2023}
}
@phdthesis{DBLP:phd/us/Huang23,
author = {Xingfan Huang},
title = {Computational methods for analyzing high-dimensional datasets derived
from molecular profiling of biological systems},
school = {University of Washington, {USA}},
year = {2023}
}
@article{DBLP:journals/access/ZenboutBMA23,
author = {Imene Zenbout and
Abdelkrim Bouramoul and
Souham Meshoul and
Mounira Amrane},
title = {Efficient Bioinspired Feature Selection and Machine Learning Based
Framework Using Omics Data and Biological Knowledge Data Bases in
Cancer Clinical Endpoint Prediction},
journal = {{IEEE} Access},
volume = {11},
pages = {2674--2699},
year = {2023}
}
@article{DBLP:journals/bib/BaoCZSSL23,
author = {Jingxuan Bao and
Changgee Chang and
Qiyiwen Zhang and
Andrew J. Saykin and
Li Shen and
Qi Long},
title = {Integrative analysis of multi-omics and imaging data with incorporation
of biological information via structural Bayesian factor analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023}
}
@article{DBLP:journals/bib/KobetsUGDMGSRK23,
author = {Victoria A Kobets and
Sergey V. Ulianov and
Aleksandra A. Galitsyna and
Semen A. Doronin and
Elena A. Mikhaleva and
Mikhail S. Gelfand and
Yuri Y. Shevelyov and
Sergey V. Razin and
Ekaterina E. Khrameeva},
title = {HiConfidence: a novel approach uncovering the biological signal in
Hi-C data affected by technical biases},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023}
}
@article{DBLP:journals/bib/ScottBoyerDBOPPD23,
author = {Marie{-}Pier Scott{-}Boyer and
Pascal Dufour and
Fran{\c{c}}ois Belleau and
R{\'{e}}gis Ongaro{-}Carcy and
Cl{\'{e}}ment Plessis and
Olivier P{\'{e}}rin and
Arnaud Droit},
title = {Use of Elasticsearch-based business intelligence tools for integration
and visualization of biological data},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023}
}
@article{DBLP:journals/bigdatasociety/Lockhart23,
author = {Jeffrey W. Lockhart},
title = {Because the machine can discriminate: How machine learning serves
and transforms biological explanations of human difference},
journal = {Big Data Soc.},
volume = {10},
number = {1},
pages = {205395172311550},
year = {2023}
}
@article{DBLP:journals/biodb/RaboneHJSG23,
author = {Muriel Rabone and
Tammy Horton and
Daniel O. B. Jones and
Erik Simon{-}Lled{\'{o}} and
Adrian G. Glover},
title = {A review of the International Seabed Authority database DeepData from
a biological perspective: challenges and opportunities in the {UN}
Ocean Decade},
journal = {Database J. Biol. Databases Curation},
volume = {2023},
year = {2023}
}
@article{DBLP:journals/biodb/ZengHCLWYM23,
author = {Zhengpeng Zeng and
Jiamin Hu and
Miyuan Cao and
Bingbing Li and
Xiting Wang and
Feng Yu and
Longfei Mao},
title = {MantaID: a machine learning-based tool to automate the identification
of biological database IDs},
journal = {Database J. Biol. Databases Curation},
volume = {2023},
year = {2023}
}
@article{DBLP:journals/bioinformatics/WangLHYFV23,
author = {Ruogu Wang and
Alex A. Lemus and
Colin M. Henneberry and
Yiming Ying and
Yunlong Feng and
Alex M. Valm},
title = {Unmixing biological fluorescence image data with sparse and low-rank
Poisson regression},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023}
}
@article{DBLP:journals/bmcbi/DaneshvarMO23,
author = {Negar Hossein{-}Nezhad Daneshvar and
Yosef Masoudi{-}Sobhanzadeh and
Yadollah Omidi},
title = {A voting-based machine learning approach for classifying biological
and clinical datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {140},
year = {2023}
}
@article{DBLP:journals/bmcbi/WysockaWZLF23,
author = {Magdalena Wysocka and
Oskar Wysocki and
Marie Zufferey and
D{\'{o}}nal Landers and
Andr{\'{e}} Freitas},
title = {A systematic review of biologically-informed deep learning models
for cancer: fundamental trends for encoding and interpreting oncology
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {198},
year = {2023}
}
@article{DBLP:journals/cbm/RasoolHJCQ23,
author = {Abdur Rasool and
Jingwei Hong and
Qingshan Jiang and
Hui Chen and
Qiang Qu},
title = {{BO-DNA:} Biologically optimized encoding model for a highly-reliable
{DNA} data storage},
journal = {Comput. Biol. Medicine},
volume = {165},
pages = {107404},
year = {2023}
}
@article{DBLP:journals/crossroads/Ge23,
author = {Xinzhou Ge},
title = {Enhancing Rigor in Computational Methods for Biological Data Analysis},
journal = {{XRDS}},
volume = {30},
number = {2},
pages = {34--37},
year = {2023}
}
@article{DBLP:journals/cssc/ZhongCH23,
author = {Yi Zhong and
Prabhakar Chalise and
Jianghua He},
title = {Nested cross-validation with ensemble feature selection and classification
model for high-dimensional biological data},
journal = {Commun. Stat. Simul. Comput.},
volume = {52},
number = {1},
pages = {110--125},
year = {2023}
}
@article{DBLP:journals/fbinf/LiMPMLD23,
author = {Wanxin Li and
Jules Mirone and
Ashok Prasad and
Nina Miolane and
Carine Legrand and
Khanh Dao Duc},
title = {Orthogonal outlier detection and dimension estimation for improved
{MDS} embedding of biological datasets},
journal = {Frontiers Bioinform.},
volume = {3},
year = {2023}
}
@article{DBLP:journals/gpb/MaZLSABXZBZ23,
author = {Lina Ma and
Dong Zou and
Lin Liu and
Huma Shireen and
Amir Ali Abbasi and
Alex Bateman and
Jing{-}Fa Xiao and
Wenming Zhao and
Yiming Bao and
Zhang Zhang},
title = {Database Commons: {A} Catalog of Worldwide Biological Databases},
journal = {Genom. Proteom. Bioinform.},
volume = {21},
number = {5},
pages = {1054--1058},
year = {2023}
}
@article{DBLP:journals/jamia/SouzaWCPCMF23,
author = {Raissa Souza and
Matthias Wilms and
Milton Camacho and
G. Bruce Pike and
Richard Camicioli and
Oury Monchi and
Nils D. Forkert},
title = {Image-encoded biological and non-biological variables may be used
as shortcuts in deep learning models trained on multisite neuroimaging
data},
journal = {J. Am. Medical Informatics Assoc.},
volume = {30},
number = {12},
pages = {1925--1933},
year = {2023}
}
@article{DBLP:journals/jbcb/HuCWYC23,
author = {Fuyan Hu and
Bifeng Chen and
Qing Wang and
Zhiyuan Yang and
Man Chu},
title = {Multi-omics data analysis reveals the biological implications of alternative
splicing events in lung adenocarcinoma},
journal = {J. Bioinform. Comput. Biol.},
volume = {21},
number = {4},
pages = {2350020:1--2350020:21},
year = {2023}
}
@article{DBLP:journals/jcheminf/GalgonekV23,
author = {Jakub Galgonek and
Jir{\'{\i}} Vondr{\'{a}}sek},
title = {A comparison of approaches to accessing existing biological and chemical
relational databases via {SPARQL}},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {61},
year = {2023}
}
@article{DBLP:journals/jise/LinC23,
author = {Hung{-}Yi Lin and
Rong{-}Chang Chen},
title = {Heuristic Feature Selection with Classification Efficiency Using Soft
Cluster Analysis for Biological Datasets},
journal = {J. Inf. Sci. Eng.},
volume = {39},
number = {4},
pages = {951--973},
year = {2023}
}
@article{DBLP:journals/ml/KaragiannakiGLPT23,
author = {Ioulia Karagiannaki and
Krystallia Gourlia and
Vincenzo Lagani and
Yannis Pantazis and
Ioannis Tsamardinos},
title = {Learning biologically-interpretable latent representations for gene
expression data},
journal = {Mach. Learn.},
volume = {112},
number = {11},
pages = {4257--4287},
year = {2023}
}
@article{DBLP:journals/nar/ChareshneuMIRHCVBS23,
author = {Aliaksei Chareshneu and
Adam Midlik and
Crina{-}Maria Ionescu and
Alexander S. Rose and
Vladim{\'{\i}}r Horsk{\'{y}} and
Alessio Cantara and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Karel Berka and
David Sehnal},
title = {Mol* Volumes and Segmentations: visualization and interpretation of
cell imaging data alongside macromolecular structure data and biological
annotations},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{W1}},
pages = {326--330},
year = {2023}
}
@article{DBLP:journals/nar/HochBBCEFGIKKMMWWYY23,
author = {Jeffrey C. Hoch and
Kumaran Baskaran and
Harrison Burr and
John Chin and
Hamid R. Eghbalnia and
Toshimichi Fujiwara and
Michael R. Gryk and
Takeshi Iwata and
Chojiro Kojima and
Genji Kurisu and
Dimitri Maziuk and
Yohei Miyanoiri and
Jonathan R. Wedell and
Colin Wilburn and
Hongyang Yao and
Masashi Yokochi},
title = {Biological Magnetic Resonance Data Bank},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {368--376},
year = {2023}
}
@article{DBLP:journals/nar/YangWHWWLWXZYNYYY23,
author = {Zhiquan Yang and
Jing Wang and
Yiming Huang and
Shengbo Wang and
Lulu Wei and
Dongxu Liu and
Yonglin Weng and
Jinhai Xiang and
Qiang Zhu and
Zhaoen Yang and
Xinhui Nie and
Yu Yu and
Zuoren Yang and
Qing{-}Yong Yang},
title = {CottonMD: a multi-omics database for cotton biological study},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {1446--1456},
year = {2023}
}
@article{DBLP:journals/nca/MafarjaTTCTHE23,
author = {Majdi M. Mafarja and
Thaer Thaher and
Jingwei Too and
Hamouda Chantar and
Hamza Turabieh and
Essam H. Houssein and
Marwa M. Emam},
title = {An Efficient High-dimensional Feature Selection Approach Driven By
Enhanced Multi-strategy Grey Wolf Optimizer for Biological Data Classification},
journal = {Neural Comput. Appl.},
volume = {35},
number = {2},
pages = {1749--1775},
year = {2023}
}
@article{DBLP:journals/pc/ZhangHCLG23,
author = {Hao Zhang and
Zhiyi Huang and
Yawen Chen and
Jianguo Liang and
Xiran Gao},
title = {{ESA:} An efficient sequence alignment algorithm for biological database
search on Sunway TaihuLight},
journal = {Parallel Comput.},
volume = {117},
pages = {103043},
year = {2023}
}
@article{DBLP:journals/ploscb/AggarwalP23,
author = {Manu Aggarwal and
Vipul Periwal},
title = {Tight basis cycle representatives for persistent homology of large
biological data sets},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {5},
year = {2023}
}
@article{DBLP:journals/ploscb/AhlquistSR23,
author = {K. D. Ahlquist and
Lauren A. Sugden and
Sohini Ramachandran},
title = {Enabling interpretable machine learning for biological data with reliability
scores},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {5},
year = {2023}
}
@article{DBLP:journals/ploscb/MassonisVB23,
author = {Gemma Massonis and
Alejandro F. Villaverde and
Julio R. Banga},
title = {Distilling identifiable and interpretable dynamic models from biological
data},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {10},
year = {2023}
}
@article{DBLP:journals/ploscb/OzaWWUWGHTIWL23,
author = {Vishal H. Oza and
Jordan H. Whitlock and
Elizabeth J. Wilk and
Angelina E. Uno{-}Antonison and
Brandon M. Wilk and
Manavalan Gajapathy and
Timothy C. Howton and
Austyn Trull and
Lara Ianov and
Elizabeth A. Worthey and
Brittany N. Lasseigne},
title = {Ten simple rules for using public biological data for your research},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {1},
year = {2023}
}
@article{DBLP:journals/siamsc/KazarnikovSHM23,
author = {Alexey Kazarnikov and
Robert Scheichl and
Heikki Haario and
Anna K. Marciniak{-}Czochra},
title = {A Bayesian Approach to Modeling Biological Pattern Formation with
Limited Data},
journal = {{SIAM} J. Sci. Comput.},
volume = {45},
number = {5},
pages = {673},
year = {2023}
}
@article{DBLP:journals/soco/LiGCWQ23,
author = {Dan Li and
Hong Gu and
Qiaozhen Chang and
Jia Wang and
Pan Qin},
title = {A joint optimization framework integrated with biological knowledge
for clustering incomplete gene expression data},
journal = {Soft Comput.},
volume = {27},
number = {18},
pages = {13639--13656},
year = {2023}
}
@article{DBLP:journals/tcbb/ZhangL23,
author = {Wenxiang Zhang and
Bin Liu},
title = {iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple
Biological Data by Ranking Framework},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {5},
pages = {3013--3019},
year = {2023}
}
@article{DBLP:journals/tpds/DuanSWSGLFXLY23,
author = {Xiaohui Duan and
Qi Shao and
Junben Weng and
Bertil Schmidt and
Lin Gan and
Guohui Li and
Haohuan Fu and
Wei Xue and
Weiguo Liu and
Guangwen Yang},
title = {Bio-ESMD: {A} Data Centric Implementation for Large-Scale Biological
System Simulation on Sunway TaihuLight Supercomputer},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {34},
number = {3},
pages = {881--893},
year = {2023}
}
@inproceedings{DBLP:conf/bcb/JamilKG23,
author = {Hasan M. Jamil and
Stephen A. Krawetz and
Alexander Gow},
title = {Leveraging Large Language Models for Automatic Hypotheses Testing
over Heterogeneous Biological Databases},
booktitle = {{BCB}},
pages = {80:1--80:2},
publisher = {{ACM}},
year = {2023}
}
@inproceedings{DBLP:conf/bibm/GhoshKK23,
author = {Tomojit Ghosh and
Karim Karimov and
Michael Kirby},
title = {Sparse Linear Centroid-Encoder: {A} Biomarker Selection tool for High
Dimensional Biological Data},
booktitle = {{BIBM}},
pages = {3012--3019},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/btw/LofflerSWKK23,
author = {Felicitas L{\"{o}}ffler and
Fateme Shafiei and
Ren{\'{e}} Witte and
Birgitta K{\"{o}}nig{-}Ries and
Friederike Klan},
title = {Semantic Search for Biological Datasets: {A} Usability Study on Modes
of Querying and Explaining Search Results},
booktitle = {{BTW}},
series = {{LNI}},
volume = {{P-331}},
pages = {851--864},
publisher = {Gesellschaft f{\"{u}}r Informatik e.V.},
year = {2023}
}
@inproceedings{DBLP:conf/cibcb/DubeSHG23,
author = {Michael Dub{\'{e}} and
James Sargant and
Sheridan K. Houghten and
Steffen Graether},
title = {From Bits to Bases: Evolving a Versatile Construct for Biological
Sequence and Network Data},
booktitle = {{CIBCB}},
pages = {1--9},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/cikm/AvesaniBPBG23,
author = {Simone Avesani and
Vincenzo Bonnici and
Simone Pernice and
Marco Beccuti and
Rosalba Giugno},
title = {{MODIMO:} Workshop on Multi-Omics Data Integration for Modelling Biological
Systems},
booktitle = {{CIKM}},
pages = {5259--5262},
publisher = {{ACM}},
year = {2023}
}
@inproceedings{DBLP:conf/complexnetworks/GuzziRCV23,
author = {Pietro Hiram Guzzi and
Arkaprava Roy and
Francesca Cortese and
Pierangelo Veltri},
title = {Non Parametric Differential Network Analysis for Biological Data},
booktitle = {{COMPLEX} {NETWORKS} {(3)}},
series = {Studies in Computational Intelligence},
volume = {1143},
pages = {114--123},
publisher = {Springer},
year = {2023}
}
@inproceedings{DBLP:conf/eusipco/BertonCLH23,
author = {Chlo{\'{e}} Berton and
Gouenou Coatrieux and
Dominique Lavenier and
Sahar Haddad},
title = {Dynamic Sliding Window Encoding for Data Storage on {DNA} Under Biological
and Indexing Constraints},
booktitle = {{EUSIPCO}},
pages = {1110--1114},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/icbbb/LinL23,
author = {Hung{-}Yi Lin and
Ting{-}Han Lin},
title = {Efficient Feature Selection based on Soft Cluster Analysis for Biological
Datasets},
booktitle = {{ICBBB}},
pages = {10--16},
publisher = {{ACM}},
year = {2023}
}
@inproceedings{DBLP:conf/iclr/DongK23,
author = {Mingze Dong and
Yuval Kluger},
title = {{GEASS:} Neural causal feature selection for high-dimensional biological
data},
booktitle = {{ICLR}},
publisher = {OpenReview.net},
year = {2023}
}
@inproceedings{DBLP:conf/icvgip/ThottupattuSK23,
author = {Alphin J. Thottupattu and
Jayanthi Sivaswamy and
Venky Krishnan},
title = {Global Space Modelling Of Biological Processes With Cross-sectional
Data},
booktitle = {{ICVGIP}},
pages = {35:1--35:8},
publisher = {{ACM}},
year = {2023}
}
@inproceedings{DBLP:conf/iecon/NomaKMOMYH23,
author = {Hiroto Noma and
Tatsuya Komatsu and
Kansei Matsumoto and
Hidetoshi Oya and
Ryotaro Miura and
Koji Yoshioka and
Yoshikatsu Hoshi},
title = {Analysis of Biological Data of Cows and Development of Detection Systems
for Calving Phase},
booktitle = {{IECON}},
pages = {1--6},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/iiwas/JamilKG23,
author = {Hasan M. Jamil and
Stephen A. Krawetz and
Alexander Gow},
title = {Automatic Hypotheses Testing Over Heterogeneous Biological Databases
Using Open Knowledge Networks},
booktitle = {iiWAS},
series = {Lecture Notes in Computer Science},
volume = {14416},
pages = {358--364},
publisher = {Springer},
year = {2023}
}
@inproceedings{DBLP:conf/ijcnn/SinghCPKY23,
author = {Dinesh Singh and
H{\'{e}}ctor Climente{-}Gonz{\'{a}}lez and
Mathis Petrovich and
Eiryo Kawakami and
Makoto Yamada},
title = {FsNet: Feature Selection Network on High-dimensional Biological Data},
booktitle = {{IJCNN}},
pages = {1--9},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/inista/JaberHK23,
author = {Iyad Jaber and
Yousef Hassouneh and
Maha Khemaja},
title = {An Enhanced Feature Selection Approach Using Capuchin Search Algorithm
for high-dimensional Biological Data Classification},
booktitle = {{INISTA}},
pages = {1--7},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/isbra/ChourasiaMAP23,
author = {Prakash Chourasia and
Taslim Murad and
Sarwan Ali and
Murray Patterson},
title = {Enhancing t-SNE Performance for Biological Sequencing Data Through
Kernel Selection},
booktitle = {{ISBRA}},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {442--452},
publisher = {Springer},
year = {2023}
}
@inproceedings{DBLP:conf/nips/0005WY023,
author = {Tianyu Liu and
Yuge Wang and
Rex Ying and
Hongyu Zhao},
title = {MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological
Graph Data},
booktitle = {NeurIPS},
year = {2023}
}
@inproceedings{DBLP:conf/sac/JamilN23,
author = {Hasan M. Jamil and
Kallol Naha},
title = {Mapping Strategies for Declarative Queries over Online Heterogeneous
Biological Databases for Intelligent Responses},
booktitle = {{SAC}},
pages = {567--574},
publisher = {{ACM}},
year = {2023}
}
@inproceedings{DBLP:conf/sbbd/VieiraAJCMHL23,
author = {Diogo Munaro Vieira and
Elvismary Molina de Armas and
Maria L. G. Jaramillo and
Marcos Catanho and
Antonio B. de Miranda and
Edward Hermann Haeusler and
S{\'{e}}rgio Lifschitz},
title = {A New Data Modeling Approach for Alignment-free Biological Applications},
booktitle = {{SBBD}},
pages = {1--13},
publisher = {{SBC}},
year = {2023}
}
@inproceedings{DBLP:conf/sccc/MariangelGAVI23,
author = {Nicol{\'{a}}s Mari{\'{a}}ngel and
Juan Giglio and
Sebasti{\'{a}}n Aliaga{-}Rojas and
Manuel Villalobos{-}Cid and
Mario Inostroza{-}Ponta},
title = {Evaluating the incorporation of Biological Knowledge in multiobjective
clustering of gene expression data},
booktitle = {{SCCC}},
pages = {1--8},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/smc/ZhanW23,
author = {Huixin Zhan and
Yifan Wang},
title = {Group Lasso with Checkpoints Selection for Biological Data Regression},
booktitle = {{SMC}},
pages = {1792--1797},
publisher = {{IEEE}},
year = {2023}
}
@inproceedings{DBLP:conf/wob/VillelaLF23,
author = {Victor Chavauty Villela and
Eduardo Silva Lira and
Andr{\'{e}} Fujita},
title = {Spectrum-Based Statistical Methods for Directed Graphs with Applications
in Biological Data},
booktitle = {{BSB}},
series = {Lecture Notes in Computer Science},
volume = {13954},
pages = {46--57},
publisher = {Springer},
year = {2023}
}
@article{DBLP:journals/corr/abs-2303-16725,
author = {Alex J. Lee and
Robert Cahill and
Reza Abbasi{-}Asl},
title = {Machine Learning for Uncovering Biological Insights in Spatial Transcriptomics
Data},
journal = {CoRR},
volume = {abs/2303.16725},
year = {2023}
}
@article{DBLP:journals/corr/abs-2305-15611,
author = {Yujun Yan and
Gaotang Li and
Danai Koutra},
title = {Size Generalizability of Graph Neural Networks on Biological Data:
Insights and Practices from the Spectral Perspective},
journal = {CoRR},
volume = {abs/2305.15611},
year = {2023}
}
@article{DBLP:journals/corr/abs-2306-17400,
author = {Ruben Glatt and
Shusen Liu},
title = {Topological Data Analysis Guided Segment Anything Model Prompt Optimization
for Zero-Shot Segmentation in Biological Imaging},
journal = {CoRR},
volume = {abs/2306.17400},
year = {2023}
}
@article{DBLP:journals/corr/abs-2308-06430,
author = {Zhendong Sha and
Li Zhu and
Zijun Jiang and
Yuanzhu Peter Chen and
Ting Hu},
title = {How complex is the microarray dataset? {A} novel data complexity metric
for biological high-dimensional microarray data},
journal = {CoRR},
volume = {abs/2308.06430},
year = {2023}
}
@article{DBLP:journals/corr/abs-2308-09791,
author = {Niloufar Mehrabi and
Sayed Pedram Haeri Boroujeni and
Elnaz Pashaei},
title = {An Efficient High-Dimensional Gene Selection Approach based on Binary
Horse Herd Optimization Algorithm for Biological Data Classification},
journal = {CoRR},
volume = {abs/2308.09791},
year = {2023}
}
@article{DBLP:journals/corr/abs-2310-02275,
author = {Tianyu Liu and
Yuge Wang and
Rex Ying and
Hongyu Zhao},
title = {MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological
Graph Data},
journal = {CoRR},
volume = {abs/2310.02275},
year = {2023}
}
@article{DBLP:journals/corr/abs-2311-05668,
author = {Terence R. Johnson and
Philip E. Bourne},
title = {The Biological Data Sustainability Paradox},
journal = {CoRR},
volume = {abs/2311.05668},
year = {2023}
}
@book{DBLP:books/hal/Poulain22,
author = {Pierre Poulain},
title = {Recyclage des donn{\'{e}}es de la recherche en biologie : vers
une bioinformatique {\'{e}}cologique? (Recycling biological research
data: towards an ecological bioinformatics?)},
year = {2022}
}
@phdthesis{DBLP:phd/basesearch/Hoffmann22,
author = {Karl B. Hoffmann},
title = {Robust Identification of Topological Defects in Discrete Vector Fields
with Applications to Biological Image Data},
school = {University of Dresden, Germany},
year = {2022}
}
@phdthesis{DBLP:phd/basesearch/Safinianaini22,
author = {Negar Safinianaini},
title = {Novel likelihood-based inference techniques for sequential data with
medical and biological applications},
school = {Royal Institute of Technology, Stockholm, Sweden},
year = {2022}
}
@phdthesis{DBLP:phd/be/Thi22,
author = {Danh Bui Thi},
title = {Biological data mining : from interestingness measure to deep learning},
school = {University of Antwerp, Belgium},
year = {2022}
}
@phdthesis{DBLP:phd/it/Leone22,
author = {Michele Leone},
title = {Genomic metadata integration and data processing methods for the analysis
of chromatin behaviour in different biological conditions},
school = {Polytechnic University of Milan, Italy},
year = {2022}
}
@article{DBLP:journals/aam/DimitrovaHLSZ22,
author = {Elena S. Dimitrova and
Jingzhen Hu and
Qingzhong Liang and
Brandilyn Stigler and
Anyu Zhang},
title = {Algebraic model selection and experimental design in biological data
science},
journal = {Adv. Appl. Math.},
volume = {133},
pages = {102282},
year = {2022}
}
@article{DBLP:journals/aei/LiHYZGWL22,
author = {Xuerui Li and
Xinggang Hou and
Mei Yang and
Lin Zhang and
Haoyue Guo and
Luyao Wang and
Xinying Li},
title = {A method of constructing an inspiration library driven by user-perceived
preference evaluation data for biologically inspired design},
journal = {Adv. Eng. Informatics},
volume = {52},
pages = {101617},
year = {2022}
}
@article{DBLP:journals/bib/RezendeXAFP22,
author = {P{\^{a}}mela M. Rezende and
Joicymara S. Xavier and
David B. Ascher and
Gabriel R. Fernandes and
Douglas E. V. Pires},
title = {Evaluating hierarchical machine learning approaches to classify biological
databases},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022}
}
@article{DBLP:journals/bib/TangYLZ22,
author = {Hui Tang and
Xiangtian Yu and
Rui Liu and
Tao Zeng},
title = {Vec2image: an explainable artificial intelligence model for the feature
representation and classification of high-dimensional biological data
by vector-to-image conversion},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022}
}
@article{DBLP:journals/bib/WangTYKP22,
author = {Lei Wang and
Yaqin Tan and
Xiaoyu Yang and
Linai Kuang and
Pengyao Ping},
title = {Review on predicting pairwise relationships between human microbes,
drugs and diseases: from biological data to computational models},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022}
}
@article{DBLP:journals/bigdata/DallAlbaCANS22,
author = {Gabriel Dall'Alba and
Pedro Lenz Casa and
Fernanda Pessi de Abreu and
Daniel Luis Notari and
Scheila de Avila e Silva},
title = {A Survey of Biological Data in a Big Data Perspective},
journal = {Big Data},
volume = {10},
number = {4},
pages = {279--297},
year = {2022}
}
@article{DBLP:journals/biodb/WrightORWTJHS22,
author = {Adam J. Wright and
Marija Orlic{-}Milacic and
Karen Rothfels and
Joel Weiser and
Quang M. Trinh and
Bijay Jassal and
Robin Haw and
Lincoln D. Stein},
title = {Evaluating the predictive accuracy of curated biological pathways
in a public knowledgebase},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022}
}
@article{DBLP:journals/bioinformatics/ChenCL22,
author = {Yang Chen and
Shue Chen and
Elissa P. Lei},
title = {DiffChIPL: a differential peak analysis method for high-throughput
sequencing data with biological replicates based on limma},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4062--4069},
year = {2022}
}
@article{DBLP:journals/bioinformatics/ChenLIWL22,
author = {Chixiang Chen and
Yuk Yee Leung and
Matei Ionita and
Li{-}San Wang and
Mingyao Li},
title = {Omnibus and robust deconvolution scheme for bulk {RNA} sequencing
data integrating multiple single-cell reference sets and prior biological
knowledge},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4530--4536},
year = {2022}
}
@article{DBLP:journals/bioinformatics/IkedaOOCNMKYOGK22,
author = {Shuya Ikeda and
Hiromasa Ono and
Tazro Ohta and
Hirokazu Chiba and
Yuki Naito and
Yuki Moriya and
Shuichi Kawashima and
Yasunori Yamamoto and
Shinobu Okamoto and
Susumu Goto and
Toshiaki Katayama},
title = {TogoID: an exploratory {ID} converter to bridge biological datasets},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4194--4199},
year = {2022}
}
@article{DBLP:journals/bioinformatics/VerschaffeltCBM22,
author = {Pieter Verschaffelt and
James H. Collier and
Alexander Botzki and
Lennart Martens and
Peter Dawyndt and
Bart Mesuere},
title = {Unipept Visualizations: an interactive visualization library for biological
data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {562--563},
year = {2022}
}
@article{DBLP:journals/biosystems/MalepathiranaSV22,
author = {Tamasha Malepathirana and
Damith A. Senanayake and
Rajith Vidanaarachchi and
Vini Gautam and
Saman K. Halgamuge},
title = {Dimensionality reduction for visualizing high-dimensional biological
data},
journal = {Biosyst.},
volume = {220},
pages = {104749},
year = {2022}
}
@article{DBLP:journals/bmcbi/FigueiredoSRHKM22,
author = {Rebeca Queiroz Figueiredo and
Sara D{\'{\i}}az del Ser and
Tamara Raschka and
Martin Hofmann{-}Apitius and
Alpha Tom Kodamullil and
Sarah Mubeen and
Daniel Domingo{-}Fern{\'{a}}ndez},
title = {Elucidating gene expression patterns across multiple biological contexts
through a large-scale investigation of transcriptomic datasets},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {231},
year = {2022}
}
@article{DBLP:journals/bmcbi/MrukwaP22,
author = {Grzegorz Mrukwa and
Joanna Polanska},
title = {DiviK: divisive intelligent K-means for hands-free unsupervised clustering
in big biological data},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {538},
year = {2022}
}
@article{DBLP:journals/bmcbi/PacinkovaP22,
author = {Anna Pac{\'{\i}}nkov{\'{a}} and
Vlad Popovici},
title = {Using empirical biological knowledge to infer regulatory networks
from multi-omics data},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {351},
year = {2022}
}
@article{DBLP:journals/bmcbi/PacinkovaP22a,
author = {Anna Pac{\'{\i}}nkov{\'{a}} and
Vlad Popovici},
title = {Correction: Using empirical biological knowledge to infer regulatory
networks from multi-omics data},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {376},
year = {2022}
}
@article{DBLP:journals/bmcbi/YangGLLWCQZWLPC22,
author = {Qing Yang and
Sunan Gao and
Junfen Lin and
Ke Lyu and
Zexu Wu and
Yuhao Chen and
Yinwei Qiu and
Yanrong Zhao and
Wei Wang and
Tianxiang Lin and
Huiyun Pan and
Ming Chen},
title = {A machine learning-based data mining in medical examination data:
a biological features-based biological age prediction model},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {411},
year = {2022}
}
@article{DBLP:journals/cea/MahjenabadiMRKR22,
author = {Vahid Alah Jahandideh Mahjenabadi and
Seyed Roohollah Mousavi and
Asghar Rahmani and
Alidad Karami and
Hadi Asadi Rahmani and
Kazem Khavazi and
Meisam Rezaei},
title = {Digital mapping of soil biological properties and wheat yield using
remotely sensed, soil chemical data and machine learning approaches},
journal = {Comput. Electron. Agric.},
volume = {197},
pages = {106978},
year = {2022}
}
@article{DBLP:journals/ewc/PawarLGUT22,
author = {Aishwarya Pawar and
Linlin Li and
Arun Gosain and
David M. Umulis and
Adrian Buganza Tepole},
title = {PDE-constrained shape registration to characterize biological growth
and morphogenesis from imaging data},
journal = {Eng. Comput.},
volume = {38},
number = {5},
pages = {3909--3924},
year = {2022}
}
@article{DBLP:journals/ewc/TacSRT22,
author = {Vahidullah Tac and
Vivek D. Sree and
Manuel K. Rausch and
Adrian Buganza Tepole},
title = {Data-driven modeling of the mechanical behavior of anisotropic soft
biological tissue},
journal = {Eng. Comput.},
volume = {38},
number = {5},
pages = {4167--4182},
year = {2022}
}
@article{DBLP:journals/fbinf/Weiskopf22,
author = {Daniel Weiskopf},
title = {Uncertainty Visualization: Concepts, Methods, and Applications in
Biological Data Visualization},
journal = {Frontiers Bioinform.},
volume = {2},
pages = {793819},
year = {2022}
}
@article{DBLP:journals/fcomp/KlatzowDMSU22,
author = {James Klatzow and
Giovanni Dalmasso and
Neus Mart{\'{\i}}nez{-}Abad{\'{\i}}as and
James Sharpe and
Virginie Uhlmann},
title = {{\(\mu\)}Match: 3D Shape Correspondence for Biological Image Data},
journal = {Frontiers Comput. Sci.},
volume = {4},
pages = {777615},
year = {2022}
}
@article{DBLP:journals/fdata/AdigaPBMR22,
author = {Abhijin Adiga and
Nicholas Palmer and
Young Yun Baek and
Henning S. Mortveit and
S. S. Ravi},
title = {Network Models and Simulation Analytics for Multi-scale Dynamics of
Biological Invasions},
journal = {Frontiers Big Data},
volume = {5},
pages = {796897},
year = {2022}
}
@article{DBLP:journals/ijcomsys/NiranjanaPS22,
author = {G. Niranjana and
A. Poongodai and
K. L. S. Soujanya},
title = {Biological inspired self-organized secure autonomous routing protocol
and secured data assured routing in {WSN:} Hybrid {EHO} and {MBO}
approach},
journal = {Int. J. Commun. Syst.},
volume = {35},
number = {4},
year = {2022}
}
@article{DBLP:journals/ijict/Saeed22,
author = {Faisal Saeed},
title = {Machine learning methods for predicting the biological activities
of molecules in high diverse databases},
journal = {Int. J. Inf. Commun. Technol.},
volume = {21},
number = {2},
pages = {170--180},
year = {2022}
}
@article{DBLP:journals/jcb/QianFLL22,
author = {Kun Qian and
Shiwei Fu and
Hongwei Li and
Wei Vivian Li},
title = {The scINSIGHT Package for Integrating Single-Cell RNA-Seq Data from
Different Biological Conditions},
journal = {J. Comput. Biol.},
volume = {29},
number = {11},
pages = {1233--1236},
year = {2022}
}
@article{DBLP:journals/jdi/GarauOSMBBMFBPR22,
author = {Noemi Garau and
Alessandro Orro and
Paul E. Summers and
Lorenza De Maria and
Raffaella Bertolotti and
Danny Bassis and
Marta Minotti and
Elvio De Fiori and
Guido Baroni and
Chiara Paganelli and
Cristiano Rampinelli},
title = {Integrating Biological and Radiological Data in a Structured Repository:
a Data Model Applied to the {COSMOS} Case Study},
journal = {J. Digit. Imaging},
volume = {35},
number = {4},
pages = {970--982},
year = {2022}
}
@article{DBLP:journals/jucs/ThaherAASTC22,
author = {Thaer Thaher and
Mohammed Awad and
Mohammed Aldasht and
Alaa F. Sheta and
Hamza Turabieh and
Hamouda Chantar},
title = {An Enhanced Evolutionary Based Feature Selection Approach Using Grey
Wolf Optimizer for the Classification of High-dimensional Biological
Data},
journal = {J. Univers. Comput. Sci.},
volume = {28},
number = {5},
pages = {499--539},
year = {2022}
}
@article{DBLP:journals/keds/PutriWRUU22,
author = {Nastiti Susetyo Fanany Putri and
Aji Prasetya Wibawa and
Harits Ar Rosyid and
Agung Bella Putra Utama and
Wako Uriu},
title = {Performance of Ensemble Classification for Agricultural and Biological
Science Journals with Scopus Index},
journal = {Knowl. Eng. Data Sci.},
volume = {5},
number = {2},
pages = {137--142},
year = {2022}
}
@article{DBLP:journals/midm/MondalDAWMBSH22,
author = {Rahul Mondal and
Minh Dung Do and
Nasimuddin Ahmed and
Daniel Walke and
Daniel Micheel and
David Broneske and
Gunter Saake and
Robert Heyer},
title = {Decision tree learning in Neo4j on homogeneous and unconnected graph
nodes from biological and clinical datasets},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {22-S},
number = {6},
pages = {347},
year = {2022}
}
@article{DBLP:journals/nar/PancsaFMSTFLSHS22,
author = {Rita Pancsa and
Erzs{\'{e}}bet Fich{\'{o}} and
Daniel Molnar and
{\'{E}}va Viola Sur{\'{a}}nyi and
Tam{\'{a}}s Trombit{\'{a}}s and
D{\'{o}}ra F{\"{u}}zesi and
Hanna L{\'{o}}czi and
P{\'{e}}ter Szijj{\'{a}}rt{\'{o}} and
Rita H{\'{\i}}rmond{\'{o}} and
Judit E. Szab{\'{o}} and
Judit T{\'{o}}th},
title = {dNTPpoolDB: a manually curated database of experimentally determined
dNTP pools and pool changes in biological samples},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {1508--1514},
year = {2022}
}
@article{DBLP:journals/nar/VaradiAABCDNNPT22,
author = {Mihaly Varadi and
Stephen Anyango and
David R. Armstrong and
John M. Berrisford and
Preeti Choudhary and
Mandar S. Deshpande and
Nurul Nadzirin and
Sreenath Nair and
Luk{\'{a}}s Pravda and
Ahsan Tanweer and
Bissan Al{-}Lazikani and
Claudia Andreini and
Geoffrey J. Barton and
David Bednar and
Karel Berka and
Tom L. Blundell and
Kelly Brock and
Jos{\'{e}} Mar{\'{\i}}a Carazo and
Jir{\'{\i}} Damborsk{\'{y}} and
Alessia David and
Sucharita Dey and
Roland L. Dunbrack Jr. and
Juan Fern{\'{a}}ndez{-}Recio and
Franca Fraternali and
Toby J. Gibson and
Manuela Helmer{-}Citterich and
David Hoksza and
Thomas A. Hopf and
David Jakubec and
Natarajan Kannan and
Radoslav Kriv{\'{a}}k and
Manjeet Kumar and
Emmanuel D. Levy and
Nir London and
Jos{\'{e}} Ram{\'{o}}n Mac{\'{\i}}as and
Mallur Srivatsan Madhusudhan and
Debora S. Marks and
Lennart Martens and
Stuart A McGowan and
Jake E. McGreig and
Vivek Modi and
R. Gonzalo Parra and
Gerardo Pepe and
Damiano Piovesan and
Jaime Prilusky and
Valeria Putignano and
Leandro G. Radusky and
Pathmanaban Ramasamy and
Atilio O. Rausch and
Nathalie Reuter and
Luis A. Rodriguez and
Nathan J. Rollins and
Antonio Rosato and
Pawel Rubach and
Luis Serrano and
Gulzar Singh and
Petr Skoda and
Carlos Oscar S{\'{a}}nchez Sorzano and
Jan Stourac and
Joanna I. Sulkowska and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Natalia Tichshenko and
Silvio C. E. Tosatto and
Wim F. Vranken and
Mark N. Wass and
Dandan Xue and
Daniel Zaidman and
Janet M. Thornton and
Michael J. E. Sternberg and
Christine A. Orengo and
Sameer Velankar},
title = {PDBe-KB: collaboratively defining the biological context of structural
data},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {534--542},
year = {2022}
}
@article{DBLP:journals/ploscb/AuerMK22,
author = {Florian Auer and
Simone Mayer and
Frank Kramer},
title = {Data-dependent visualization of biological networks in the web-browser
with NDExEdit},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {6},
year = {2022}
}
@article{DBLP:journals/symmetry/ZdimalovaCKGOKK22,
author = {M{\'{a}}ria Zd{\'{\i}}malov{\'{a}} and
Anuprava Chatterjee and
Helena Kosn{\'{a}}cov{\'{a}} and
Mridul Ghosh and
Sk Md Obaidullah and
Martin Kopani and
Daniel Kosn{\'{a}}c},
title = {Various Approaches to the Quantitative Evaluation of Biological and
Medical Data Using Mathematical Models},
journal = {Symmetry},
volume = {14},
number = {1},
pages = {7},
year = {2022}
}
@article{DBLP:journals/tcbb/Sefer22,
author = {Emre Sefer},
title = {BioCode: {A} Data-Driven Procedure to Learn the Growth of Biological
Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {6},
pages = {3103--3113},
year = {2022}
}
@inproceedings{DBLP:conf/bcb/BabjacRSE22,
author = {Ashley Babjac and
Taylor M. Royalty and
Andrew D. Steen and
Scott J. Emrich},
title = {A comparison of dimensionality reduction methods for large biological
data},
booktitle = {{BCB}},
pages = {15:1--15:7},
publisher = {{ACM}},
year = {2022}
}
@inproceedings{DBLP:conf/bibm/AlipourfardG22,
author = {Borzou Alipourfard and
Jean Gao},
title = {Causal Discovery in Biological Data Using Directed Topological Overlap
Matrix},
booktitle = {{BIBM}},
pages = {908--915},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/bigdataconf/ChourasiaAP22,
author = {Prakash Chourasia and
Sarwan Ali and
Murray Patterson},
title = {Informative Initialization and Kernel Selection Improves t-SNE for
Biological Sequences},
booktitle = {{IEEE} Big Data},
pages = {101--106},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/bigdataconf/FuH22,
author = {Dongqi Fu and
Jingrui He},
title = {{DPPIN:} {A} Biological Repository of Dynamic Protein-Protein Interaction
Network Data},
booktitle = {{IEEE} Big Data},
pages = {5269--5277},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/cibcb/Demir22,
author = {Esra Demir},
title = {Big Biological Data: Need for a Reorientation of the Governance Framework},
booktitle = {{CIBCB}},
pages = {1--7},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/codit/RistevskiSS22,
author = {Blagoj Ristevski and
Snezana Savoska and
Zlatko Savoski},
title = {Using Graph Databases for Portraying and Analysing Biological and
Biomedical Networks},
booktitle = {CoDIT},
pages = {565--568},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/embc/MatsudaNT22,
author = {Naoya Matsuda and
Iko Nakari and
Keiki Takadama},
title = {Unstable Circadian Rhythm of Heart Rate of Alzheimer Dementia Based
on Biological Data of Mattress Sensor},
booktitle = {{EMBC}},
pages = {1129--1132},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/embc/NakariMT22,
author = {Iko Nakari and
Naoya Matsuda and
Keiki Takadama},
title = {Non-Contact {REM} Sleep Estimation Correction by Time-Series Confidence
of Predictions: From Binary to Continuous Prediction in Machine Learning
for Biological Data},
booktitle = {{EMBC}},
pages = {1008--1011},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/gptp/KotanchekKK22,
author = {Mark E. Kotanchek and
Theresa Kotanchek and
Kelvin Kotanchek},
title = {Biological Strategies ParetoGP Enables Analysis of Wide and Ill-Conditioned
Data from Nonlinear Systems},
booktitle = {{GPTP}},
pages = {91--116},
publisher = {Springer},
year = {2022}
}
@inproceedings{DBLP:conf/huc/Young-NgCKGSV22,
author = {Meredith Young{-}Ng and
Grace Chen and
Danielle Kiyama and
Anna{-}Sofia Giannicola and
Erkin Seker and
Katia Vega},
title = {Sweatcessory: a Wearable Necklace for Sensing Biological Data in Sweat},
booktitle = {UbiComp/ISWC Adjunct},
pages = {141--143},
publisher = {{ACM}},
year = {2022}
}
@inproceedings{DBLP:conf/icann/ItoUTTKON22,
author = {Eisuke Ito and
Takaya Ueda and
Ryo Takano and
Yukako Tohsato and
Koji Kyoda and
Shuichi Onami and
Ikuko Nishikawa},
title = {Phenotype Anomaly Detection for Biological Dynamics Data Using a Deep
Generative Model},
booktitle = {{ICANN} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {13530},
pages = {432--444},
publisher = {Springer},
year = {2022}
}
@inproceedings{DBLP:conf/ispa/JamilN22,
author = {Hasan M. Jamil and
Kallol Naha},
title = {Mapping Declarative Queries to Heterogeneous Biological Databases
using Schema Graphs for Intelligent Responses},
booktitle = {ISPA/BDCloud/SocialCom/SustainCom},
pages = {147--154},
publisher = {{IEEE}},
year = {2022}
}
@inproceedings{DBLP:conf/midl/DmitrenkoMZ22,
author = {Andrei Dmitrenko and
Mauro M. Masiero and
Nicola Zamboni},
title = {Comparing representations of biological data learned with different
{AI} paradigms, augmenting and cropping strategies},
booktitle = {{MIDL}},
series = {Proceedings of Machine Learning Research},
volume = {172},
pages = {353--369},
publisher = {{PMLR}},
year = {2022}
}
@inproceedings{DBLP:conf/mlcb/LalchandRDKSLMT22,
author = {Vidhi Lalchand and
Aditya Ravuri and
Emma Dann and
Natsuhiko Kumasaka and
Dinithi Sumanaweera and
Rik G. H. Lindeboom and
Shaista Madad and
Sarah A. Teichmann and
Neil D. Lawrence},
title = {Modelling Technical and Biological Effects in scRNA-seq data with
Scalable GPLVMs},
booktitle = {{MLCB}},
series = {Proceedings of Machine Learning Research},
volume = {200},
pages = {46--60},
publisher = {{PMLR}},
year = {2022}
}
@inproceedings{DBLP:conf/recomb/QianFLL22,
author = {Kun Qian and
Shiwei Fu and
Hongwei Li and
Wei Vivian Li},
title = {A Novel Matrix Factorization Model for Interpreting Single-Cell Gene
Expression from Biologically Heterogeneous Data},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {13278},
pages = {353--355},
publisher = {Springer},
year = {2022}
}
@article{DBLP:journals/corr/abs-2203-03708,
author = {Cheng Hua and
Dandan Wang},
title = {Biological, Family and Cultural Predictors of Personality Structure
analysis based on personality prediction models constructed by open
data source},
journal = {CoRR},
volume = {abs/2203.03708},
year = {2022}
}
@article{DBLP:journals/corr/abs-2203-04107,
author = {Andrei Dmitrenko and
Mauro M. Masiero and
Nicola Zamboni},
title = {Comparing representations of biological data learned with different
{AI} paradigms, augmenting and cropping strategies},
journal = {CoRR},
volume = {abs/2203.04107},
year = {2022}
}
@article{DBLP:journals/corr/abs-2207-00812,
author = {Magdalena Wysocka and
Oskar Wysocki and
Marie Zufferey and
D{\'{o}}nal Landers and
Andr{\'{e}} Freitas},
title = {Biologically-informed deep learning models for cancer: fundamental
trends for encoding and interpreting oncology data},
journal = {CoRR},
volume = {abs/2207.00812},
year = {2022}
}
@article{DBLP:journals/corr/abs-2208-04720,
author = {Richard Tj{\"{o}}rnhammar},
title = {Clustering Optimisation Method for Highly Connected Biological Data},
journal = {CoRR},
volume = {abs/2208.04720},
year = {2022}
}
@article{DBLP:journals/corr/abs-2209-06716,
author = {Vidhi Lalchand and
Aditya Ravuri and
Emma Dann and
Natsuhiko Kumasaka and
Dinithi Sumanaweera and
Rik G. H. Lindeboom and
Shaista Madad and
Sarah A. Teichmann and
Neil D. Lawrence},
title = {Modelling Technical and Biological Effects in scRNA-seq data with
Scalable GPLVMs},
journal = {CoRR},
volume = {abs/2209.06716},
year = {2022}
}
@article{DBLP:journals/corr/abs-2211-02537,
author = {Nicholas Pellegrino and
Zahra Gharaee and
Paul W. Fieguth},
title = {Machine Learning Challenges of Biological Factors in Insect Image
Data},
journal = {CoRR},
volume = {abs/2211.02537},
year = {2022}
}
@phdthesis{DBLP:phd/basesearch/Zobolas21,
author = {John Zobolas},
title = {Software implementations allowing new approaches toward data analysis,
modeling and curation of biological knowledge for Systems Medicine},
school = {Norwegian University of Science and Technology, Trondheim, Norway},
year = {2021}
}
@phdthesis{DBLP:phd/dnb/Becker21a,
author = {Katinka Becker},
title = {Logical Analysis of Biological Data},
school = {Free University of Berlin, Germany},
year = {2021}
}
@phdthesis{DBLP:phd/ethos/Hathway21,
author = {Pamela Hathway},
title = {Biologically-inspired machine learning approaches to large-scale neural
data analysis},
school = {Imperial College London, {UK}},
year = {2021}
}
@phdthesis{DBLP:phd/hal/Andrieu21,
author = {Pierre Andrieu},
title = {Passage {\`{a}} l'{\'{e}}chelle, propri{\'{e}}t{\'{e}}s
et qualit{\'{e}} des algorithmes de classements consensuels pour
les donn{\'{e}}es biologiques massives. (Scalability, features
and quality aspects of consensus algorithms for big biological data
sets)},
school = {University of Paris-Saclay, France},
year = {2021}
}
@phdthesis{DBLP:phd/hal/Cabeli21,
author = {Vincent Cabeli},
title = {Learning causal graphs from continuous or mixed datasets of biological
or clinical interest. (Apprentissage de graphes causaux {\`{a}} partir
de donn{\'{e}}es continues ou mixtes d'int{\'{e}}r{\^{e}}t
biologique ou clinique)},
school = {Sorbonne University, Paris, France},
year = {2021}
}
@phdthesis{DBLP:phd/il/Anavy21,
author = {Leon Anavy},
title = {Synthetic {DNA} libraries and their applications in data storage and
biological assays},
school = {Technion - Israel Institute of Technology, Israel},
year = {2021}
}
@phdthesis{DBLP:phd/it/Ceddia21,
author = {Gaia Ceddia},
title = {Computational methods for data-driven predictions and understanding
of biological interactions},
school = {Polytechnic University of Milan, Italy},
year = {2021}
}
@phdthesis{DBLP:phd/us/Chan21,
author = {Jeffrey Chan},
title = {Scalable Machine Learning Algorithms for Biological Sequence Data},
school = {University of California, Berkeley, {USA}},
year = {2021}
}
@article{DBLP:journals/aai/TooM21,
author = {Jingwei Too and
Seyedali Mirjalili},
title = {General Learning Equilibrium Optimizer: {A} New Feature Selection
Method for Biological Data Classification},
journal = {Appl. Artif. Intell.},
volume = {35},
number = {3},
pages = {247--263},
year = {2021}
}
@article{DBLP:journals/adac/ParvasidehR21,
author = {Parvaneh Parvasideh and
Mansoor Rezghi},
title = {A novel dictionary learning method based on total least squares approach
with application in high dimensional biological data},
journal = {Adv. Data Anal. Classif.},
volume = {15},
number = {3},
pages = {575--597},
year = {2021}
}
@article{DBLP:journals/asc/MaatoukABD21,
author = {Ons Ma{\^{a}}touk and
Wassim Ayadi and
Hend Bouziri and
B{\'{e}}atrice Duval},
title = {Evolutionary Local Search Algorithm for the biclustering of gene expression
data based on biological knowledge},
journal = {Appl. Soft Comput.},
volume = {104},
pages = {107177},
year = {2021}
}
@article{DBLP:journals/bib/ToureFNVK21,
author = {Vasundra Tour{\'{e}} and
{\AA}smund Flobak and
Anna Niarakis and
Steven Vercruysse and
Martin Kuiper},
title = {The status of causality in biological databases: data resources and
data retrieval possibilities to support logical modeling},
journal = {Briefings Bioinform.},
volume = {22},
number = {4},
year = {2021}
}
@article{DBLP:journals/bib/WenYDLWW21,
author = {Zhongqi Wen and
Cheng Yan and
Guihua Duan and
Suning Li and
Fang{-}Xiang Wu and
Jianxin Wang},
title = {A survey on predicting microbe-disease associations: biological data
and computational methods},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021}
}
@article{DBLP:journals/biodb/AhmedK21,
author = {Mahmoud Ahmed and
Deok Ryong Kim},
title = {{LINPS:} a database for cancer-cell-specific perturbations of biological
networks},
journal = {Database J. Biol. Databases Curation},
volume = {2021},
year = {2021}
}
@article{DBLP:journals/biodb/GuoDJZYCYRTC21,
author = {Wen{-}Ping Guo and
Xiao{-}Bao Ding and
Jie Jin and
Hai{-}bo Zhang and
Qiao{-}lei Yang and
Peng{-}Cheng Chen and
Heng Yao and
Li Ruan and
Yu{-}Tian Tao and
Xin Chen},
title = {{HIR} {V2:} a human interactome resource for the biological interpretation
of differentially expressed genes via gene set linkage analysis},
journal = {Database J. Biol. Databases Curation},
volume = {2021},
year = {2021}
}
@article{DBLP:journals/bioinformatics/DragerHBBCCHKNM21,
author = {Andreas Dr{\"{a}}ger and
Tom{\'{a}}s Helikar and
Matteo Barberis and
Marc R. Birtwistle and
Laurence Calzone and
Claudine Chaouiya and
Jan Hasenauer and
Jonathan R. Karr and
Anna Niarakis and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez and
Julio Saez{-}Rodriguez and
Juilee Thakar},
title = {SysMod: the {ISCB} community for data-driven computational modelling
and multi-scale analysis of biological systems},
journal = {Bioinform.},
volume = {37},
number = {21},
pages = {3702--3706},
year = {2021}
}
@article{DBLP:journals/bioinformatics/Ovando-VazquezC21,
author = {Cesar{\'{e}} Ovando{-}V{\'{a}}zquez and
Daniel C{\'{a}}zarez{-}Garc{\'{\i}}a and
Robert Winkler},
title = {Target-Decoy MineR for determining the biological relevance of variables
in noisy datasets},
journal = {Bioinform.},
volume = {37},
number = {20},
pages = {3595--3603},
year = {2021}
}
@article{DBLP:journals/bioinformatics/ZhangLKLWZYXYC21,
author = {Le Zhang and
Guangdi Liu and
Meijing Kong and
Tingting Li and
Dan Wu and
Xiaobo Zhou and
Chuanwei Yang and
Lei Xia and
Zhenzhou Yang and
Luonan Chen},
title = {Revealing dynamic regulations and the related key proteins of myeloma-initiating
cells by integrating experimental data into a systems biological model},
journal = {Bioinform.},
volume = {37},
number = {11},
pages = {1554--1561},
year = {2021}
}
@article{DBLP:journals/bmcbi/AlexandreCH21,
author = {Leonardo Alexandre and
Rafael S. Costa and
Rui Henriques},
title = {{DI2:} prior-free and multi-item discretization of biological data
and its applications},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {426},
year = {2021}
}
@article{DBLP:journals/bmcbi/FerravanteMPCLD21,
author = {Carlo Ferravante and
Domenico Memoli and
Domenico A. Palumbo and
Paolo Ciaramella and
Antonio Di Loria and
Ylenia D'Agostino and
Giovanni Nassa and
Francesca Rizzo and
Roberta Tarallo and
Alessandro Weisz and
Giorgio Giurato},
title = {{HOME-BIO} (sHOtgun MEtagenomic analysis of BIOlogical entities):
a specific and comprehensive pipeline for metagenomic shotgun sequencing
data analysis},
journal = {{BMC} Bioinform.},
volume = {22-S},
number = {7},
pages = {106},
year = {2021}
}
@article{DBLP:journals/bmcbi/GuM21,
author = {Shawn Gu and
Tijana Milenkovic},
title = {Data-driven biological network alignment that uses topological, sequence,
and functional information},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {34},
year = {2021}
}
@article{DBLP:journals/bmcbi/KavranC21,
author = {Andrew J. Kavran and
Aaron Clauset},
title = {Denoising large-scale biological data using network filters},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {157},
year = {2021}
}
@article{DBLP:journals/bmcbi/LicheriBBG21,
author = {Nicola Licheri and
Vincenzo Bonnici and
Marco Beccuti and
Rosalba Giugno},
title = {{GRAPES-DD:} exploiting decision diagrams for index-driven search
in biological graph databases},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {209},
year = {2021}
}
@article{DBLP:journals/bmcbi/WillforssSL21,
author = {Jakob Willforss and
Valentina Siino and
Fredrik Levander},
title = {OmicLoupe: facilitating biological discovery by interactive exploration
of multiple omic datasets and statistical comparisons},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {107},
year = {2021}
}
@article{DBLP:journals/cin/ShariatmadarF21,
author = {Zahra Sadat Shariatmadar and
Karim Faez},
title = {A Data-Driven and Biologically Inspired Preprocessing Scheme to Improve
Visual Object Recognition},
journal = {Comput. Intell. Neurosci.},
volume = {2021},
pages = {6699335:1--6699335:13},
year = {2021}
}
@article{DBLP:journals/cogcom/MahmudKMH21,
author = {Mufti Mahmud and
M. Shamim Kaiser and
T. Martin McGinnity and
Amir Hussain},
title = {Deep Learning in Mining Biological Data},
journal = {Cogn. Comput.},
volume = {13},
number = {1},
pages = {1--33},
year = {2021}
}
@article{DBLP:journals/datasci/Hulsen21,
author = {Tim Hulsen},
title = {BioVenn - an {R} and Python package for the comparison and visualization
of biological lists using area-proportional Venn diagrams},
journal = {Data Sci.},
volume = {4},
number = {1},
pages = {51--61},
year = {2021}
}
@article{DBLP:journals/entropy/YousefKB21,
author = {Malik Yousef and
Abhishek Kumar and
Burcu Bakir{-}Gungor},
title = {Application of Biological Domain Knowledge Based Feature Selection
on Gene Expression Data},
journal = {Entropy},
volume = {23},
number = {1},
pages = {2},
year = {2021}
}
@article{DBLP:journals/fdata/NguyenBYWC21,
author = {Thanh Nguyen and
Samuel Bharti and
Zongliang Yue and
Christopher D. Willey and
Jake Y. Chen},
title = {Statistical Enrichment Analysis of Samples: {A} General-Purpose Tool
to Annotate Metadata Neighborhoods of Biological Samples},
journal = {Frontiers Big Data},
volume = {4},
pages = {725276},
year = {2021}
}
@article{DBLP:journals/fdata/NguyenBYWC21a,
author = {Thanh Nguyen and
Samuel Bharti and
Zongliang Yue and
Christopher D. Willey and
Jake Y. Chen},
title = {Corrigendum: Statistical Enrichment Analysis of Samples: {A} General-Purpose
Tool to Annotate Metadata Neighborhoods of Biological Samples},
journal = {Frontiers Big Data},
volume = {4},
pages = {804141},
year = {2021}
}
@article{DBLP:journals/fgcs/AndrieuBBCDPV21,
author = {Pierre Andrieu and
Bryan Brancotte and
Laurent Bulteau and
Sarah Cohen{-}Boulakia and
Alain Denise and
Adeline Pierrot and
St{\'{e}}phane Vialette},
title = {Efficient, robust and effective rank aggregation for massive biological
datasets},
journal = {Future Gener. Comput. Syst.},
volume = {124},
pages = {406--421},
year = {2021}
}
@article{DBLP:journals/fgcs/LiuXY21,
author = {Yi Liu and
Jie Xu and
Weijie Yi},
title = {Massive-scale carbon pollution control and biological fusion under
big data context},
journal = {Future Gener. Comput. Syst.},
volume = {118},
pages = {257--262},
year = {2021}
}
@article{DBLP:journals/gpb/CuiLL21,
author = {Ya Cui and
Jason Sheng Li and
Wei Li},
title = {From Reads to Insights: Integrative Pipelines for Biological Interpretation
of ATAC-seq Data},
journal = {Genom. Proteom. Bioinform.},
volume = {19},
number = {4},
pages = {519--521},
year = {2021}
}
@article{DBLP:journals/ida/LiPLK21,
author = {Bentian Li and
Dechang Pi and
Yunxia Lin and
Izhar Ahmed Khan},
title = {Biogc: {A} novel framework for biological network classification via
machine learning},
journal = {Intell. Data Anal.},
volume = {25},
number = {5},
pages = {1153--1168},
year = {2021}
}
@article{DBLP:journals/ijaci/ChowdhuryKRPHAC21,
author = {Linkon Chowdhury and
Md Sarwar Kamal and
Shamim Hasnat Ripon and
Sazia Parvin and
Omar Khadeer Hussain and
Amira S. Ashour and
Bristy Roy Chowdhury},
title = {A Biological Data-Driven Mining Technique by Using Hybrid Classifiers
With Rough Set},
journal = {Int. J. Ambient Comput. Intell.},
volume = {12},
number = {3},
pages = {123--139},
year = {2021}
}
@article{DBLP:journals/jbi/KosvyraNC21,
author = {Alexandra Kosvyra and
Eleni Ntzioni and
Ioanna Chouvarda},
title = {Network analysis with biological data of cancer patients: {A} scoping
review},
journal = {J. Biomed. Informatics},
volume = {120},
pages = {103873},
year = {2021}
}
@article{DBLP:journals/jcb/Thapa021,
author = {Ishwor Thapa and
Hesham Ali},
title = {A Multiomics Graph Database System for Biological Data Integration
and Cancer Informatics},
journal = {J. Comput. Biol.},
volume = {28},
number = {2},
pages = {209--219},
year = {2021}
}
@article{DBLP:journals/jcc/CrowetBBSLD21,
author = {Jean{-}Marc Crowet and
S{\'{e}}bastien Buchoux and
Nicolas Belloy and
Catherine Sarazin and
Laurence Lins and
Manuel Dauchez},
title = {{LIMONADA:} {A} database dedicated to the simulation of biological
membranes},
journal = {J. Comput. Chem.},
volume = {42},
number = {14},
pages = {1028--1033},
year = {2021}
}
@article{DBLP:journals/jois/BegumSCM21,
author = {Shemim Begum and
Ram Sarkar and
Debasis Chakraborty and
Ujjwal Maulik},
title = {Identification of Biomarker on Biological and Gene Expression data
using Fuzzy Preference Based Rough Set},
journal = {J. Intell. Syst.},
volume = {30},
number = {1},
pages = {130--141},
year = {2021}
}
@article{DBLP:journals/nar/BurleyBBB0CCDCD21,
author = {Stephen K. Burley and
Charmi Bhikadiya and
Chunxiao Bi and
Sebastian Bittrich and
Li Chen and
Gregg V. Crichlow and
Cole H. Christie and
Kenneth Dalenberg and
Luigi Di Costanzo and
Jose M. Duarte and
Shuchismita Dutta and
Zukang Feng and
Sai Ganesan and
David S. Goodsell and
Sutapa Ghosh and
Rachel Kramer Green and
Vladimir Guranovic and
Dmytro Guzenko and
Brian P. Hudson and
Catherine L. Lawson and
Yuhe Liang and
Robert Lowe and
Harry Namkoong and
Ezra Peisach and
Irina Persikova and
Christopher Randle and
Alexander S. Rose and
Yana Rose and
Andrej Sali and
Joan Segura and
Monica Sekharan and
Chenghua Shao and
Yi{-}Ping Tao and
Maria Voigt and
John D. Westbrook and
Jasmine Young and
Christine Zardecki and
Marina Zhuravleva},
title = {{RCSB} Protein Data Bank: powerful new tools for exploring 3D structures
of biological macromolecules for basic and applied research and education
in fundamental biology, biomedicine, biotechnology, bioengineering
and energy sciences},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D437--D451},
year = {2021}
}
@article{DBLP:journals/npjdm/WalJLNRRTW0FMSS21,
author = {Douwe van der Wal and
Iny Jhun and
Israa Laklouk and
Jeffrey J. Nirschl and
Lara Richer and
Rebecca Rojansky and
Talent Theparee and
Joshua Wheeler and
J{\"{o}}rg Sander and
Felix Y. Feng and
Osama Mohamad and
Silvio Savarese and
Richard Socher and
Andre Esteva},
title = {Biological data annotation via a human-augmenting AI-based labeling
system},
journal = {npj Digit. Medicine},
volume = {4},
year = {2021}
}
@article{DBLP:journals/ploscb/GuoYSLZZ21,
author = {Weifeng Guo and
Xiangtian Yu and
Qianqian Shi and
Jing Liang and
Shao{-}Wu Zhang and
Tao Zeng},
title = {Performance assessment of sample-specific network control methods
for bulk and single-cell biological data analysis},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {5},
year = {2021}
}
@article{DBLP:journals/ploscb/HattabRH21,
author = {Georges Hattab and
Theresa{-}Marie Rhyne and
Dominik Heider},
title = {Correction: Ten simple rules to colorize biological data visualization},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {4},
year = {2021}
}
@article{DBLP:journals/ploscb/LimQ21,
author = {Hong Seo Lim and
Peng Qiu},
title = {{JSOM:} Jointly-evolving self-organizing maps for alignment of biological
datasets and identification of related clusters},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {3},
year = {2021}
}
@article{DBLP:journals/ploscb/WaschkeHATRHS21,
author = {Johannes Waschke and
Mario Hlawitschka and
Kerim Anlas and
Vikas Trivedi and
Ingo Roeder and
Jan Huisken and
Nico Scherf},
title = {linus: Conveniently explore, share, and present large-scale biological
trajectory data in a web browser},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {11},
year = {2021}
}
@article{DBLP:journals/quanbio/Neuwald21,
author = {Andrew F. Neuwald},
title = {Reflections on the quest to obtain biological information from genomic
data},
journal = {Quant. Biol.},
volume = {9},
number = {3},
pages = {251--254},
year = {2021}
}
@article{DBLP:journals/ral/BirdPFEF21,
author = {Jordan J. Bird and
Michael Pritchard and
Antonio Fratini and
Anik{\'{o}} Ek{\'{a}}rt and
Diego R. Faria},
title = {Synthetic Biological Signals Machine-Generated by {GPT-2} Improve
the Classification of {EEG} and {EMG} Through Data Augmentation},
journal = {{IEEE} Robotics Autom. Lett.},
volume = {6},
number = {2},
pages = {3498--3504},
year = {2021}
}
@article{DBLP:journals/remotesensing/KerfootHSRRBGCS21,
author = {W. Charles Kerfoot and
Martin M. Hobmeier and
Gary Swain and
Robert Regis and
Varsha K. Raman and
Colin N. Brooks and
Amanda Grimm and
Chris Cook and
Robert A. Shuchman and
Molly K. Reif},
title = {Coastal Remote Sensing: Merging Physical, Chemical, and Biological
Data as Tailings Drift onto Buffalo Reef, Lake Superior},
journal = {Remote. Sens.},
volume = {13},
number = {13},
pages = {2434},
year = {2021}
}
@article{DBLP:journals/remotesensing/RieserVTS21,
author = {Jakob Rieser and
Maik Veste and
Michael Thiel and
Sarah Sch{\"{o}}nbrodt{-}Stitt},
title = {Coverage and Rainfall Response of Biological Soil Crusts Using Multi-Temporal
Sentinel-2 Data in a Central European Temperate Dry Acid Grassland},
journal = {Remote. Sens.},
volume = {13},
number = {16},
pages = {3093},
year = {2021}
}
@article{DBLP:journals/simods/CowenDHMW21,
author = {Lenore Cowen and
Kapil Devkota and
Xiaozhe Hu and
James M. Murphy and
Kaiyi Wu},
title = {Diffusion State Distances: Multitemporal Analysis, Fast Algorithms,
and Applications to Biological Networks},
journal = {{SIAM} J. Math. Data Sci.},
volume = {3},
number = {1},
pages = {142--170},
year = {2021}
}
@article{DBLP:journals/tbd/ZuckerPTBKBTHON21,
author = {Jeremy Zucker and
Kaushal Paneri and
Sara Mohammad Taheri and
Somya Bhargava and
Pallavi Kolambkar and
Craig Bakker and
Jeremy Teuton and
Charles Tapley Hoyt and
Kristie L. Oxford and
Robert Osazuwa Ness and
Olga Vitek},
title = {Leveraging Structured Biological Knowledge for Counterfactual Inference:
{A} Case Study of Viral Pathogenesis},
journal = {{IEEE} Trans. Big Data},
volume = {7},
number = {1},
pages = {25--37},
year = {2021}
}
@article{DBLP:journals/tit/BergerWY21,
author = {Bonnie Berger and
Michael S. Waterman and
Yun William Yu},
title = {Levenshtein Distance, Sequence Comparison and Biological Database
Search},
journal = {{IEEE} Trans. Inf. Theory},
volume = {67},
number = {6},
pages = {3287--3294},
year = {2021}
}
@article{DBLP:journals/tkde/MinLZ21,
author = {Wenwen Min and
Juan Liu and
Shihua Zhang},
title = {Group-Sparse {SVD} Models via {\textdollar}L{\_}1{\textdollar}L1-
and {\textdollar}L{\_}0{\textdollar}L0-norm Penalties and their Applications
in Biological Data},
journal = {{IEEE} Trans. Knowl. Data Eng.},
volume = {33},
number = {2},
pages = {536--550},
year = {2021}
}
@inproceedings{DBLP:conf/aaaiss/HeHC21,
author = {Xiaolong He and
Qizhi He and
Jiun{-}Shyan Chen},
title = {Deep Autoencoders for Nonlinear Physics-Constrained Data-Driven Computational
Framework with Application to Biological Tissue Modeling},
booktitle = {{AAAI} Spring Symposium: {MLPS}},
series = {{CEUR} Workshop Proceedings},
volume = {2964},
publisher = {CEUR-WS.org},
year = {2021}
}
@inproceedings{DBLP:conf/bcb/KesimogluB21,
author = {Ziynet Nesibe Kesimoglu and
Serdar Bozdag},
title = {{SUPREME:} a cancer subtype prediction methodology integrating multiple
biological datatypes using graph convolutional neural networks},
booktitle = {{BCB}},
pages = {83:1},
publisher = {{ACM}},
year = {2021}
}
@inproceedings{DBLP:conf/bibm/ZhangTYLLLXGXFZ21,
author = {Shilong Zhang and
Yue Tang and
Jing Yan and
Linye Li and
Tong Li and
Jixiang Li and
Peilin Xie and
Yuanshuai Gu and
Jiakang Xu and
Zaiwen Feng and
Wen Zhang and
Jingbo Xia and
Wolfgang Mayer and
Hong{-}Yu Zhang and
Guang{-}Cun He and
Keqing He},
title = {A Graph-based Approach for Integrating Biological Heterogeneous Data
Based on Connecting Ontology},
booktitle = {{BIBM}},
pages = {600--607},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/cibb/CruzVH21,
author = {Beatriz Garcia Santa Cruz and
Carlos Vega and
Frank Hertel},
title = {The Need of Standardised Metadata to Encode Causal Relationships:
Towards Safer Data-Driven Machine Learning Biological Solutions},
booktitle = {{CIBB}},
series = {Lecture Notes in Computer Science},
volume = {13483},
pages = {200--216},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/cikm/BeccutiBG21,
author = {Marco Beccuti and
Vincenzo Bonnici and
Rosalba Giugno},
title = {{MODIMO:} Workshop on Multi-Omics Data Integration for Modelling Biological
Systems},
booktitle = {{CIKM}},
pages = {4870--4871},
publisher = {{ACM}},
year = {2021}
}
@inproceedings{DBLP:conf/cikm/LicheriABGB21,
author = {Nicola Licheri and
Elvio Amparone and
Vincenzo Bonnici and
Rosalba Giugno and
Marco Beccuti},
title = {An Entropy Heuristic to Optimize Decision Diagrams for Index-driven
Search in Biological Graph Databases},
booktitle = {{CIKM} Workshops},
series = {{CEUR} Workshop Proceedings},
volume = {3052},
publisher = {CEUR-WS.org},
year = {2021}
}
@inproceedings{DBLP:conf/cmis/MartsenyukKSBBW21,
author = {Vasyl P. Martsenyuk and
Aleksandra Klos{-}Witkowska and
Andriy Sverstiuk and
Oksana Bahrii{-}Zaiats and
Marcin Bernas and
Krzysztof Witos},
title = {Intelligent Big Data System Based on Scientific Machine Learning of
Cyber-physical Systems of Medical and Biological Processes},
booktitle = {{CMIS}},
series = {{CEUR} Workshop Proceedings},
volume = {2864},
pages = {34--48},
publisher = {CEUR-WS.org},
year = {2021}
}
@inproceedings{DBLP:conf/embc/MelanitisNLSFN21,
author = {Nikos Melanitis and
Giorgos Nakopoulos and
Antonio Lozano and
Cristina Soto{-}S{\'{a}}nchez and
Eduardo Fern{\'{a}}ndez and
Konstantina S. Nikita},
title = {Using Biologically-inspired Image Features to Model Retinal Response:
Evidence from Biological Datasets},
booktitle = {{EMBC}},
pages = {3378--3381},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/etfa/ZhengMGHG21,
author = {Tao Zheng and
Zuyao Meng and
Qing Gu and
Fei Huang and
Mikael Gidlund},
title = {A Preliminary Prototype Based on Biological Mimicry for Hardware Data
Acquisition},
booktitle = {{ETFA}},
pages = {1--4},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/eurova-ws/RipkenTT21,
author = {Christine Ripken and
Sebastian Tusk and
Christian Tominski},
title = {Immersive Analytics of Heterogeneous Biological Data Informed through
Need-finding Interviews},
booktitle = {EuroVA@EuroVis},
pages = {13--17},
publisher = {Eurographics Association},
year = {2021}
}
@inproceedings{DBLP:conf/icaai/LiuS21,
author = {Zheng Liu and
Jiayuan Song},
title = {Comparison of Tree-based Feature Selection Algorithms on Biological
Omics Dataset},
booktitle = {{ICAAI}},
pages = {165--169},
publisher = {{ACM}},
year = {2021}
}
@inproceedings{DBLP:conf/icaip/SongL21,
author = {Jiayuan Song and
Zheng Liu},
title = {Comparison of Norm-Based Feature Selection Methods on Biological Omics
Data},
booktitle = {{ICAIP}},
pages = {109--112},
publisher = {{ACM}},
year = {2021}
}
@inproceedings{DBLP:conf/ictc/LeePL21a,
author = {Jiwoo Lee and
SoHyeon Park and
Eun{-}Kyu Lee},
title = {Behavior-based Authentication using User Biological Data to IoT Device
having Touchscreen},
booktitle = {{ICTC}},
pages = {750--752},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/iddm/KomlevoiKLZ21,
author = {Oleksandr Komlevoi and
Nataliia O. Komleva and
Vira Liubchenko and
Svitlana Zinovatna},
title = {Biological Data Mining and Its Applications in Pulmonology},
booktitle = {{IDDM}},
series = {{CEUR} Workshop Proceedings},
volume = {3038},
pages = {44--53},
publisher = {CEUR-WS.org},
year = {2021}
}
@inproceedings{DBLP:conf/ijcnn/XiangHLTW21,
author = {Mingrong Xiang and
Jingyu Hou and
Wei Luo and
Wenjing Tao and
Deshou Wang},
title = {Impute Gene Expression Missing Values via Biological Networks: Optimal
Fusion of Data and Knowledge},
booktitle = {{IJCNN}},
pages = {1--8},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/intellisys/YanD21,
author = {Runze Yan and
Afsaneh Doryab},
title = {Towards a Computational Framework for Automated Discovery and Modeling
of Biological Rhythms from Wearable Data Streams},
booktitle = {IntelliSys {(3)}},
series = {Lecture Notes in Networks and Systems},
volume = {296},
pages = {643--661},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/ipaw/WittnerHMGGSPFM21,
author = {Rudolf Wittner and
Petr Holub and
Heimo M{\"{u}}ller and
J{\"{o}}rg Geiger and
Carole A. Goble and
Stian Soiland{-}Reyes and
Luca Pireddu and
Francesca Frexia and
Cecilia Mascia and
Elliot Fairweather and
Jason R. Swedlow and
Josh Moore and
Caterina Strambio{-}De{-}Castillia and
David Grunwald and
Hiroki Nakae},
title = {{ISO} 23494: Biotechnology - Provenance Information Model for Biological
Specimen And Data},
booktitle = {{IPAW}},
series = {Lecture Notes in Computer Science},
volume = {12839},
pages = {222--225},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/jowo/ShafieiLTOGRK21,
author = {Fateme Shafiei and
Felicitas L{\"{o}}ffler and
Sven Thiel and
Kobkaew Opasjumruskit and
Denis Grabiger and
Pauline Rauh and
Birgitta K{\"{o}}nig{-}Ries},
title = {[Dai: Si] - {A} Modular Dataset Retrieval Framework with a Semantic
Search for Biological Data},
booktitle = {{JOWO}},
series = {{CEUR} Workshop Proceedings},
volume = {2969},
publisher = {CEUR-WS.org},
year = {2021}
}
@inproceedings{DBLP:conf/memea/FirouzehCR21,
author = {Fereshteh Fakhar Firouzeh and
John W. Chinneck and
Sreeraman Rajan},
title = {Biological Data Classification via Faster MAXimum Feasible Subsystem
Algorithm},
booktitle = {MeMeA},
pages = {1--5},
publisher = {{IEEE}},
year = {2021}
}
@inproceedings{DBLP:conf/mtsr/InizanFGSS21,
author = {Olivier Inizan and
Vincent Fromion and
Anne Goelzer and
Fatiha Sa{\"{\i}}s and
Danai Symeonidou},
title = {An Ontology to Structure Biological Data: The Contribution of Mathematical
Models},
booktitle = {{MTSR}},
series = {Communications in Computer and Information Science},
volume = {1537},
pages = {57--64},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/ola/VaginayBS21,
author = {Ath{\'{e}}na{\"{\i}}s Vaginay and
Taha Boukhobza and
Malika Sma{\"{\i}}l{-}Tabbone},
title = {Automatic Synthesis of Boolean Networks from Biological Knowledge
and Data},
booktitle = {{OLA}},
series = {Communications in Computer and Information Science},
volume = {1443},
pages = {156--170},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/spml/Tong21,
author = {Fu Tong},
title = {A Comprehensive Comparison of Neural Network-Based Feature Selection
Methods in Biological Omics Datasets},
booktitle = {{SPML}},
pages = {77--81},
publisher = {{ACM}},
year = {2021}
}
@article{DBLP:journals/corr/abs-2103-08335,
author = {Xuequan Lu and
Yihao Wang and
Sheldon Fung and
Xue Qing},
title = {I-Nema: {A} Biological Image Dataset for Nematode Recognition},
journal = {CoRR},
volume = {abs/2103.08335},
year = {2021}
}
@article{DBLP:journals/corr/abs-2107-02168,
author = {Dongqi Fu and
Jingrui He},
title = {{DPPIN:} {A} Biological Dataset of Dynamic Protein-Protein Interaction
Networks},
journal = {CoRR},
volume = {abs/2107.02168},
year = {2021}
}
@article{DBLP:journals/corr/abs-2107-05388,
author = {Vahidullah Tac and
Vivek D. Sree and
Manuel K. Rausch and
Adrian Buganza Tepole},
title = {Data-driven Modeling of the Mechanical Behavior of Anisotropic Soft
Biological Tissue},
journal = {CoRR},
volume = {abs/2107.05388},
year = {2021}
}
@article{DBLP:journals/corr/abs-2107-13822,
author = {Erik Esche and
Torben Talis and
Joris Weigert and
Gerardo Brand{-}Rihm and
Byungjun You and
Christian Hoffmann and
Jens{-}Uwe Repke},
title = {Semi-supervised Learning for Data-driven Soft-sensing of Biological
and Chemical Processes},
journal = {CoRR},
volume = {abs/2107.13822},
year = {2021}
}
@article{DBLP:journals/corr/abs-2109-06177,
author = {Runze Yan and
Afsaneh Doryab},
title = {Towards a Computational Framework for Automated Discovery and Modeling
of Biological Rhythms from Wearable Data Streams},
journal = {CoRR},
volume = {abs/2109.06177},
year = {2021}
}
@article{DBLP:journals/corr/abs-2110-12058,
author = {Satoshi Kume and
Hiroshi Masuya and
Mitsuyo Maeda and
Mitsuo Suga and
Yosky Kataoka and
Norio Kobayashi},
title = {Development of Semantic Web-based Imaging Database for Biological
Morphome},
journal = {CoRR},
volume = {abs/2110.12058},
year = {2021}
}
@article{DBLP:journals/corr/abs-2112-07173,
author = {Binxu Wang and
David Mayo and
Arturo Deza and
Andrei Barbu and
Colin Conwell},
title = {On the use of Cortical Magnification and Saccades as Biological Proxies
for Data Augmentation},
journal = {CoRR},
volume = {abs/2112.07173},
year = {2021}
}
@article{DBLP:journals/dagstuhl-reports/KleinMNZ21,
author = {Karsten Klein and
Georgeta Elisabeta Marai and
Kay Katja Nieselt and
Blaz Zupan},
title = {Visualization of Biological Data - From Analysis to Communication
(Dagstuhl Seminar 21401)},
journal = {Dagstuhl Reports},
volume = {11},
number = {9},
pages = {1--27},
year = {2021}
}
@phdthesis{DBLP:phd/au/Lee20,
author = {Stuart Lee},
title = {Fluent statistical computing interfaces for biological data analysis},
school = {Monash University, Australia},
year = {2020}
}
@phdthesis{DBLP:phd/basesearch/Chen20n,
author = {Junfang Chen},
title = {Biologically informed risk scoring in schizophrenia based on genome-wide
omics data},
school = {Heidelberg University, Germany},
year = {2020}
}
@phdthesis{DBLP:phd/ethos/Robinson20,
author = {Scott W. Robinson},
title = {The integration of large biological and clinical datasets towards
the understanding of human disease},
school = {University of Glasgow, {UK}},
year = {2020}
}
@phdthesis{DBLP:phd/gr/Vlastaridis20,
author = {Panayotis Vlastaridis},
title = {Bioinformatics analysis, management and organization of biological
data related to post-translational regulation},
school = {University of Thessaly, Greece},
year = {2020}
}
@article{DBLP:journals/ans/MalekZG20,
author = {Maria Malek and
Simone Zorzan and
Mohammad Ghoniem},
title = {A methodology for multilayer networks analysis in the context of open
and private data: biological application},
journal = {Appl. Netw. Sci.},
volume = {5},
number = {1},
pages = {41},
year = {2020}
}
@article{DBLP:journals/biodb/CowmanCGK20,
author = {Tyler Cowman and
Mustafa Coskun and
Ananth Grama and
Mehmet Koyut{\"{u}}rk},
title = {Integrated querying and version control of context-specific biological
networks},
journal = {Database J. Biol. Databases Curation},
volume = {2020},
year = {2020}
}
@article{DBLP:journals/biodb/SpoorWSCACHHJSW20,
author = {Shawna Spoor and
Connor Wytko and
Brian Soto and
Ming Chen and
Abdullah Almsaeed and
Bradford Condon and
Nic Herndon and
Heidi Hough and
Sook Jung and
Meg Staton and
Jill L. Wegrzyn and
Dorrie Main and
F. Alex Feltus and
Stephen P. Ficklin},
title = {Tripal and Galaxy: supporting reproducible scientific workflows for
community biological databases},
journal = {Database J. Biol. Databases Curation},
volume = {2020},
year = {2020}
}
@article{DBLP:journals/biodb/WuWYT20,
author = {Wei{-}Sheng Wu and
Lai{-}Ji Wang and
Han{-}Chen Yen and
Yan Yuan Tseng},
title = {{YQFC:} a web tool to compare quantitative biological features between
two yeast gene lists},
journal = {Database J. Biol. Databases Curation},
volume = {2020},
year = {2020}
}
@article{DBLP:journals/biodb/XuCZDLZ20,
author = {Tingjun Xu and
Weiming Chen and
Junhong Zhou and
Jingfang Dai and
Yingyong Li and
Yingli Zhao},
title = {{NPBS} database: a chemical data resource with relational data between
natural products and biological sources},
journal = {Database J. Biol. Databases Curation},
volume = {2020},
year = {2020}
}
@article{DBLP:journals/bioinformatics/BoileauHD20,
author = {Philippe Boileau and
Nima S. Hejazi and
Sandrine Dudoit},
title = {Exploring high-dimensional biological data with sparse contrastive
principal component analysis},
journal = {Bioinform.},
volume = {36},
number = {11},
pages = {3422--3430},
year = {2020}
}
@article{DBLP:journals/bioinformatics/DemeoB20,
author = {Benjamin Demeo and
Bonnie Berger},
title = {Hopper: a mathematically optimal algorithm for sketching biological
data},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i236--i241},
year = {2020}
}
@article{DBLP:journals/bioinformatics/GardiniGDC20,
author = {Erika Gardini and
Federico M. Giorgi and
Sergio Decherchi and
Andrea Cavalli},
title = {Spathial: an {R} package for the evolutionary analysis of biological
data},
journal = {Bioinform.},
volume = {36},
number = {17},
pages = {4664--4667},
year = {2020}
}
@article{DBLP:journals/bioinformatics/PikeKPTMRPS20,
author = {Jeremy A. Pike and
Abdullah O. Khan and
Chiara Pallini and
Steven G. Thomas and
Markus Mund and
Jonas Ries and
Natalie S. Poulter and
Iain B. Styles},
title = {Topological data analysis quantifies biological nano-structure from
single molecule localization microscopy},
journal = {Bioinform.},
volume = {36},
number = {5},
pages = {1614--1621},
year = {2020}
}
@article{DBLP:journals/bioinformatics/SeifertGJSM20,
author = {Stephan Seifert and
Sven Gundlach and
Olaf Junge and
Silke Szymczak and
Luigi Martelli},
title = {Integrating biological knowledge and gene expression data using pathway-guided
random forests: a benchmarking study},
journal = {Bioinform.},
volume = {36},
number = {15},
pages = {4301--4308},
year = {2020}
}
@article{DBLP:journals/bioinformatics/YaoQH20,
author = {Ruijie Yao and
Jiaqiang Qian and
Qiang Huang},
title = {Deep-learning with synthetic data enables automated picking of cryo-EM
particle images of biological macromolecules},
journal = {Bioinform.},
volume = {36},
number = {4},
pages = {1252--1259},
year = {2020}
}
@article{DBLP:journals/bmcbi/AcharyaCP20a,
author = {Sudipta Acharya and
Laizhong Cui and
Yi Pan},
title = {Multi-view feature selection for identifying gene markers: a diversified
biological data driven approach},
journal = {{BMC} Bioinform.},
volume = {21-S},
number = {18},
pages = {483},
year = {2020}
}
@article{DBLP:journals/bmcbi/WuSYWLZ20,
author = {Wenting Wu and
Lei Song and
Yongtao Yang and
Jianxin Wang and
Hongtu Liu and
Le Zhang},
title = {Exploring the dynamics and interplay of human papillomavirus and cervical
tumorigenesis by integrating biological data into a mathematical model},
journal = {{BMC} Bioinform.},
volume = {21-S},
number = {7},
pages = {152},
year = {2020}
}
@article{DBLP:journals/candc/ZhangCZLZZZZ20,
author = {Tianyue Zhang and
Haowu Chang and
Borui Zhang and
Sifei Liu and
Tianheng Zhao and
Enshuang Zhao and
Hengyi Zhao and
Hao Zhang},
title = {Transboundary Pathogenic microRNA Analysis Framework for Crop Fungi
Driven by Biological Big Data and Artificial Intelligence Model},
journal = {Comput. Biol. Chem.},
volume = {89},
pages = {107401},
year = {2020}
}
@article{DBLP:journals/cce/SunB20,
author = {Weike Sun and
Richard D. Braatz},
title = {Opportunities in tensorial data analytics for chemical and biological
manufacturing processes},
journal = {Comput. Chem. Eng.},
volume = {143},
pages = {107099},
year = {2020}
}
@article{DBLP:journals/cmmm/WeylandTNBUPLFS20,
author = {Mathias S. Weyland and
Pauline Thumser{-}Henner and
Katarzyna J. Nytko and
Carla Rohrer Bley and
Simone Ulzega and
Alke Petri{-}Fink and
Marco Lattuada and
Rudolf M. F{\"{u}}chslin and
Stephan Scheidegger},
title = {Holistic View on Cell Survival and {DNA} Damage: How Model-Based Data
Analysis Supports Exploration of Dynamics in Biological Systems},
journal = {Comput. Math. Methods Medicine},
volume = {2020},
pages = {5972594:1--5972594:11},
year = {2020}
}
@article{DBLP:journals/el/YoonK20,
author = {Ayoung Yoon and
Youngseek Kim},
title = {The role of data-reuse experience in biological scientists' data sharing:
an empirical analysis},
journal = {Electron. Libr.},
volume = {38},
number = {1},
pages = {186--208},
year = {2020}
}
@article{DBLP:journals/entropy/DasR20,
author = {Samarendra Das and
Shesh N. Rai},
title = {Statistical Approach for Biologically Relevant Gene Selection from
High-Throughput Gene Expression Data},
journal = {Entropy},
volume = {22},
number = {11},
pages = {1205},
year = {2020}
}
@article{DBLP:journals/gpb/ChenBEJLMORSZV20,
author = {Qingyu Chen and
Ramona Britto and
Ivan Erill and
Constance J. Jeffery and
Arthur Liberzon and
Michele Magrane and
Jun{-}ichi Onami and
Marc Robinson{-}Rechavi and
Jana Sponarova and
Justin Zobel and
Karin Verspoor},
title = {Quality Matters: Biocuration Experts on the Impact of Duplication
and Other Data Quality Issues in Biological Databases},
journal = {Genom. Proteom. Bioinform.},
volume = {18},
number = {2},
pages = {91--103},
year = {2020}
}
@article{DBLP:journals/ijncr/VaniKKPA20,
author = {Koneru Suvarna Vani and
K. Praveen Kumar and
Geethika Kodali and
Naveen Pothineni and
Sri Chaitanya Aravapalli},
title = {An Exploration of Mixed {DNA} Samples by Forensic Biological Data},
journal = {Int. J. Nat. Comput. Res.},
volume = {9},
number = {2},
pages = {1--13},
year = {2020}
}
@article{DBLP:journals/ijoci/BoufenaraBB20,
author = {Mohamed Nadjib Boufenara and
Mahmoud Boufa{\"{\i}}da and
Mohamed Lamine Berkane},
title = {A Prediction Approach Based on Self-Training and Deep Learning for
Biological Data},
journal = {Int. J. Organ. Collect. Intell.},
volume = {10},
number = {4},
pages = {50--64},
year = {2020}
}
@article{DBLP:journals/jifs/AhmadJKK20,
author = {Shabir Ahmad and
Faisal Jamil and
Azimbek Khudoyberdiev and
Dohyeun Kim},
title = {Accident risk prediction and avoidance in intelligent semi-autonomous
vehicles based on road safety data and driver biological behaviours},
journal = {J. Intell. Fuzzy Syst.},
volume = {38},
number = {4},
pages = {4591--4601},
year = {2020}
}
@article{DBLP:journals/jifs/ShuklaPGRT20,
author = {Alok Kumar Shukla and
Sanjeev Kumar Pippal and
Srishti Gupta and
B. Ramachandra Reddy and
Diwakar Tripathi},
title = {Knowledge discovery in medical and biological datasets by integration
of Relief-F and correlation feature selection techniques},
journal = {J. Intell. Fuzzy Syst.},
volume = {38},
number = {5},
pages = {6637--6648},
year = {2020}
}
@article{DBLP:journals/jmihi/AhmadIB20,
author = {Iftikhar Ahmad and
Muhammad Javed Iqbal and
Mohammad Basheri},
title = {Biological Data Classification and Analysis Using Convolutional Neural
Network},
journal = {J. Medical Imaging Health Informatics},
volume = {10},
number = {10},
pages = {2459--2465},
year = {2020}
}
@article{DBLP:journals/jmihi/AhmadIB20a,
author = {Iftikhar Ahmad and
Muhammad Javed Iqbal and
Mohammad Basheri},
title = {Biological Data Classification and Analysis Using Convolutional Neural
Network},
journal = {J. Medical Imaging Health Informatics},
volume = {10},
number = {10},
pages = {2459--2465},
year = {2020}
}
@article{DBLP:journals/jms/AlbahriHAAZZAAK20,
author = {Ahmed Shihab Albahri and
Rula A. Hamid and
Jwan K. Alwan and
Z. T. Al{-}qays and
A. A. Zaidan and
B. B. Zaidan and
Osamah Shihab Albahri and
Abdullah Hussein Alamoodi and
Jamal Mawlood Khlaf and
E. M. Almahdi and
Eman Thabet and
Suha M. Hadi and
K. I. Mohammed and
M. A. Alsalem and
Jameel R. Al{-}Obaidi and
H. T. Madhloom},
title = {Role of biological Data Mining and Machine Learning Techniques in
Detecting and Diagnosing the Novel Coronavirus {(COVID-19):} {A} Systematic
Review},
journal = {J. Medical Syst.},
volume = {44},
number = {7},
pages = {122},
year = {2020}
}
@article{DBLP:journals/jossw/KellyB20,
author = {Simon Thomas Kelly and
Michael A. Black},
title = {graphsim: An {R} package for simulating gene expression data from
graph structures of biological pathways},
journal = {J. Open Source Softw.},
volume = {5},
number = {51},
pages = {2161},
year = {2020}
}
@article{DBLP:journals/nn/BaxterL20,
author = {Robert A. Baxter and
William B. Levy},
title = {Constructing multilayered neural networks with sparse, data-driven
connectivity using biologically-inspired, complementary, homeostatic
mechanisms},
journal = {Neural Networks},
volume = {122},
pages = {68--93},
year = {2020}
}
@article{DBLP:journals/patterns/ShahLLCGCHZ20,
author = {Najeebullah Shah and
Jiaqi Li and
Fanhong Li and
Wenchang Chen and
Haoxiang Gao and
Sijie Chen and
Kui Hua and
Xuegong Zhang},
title = {An Experiment on \emph{Ab Initio} Discovery of Biological Knowledge
from scRNA-Seq Data Using Machine Learning},
journal = {Patterns},
volume = {1},
number = {5},
pages = {100071},
year = {2020}
}
@article{DBLP:journals/ploscb/HattabRH20,
author = {Georges Hattab and
Theresa{-}Marie Rhyne and
Dominik Heider},
title = {Ten simple rules to colorize biological data visualization},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {10},
year = {2020}
}
@article{DBLP:journals/ploscb/LagergrenNBSF20,
author = {John H. Lagergren and
John T. Nardini and
Ruth E. Baker and
Matthew J. Simpson and
Kevin B. Flores},
title = {Biologically-informed neural networks guide mechanistic modeling from
sparse experimental data},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {12},
year = {2020}
}
@article{DBLP:journals/ploscb/TerkelsenKP20,
author = {Thilde Terkelsen and
Anders Krogh and
Elena Papaleo},
title = {CAncer bioMarker Prediction Pipeline {(CAMPP)} - {A} standardized
framework for the analysis of quantitative biological data},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {3},
year = {2020}
}
@article{DBLP:journals/remotesensing/GauthreauxD20,
author = {Sidney Gauthreaux and
Robert Diehl},
title = {Discrimination of Biological Scatterers in Polarimetric Weather Radar
Data: Opportunities and Challenges},
journal = {Remote. Sens.},
volume = {12},
number = {3},
pages = {545},
year = {2020}
}
@article{DBLP:journals/tbd/ZhangLZSKYJ20,
author = {Wenlu Zhang and
Rongjian Li and
Tao Zeng and
Qian Sun and
Sudhir Kumar and
Jieping Ye and
Shuiwang Ji},
title = {Deep Model Based Transfer and Multi-Task Learning for Biological Image
Analysis},
journal = {{IEEE} Trans. Big Data},
volume = {6},
number = {2},
pages = {322--333},
year = {2020}
}
@article{DBLP:journals/tcbb/LiuLZSL20,
author = {Jian Liu and
Qiuru Liu and
Lei Zhang and
Shuhui Su and
Yongzhuang Liu},
title = {Enabling Massive XML-Based Biological Data Management in HBase},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {17},
number = {6},
pages = {1994--2004},
year = {2020}
}
@article{DBLP:journals/tcbb/LiuNW20,
author = {Ye Liu and
Michael K. Ng and
Stephen Wu},
title = {Multi-Domain Networks Association for Biological Data Using Block
Signed Graph Clustering},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {17},
number = {2},
pages = {435--448},
year = {2020}
}
@article{DBLP:journals/tcbb/MarczykJPP20,
author = {Michal Marczyk and
Roman Jaksik and
Andrzej Polanski and
Joanna Polanska},
title = {GaMRed - Adaptive Filtering of High-Throughput Biological Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {17},
number = {1},
pages = {149--157},
year = {2020}
}
@inproceedings{DBLP:conf/bibm/Hoard20,
author = {Brittany R. Hoard},
title = {Biological Rule-Based Modeling of Experimental Cell Secretion Data},
booktitle = {{BIBM}},
pages = {1245--1252},
publisher = {{IEEE}},
year = {2020}
}
@inproceedings{DBLP:conf/cikm/WalshMN20,
author = {Brian Walsh and
Sameh K. Mohamed and
V{\'{\i}}t Nov{\'{a}}cek},
title = {BioKG: {A} Knowledge Graph for Relational Learning On Biological Data},
booktitle = {{CIKM}},
pages = {3173--3180},
publisher = {{ACM}},
year = {2020}
}
@inproceedings{DBLP:conf/cogsci/TsvetkovMEB20,
author = {Christian Tsvetkov and
Gaurav Malhotra and
Benjamin Evans and
Jeffrey S. Bowers},
title = {Adding biological constraints to deep neural networks reduces their
capacity to learn unstructured data},
booktitle = {CogSci},
publisher = {cognitivesciencesociety.org},
year = {2020}
}
@inproceedings{DBLP:conf/embc/HaKBLLS20,
author = {Junhyoung Ha and
Soonkyum Kim and
YaeJun Baik and
Dohee Lee and
Woosub Lee and
SeungBeum Suh},
title = {Artificial Neural Network enabling Clinically Meaningful Biological
Image Data Generation},
booktitle = {{EMBC}},
pages = {2404--2407},
publisher = {{IEEE}},
year = {2020}
}
@inproceedings{DBLP:conf/er/AgapitoC20,
author = {Giuseppe Agapito and
Mario Cannataro},
title = {Using BioPAX-Parser (BiP) to Annotate Lists of Biological Entities
with Pathway Data},
booktitle = {{ER} (Workshops)},
series = {Lecture Notes in Computer Science},
volume = {12584},
pages = {92--101},
publisher = {Springer},
year = {2020}
}
@inproceedings{DBLP:conf/icann/UedaTN20,
author = {Takaya Ueda and
Yukako Tohsato and
Ikuko Nishikawa},
title = {Temporal Anomaly Detection by Deep Generative Models with Applications
to Biological Data},
booktitle = {{ICANN} {(1)}},
series = {Lecture Notes in Computer Science},
volume = {12396},
pages = {553--565},
publisher = {Springer},
year = {2020}
}
@inproceedings{DBLP:conf/icbet/WangZWCF20,
author = {Ningya Wang and
Wenbin Zhou and
Jiamin Wu and
Shengjia Chen and
Ziling Fan},
title = {Comparison of Penalty-based Feature Selection Approach on High Throughput
Biological Data},
booktitle = {{ICBET}},
pages = {176--183},
publisher = {{ACM}},
year = {2020}
}
@inproceedings{DBLP:conf/icbet/WuCZWF20,
author = {Jiamin Wu and
Shengjia Chen and
Wenbin Zhou and
Ningya Wang and
Ziling Fan},
title = {Evaluation of Feature Selection Methods using Bagging and Boosting
Ensemble Techniques on High Throughput Biological Data},
booktitle = {{ICBET}},
pages = {170--175},
publisher = {{ACM}},
year = {2020}
}
@inproceedings{DBLP:conf/iccai/DengZCLQ20a,
author = {Jianzhi Deng and
Yuehan Zhou and
Xiaohui Cheng and
Tianyu Li and
Chuling Qin},
title = {Biological Big Data Analysis of Competing Endogenous {RNA} Network
and mRNA Biomarker in Liver Cancer},
booktitle = {{ICCAI}},
pages = {94--98},
publisher = {{ACM}},
year = {2020}
}
@inproceedings{DBLP:conf/icpr/KokerCWTWCW20,
author = {T. E. Koker and
S. S. Chintapalli and
S. Wang and
Blake A. Talbot and
D. Wainstock and
Marcelo Cicconet and
M. C. Walsh},
title = {On Identification and Retrieval of Near-Duplicate Biological Images:
a New Dataset and Protocol},
booktitle = {{ICPR}},
pages = {3114--3121},
publisher = {{IEEE}},
year = {2020}
}
@inproceedings{DBLP:conf/ifip12/AlshammaryIMV20,
author = {Miznah H. Alshammary and
Costas S. Iliopoulos and
Manal Mohamed and
Fatima Vayani},
title = {Application and Algorithm: Maximal Motif Discovery for Biological
Data in a Sliding Window},
booktitle = {{AIAI} Workshops},
series = {{IFIP} Advances in Information and Communication Technology},
volume = {585},
pages = {213--224},
publisher = {Springer},
year = {2020}
}
@inproceedings{DBLP:conf/mm/Baird20,
author = {Alice Baird},
title = {Extending Multimodal Emotion Recognition with Biological Signals:
Presenting a Novel Dataset and Recent Findings},
booktitle = {MuSe @ {ACM} Multimedia},
pages = {7},
publisher = {{ACM}},
year = {2020}
}
@inproceedings{DBLP:conf/scisisis/ParkJJ20,
author = {Sung Min Park and
Junghyun Jung and
Jong Wha Joanne Joo},
title = {Integrative Meta-analysis of Transcriptome Data for Unmasking Biological
Mechanism of Idiopathic pulmonary fibrosis},
booktitle = {{SCIS/ISIS}},
pages = {1--3},
publisher = {{IEEE}},
year = {2020}
}
@inproceedings{DBLP:conf/semco/AngeloIASOAHB20,
author = {Rafaela M. Angelo and
Andreia K. Io and
Matheus P. Almeida and
Rafael G. Silveira and
Patr{\'{\i}}cia R. Oliveira and
Jose J. P. Alcazar and
K{\'{a}}thia Maria Hon{\'{o}}rio and
Fernanda Bettanin},
title = {OntoQSAR: an Ontology for Interpreting Chemical and Biological Data
in Quantitative Structure-Activity Relationship Studies},
booktitle = {{ICSC}},
pages = {203--206},
publisher = {{IEEE}},
year = {2020}
}
@inproceedings{DBLP:conf/systor/KaplanYG20,
author = {Roman Kaplan and
Leonid Yavits and
Ran Ginosar},
title = {BioSEAL: In-Memory Biological Sequence Alignment Accelerator for Large-Scale
Genomic Data},
booktitle = {{SYSTOR}},
pages = {36--48},
publisher = {{ACM}},
year = {2020}
}
@article{DBLP:journals/corr/abs-2001-08322,
author = {Dinesh Singh and
Makoto Yamada},
title = {FsNet: Feature Selection Network on High-dimensional Biological Data},
journal = {CoRR},
volume = {abs/2001.08322},
year = {2020}
}
@article{DBLP:journals/corr/abs-2002-07064,
author = {Michele Gentili and
Leonardo Martini and
Manuela Petti and
Lorenzo Farina and
Luca Becchetti},
title = {Biological Random Walks: integrating heterogeneous data in disease
gene prioritization},
journal = {CoRR},
volume = {abs/2002.07064},
year = {2020}
}
@article{DBLP:journals/corr/abs-2003-00108,
author = {Mufti Mahmud and
M. Shamim Kaiser and
Amir Hussain},
title = {Deep Learning in Mining Biological Data},
journal = {CoRR},
volume = {abs/2003.00108},
year = {2020}
}
@phdthesis{DBLP:phd/basesearch/Watford19,
author = {Sean Watford},
title = {Interoperability in Toxicology: Connecting Chemical, biological, and
Complex disease Data},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2019}
}
@phdthesis{DBLP:phd/hal/Lima19,
author = {Leandro Ishi Soares de Lima},
title = {De novo algorithms to identify patterns associated with biological
events in de Bruijn graphs built from {NGS} data. (Algorithmes de
novo pour l'identification de motifs associ{\'{e}}s {\`{a}} des
{\'{e}}v{\'{e}}nements biologiques dans les graphes de De
Bruijn construits {\`{a}} partir de donn{\'{e}}es {NGS)}},
school = {University of Lyon, France},
year = {2019}
}
@phdthesis{DBLP:phd/hal/Soret19,
author = {Perrine Soret},
title = {R{\'{e}}gression p{\'{e}}nalis{\'{e}}e de type Lasso
pour l'analyse de donn{\'{e}}es biologiques de grande dimension
: application {\`{a}} la charge virale du {VIH} censur{\'{e}}e
par une limite de quantification et aux donn{\'{e}}es compositionnelles
du microbiote. (Penalized Lasso regression for the analysis of high-dimensional
biological data: application to {HIV} viral load censored by a limit
of quantification and to microbiota compositional data)},
school = {University of Bordeaux, France},
year = {2019}
}
@article{DBLP:journals/access/ChenLC19a,
author = {Shih{-}Yeh Chen and
Chin{-}Feng Lai and
Chi{-}Cheng Chang},
title = {A Hybrid Biological Data Analysis Approach for Students' Learning
Creative Characteristics Recognition},
journal = {{IEEE} Access},
volume = {7},
pages = {134411--134421},
year = {2019}
}
@article{DBLP:journals/aslib/JuK19,
author = {Boryung Ju and
Youngseek Kim},
title = {The formation of research ethics for data sharing by biological scientists:
an empirical analysis},
journal = {Aslib J. Inf. Manag.},
volume = {71},
number = {5},
pages = {583--600},
year = {2019}
}
@article{DBLP:journals/bib/CruzAM19,
author = {Ant{\'{o}}nio Cruz and
Joel P. Arrais and
Penousal Machado},
title = {Interactive and coordinated visualization approaches for biological
data analysis},
journal = {Briefings Bioinform.},
volume = {20},
number = {4},
pages = {1513--1523},
year = {2019}
}
@article{DBLP:journals/bib/XieMFMZ19,
author = {Juan Xie and
Anjun Ma and
Anne Fennell and
Qin Ma and
Jing Zhao},
title = {It is time to apply biclustering: a comprehensive review of biclustering
applications in biological and biomedical data},
journal = {Briefings Bioinform.},
volume = {20},
number = {4},
pages = {1449--1464},
year = {2019}
}
@article{DBLP:journals/biodb/HoytDAXKSWBGGH19,
author = {Charles Tapley Hoyt and
Daniel Domingo{-}Fern{\'{a}}ndez and
Rana Aldisi and
Lingling Xu and
Kristian Kolpeja and
Sandra Spalek and
Esther Wollert and
John A. Bachman and
Benjamin M. Gyori and
Patrick Greene and
Martin Hofmann{-}Apitius},
title = {Re-curation and rational enrichment of knowledge graphs in Biological
Expression Language},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz068},
year = {2019}
}
@article{DBLP:journals/biodb/MadanSETAQRHF19,
author = {Sumit Madan and
Justyna Szostak and
Ravikumar Komandur Elayavilli and
Richard Tzong{-}Han Tsai and
Mehdi Ali and
Longhua Qian and
Majid Rastegar{-}Mojarad and
Julia Hoeng and
Juliane Fluck},
title = {The extraction of complex relationships and their conversion to biological
expression language {(BEL)} overview of the BioCreative {VI} {(2017)}
{BEL} track},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz084},
year = {2019}
}
@article{DBLP:journals/biodb/SpoorCSCACBRJMB19,
author = {Shawna Spoor and
Chun{-}Huai Cheng and
Lacey{-}Anne Sanderson and
Bradford Condon and
Abdullah Almsaeed and
Ming Chen and
Anthony Bretaudeau and
Helena Rasche and
Sook Jung and
Dorrie Main and
Kirstin E. Bett and
Margaret Staton and
Jill L. Wegrzyn and
F. Alex Feltus and
Stephen P. Ficklin},
title = {Tripal v3: an ontology-based toolkit for construction of {FAIR} biological
community databases},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz077},
year = {2019}
}
@article{DBLP:journals/bioinformatics/BraunSPAS19,
author = {Bremen L. Braun and
David A. Schott and
John L. Portwood II and
Carson M. Andorf and
Taner Z. Sen},
title = {PedigreeNet: a web-based pedigree viewer for biological databases},
journal = {Bioinform.},
volume = {35},
number = {20},
pages = {4184--4186},
year = {2019}
}
@article{DBLP:journals/bioinformatics/WangFWC19,
author = {Yue Wang and
Jennifer M. Franks and
Michael L. Whitfield and
Chao Cheng},
title = {BioMethyl: an {R} package for biological interpretation of {DNA} methylation
data},
journal = {Bioinform.},
volume = {35},
number = {19},
pages = {3635--3641},
year = {2019}
}
@article{DBLP:journals/bioinformatics/WenHTH19,
author = {Zeyu Wen and
Jiahua He and
Huanyu Tao and
Sheng{-}You Huang},
title = {PepBDB: a comprehensive structural database of biological peptide-protein
interactions},
journal = {Bioinform.},
volume = {35},
number = {1},
pages = {175--177},
year = {2019}
}
@article{DBLP:journals/bmcbi/BouadjenekZV19,
author = {Mohamed Reda Bouadjenek and
Justin Zobel and
Karin Verspoor},
title = {Automated assessment of biological database assertions using the scientific
literature},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {216:1--216:22},
year = {2019}
}
@article{DBLP:journals/bmcbi/ChungMSG19,
author = {Neo Christopher Chung and
Blazej Miasojedow and
Michal Startek and
Anna Gambin},
title = {Jaccard/Tanimoto similarity test and estimation methods for biological
presence-absence data},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {15},
pages = {644},
year = {2019}
}
@article{DBLP:journals/bmcbi/DirmeierEDB19,
author = {Simon Dirmeier and
Mario Emmenlauer and
Christoph Dehio and
Niko Beerenwinkel},
title = {PyBDA: a command line tool for automated analysis of big biological
data sets},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {564:1--564:6},
year = {2019}
}
@article{DBLP:journals/bmcbi/HanL19a,
author = {Henry Han and
Wenbin Liu},
title = {The coming era of artificial intelligence in biological data science},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {22},
pages = {712},
year = {2019}
}
@article{DBLP:journals/bmcbi/KinalisNWB19,
author = {Savvas Kinalis and
Finn Cilius Nielsen and
Ole Winther and
Frederik Otzen Bagger},
title = {Deconvolution of autoencoders to learn biological regulatory modules
from single cell mRNA sequencing data},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {379:1--379:9},
year = {2019}
}
@article{DBLP:journals/bmcbi/LuPL19,
author = {Yuping Lu and
Charles A. Phillips and
Michael A. Langston},
title = {A robustness metric for biological data clustering algorithms},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {15},
pages = {503},
year = {2019}
}
@article{DBLP:journals/bmcbi/Perez-GilLDMRM19,
author = {Daniel Perez{-}Gil and
Francisco J. Lopez and
Joaqu{\'{\i}}n Dopazo and
Pablo Mar{\'{\i}}n{-}Garc{\'{\i}}a and
Augusto Rendon and
Ignacio Medina},
title = {PyCellBase, an efficient python package for easy retrieval of biological
data from heterogeneous sources},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {159:1--159:5},
year = {2019}
}
@article{DBLP:journals/bmcbi/WangJPZW19a,
author = {Yongtian Wang and
Liran Juan and
Jiajie Peng and
Tianyi Zang and
Yadong Wang},
title = {LncDisAP: a computation model for LncRNA-disease association prediction
based on multiple biological datasets},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {16},
pages = {582:1--582:11},
year = {2019}
}
@article{DBLP:journals/bmcbi/ZhangLB19,
author = {Wenxiang Zhang and
Xiujuan Lei and
Chen Bian},
title = {Identifying Cancer genes by combining two-rounds {RWR} based on multiple
biological data},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {18},
pages = {518:1--518:12},
year = {2019}
}
@article{DBLP:journals/bmcbi/ZhangPCC19,
author = {Jimmy F. Zhang and
Alex R. Paciorkowski and
Paul A. Craig and
Feng Cui},
title = {BioVR: a platform for virtual reality assisted biological data integration
and visualization},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {78:1--78:10},
year = {2019}
}
@article{DBLP:journals/cluster/Bo19a,
author = {Yang Bo},
title = {The data clustering based dynamic risk identification of biological
immune system: mechanism, method and simulation},
journal = {Clust. Comput.},
volume = {22},
number = {Supplement},
pages = {6253--6266},
year = {2019}
}
@article{DBLP:journals/cogsr/OgielaO19,
author = {Lidia Ogiela and
Urszula Ogiela},
title = {Cognitive and biologically cryptographic protocols for data security},
journal = {Cogn. Syst. Res.},
volume = {56},
pages = {1--6},
year = {2019}
}
@article{DBLP:journals/dim/XuGJTLR19,
author = {Weijia Xu and
Amit Gupta and
Pankaj Jaiswal and
Crispin Taylor and
Patti Lockhart and
Jennifer Regala},
title = {Improving Publication Pipeline with Automated Biological Entity Detection
and Validation Service},
journal = {Data Inf. Manag.},
volume = {3},
number = {1},
pages = {3--17},
year = {2019}
}
@article{DBLP:journals/ijcini/Hiraishi19,
author = {Hironori Hiraishi},
title = {Qualitative and Cognitive Analysis and Modeling Tool for Biological
Data},
journal = {Int. J. Cogn. Informatics Nat. Intell.},
volume = {13},
number = {2},
pages = {30--47},
year = {2019}
}
@article{DBLP:journals/ijmdem/HosseinkhaniJ19,
author = {Jila Hosseinkhani and
Chris Joslin},
title = {A Biologically Inspired Saliency Priority Extraction Using Bayesian
Framework},
journal = {Int. J. Multim. Data Eng. Manag.},
volume = {10},
number = {2},
pages = {1--20},
year = {2019}
}
@article{DBLP:journals/ijon/WuL19,
author = {Fang{-}Xiang Wu and
Min Li},
title = {Deep learning for biological/clinical data},
journal = {Neurocomputing},
volume = {324},
pages = {1--2},
year = {2019}
}
@article{DBLP:journals/jcisd/TarasovaBFPN19,
author = {Olga A. Tarasova and
Nadezhda Yu. Biziukova and
Dmitry Filimonov and
Vladimir Poroikov and
Marc C. Nicklaus},
title = {Data Mining Approach for Extraction of Useful Information About Biologically
Active Compounds from Publications},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {9},
pages = {3635--3644},
year = {2019}
}
@article{DBLP:journals/jib/PerscheidGU19,
author = {Cindy Perscheid and
Bastien Grasnick and
Matthias Uflacker},
title = {Integrative Gene Selection on Gene Expression Data: Providing Biological
Context to Traditional Approaches},
journal = {J. Integr. Bioinform.},
volume = {16},
number = {1},
year = {2019}
}
@article{DBLP:journals/jsjkx/LiuWGYL19,
author = {Yuan Liu and
Xin Wang and
Ying Gan and
Chaozhou Yang and
Weixi Li},
title = {BioPW+: {\unicode{22522}}{\unicode{20110}}Linked Data{\unicode{30340}}{\unicode{29983}}{\unicode{29289}}{\unicode{36884}}{\unicode{24452}}{\unicode{25968}}{\unicode{25454}}{\unicode{21487}}{\unicode{35270}}{\unicode{21270}}{\unicode{31995}}{\unicode{32479}}
(BioPW+: Biological Pathway Data Visualization System Based on Linked
Data)},
journal = {{\unicode{35745}}{\unicode{31639}}{\unicode{26426}}{\unicode{31185}}{\unicode{23398}}},
volume = {46},
number = {2},
pages = {18--23},
year = {2019}
}
@article{DBLP:journals/nar/BurleyBBBCCCDDD19,
author = {Stephen K. Burley and
Helen M. Berman and
Charmi Bhikadiya and
Chunxiao Bi and
Li Chen and
Luigi Di Costanzo and
Cole H. Christie and
Kenneth Dalenberg and
Jose M. Duarte and
Shuchismita Dutta and
Zukang Feng and
Sutapa Ghosh and
David S. Goodsell and
Rachel Kramer Green and
Vladimir Guranovic and
Dmytro Guzenko and
Brian P. Hudson and
Tara Kalro and
Yuhe Liang and
Robert Lowe and
Harry Namkoong and
Ezra Peisach and
Irina Periskova and
Andreas Prlic and
Christopher Randle and
Alexander S. Rose and
Peter W. Rose and
Raul Sala and
Monica Sekharan and
Chenghua Shao and
Lihua Tan and
Yi{-}Ping Tao and
Yana Valasatava and
Maria Voigt and
John D. Westbrook and
Jesse Woo and
Huanwang Yang and
Jasmine Young and
Marina Zhuravleva and
Christine Zardecki},
title = {{RCSB} Protein Data Bank: biological macromolecular structures enabling
research and education in fundamental biology, biomedicine, biotechnology
and energy},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D464--D474},
year = {2019}
}
@article{DBLP:journals/paa/HoseiniM19,
author = {Elham Hoseini and
Eghbal G. Mansoori},
title = {Unsupervised feature selection in linked biological data},
journal = {Pattern Anal. Appl.},
volume = {22},
number = {3},
pages = {999--1013},
year = {2019}
}
@article{DBLP:journals/tbe/YangHCC19,
author = {Xi Yang and
Guoqiang Han and
Jiazhou Chen and
Hongmin Cai},
title = {Finding Correlated Patterns via High-Order Matching for Multiple Sourced
Biological Data},
journal = {{IEEE} Trans. Biomed. Eng.},
volume = {66},
number = {4},
pages = {1017--1025},
year = {2019}
}
@article{DBLP:journals/tcbb/CaiMR19,
author = {Xingyu Cai and
Abdullah{-}Al Mamun and
Sanguthevar Rajasekaran},
title = {Efficient Algorithms for Finding the Closest {\textdollar}l{\textdollar}l-Mers
in Biological Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {6},
pages = {1912--1921},
year = {2019}
}
@article{DBLP:journals/tnn/Feng0LGZ19,
author = {Chun{-}Mei Feng and
Yong Xu and
Jin{-}Xing Liu and
Ying{-}Lian Gao and
Chun{-}Hou Zheng},
title = {Supervised Discriminative Sparse {PCA} for Com-Characteristic Gene
Selection and Tumor Classification on Multiview Biological Data},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {30},
number = {10},
pages = {2926--2937},
year = {2019}
}
@inproceedings{DBLP:conf/IEEEpact/KaplanYG19,
author = {Roman Kaplan and
Leonid Yavits and
Ran Ginosar},
title = {{POSTER:} BioSEAL: In-Memory Biological Sequence Alignment Accelerator
for Large-Scale Genomic Data},
booktitle = {{PACT}},
pages = {459--460},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/acsw/ZarnegarJVS19,
author = {Armita Zarnegar and
Herbert F. Jelinek and
Peter Vamplew and
Andrew Stranieri},
title = {Integrating Biological Heuristics and Gene Expression Data for Gene
Regulatory Network Inference},
booktitle = {{ACSW}},
pages = {37:1--37:10},
publisher = {{ACM}},
year = {2019}
}
@inproceedings{DBLP:conf/bcb/Tillquist19,
author = {Richard C. Tillquist},
title = {Low-Dimensional Representation of Biological Sequence Data},
booktitle = {{BCB}},
pages = {555},
publisher = {{ACM}},
year = {2019}
}
@inproceedings{DBLP:conf/bigdataconf/IshaqSD19,
author = {Najib Ishaq and
George Student and
Noah M. Daniels},
title = {Clustered Hierarchical Entropy-Scaling Search of Astronomical and
Biological Data},
booktitle = {{IEEE} BigData},
pages = {780--789},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/bigdataconf/IshaqSD19a,
author = {Najib Ishaq and
George Student and
Noah M. Daniels},
title = {Clustered Hierarchical Entropy-Scaling Search of Astronomical and
Biological Data},
booktitle = {{IEEE} BigData},
pages = {6077},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/carla/Alfaro-BadillaA19,
author = {Kaleb Alfaro{-}Badilla and
Andr{\'{e}}s Arroyo{-}Romero and
Carlos Salazar{-}Garc{\'{\i}}a and
Luis G. Le{\'{o}}n{-}Vega and
Javier Espinoza{-}Gonz{\'{a}}lez and
Franklin Hern{\'{a}}ndez{-}Castro and
Alfonso Chac{\'{o}}n{-}Rodr{\'{\i}}guez and
Georgios Smaragdos and
Christos Strydis},
title = {Improving the Simulation of Biologically Accurate Neural Networks
Using Data Flow {HLS} Transformations on Heterogeneous SoC-FPGA Platforms},
booktitle = {{CARLA}},
series = {Communications in Computer and Information Science},
volume = {1087},
pages = {185--199},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/cibcb/GentiliMPFB19,
author = {Michele Gentili and
Leonardo Martini and
Manuela Petti and
Lorenzo Farina and
Luca Becchetti},
title = {Biological Random Walks: Integrating heterogeneous data in disease
gene prioritization},
booktitle = {{CIBCB}},
pages = {1--8},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/eScience/AndrieuBBCDPV19,
author = {Pierre Andrieu and
Bryan Brancotte and
Laurent Bulteau and
Sarah Cohen{-}Boulakia and
Alain Denise and
Adeline Pierrot and
St{\'{e}}phane Vialette},
title = {Reliability-Aware and Graph-Based Approach for Rank Aggregation of
Biological Data},
booktitle = {eScience},
pages = {136--145},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/hucc/YangMLZX19,
author = {Minglang Yang and
Yi Man and
Ningning Liu and
Yixin Zhang and
Xiao Xing},
title = {Design of Searchable Algorithm for Biological Databased on Homomorphic
Encryption},
booktitle = {{HCC}},
series = {Lecture Notes in Computer Science},
volume = {11956},
pages = {537--545},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/hucc/ZhangMHGX19,
author = {Changwen Zhang and
Yi Man and
Jin He and
Jieming Gu and
Xiao Xing},
title = {Biological Data Migration Method Based on {IPFS} System},
booktitle = {{HCC}},
series = {Lecture Notes in Computer Science},
volume = {11956},
pages = {588--599},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/icann/SchneiderWM19,
author = {Michael Schneider and
Lichao Wang and
Carsten Marr},
title = {Evaluation of Domain Adaptation Approaches for Robust Classification
of Heterogeneous Biological Data Sets},
booktitle = {{ICANN} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {11728},
pages = {673--686},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/iccabs/ThapaA19,
author = {Ishwor Thapa and
Hesham Ali},
title = {A New Graph Database System for Multi-omics Data Integration and Mining
Complex Biological Information},
booktitle = {{ICCABS}},
series = {Lecture Notes in Computer Science},
volume = {12029},
pages = {171--183},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/iceis/SchmidtsKSZ19,
author = {Oliver Schmidts and
Bodo Kraft and
Ines Siebigteroth and
Albert Z{\"{u}}ndorf},
title = {Schema Matching with Frequent Changes on Semi-Structured Input Files:
{A} Machine Learning Approach on Biological Product Data},
booktitle = {{ICEIS} {(1)}},
pages = {208--215},
publisher = {SciTePress},
year = {2019}
}
@inproceedings{DBLP:conf/ichi/GuzziTV19,
author = {Pietro Hiram Guzzi and
Giuseppe Tradigo and
Pierangelo Veltri},
title = {Using Dual Networks for the Integration of Clinical and Biological
Data},
booktitle = {{ICHI}},
pages = {1--2},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/iclr/XiaoCLP19,
author = {Will Xiao and
Honglin Chen and
Qianli Liao and
Tomaso A. Poggio},
title = {Biologically-Plausible Learning Algorithms Can Scale to Large Datasets},
booktitle = {{ICLR} (Poster)},
publisher = {OpenReview.net},
year = {2019}
}
@inproceedings{DBLP:conf/icnc/UedaSTN19,
author = {Takaya Ueda and
Masataka Seo and
Yukako Tohsato and
Ikuko Nishikawa},
title = {Analysis of Time Series Anomalies Using Causal InfoGAN and Its Application
to Biological Data},
booktitle = {{ICNC-FSKD}},
series = {Advances in Intelligent Systems and Computing},
volume = {1074},
pages = {609--617},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/iconference/Kim19,
author = {Youngseek Kim},
title = {A Comparative Study of Biological Scientists' Data Sharing Between
Genome Sequence Data and Lab Experiment Data},
booktitle = {iConference},
series = {Lecture Notes in Computer Science},
volume = {11420},
pages = {3--14},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/ijcnn/AlberganteBZ19,
author = {Luca Albergante and
Jonathan Bac and
Andrei Yu. Zinovyev},
title = {Estimating the effective dimension of large biological datasets using
Fisher separability analysis},
booktitle = {{IJCNN}},
pages = {1--8},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/isbi/MedelaPSBCCBG19,
author = {Alfonso Medela and
Artzai Pic{\'{o}}n and
Cristina L{\'{o}}pez Saratxaga and
Oihana Belar and
Virginia Cabez{\'{o}}n and
Riccardo Cicchi and
Roberto Bilbao and
Ben Glover},
title = {Few Shot Learning in Histopathological Images: Reducing the Need of
Labeled Data on Biological Datasets},
booktitle = {{ISBI}},
pages = {1860--1864},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/kdd/YangSLPB19,
author = {Laurence Yang and
Michael A. Saunders and
Jean{-}Christophe Lachance and
Bernhard O. Palsson and
Jos{\'{e}} Bento},
title = {Estimating Cellular Goals from High-Dimensional Biological Data},
booktitle = {{KDD}},
pages = {2202--2211},
publisher = {{ACM}},
year = {2019}
}
@inproceedings{DBLP:conf/mmsp/BairdABSS19,
author = {Alice Baird and
Shahin Amiriparian and
Miriam Berschneider and
Maximilian Schmitt and
Bj{\"{o}}rn W. Schuller},
title = {Predicting Biological Signals from Speech: Introducing a Novel Multimodal
Dataset and Results},
booktitle = {{MMSP}},
pages = {1--5},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/pkdd/SchallnerRSS19,
author = {Ludwig Schallner and
Johannes Rabold and
Oliver Scholz and
Ute Schmid},
title = {Effect of Superpixel Aggregation on Explanations in {LIME} - {A} Case
Study with Biological Data},
booktitle = {{PKDD/ECML} Workshops {(1)}},
series = {Communications in Computer and Information Science},
volume = {1167},
pages = {147--158},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/recomb/ThompsonCRH19,
author = {Mike Thompson and
Zeyuan Johnson Chen and
Elior Rahmani and
Eran Halperin},
title = {Distinguishing Biological from Technical Sources of Variation Using
a Combination of Methylation Datasets},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {11467},
pages = {316--317},
publisher = {Springer},
year = {2019}
}
@inproceedings{DBLP:conf/sac/BouaskerYD19,
author = {Souad Bouasker and
Sadok Ben Yahia and
Gayo Diallo},
title = {An insight into biological datamining based on rarity and correlation
as constraints},
booktitle = {{SAC}},
pages = {3--10},
publisher = {{ACM}},
year = {2019}
}
@inproceedings{DBLP:conf/ssci/NakariMKST19,
author = {Iko Nakari and
Akinori Murata and
Eiki Kitajima and
Hiroyuki Sato and
Keiki Takadama},
title = {Sleep Apnea Syndrome Detection based on Biological Vibration Data
from Mattress Sensor},
booktitle = {{SSCI}},
pages = {550--556},
publisher = {{IEEE}},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Agapito19,
author = {Giuseppe Agapito},
title = {Standards and Models for Biological Data: {SBML}},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {142--146},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Agapito19a,
author = {Giuseppe Agapito},
title = {Standards and Models for Biological Data: BioPAX},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {147--153},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Calabrese19,
author = {Barbara Calabrese},
title = {Experimental Platforms for Extracting Biological Data: Mass Spectrometry,
Microarray, Next Generation Sequencing},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {126--129},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Calabrese19a,
author = {Barbara Calabrese},
title = {Standards and Models for Biological Data: Common Formats},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {130--136},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Calabrese19b,
author = {Barbara Calabrese},
title = {Standards and Models for Biological Data: {FGED} and {HUPO}},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {137--141},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Dhillon19,
author = {Sarinder Kaur Dhillon},
title = {Biological Databases},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(2)}},
pages = {96--117},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/Muhammad19,
author = {Nor Azlan Nor Muhammad},
title = {Biological Database Searching},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(3)}},
pages = {29--38},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/RahmatiPRJ19,
author = {Sara Rahmati and
Chiara Pastrello and
Andrea E. M. Rossos and
Igor Jurisica},
title = {Two Decades of Biological Pathway Databases: Results and Challenges},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {1071--1084},
publisher = {Elsevier},
year = {2019}
}
@incollection{DBLP:reference/bioinf/VenkataG19,
author = {Ramakanth Chirravuri Venkata and
Dario Ghersi},
title = {Biological Pathway Data Formats and Standards},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology {(1)}},
pages = {1063--1066},
publisher = {Elsevier},
year = {2019}
}
@article{DBLP:journals/corr/abs-1901-05959,
author = {Roman Kaplan and
Leonid Yavits and
Ran Ginosar},
title = {BioSEAL: In-Memory Biological Sequence Alignment Accelerator for Large-Scale
Genomic Data},
journal = {CoRR},
volume = {abs/1901.05959},
year = {2019}
}
@article{DBLP:journals/corr/abs-1901-06328,
author = {Luca Albergante and
Jonathan Bac and
Andrei Yu. Zinovyev},
title = {Estimating the effective dimension of large biological datasets using
Fisher separability analysis},
journal = {CoRR},
volume = {abs/1901.06328},
year = {2019}
}
@article{DBLP:journals/corr/abs-1905-11837,
author = {Chun{-}Mei Feng and
Yong Xu and
Jin{-}Xing Liu and
Ying{-}Lian Gao and
Chun{-}Hou Zheng},
title = {Supervised Discriminative Sparse {PCA} for Com-Characteristic Gene
Selection and Tumor Classification on Multiview Biological Data},
journal = {CoRR},
volume = {abs/1905.11837},
year = {2019}
}
@article{DBLP:journals/corr/abs-1906-07289,
author = {Nhat Tran and
Ishfaq Ahmad and
Jean Gao},
title = {rna2rna: Predicting lncRNA-microRNA-mRNA Interactions from Sequence
with Integration of Interactome and Biological Annotation Data},
journal = {CoRR},
volume = {abs/1906.07289},
year = {2019}
}
@article{DBLP:journals/corr/abs-1908-08551,
author = {Najib Ishaq and
George Student and
Noah M. Daniels},
title = {Clustered Hierarchical Entropy-Scaling Search of Astronomical and
Biological Data},
journal = {CoRR},
volume = {abs/1908.08551},
year = {2019}
}
@article{DBLP:journals/corr/abs-1910-07856,
author = {Ludwig Schallner and
Johannes Rabold and
Oliver Scholz and
Ute Schmid},
title = {Effect of Superpixel Aggregation on Explanations in {LIME} - {A} Case
Study with Biological Data},
journal = {CoRR},
volume = {abs/1910.07856},
year = {2019}
}
@article{DBLP:journals/corr/abs-1911-04389,
author = {Niklas T. Rindtorff and
Mingyu Lu and
Nisarg A. Patel and
Huahua Zheng and
Alexander D'Amour},
title = {A Biologically Plausible Benchmark for Contextual Bandit Algorithms
in Precision Oncology Using in vitro Data},
journal = {CoRR},
volume = {abs/1911.04389},
year = {2019}
}
@article{DBLP:journals/corr/abs-1911-10617,
author = {Claas Flint and
Katharina F{\"{o}}rster and
Sophie A. Koser and
Carsten Konrad and
Pienie Zwitserlood and
Klaus Berger and
Marco Hermesdorf and
Tilo Kircher and
Igor Nenadic and
Axel Krug and
Bernhard T. Baune and
Katharina Dohm and
Ronny Redlich and
Nils Opel and
Tim Hahn and
Xiaoyi Jiang and
Udo Dannlowski and
Dominik Grotegerd},
title = {Biological sex classification with structural {MRI} data shows increased
misclassification in transgender women},
journal = {CoRR},
volume = {abs/1911.10617},
year = {2019}
}
@phdthesis{DBLP:phd/basesearch/Tini18,
author = {Giulia Tini},
title = {The influence of the inclusion of biological knowledge in statistical
methods to integrate multi-omics data},
school = {University of Trento, Italy},
year = {2018}
}
@phdthesis{DBLP:phd/basesearch/Zhong18,
author = {Yi Zhong},
title = {Feature selection and classification for high-dimensional biological
data under cross-validation framework},
school = {University of Kansas, {USA}},
year = {2018}
}
@article{DBLP:journals/ac/Gharajeh18,
author = {Mohammad Samadi Gharajeh},
title = {Chapter Eight - Biological Big Data Analytics},
journal = {Adv. Comput.},
volume = {109},
pages = {321--355},
year = {2018}
}
@article{DBLP:journals/access/KimYKSS18,
author = {Seongjung Kim and
Seongkyu Yeom and
Oh{-}Jin Kwon and
Dongil Shin and
Dongkyoo Shin},
title = {Ubiquitous Healthcare System for Analysis of Chronic Patients' Biological
and Lifelog Data},
journal = {{IEEE} Access},
volume = {6},
pages = {8909--8915},
year = {2018}
}
@article{DBLP:journals/bib/LiWN18,
author = {Yifeng Li and
Fang{-}Xiang Wu and
Alioune Ngom},
title = {A review on machine learning principles for multi-view biological
data integration},
journal = {Briefings Bioinform.},
volume = {19},
number = {2},
pages = {325--340},
year = {2018}
}
@article{DBLP:journals/biodatamining/BouzagloCT18,
author = {David Bouzaglo and
Israel Chasida and
Elishai Ezra Tsur},
title = {Distributed retrieval engine for the development of cloud-deployed
biological databases},
journal = {BioData Min.},
volume = {11},
number = {1},
pages = {26:1--26:10},
year = {2018}
}
@article{DBLP:journals/biodb/HoytDH18,
author = {Charles Tapley Hoyt and
Daniel Domingo{-}Fern{\'{a}}ndez and
Martin Hofmann{-}Apitius},
title = {{BEL} Commons: an environment for exploration and analysis of networks
encoded in Biological Expression Language},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay126},
year = {2018}
}
@article{DBLP:journals/biodb/JorqueraGCPH18,
author = {Roddy Jorquera and
Carolina Gonz{\'{a}}lez and
Philip T. L. C. Clausen and
Bent Petersen and
David S. Holmes},
title = {Improved ontology for eukaryotic single-exon coding sequences in biological
databases},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay089},
year = {2018}
}
@article{DBLP:journals/bioinformatics/GorenLWW18,
author = {Emily Goren and
Peng Liu and
Chao Wang and
Chong Wang},
title = {BinQuasi: a peak detection method for ChIP-sequencing data with biological
replicates},
journal = {Bioinform.},
volume = {34},
number = {17},
pages = {2909--2917},
year = {2018}
}
@article{DBLP:journals/bioinformatics/RuszczyckiB18,
author = {Blazej Ruszczycki and
Tytus Bernas},
title = {Quality of biological images, reconstructed using localization microscopy
data},
journal = {Bioinform.},
volume = {34},
number = {5},
pages = {845--852},
year = {2018}
}
@article{DBLP:journals/bioinformatics/WuTHHLTC18,
author = {Han{-}Ming Wu and
Yin{-}Jing Tien and
Meng{-}Ru Ho and
Hai{-}Gwo Hwu and
Wen{-}Chang Lin and
Mi{-}Hua Tao and
Chun{-}Houh Chen},
title = {Covariate-adjusted heatmaps for visualizing biological data via correlation
decomposition},
journal = {Bioinform.},
volume = {34},
number = {20},
pages = {3529--3538},
year = {2018}
}
@article{DBLP:journals/bioinformatics/YiRZAL18,
author = {Haidong Yi and
Ayush T. Raman and
Han Zhang and
Genevera I. Allen and
Zhandong Liu},
title = {Detecting hidden batch factors through data-adaptive adjustment for
biological effects},
journal = {Bioinform.},
volume = {34},
number = {7},
pages = {1141--1147},
year = {2018}
}
@article{DBLP:journals/biosystems/BarbosaNWMT18,
author = {Sara Barbosa and
Bastian Niebel and
Sebastian Wolf and
Klaus Mauch and
Ralf Takors},
title = {A guide to gene regulatory network inference for obtaining predictive
solutions: Underlying assumptions and fundamental biological and data
constraints},
journal = {Biosyst.},
volume = {174},
pages = {37--48},
year = {2018}
}
@article{DBLP:journals/biosystems/Slijepcevic18,
author = {Predrag Slijepcevic},
title = {Evolutionary epistemology: Reviewing and reviving with new data the
research programme for distributed biological intelligence},
journal = {Biosyst.},
volume = {163},
pages = {23--35},
year = {2018}
}
@article{DBLP:journals/bmcbi/IuchiST18,
author = {Hitoshi Iuchi and
Masahiro Sugimoto and
Masaru Tomita},
title = {{MICOP:} Maximal information coefficient-based oscillation prediction
to detect biological rhythms in proteomics data},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {249:1--249:11},
year = {2018}
}
@article{DBLP:journals/bmcsb/LiuCHS18,
author = {Fei Liu and
Siyuan Chen and
Monika Heiner and
Hengjie Song},
title = {Modeling biological systems with uncertain kinetic data using fuzzy
continuous Petri nets},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {4},
pages = {63--74},
year = {2018}
}
@article{DBLP:journals/ijdmb/SulaimanyKM18,
author = {Sadegh Sulaimany and
Mohammad Khansari and
Ali Masoudi{-}Nejad},
title = {Link prediction potentials for biological networks},
journal = {Int. J. Data Min. Bioinform.},
volume = {20},
number = {2},
pages = {161--184},
year = {2018}
}
@article{DBLP:journals/ijdmb/ZuallaertKSSN18,
author = {Jasper Zuallaert and
Mijung Kim and
Arne Soete and
Yvan Saeys and
Wesley De Neve},
title = {TISRover: ConvNets learn biologically relevant features for effective
translation initiation site prediction},
journal = {Int. J. Data Min. Bioinform.},
volume = {20},
number = {3},
pages = {267--284},
year = {2018}
}
@article{DBLP:journals/ijict/GheraibiaKMM18,
author = {Youcef Gheraibia and
Sohag Kabir and
Abdelouahab Moussaoui and
Smaine Mazouzi},
title = {Optimised cost considering Huffman code for biological data compression},
journal = {Int. J. Inf. Commun. Technol.},
volume = {13},
number = {3},
pages = {275--290},
year = {2018}
}
@article{DBLP:journals/jdiq/ChenWZLZV18,
author = {Qingyu Chen and
Yu Wan and
Xiuzhen Zhang and
Yang Lei and
Justin Zobel and
Karin Verspoor},
title = {Comparative Analysis of Sequence Clustering Methods for Deduplication
of Biological Databases},
journal = {{ACM} J. Data Inf. Qual.},
volume = {9},
number = {3},
pages = {17},
year = {2018}
}
@article{DBLP:journals/jhir/CakinGBZL18,
author = {Hande Cakin and
Berk G{\"{o}}rg{\"{u}}l{\"{u}} and
Mustafa G{\"{o}}k{\c{c}}e Baydogan and
Na Zou and
Jing Li},
title = {A Data Adaptive Biological Sequence Representation for Supervised
Learning},
journal = {J. Heal. Informatics Res.},
volume = {2},
number = {4},
pages = {448--471},
year = {2018}
}
@article{DBLP:journals/jib/BrandiziSRH18,
author = {Marco Brandizi and
Ajit Singh and
Christopher J. Rawlings and
Keywan Hassani{-}Pak},
title = {Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked
Data and Graph Database Approach},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {3},
year = {2018}
}
@article{DBLP:journals/jwscg/Somogyi18,
author = {Endre T. Somogyi},
title = {A Dynamic Non-Manifold Mesh Data Structure to Represent Biological
Materials},
journal = {J. {WSCG}},
volume = {26},
number = {1},
year = {2018}
}
@article{DBLP:journals/midm/ManhasDPLACT18,
author = {Kiran Pohar Manhas and
Shawn X. Dodd and
Stacey Page and
Nicole Letourneau and
Carol E. Adair and
Xinjie Cui and
Suzanne Tough},
title = {Sharing longitudinal, non-biological birth cohort data: a cross-sectional
analysis of parent consent preferences},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {18},
number = {1},
pages = {97:1--97:11},
year = {2018}
}
@article{DBLP:journals/nar/Lee0ALBBDSLBNUM18,
author = {Sunjae Lee and
Cheng Zhang and
Muhammad Arif and
Zhengtao Liu and
Rui Benfeitas and
Gholamreza Bidkhori and
Sumit Deshmukh and
Mohamed Al Shobky and
Alen Lovric and
Jan Boren and
Jens Nielsen and
Mathias Uhlen and
Adil Mardinoglu},
title = {{TCSBN:} a database of tissue and cancer specific biological networks},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D595--D600},
year = {2018}
}
@article{DBLP:journals/nar/PutignanoRBA18,
author = {Valeria Putignano and
Antonio Rosato and
Lucia Banci and
Claudia Andreini},
title = {MetalPDB in 2018: a database of metal sites in biological macromolecular
structures},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D459--D464},
year = {2018}
}
@article{DBLP:journals/nca/DwivediTKBM18,
author = {Vivek Dhar Dwivedi and
Indra Prasad Tripathi and
Aman Chandra Kaushik and
Shiv Bharadwaj and
Sarad Kumar Mishra},
title = {Biological Data Analysis Program {(BDAP):} a multitasking biological
sequence analysis program},
journal = {Neural Comput. Appl.},
volume = {30},
number = {5},
pages = {1493--1501},
year = {2018}
}
@article{DBLP:journals/ploscb/LunPS18,
author = {Aaron T. L. Lun and
Herv{\'{e}} Pag{\`{e}}s and
Mike L. Smith},
title = {beachmat: {A} Bioconductor {C++} {API} for accessing high-throughput
biological data from a variety of {R} matrix types},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {5},
year = {2018}
}
@article{DBLP:journals/tcbb/LealeBMGS18,
author = {Guillermo Leale and
Ariel E. Bay{\'{a}} and
Diego H. Milone and
Pablo M. Granitto and
Georgina Stegmayer},
title = {Inferring Unknown Biological Function by Integration of {GO} Annotations
and Gene Expression Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {1},
pages = {168--180},
year = {2018}
}
@article{DBLP:journals/tcbb/PeaseR18,
author = {James B. Pease and
Benjamin K. Rosenzweig},
title = {Encoding Data Using Biological Principles: The Multisample Variant
Format for Phylogenomics and Population Genomics},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {4},
pages = {1231--1238},
year = {2018}
}
@article{DBLP:journals/tkde/YamadaTLHSSOYMS18,
author = {Makoto Yamada and
Jiliang Tang and
Jose Lugo{-}Martinez and
Ermin Hodzic and
Raunak Shrestha and
Avishek Saha and
Hua Ouyang and
Dawei Yin and
Hiroshi Mamitsuka and
S{\"{u}}leyman Cenk Sahinalp and
Predrag Radivojac and
Filippo Menczer and
Yi Chang},
title = {Ultra High-Dimensional Nonlinear Feature Selection for Big Biological
Data},
journal = {{IEEE} Trans. Knowl. Data Eng.},
volume = {30},
number = {7},
pages = {1352--1365},
year = {2018}
}
@article{DBLP:journals/tnn/MahmudKHV18,
author = {Mufti Mahmud and
M. Shamim Kaiser and
Amir Hussain and
Stefano Vassanelli},
title = {Applications of Deep Learning and Reinforcement Learning to Biological
Data},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {29},
number = {6},
pages = {2063--2079},
year = {2018}
}
@inproceedings{DBLP:conf/aaaiss/UwanoT18,
author = {Fumito Uwano and
Keiki Takadama},
title = {Ensemble Heart Rate Extraction Method for Biological Data from Water
Pressure Sensor},
booktitle = {{AAAI} Spring Symposia},
publisher = {{AAAI} Press},
year = {2018}
}
@inproceedings{DBLP:conf/asist/JuK18,
author = {Boryung Ju and
Youngseek Kim},
title = {Conceptualizing research ethics on scientific data sharing: Evidence
from biological scientists},
booktitle = {{ASIST}},
series = {Proc. Assoc. Inf. Sci. Technol.},
volume = {55},
number = {1},
pages = {834--836},
publisher = {Wiley},
year = {2018}
}
@inproceedings{DBLP:conf/bdccf/Tang0NZL18,
author = {Jianan Tang and
Pengfei Xu and
Weike Nie and
Yi Zhang and
Ruyi Liu},
title = {A Review of Recent Advances in Identity Identification Technology
Based on Biological Features},
booktitle = {Big Data {(CCF)}},
series = {Communications in Computer and Information Science},
volume = {945},
pages = {178--195},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/bibm/TranPA18,
author = {Truong X. Tran and
Marc L. Pusey and
Ramazan S. Ayg{\"{u}}n},
title = {Else-Tree Classifier for Minimizing Misclassification of Biological
Data},
booktitle = {{BIBM}},
pages = {2301--2308},
publisher = {{IEEE} Computer Society},
year = {2018}
}
@inproceedings{DBLP:conf/bibm/ZengLNXJ18,
author = {Shuai Zeng and
Zhen Lyu and
Siva Ratna Kumari Narisetti and
Dong Xu and
Trupti Joshi},
title = {Knowledge Base Commons (KBCommons) v1.0: {A} multi OMICS' web-based
data integration framework for biological discoveries},
booktitle = {{BIBM}},
pages = {589--594},
publisher = {{IEEE} Computer Society},
year = {2018}
}
@inproceedings{DBLP:conf/bibm/ZhangL18,
author = {Wenxiang Zhang and
Xiujuan Lei},
title = {Two-step Random Walk Algorithm to Identify Cancer Genes Based on Various
Biological Data},
booktitle = {{BIBM}},
pages = {1296--1301},
publisher = {{IEEE} Computer Society},
year = {2018}
}
@inproceedings{DBLP:conf/bigdataconf/ChenSWC18,
author = {Huaming Chen and
Jun Shen and
Lei Wang and
Chi{-}Hung Chi},
title = {Towards Biological Sequence Data Service with Insights},
booktitle = {{IEEE} BigData},
pages = {2847--2854},
publisher = {{IEEE}},
year = {2018}
}
@inproceedings{DBLP:conf/bigdatasec/ZhaiLHDHYW18,
author = {Xing Zhai and
Junnan Liu and
Aiqing Han and
Shuang Ding and
Youliang Huang and
Peng Yin and
Min Wang},
title = {Research on the Biological Basis of Treating Different Diseases with
Same Method Based on Big Data Mining and Complex Network},
booktitle = {BigDataSecurity/HPSC/IDS},
pages = {264--269},
publisher = {{IEEE}},
year = {2018}
}
@inproceedings{DBLP:conf/cdc/TuzaS18,
author = {Zolt{\'{a}}n A. Tuza and
Guy{-}Bart Stan},
title = {Characterization of Biologically Relevant Network Structures form
Time-series Data},
booktitle = {{CDC}},
pages = {1089--1095},
publisher = {{IEEE}},
year = {2018}
}
@inproceedings{DBLP:conf/complexnetworks/KarimKA18,
author = {Mohammad Bozlul Karim and
Shigehiko Kanaya and
Md. Altaf{-}Ul{-}Amin},
title = {Comparison of BiClusO with Five Different Biclustering Algorithms
Using Biological and Synthetic Data},
booktitle = {{COMPLEX} {NETWORKS} {(2)}},
series = {Studies in Computational Intelligence},
volume = {813},
pages = {575--585},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/dcai/PerscheidU18,
author = {Cindy Perscheid and
Matthias Uflacker},
title = {Integrating Biological Context into the Analysis of Gene Expression
Data},
booktitle = {{DCAI} (Special Sessions)},
series = {Advances in Intelligent Systems and Computing},
volume = {801},
pages = {339--343},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/dils/WieseWSSG18,
author = {Lena Wiese and
Chimi Wangmo and
Lukas Steuernagel and
Armin Otto Schmitt and
Mehmet G{\"{u}}ltas},
title = {Construction and Visualization of Dynamic Biological Networks: Benchmarking
the Neo4J Graph Database},
booktitle = {{DILS}},
series = {Lecture Notes in Computer Science},
volume = {11371},
pages = {33--43},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/dsmp/PerovaLBBZM18,
author = {Iryna Perova and
Olena Litovchenko and
Yevgeniy V. Bodyanskiy and
Yelizaveta Brazhnykova and
Igor Zavgorodnii and
Pavlo Mulesa},
title = {Medical Data-Stream Mining in the Area of Electromagnetic Radiation
and Low Temperature Influence on Biological Objects},
booktitle = {{DSMP}},
pages = {3--6},
publisher = {{IEEE}},
year = {2018}
}
@inproceedings{DBLP:conf/hicss/SimekDHMOPW18,
author = {Olga Simek and
Curtis Davis and
Andrew Heier and
Sanjeev Mohindra and
Kyle O'Brien and
John Passarelli and
Frederick R. Waugh},
title = {XLab: Early Indications {\&} Warnings from Open Source Data with
Application to Biological Threat},
booktitle = {{HICSS}},
pages = {1--10},
publisher = {ScholarSpace / {AIS} Electronic Library (AISeL)},
year = {2018}
}
@inproceedings{DBLP:conf/icete/SaibeneCDFG18,
author = {Aurora Saibene and
Silvia Corchs and
Roberta Daini and
Alessio Facchin and
Francesca Gasparini},
title = {{EEG} Data of Face Recognition in Case of Biological Compatible Changes:
{A} Pilot Study on Healthy People},
booktitle = {{ICETE} {(1)}},
pages = {580--586},
publisher = {SciTePress},
year = {2018}
}
@inproceedings{DBLP:conf/icic/HuertaMA18,
author = {Edmundo Bonilla Huerta and
Roberto Morales{-}Caporal and
M. Antonio Arjona{-}L{\'{o}}pez},
title = {Exploration and Exploitation of High Dimensional Biological Datasets
Using a Wrapper Approach Based on Strawberry Plant Algorithm},
booktitle = {{ICIC} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {10955},
pages = {307--317},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/isda/VanahalliP18,
author = {Manjunath K. Vanahalli and
Nagamma Patil},
title = {Distributed Mining of Significant Frequent Colossal Closed Itemsets
from Long Biological Dataset},
booktitle = {{ISDA} {(1)}},
series = {Advances in Intelligent Systems and Computing},
volume = {940},
pages = {891--902},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/iwbbio/MeerMUMB18,
author = {Hossam Al Meer and
Raghvendra Mall and
Ehsan Ullah and
Nasreddine Megrez and
Halima Bensmail},
title = {ISaaC: Identifying Structural Relations in Biological Data with Copula-Based
Kernel Dependency Measures},
booktitle = {{IWBBIO} {(1)}},
series = {Lecture Notes in Computer Science},
volume = {10813},
pages = {71--82},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/iwci/ParvezHGR18,
author = {H. M. Shahriar Parvez and
Saqib Hakak and
Gulshan Amin Gilkar and
Mahmud Abdur Rahman},
title = {Factorial Analysis of Biological Datasets},
booktitle = {{IJCCI}},
series = {Algorithms for Intelligent Systems},
pages = {1--9},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/mldm/SokolovskaPFZ18,
author = {Nataliya Sokolovska and
Olga Permiakova and
Sofia K. Forslund and
Jean{-}Daniel Zucker},
title = {A Semi-supervised Approach to Discover Bivariate Causality in Large
Biological Data},
booktitle = {{MLDM} {(1)}},
series = {Lecture Notes in Computer Science},
volume = {10934},
pages = {406--420},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/mln/AzzawiHAX18,
author = {Hasseeb Azzawi and
Jingyu Hou and
Russul Alanni and
Yong Xiang},
title = {A Hybrid Neural Network Approach for Lung Cancer Classification with
Gene Expression Dataset and Prior Biological Knowledge},
booktitle = {{MLN}},
series = {Lecture Notes in Computer Science},
volume = {11407},
pages = {279--293},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/pacbb/ZakiTAJA18,
author = {Nazar Zaki and
Chandana Tennakoon and
Hany Al Ashwal and
Alanoud Al Jaberi and
Amel Al Ameri},
title = {Methods of Creating Knowledge Graph by Linking Biological Databases},
booktitle = {{PACBB}},
series = {Advances in Intelligent Systems and Computing},
volume = {803},
pages = {52--62},
publisher = {Springer},
year = {2018}
}
@inproceedings{DBLP:conf/sca2/AndaloussiKH18,
author = {Ouissam El Andaloussi and
M'hamed A{\"{\i}}t Kbir and
Badr Din Rossi Hassani},
title = {Biological data annotation using complementary and alternative Medicine
with a collection tracking system (Hirbalink)},
booktitle = {{SCA}},
pages = {61:1--61:5},
publisher = {{ACM}},
year = {2018}
}
@inproceedings{DBLP:conf/sca2/HanafiRHK18,
author = {Hamza Hanafi and
Fadoua Rafii and
Badr Dine Rossi Hassani and
M'hamed A{\"{\i}}t Kbir},
title = {A graph based model for multiple biological data sources integration},
booktitle = {{SCA}},
pages = {49:1--49:5},
publisher = {{ACM}},
year = {2018}
}
@inproceedings{DBLP:conf/spawc/MertzanisPSK18,
author = {Lambros Mertzanis and
Athina Panotopoulou and
Maria Skoularidou and
Ioannis Kontoyiannis},
title = {Deep Tree Models for 'Big' Biological Data},
booktitle = {{SPAWC}},
pages = {1--5},
publisher = {{IEEE}},
year = {2018}
}
@inproceedings{DBLP:conf/vcbm/KnotelBSB18,
author = {David Kn{\"{o}}tel and
Carola Becker and
Gerhard Scholtz and
Daniel Baum},
title = {Global and Local Mesh Morphing for Complex Biological Objects from
{\(\mathrm{\mu}\)}CT Data},
booktitle = {VCBM@MICCAI},
pages = {179--183},
publisher = {Eurographics Association},
year = {2018}
}
@incollection{DBLP:books/sp/18/MallikBSBC18,
author = {Saurav Mallik and
Tapas Bhadra and
Soumita Seth and
Sanghamitra Bandyopadhyay and
Jianjiao Chen},
title = {Multi-Objective Optimization Approaches in Biological Learning System
on Microarray Data},
booktitle = {Multi-Objective Optimization},
pages = {159--180},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/0001L18,
author = {Arnab Bhattacharya and
Vebjorn Ljosa},
title = {Image Management for Biological Data},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/Gupta18a,
author = {Amarnath Gupta},
title = {Biological Networks},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/Gupta18b,
author = {Amarnath Gupta},
title = {Biological Sequences},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/Kahveci18,
author = {Tamer Kahveci},
title = {Index Structures for Biological Sequences},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/LacroixKMRWFB18,
author = {Zo{\'{e}} Lacroix and
Cartik R. Kothari and
Peter Mork and
Rami Rifaieh and
Mark D. Wilkinson and
Juliana Freire and
Sarah Cohen Boulakia},
title = {Biological Resource Discovery},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/LacroixKMWB18,
author = {Zo{\'{e}} Lacroix and
Cartik R. Kothari and
Peter Mork and
Mark D. Wilkinson and
Sarah Cohen Boulakia},
title = {Biological Metadata Management},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/Srinivasan18,
author = {Padmini Srinivasan},
title = {Text Mining of Biological Resources},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@incollection{DBLP:reference/db/TataP18,
author = {Sandeep Tata and
Jignesh M. Patel},
title = {Query Languages and Evaluation Techniques for Biological Sequence
Data},
booktitle = {Encyclopedia of Database Systems (2nd ed.)},
publisher = {Springer},
year = {2018}
}
@article{DBLP:journals/corr/abs-1807-07127,
author = {Erin Connelly and
Charo I. Del Genio and
Freya Harrison},
title = {Datamining a medieval medical text reveals patterns in ingredient
choice that reflect biological activity against the causative agents
of specified infections},
journal = {CoRR},
volume = {abs/1807.07127},
year = {2018}
}
@article{DBLP:journals/corr/abs-1807-10956,
author = {Wenwen Min and
Juan Liu and
Shihua Zhang},
title = {Group-sparse {SVD} Models and Their Applications in Biological Data},
journal = {CoRR},
volume = {abs/1807.10956},
year = {2018}
}
@article{DBLP:journals/corr/abs-1808-08124,
author = {Charles B. Delahunt and
J. Nathan Kutz},
title = {Insect cyborgs: Biological feature generators improve machine learning
accuracy on limited data},
journal = {CoRR},
volume = {abs/1808.08124},
year = {2018}
}
@article{DBLP:journals/corr/abs-1809-08862,
author = {Zolt{\'{a}}n A. Tuza and
Guy{-}Bart Stan},
title = {Characterization of Biologically Relevant Network Structures form
Time-series Data},
journal = {CoRR},
volume = {abs/1809.08862},
year = {2018}
}
@article{DBLP:journals/corr/abs-1811-03567,
author = {Will Xiao and
Honglin Chen and
Qianli Liao and
Tomaso A. Poggio},
title = {Biologically-plausible learning algorithms can scale to large datasets},
journal = {CoRR},
volume = {abs/1811.03567},
year = {2018}
}
@article{DBLP:journals/corr/abs-1812-04778,
author = {Tzu{-}Yu Liu and
Ajay Kannan and
Adam Drake and
Marvin Bertin and
Nathan Wan},
title = {Bridging the Generalization Gap: Training Robust Models on Confounded
Biological Data},
journal = {CoRR},
volume = {abs/1812.04778},
year = {2018}
}
@article{DBLP:journals/dagstuhl-reports/AertsGMN18,
author = {Jan Aerts and
Nils Gehlenborg and
Georgeta Elisabeta Marai and
Kay Katja Nieselt},
title = {Visualization of Biological Data - Crossroads (Dagstuhl Seminar 18161)},
journal = {Dagstuhl Reports},
volume = {8},
number = {4},
pages = {32--71},
year = {2018}
}
@article{DBLP:journals/f1000research/GodardE18,
author = {Patrice Godard and
Jonathan van Eyll},
title = {{BED:} a Biological Entity Dictionary based on a graph data model},
journal = {F1000Research},
volume = {7},
pages = {195},
year = {2018}
}
@phdthesis{DBLP:phd/basesearch/Chen17c,
author = {Qingyu Chen},
title = {Duplication in biological databases: definitions, impacts and methods},
school = {University of Melbourne, Parkville, Victoria, Australia},
year = {2017}
}
@phdthesis{DBLP:phd/basesearch/Ghazanfar17,
author = {Shila Ghazanfar},
title = {Statistical approaches to harness high throughput sequencing data
in diverse biological systems},
school = {University of Sydney, Australia},
year = {2017}
}
@phdthesis{DBLP:phd/basesearch/Hou17,
author = {Wenpin Hou},
title = {Mathematical modelling and optimization in biological networks and
data},
school = {University of Hong Kong, Pokfulam, Hong Kong},
year = {2017}
}
@phdthesis{DBLP:phd/hal/Chambon17,
author = {Arthur Chambon},
title = {Caract{\'{e}}risation logique de donn{\'{e}}es : application
aux donn{\'{e}}es biologiques. (Logical Characterization of Data
: application to Biological Data)},
school = {University of Angers, France},
year = {2017}
}
@article{DBLP:journals/algorithms/AbdallahRMRI17,
author = {Emna Ben Abdallah and
Tony Ribeiro and
Morgan Magnin and
Olivier H. Roux and
Katsumi Inoue},
title = {Modeling Delayed Dynamics in Biological Regulatory Networks from Time
Series Data},
journal = {Algorithms},
volume = {10},
number = {1},
pages = {8},
year = {2017}
}
@article{DBLP:journals/asc/PashaeiA17,
author = {Elnaz Pashaei and
Nizamettin Aydin},
title = {Binary black hole algorithm for feature selection and classification
on biological data},
journal = {Appl. Soft Comput.},
volume = {56},
pages = {94--106},
year = {2017}
}
@article{DBLP:journals/bib/Abriata17,
author = {Luciano A. Abriata},
title = {Structural database resources for biological macromolecules},
journal = {Briefings Bioinform.},
volume = {18},
number = {4},
pages = {659--669},
year = {2017}
}
@article{DBLP:journals/bib/TaylorRKWK17,
author = {Sandra L. Taylor and
L. Renee Ruhaak and
Karen Kelly and
Robert H. Weiss and
Kyoungmi Kim},
title = {Effects of imputation on correlation: implications for analysis of
mass spectrometry data from multiple biological matrices},
journal = {Briefings Bioinform.},
volume = {18},
number = {2},
pages = {312--320},
year = {2017}
}
@article{DBLP:journals/biodb/GuntschHHCR17,
author = {Anton G{\"{u}}ntsch and
Roger Hyam and
Gregor Hagedorn and
Simon Chagnoux and
Dominik R{\"{o}}pert and
Ana Casino and
Gabi Droege and
Falko Gl{\"{o}}ckler and
Karsten G{\"{o}}dderz and
Quentin Groom and
Jana Hoffmann and
Ayco Holleman and
Mat{\'{u}}s Kempa and
Hanna Koivula and
Karol Marhold and
Nicky Nicolson and
Vincent S. Smith and
Dagmar Triebel},
title = {Actionable, long-term stable and semantic web compatible identifiers
for access to biological collection objects},
journal = {Database J. Biol. Databases Curation},
volume = {2017},
pages = {bax003},
year = {2017}
}
@article{DBLP:journals/biodb/RavikumarRL17,
author = {K. E. Ravikumar and
Majid Rastegar{-}Mojarad and
Hongfang Liu},
title = {BELMiner: adapting a rule-based relation extraction system to extract
biological expression language statements from bio-medical literature
evidence sentences},
journal = {Database J. Biol. Databases Curation},
volume = {2017},
pages = {baw156},
year = {2017}
}
@article{DBLP:journals/bioinformatics/BerchtoldCZ17,
author = {Evi Berchtold and
Gergely Csaba and
Ralf Zimmer},
title = {RelExplain - integrating data and networks to explain biological processes},
journal = {Bioinform.},
volume = {33},
number = {12},
pages = {1837--1844},
year = {2017}
}
@article{DBLP:journals/bioinformatics/JurtzJNANSWS17,
author = {Vanessa Isabell Jurtz and
Alexander Rosenberg Johansen and
Morten Nielsen and
Jos{\'{e}} Juan Almagro Armenteros and
Henrik Nielsen and
Casper Kaae S{\o}nderby and
Ole Winther and
S{\o}ren Kaae S{\o}nderby},
title = {An introduction to deep learning on biological sequence data: examples
and solutions},
journal = {Bioinform.},
volume = {33},
number = {22},
pages = {3685--3690},
year = {2017}
}
@article{DBLP:journals/bioinformatics/KleinSBAR17,
author = {Max Klein and
Rati Sharma and
Christopher Herrick Bohrer and
Cameron M. Avelis and
Elijah Roberts},
title = {Biospark: scalable analysis of large numerical datasets from biological
simulations and experiments using Hadoop and Spark},
journal = {Bioinform.},
volume = {33},
number = {2},
pages = {303--305},
year = {2017}
}
@article{DBLP:journals/bioinformatics/RussoKWPSSHZ17,
author = {Daniel P. Russo and
Marlene T. Kim and
Wenyi Wang and
Daniel Pinolini and
Sunil M. Shende and
Judy Strickland and
Thomas Hartung and
Hao Zhu},
title = {CIIPro: a new read-across portal to fill data gaps using public large-scale
chemical and biological data},
journal = {Bioinform.},
volume = {33},
number = {3},
pages = {464--466},
year = {2017}
}
@article{DBLP:journals/bioinformatics/SalviatoDCR17,
author = {Elisa Salviato and
Vera Djordjilovic and
Monica Chiogna and
Chiara Romualdi},
title = {simPATHy: a new method for simulating data from perturbed biological
PATHways},
journal = {Bioinform.},
volume = {33},
number = {3},
pages = {456--457},
year = {2017}
}
@article{DBLP:journals/bioinformatics/SeversonMLB17,
author = {Kristen A. Severson and
Brinda Monian and
J. Christopher Love and
Richard D. Braatz},
title = {A method for learning a sparse classifier in the presence of missing
data for high-dimensional biological datasets},
journal = {Bioinform.},
volume = {33},
number = {18},
pages = {2897--2905},
year = {2017}
}
@article{DBLP:journals/bioinformatics/TaylorRWKK17,
author = {Sandra L. Taylor and
L. Renee Ruhaak and
Robert H. Weiss and
Karen Kelly and
Kyoungmi Kim},
title = {Multivariate two-part statistics for analysis of correlated mass spectrometry
data from multiple biological specimens},
journal = {Bioinform.},
volume = {33},
number = {1},
pages = {17--25},
year = {2017}
}
@article{DBLP:journals/bmcbi/GuhlinSZTY17,
author = {Joseph Guhlin and
Kevin A. T. Silverstein and
Peng Zhou and
Peter Tiffin and
Nevin D. Young},
title = {{ODG:} Omics database generator - a tool for generating, querying,
and analyzing multi-omics comparative databases to facilitate biological
understanding},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {367:1--367:8},
year = {2017}
}
@article{DBLP:journals/bmcbi/HenriquesFM17,
author = {Rui Henriques and
Francisco L. Ferreira and
Sara C. Madeira},
title = {BicPAMS: software for biological data analysis with pattern-based
biclustering},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {82:1--82:16},
year = {2017}
}
@article{DBLP:journals/bmcbi/HenriquesFM17a,
author = {Rui Henriques and
Francisco L. Ferreira and
Sara C. Madeira},
title = {Erratum to: BicPAMS: software for biological data analysis with pattern-based
biclustering},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {162:1--162:2},
year = {2017}
}
@article{DBLP:journals/bmcbi/KangDZZZ17,
author = {Tianyu Kang and
Wei Ding and
Luoyan Zhang and
Daniel Ziemek and
Kourosh Zarringhalam},
title = {A biological network-based regularized artificial neural network model
for robust phenotype prediction from gene expression data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {565:1--565:11},
year = {2017}
}
@article{DBLP:journals/bmcbi/LiSL17,
author = {Ziyi Li and
Sandra E. Safo and
Qi Long},
title = {Incorporating biological information in sparse principal component
analysis with application to genomic data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {332},
year = {2017}
}
@article{DBLP:journals/bmcbi/LowKT17,
author = {Joel Z. B. Low and
Tsung Fei Khang and
Martti T. Tammi},
title = {{CORNAS:} coverage-dependent RNA-Seq analysis of gene expression data
without biological replicates},
journal = {{BMC} Bioinform.},
volume = {18},
number = {16},
pages = {243--253},
year = {2017}
}
@article{DBLP:journals/bmcbi/MurrayMF17,
author = {Paul Murray and
Fintan McGee and
Angus Graeme Forbes},
title = {A taxonomy of visualization tasks for the analysis of biological pathway
data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {{S-2}},
pages = {21:1--21:13},
year = {2017}
}
@article{DBLP:journals/bmcbi/SmelterAM17,
author = {Andrey Smelter and
Morgan Astra and
Hunter N. B. Moseley},
title = {A fast and efficient python library for interfacing with the Biological
Magnetic Resonance Data Bank},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {175:1--175:12},
year = {2017}
}
@article{DBLP:journals/bmcbi/ZakiT17,
author = {Nazar Zaki and
Chandana Tennakoon},
title = {BioCarian: search engine for exploratory searches in heterogeneous
biological databases},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {435:1--435:15},
year = {2017}
}
@article{DBLP:journals/bmcbi/ZhangCLLTL17,
author = {Wen Zhang and
Yanlin Chen and
Feng Liu and
Fei Luo and
Gang Tian and
Xiaohong Li},
title = {Predicting potential drug-drug interactions by integrating chemical,
biological, phenotypic and network data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {18:1--18:12},
year = {2017}
}
@article{DBLP:journals/bmcsb/WangZC17,
author = {Yong Wang and
Xiang{-}Sun Zhang and
Luonan Chen},
title = {Understanding biological systems through the lens of data},
journal = {{BMC} Syst. Biol.},
volume = {11},
number = {{S-4}},
pages = {77:1--77:2},
year = {2017}
}
@article{DBLP:journals/data/SubramanianG17,
author = {Sandeep Subramanian and
Madhavi K. Ganapathiraju},
title = {Antibody Exchange: Information Extraction of Biological Antibody Donation
and a Web-Portal to Find Donors and Seekers},
journal = {Data},
volume = {2},
number = {4},
pages = {38},
year = {2017}
}
@article{DBLP:journals/ejes/WangHC17,
author = {Shujuan Wang and
Long He and
Guiru Cheng},
title = {Energy consumption optimization management mechanism based on drug
green crowd data in biological pharmaceutical cloud environment},
journal = {{EURASIP} J. Embed. Syst.},
volume = {2017},
pages = {21},
year = {2017}
}
@article{DBLP:journals/fgcs/PedersenB17,
author = {Edvard Pedersen and
Lars Ailo Bongo},
title = {Large-scale biological meta-database management},
journal = {Future Gener. Comput. Syst.},
volume = {67},
pages = {481--489},
year = {2017}
}
@article{DBLP:journals/ijbra/LuWK17,
author = {Jing Lu and
Cuiqing Wang and
Malcolm Keech},
title = {A novel approach to knowledge discovery and representation in biological
databases},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {13},
number = {4},
pages = {352--375},
year = {2017}
}
@article{DBLP:journals/ijdmb/HuangLLL17,
author = {Hai{-}Hui Huang and
Xiao{-}Ying Liu and
Hui{-}Min Li and
Yong Liang},
title = {Molecular pathway identification using a new L\({}_{\mbox{1/2}}\)
solver and biological network-constrained model},
journal = {Int. J. Data Min. Bioinform.},
volume = {17},
number = {3},
pages = {189--205},
year = {2017}
}
@article{DBLP:journals/ijdmb/Raza17,
author = {Khalid Raza},
title = {Formal concept analysis for knowledge discovery from biological data},
journal = {Int. J. Data Min. Bioinform.},
volume = {18},
number = {4},
pages = {281--300},
year = {2017}
}
@article{DBLP:journals/jbi/BouadjenekVZ17,
author = {Mohamed Reda Bouadjenek and
Karin Verspoor and
Justin Zobel},
title = {Automated detection of records in biological sequence databases that
are inconsistent with the literature},
journal = {J. Biomed. Informatics},
volume = {71},
pages = {229--240},
year = {2017}
}
@article{DBLP:journals/jcb/GogoshinBR17,
author = {Grigoriy Gogoshin and
Eric Boerwinkle and
Andrei S. Rodin},
title = {New Algorithm and Software (BNOmics) for Inferring and Visualizing
Bayesian Networks from Heterogeneous Big Biological and Genetic Data},
journal = {J. Comput. Biol.},
volume = {24},
number = {4},
pages = {340--356},
year = {2017}
}
@article{DBLP:journals/jcc/JungS17,
author = {Jaewoon Jung and
Yuji Sugita},
title = {Multiple program/multiple data molecular dynamics method with multiple
time step integrator for large biological systems},
journal = {J. Comput. Chem.},
volume = {38},
number = {16},
pages = {1410--1418},
year = {2017}
}
@article{DBLP:journals/jib/ChenHSO17,
author = {Ming Chen and
Andrew P. Harrison and
Hugh P. Shanahan and
Yuriy L. Orlov},
title = {Biological Big Bytes: Integrative Analysis of Large Biological Datasets},
journal = {J. Integr. Bioinform.},
volume = {14},
number = {3},
year = {2017}
}
@article{DBLP:journals/jib/Hassani-PakR17,
author = {Keywan Hassani{-}Pak and
Christopher J. Rawlings},
title = {Knowledge Discovery in Biological Databases for Revealing Candidate
Genes Linked to Complex Phenotypes},
journal = {J. Integr. Bioinform.},
volume = {14},
number = {1},
year = {2017}
}
@article{DBLP:journals/nar/Dabrowski-Tumanski17,
author = {Pawel Dabrowski{-}Tumanski and
Aleksandra I. Jarmolinska and
Wanda Niemyska and
Eric J. Rawdon and
Kenneth C. Millett and
Joanna I. Sulkowska},
title = {LinkProt: a database collecting information about biological links},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D243--D249},
year = {2017}
}
@article{DBLP:journals/nar/ParkSBGL17,
author = {Young Mi Park and
Silvano Squizzato and
Nicola Buso and
Tamer Gur and
Rodrigo Lopez},
title = {The {EBI} search engine: {EBI} search as a service - making biological
data accessible for all},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Webserver-Issue},
pages = {W545--W549},
year = {2017}
}
@article{DBLP:journals/neuroimage/HuertasOOGMBM17,
author = {Ismael Huertas and
Marianne Oldehinkel and
Erik S. B. van Oort and
David Garcia{-}Solis and
Pablo Mir and
Christian F. Beckmann and
Andre F. Marquand},
title = {A Bayesian spatial model for neuroimaging data based on biologically
informed basis functions},
journal = {NeuroImage},
volume = {161},
pages = {134--148},
year = {2017}
}
@article{DBLP:journals/pieee/NguyenMTD17,
author = {Tin Chi Nguyen and
Cristina Mitrea and
Rebecca Tagett and
Sorin Draghici},
title = {{DANUBE:} Data-Driven Meta-ANalysis Using UnBiased Empirical Distributions
- Applied to Biological Pathway Analysis},
journal = {Proc. {IEEE}},
volume = {105},
number = {3},
pages = {496--515},
year = {2017}
}
@article{DBLP:journals/ploscb/BaroneWM17,
author = {Lindsay Barone and
Jason Williams and
David Micklos},
title = {Unmet needs for analyzing biological big data: {A} survey of 704 {NSF}
principal investigators},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017}
}
@article{DBLP:journals/ploscb/LiJCLM17,
author = {Yang Li and
Alexis A. Jourdain and
Sarah E. Calvo and
Jun S. Liu and
Vamsi K. Mootha},
title = {CLIC, a tool for expanding biological pathways based on co-expression
across thousands of datasets},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {7},
year = {2017}
}
@article{DBLP:journals/ploscb/WangHZKBG17,
author = {Bo Wang and
Lin Huang and
Yuke Zhu and
Anshul Kundaje and
Serafim Batzoglou and
Anna Goldenberg},
title = {Vicus: Exploiting local structures to improve network-based analysis
of biological data},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017}
}
@article{DBLP:journals/tcbb/00010WN17,
author = {Fei Wang and
Xiaoli Li and
Jason T. L. Wang and
See{-}Kiong Ng},
title = {Guest Editorial: Special Section on Biological Data Mining and Its
Applications in Healthcare},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {14},
number = {3},
pages = {501--502},
year = {2017}
}
@article{DBLP:journals/tcbb/WangDLWZ17,
author = {Chao Wang and
Dong Dai and
Xi Li and
Aili Wang and
Xuehai Zhou},
title = {SuperMIC: Analyzing Large Biological Datasets in Bioinformatics with
Maximal Information Coefficient},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {14},
number = {4},
pages = {783--795},
year = {2017}
}
@inproceedings{DBLP:conf/amcc/AchantaMV17,
author = {Hema Kumari Achanta and
Burook Misganaw and
Mathukumalli Vidyasagar},
title = {A multi-view {\(\mathscr{l}\)}1-norm {SVM} algorithm for data integration
in biological applications},
booktitle = {{ACC}},
pages = {3753--3757},
publisher = {{IEEE}},
year = {2017}
}
@inproceedings{DBLP:conf/amia/MayoCTJSDH17,
author = {Kelsey R. Mayo and
Robert J. Carroll and
Jason Tan and
Rebecca Johnston and
Celecia M. Scott and
Joshua C. Denny and
Paul A. Harris},
title = {HealthPro: An integrated web application for essential health data
and biological specimen collection in the Precision Medicine Initiative},
booktitle = {{AMIA}},
publisher = {{AMIA}},
year = {2017}
}
@inproceedings{DBLP:conf/apweb/LiuWX17,
author = {Yuan Liu and
Xin Wang and
Qiang Xu},
title = {BioPW: An Interactive Tool for Biological Pathway Visualization on
Linked Data},
booktitle = {APWeb/WAIM {(2)}},
series = {Lecture Notes in Computer Science},
volume = {10367},
pages = {333--336},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/bcb/Jamil17,
author = {Hasan M. Jamil},
title = {Knowledge Rich Natural Language Queries over Structured Biological
Databases},
booktitle = {{BCB}},
pages = {352--361},
publisher = {{ACM}},
year = {2017}
}
@inproceedings{DBLP:conf/bibm/CaiMR17,
author = {Xingyu Cai and
Abdullah{-}Al Mamun and
Sanguthevar Rajasekaran},
title = {Novel algorithms for finding the closest l-mers in biological data},
booktitle = {{BIBM}},
pages = {525--528},
publisher = {{IEEE} Computer Society},
year = {2017}
}
@inproceedings{DBLP:conf/bibm/HuffC17,
author = {Grogan W. Huff and
Kathryn M. Cooper},
title = {Correlation networks: Biologically driven relationships from gene
expression data},
booktitle = {{BIBM}},
pages = {1712--1715},
publisher = {{IEEE} Computer Society},
year = {2017}
}
@inproceedings{DBLP:conf/bigdata/LiSLLWWS17,
author = {Liang Li and
Zhihong Shen and
Jianhui Li and
Dongjiang Liu and
Huajin Wang and
Lipeng Wang and
Qinglan Sun},
title = {A Resilient Index Graph for Querying Large Biological Scientific Data},
booktitle = {BigData Congress},
pages = {435--443},
publisher = {{IEEE} Computer Society},
year = {2017}
}
@inproceedings{DBLP:conf/biostec/NeelyA17,
author = {Benjamin A. Neely and
Paul E. Anderson},
title = {Complementary Domain Prioritization: {A} Method to Improve Biologically
Relevant Detection in Multi-Omic Data Sets},
booktitle = {{BIOINFORMATICS}},
pages = {68--80},
publisher = {SciTePress},
year = {2017}
}
@inproceedings{DBLP:conf/ccta/AchantaMV17,
author = {Hema Kumari Achanta and
Burook Misganaw and
M. Vidyasagar},
title = {Integrating biological data across multiple platforms using importance-weighted
transfer learning and applications to breast cancer data sets},
booktitle = {{CCTA}},
pages = {955--960},
publisher = {{IEEE}},
year = {2017}
}
@inproceedings{DBLP:conf/cibb/FioriniTSB17,
author = {Samuele Fiorini and
Federico Tomasi and
Margherita Squillario and
Annalisa Barla},
title = {Adenine: {A} HPC-Oriented Tool for Biological Data Exploration},
booktitle = {{CIBB}},
series = {Lecture Notes in Computer Science},
volume = {10834},
pages = {51--59},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/dexaw/BalderasBHG17,
author = {Eva C. Serrano Balderas and
Laure Berti{-}{\'{E}}quille and
Maria Aurora Armienta Hernandez and
Corinne Grac},
title = {Principled Data Preprocessing: Application to Biological Aquatic Indicators
of Water Pollution},
booktitle = {{DEXA} Workshops},
pages = {52--56},
publisher = {{IEEE} Computer Society},
year = {2017}
}
@inproceedings{DBLP:conf/embc/BrusseauBMFNB17,
author = {Elisabeth Brusseau and
Adeline Bernard and
Cyril Meynier and
Guillaume F{\'{e}}rin and
An Nguyen{-}Dinh and
Olivier Basset},
title = {Radiofrequency ultrasound data acquisition with a 640-element array
transducer for strain imaging: Experimental results with phantoms
and biological tissue samples},
booktitle = {{EMBC}},
pages = {2996--2999},
publisher = {{IEEE}},
year = {2017}
}
@inproceedings{DBLP:conf/esws/LofflerOKFSKMD17,
author = {Felicitas L{\"{o}}ffler and
Kobkaew Opasjumruskit and
Naouel Karam and
David Fichtm{\"{u}}ller and
Uwe Schindler and
Friederike Klan and
Claudia M{\"{u}}ller{-}Birn and
Michael Diepenbroek},
title = {Honey Bee Versus Apis Mellifera: {A} Semantic Search for Biological
Data},
booktitle = {{ESWC} (Satellite Events)},
series = {Lecture Notes in Computer Science},
volume = {10577},
pages = {98--103},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/eva/Stadon17,
author = {Julian Stadon},
title = {Data Body Trader: Identity Augmentation and Post-Biological Organ
Trade},
booktitle = {{EVA}},
series = {Workshops in Computing},
publisher = {{BCS}},
year = {2017}
}
@inproceedings{DBLP:conf/evoW/BaronLB17,
author = {Simon Baron and
Nicola Lazzarini and
Jaume Bacardit},
title = {Characterising the Influence of Rule-Based Knowledge Representations
in Biological Knowledge Extraction from Transcriptomics Data},
booktitle = {EvoApplications {(1)}},
series = {Lecture Notes in Computer Science},
volume = {10199},
pages = {125--141},
year = {2017}
}
@inproceedings{DBLP:conf/ijcai/0001ZWZV17,
author = {Qingyu Chen and
Xiuzhen Zhang and
Yu Wan and
Justin Zobel and
Karin Verspoor},
title = {Sequence Clustering Methods and Completeness of Biological Database
Search},
booktitle = {BAI@IJCAI},
series = {{CEUR} Workshop Proceedings},
volume = {1942},
pages = {8--14},
publisher = {CEUR-WS.org},
year = {2017}
}
@inproceedings{DBLP:conf/iwbbio/FiannacaPRMRSU17,
author = {Antonino Fiannaca and
Laura La Paglia and
Massimo La Rosa and
Antonio Messina and
Riccardo Rizzo and
Dario Stabile and
Alfonso Urso},
title = {Gremlin Language for Querying the BiographDB Integrated Biological
Database},
booktitle = {{IWBBIO} {(1)}},
series = {Lecture Notes in Computer Science},
volume = {10208},
pages = {303--313},
year = {2017}
}
@inproceedings{DBLP:conf/iwcia/JimenezRVGE17,
author = {Mar{\'{\i}}a Jos{\'{e}} Jim{\'{e}}nez and
Matteo Rucco and
Pablo Vicente{-}Munuera and
Pedro G{\'{o}}mez{-}G{\'{a}}lvez and
Luis M. Escudero},
title = {Topological Data Analysis for Self-organization of Biological Tissues},
booktitle = {{IWCIA}},
series = {Lecture Notes in Computer Science},
volume = {10256},
pages = {229--242},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/jist/KumeMMSKK17,
author = {Satoshi Kume and
Hiroshi Masuya and
Mitsuyo Maeda and
Mitsuo Suga and
Yosky Kataoka and
Norio Kobayashi},
title = {Development of Semantic Web-Based Imaging Database for Biological
Morphome},
booktitle = {{JIST}},
series = {Lecture Notes in Computer Science},
volume = {10675},
pages = {277--285},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/jowo/ZarateBF17,
author = {Marcos Daniel Z{\'{a}}rate and
Agustina Buccella and
Pablo R. Fillottrani},
title = {BioOnto: Towards an Integration of Biological and Biogeographic Data},
booktitle = {{JOWO}},
series = {{CEUR} Workshop Proceedings},
volume = {2050},
publisher = {CEUR-WS.org},
year = {2017}
}
@inproceedings{DBLP:conf/pacbb/ZylaMP17,
author = {Joanna Zyla and
Michal Marczyk and
Joanna Polanska},
title = {Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis},
booktitle = {{PACBB}},
series = {Advances in Intelligent Systems and Computing},
volume = {616},
pages = {146--154},
publisher = {Springer},
year = {2017}
}
@inproceedings{DBLP:conf/ppdp/AngelopoulosW17,
author = {Nicos Angelopoulos and
Jan Wielemaker},
title = {Accessing biological data as Prolog facts},
booktitle = {{PPDP}},
pages = {29--38},
publisher = {{ACM}},
year = {2017}
}
@inproceedings{DBLP:conf/sigmod/LianK17,
author = {Xiang Lian and
Dongchul Kim},
title = {Efficient Ad-Hoc Graph Inference and Matching in Biological Databases},
booktitle = {{SIGMOD} Conference},
pages = {359--373},
publisher = {{ACM}},
year = {2017}
}
@inproceedings{DBLP:conf/swat4ls/MillerSKMSEW17,
author = {Ryan A. Miller and
Denise N. Slenter and
Martina Kutmon and
Jonathan M{\'{e}}lius and
Georg Summer and
Chris T. A. Evelo and
Egon L. Willighagen},
title = {Visualizing Metabolomics Data in Directed Biological Networks},
booktitle = {{SWAT4LS}},
series = {{CEUR} Workshop Proceedings},
volume = {2042},
publisher = {CEUR-WS.org},
year = {2017}
}
@inproceedings{DBLP:conf/vissym/KerrenKLS17,
author = {Andreas Kerren and
Kostiantyn Kucher and
Yuan{-}Fang Li and
Falk Schreiber},
title = {MDS-based Visual Survey of Biological Data Visualization Techniques},
booktitle = {EuroVis (Posters)},
pages = {85--87},
publisher = {Eurographics Association},
year = {2017}
}
@incollection{DBLP:reference/gis/X17cw,
title = {Biological Data Mining},
booktitle = {Encyclopedia of {GIS}},
pages = {127},
publisher = {Springer},
year = {2017}
}
@incollection{DBLP:reference/ml/Gerstner17,
author = {Wulfram Gerstner},
title = {Biological Learning: Synaptic Plasticity, Hebb Rule and Spike Timing
Dependent Plasticity},
booktitle = {Encyclopedia of Machine Learning and Data Mining},
pages = {140--143},
publisher = {Springer},
year = {2017}
}
@incollection{DBLP:reference/ml/NobleL17,
author = {William Stafford Noble and
Christina S. Leslie},
title = {Learning Models of Biological Sequences},
booktitle = {Encyclopedia of Machine Learning and Data Mining},
pages = {723--729},
publisher = {Springer},
year = {2017}
}
@article{DBLP:journals/corr/Jamil17,
author = {Hasan M. Jamil},
title = {Knowledge Rich Natural Language Queries over Structured Biological
Databases},
journal = {CoRR},
volume = {abs/1703.10692},
year = {2017}
}
@article{DBLP:journals/corr/PerrinDGcDHPDDG17,
author = {Helene Perrin and
Marion Denorme and
Julien Grosjean and
OMICtools community and
Emeric Dynomant and
Vincent J. Henry and
Fabien Pichon and
St{\'{e}}fan Jacques Darmoni and
Arnaud Desfeux and
Bruno J. Gonzalez},
title = {OMICtools: a community-driven search engine for biological data analysis},
journal = {CoRR},
volume = {abs/1707.03659},
year = {2017}
}
@article{DBLP:journals/corr/abs-1711-03985,
author = {Mufti Mahmud and
M. Shamim Kaiser and
Amir Hussain and
Stefano Vassanelli},
title = {Applications of Deep Learning and Reinforcement Learning to Biological
Data},
journal = {CoRR},
volume = {abs/1711.03985},
year = {2017}
}
@phdthesis{DBLP:phd/basesearch/Hagen16,
author = {Matthew Hagen},
title = {Biological and clinical data integration and its applications in healthcare},
school = {Georgia Institute of Technology, Atlanta, GA, {USA}},
year = {2016}
}
@phdthesis{DBLP:phd/basesearch/Soufan16,
author = {Othman Soufan},
title = {Novel Data Mining Methods for Virtual Screening of Biological Active
Chemical Compounds},
school = {King Abdullah University of Science and Technology, Thuwal, Saudi
Arabia},
year = {2016}
}
@phdthesis{DBLP:phd/gr/Sfakianakis16,
author = {Stelios Sfakianakis},
title = {Exploration of disease-specific biomarkers in cancer research by integrating
biological knowledge and high throughput data},
school = {Technical University of Crete, Greece},
year = {2016}
}
@article{DBLP:journals/almob/HenriquesM16a,
author = {Rui Henriques and
Sara C. Madeira},
title = {BiC2PAM: constraint-guided biclustering for biological data analysis
with domain knowledge},
journal = {Algorithms Mol. Biol.},
volume = {11},
pages = {23},
year = {2016}
}
@article{DBLP:journals/biodatamining/DenaxasAM16,
author = {Spiros C. Denaxas and
Folkert W. Asselbergs and
Jason H. Moore},
title = {The tip of the iceberg: challenges of accessing hospital electronic
health record data for biological data mining},
journal = {BioData Min.},
volume = {9},
pages = {29},
year = {2016}
}
@article{DBLP:journals/biodatamining/LynchM16,
author = {Shannon M. Lynch and
Jason H. Moore},
title = {A call for biological data mining approaches in epidemiology},
journal = {BioData Min.},
volume = {9},
pages = {1},
year = {2016}
}
@article{DBLP:journals/biodb/ChoiLBZV16,
author = {Miji Choi and
Haibin Liu and
William A. Baumgartner Jr. and
Justin Zobel and
Karin Verspoor},
title = {Coreference resolution improves extraction of Biological Expression
Language statements from texts},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016}
}
@article{DBLP:journals/biodb/FluckMAKKRCHSHP16,
author = {Juliane Fluck and
Sumit Madan and
Sam Ansari and
Alpha Tom Kodamullil and
Reagon Karki and
Majid Rastegar{-}Mojarad and
Natalie L. Catlett and
William Hayes and
Justyna Szostak and
Julia Hoeng and
Manuel C. Peitsch},
title = {Training and evaluation corpora for the extraction of causal relationships
encoded in biological expression language {(BEL)}},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016}
}
@article{DBLP:journals/biodb/LaiLHHT16,
author = {Po{-}Ting Lai and
Yu{-}Yan Lo and
Ming{-}Siang Huang and
Yu{-}Cheng Hsiao and
Richard Tzong{-}Han Tsai},
title = {BelSmile: a biomedical semantic role labeling approach for extracting
biological expression language from text},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016}
}
@article{DBLP:journals/biodb/RinaldiEMCLMF16,
author = {Fabio Rinaldi and
Tilia Renate Ellendorff and
Sumit Madan and
Simon Clematide and
Adrian Van der Lek and
Heinz{-}Theodor Mevissen and
Juliane Fluck},
title = {BioCreative {V} track 4: a shared task for the extraction of causal
network information using the Biological Expression Language},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016}
}
@article{DBLP:journals/bioinformatics/CuiCLFLHYZC16,
author = {Ya Cui and
Xiaowei Chen and
Huaxia Luo and
Zhen Fan and
Jianjun Luo and
Shunmin He and
Haiyan Yue and
Peng Zhang and
Runsheng Chen},
title = {BioCircos.js: an interactive Circos JavaScript library for biological
data visualization on web applications},
journal = {Bioinform.},
volume = {32},
number = {11},
pages = {1740--1742},
year = {2016}
}
@article{DBLP:journals/bioinformatics/CuiMZCH16,
author = {Xiaodong Cui and
Jia Meng and
Shaowu Zhang and
Yidong Chen and
Yufei Huang},
title = {A novel algorithm for calling mRNA m\({}^{\mbox{6}}\)A peaks by modeling
biological variances in MeRIP-seq data},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {378--385},
year = {2016}
}
@article{DBLP:journals/bioinformatics/DadaevLSEK16,
author = {Tokhir Dadaev and
Daniel A. Leongamornlert and
Edward J. Saunders and
Rosalind A. Eeles and
Zsofia Kote{-}Jarai},
title = {LocusExplorer: a user-friendly tool for integrated visualization of
human genetic association data and biological annotations},
journal = {Bioinform.},
volume = {32},
number = {6},
pages = {949--951},
year = {2016}
}
@article{DBLP:journals/bioinformatics/DaoFHLSC16,
author = {David Dao and
Adam Fraser and
Jane Hung and
Vebjorn Ljosa and
Shantanu Singh and
Anne E. Carpenter},
title = {CellProfiler Analyst: interactive data exploration, analysis and classification
of large biological image sets},
journal = {Bioinform.},
volume = {32},
number = {20},
pages = {3210--3212},
year = {2016}
}
@article{DBLP:journals/bioinformatics/DingSC16,
author = {Jiarui Ding and
Sohrab P. Shah and
Anne Condon},
title = {densityCut: an efficient and versatile topological approach for automatic
clustering of biological data},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {2567--2576},
year = {2016}
}
@article{DBLP:journals/bioinformatics/HayakawaFM16,
author = {Eisuke Hayakawa and
Yoshinori Fujimura and
Daisuke Miura},
title = {MSIdV: a versatile tool to visualize biological indices from mass
spectrometry imaging data},
journal = {Bioinform.},
volume = {32},
number = {24},
pages = {3852--3854},
year = {2016}
}
@article{DBLP:journals/bioinformatics/ThabenW16,
author = {Paul Florian Thaben and
P{\aa}l O. Westermark},
title = {Differential rhythmicity: detecting altered rhythmicity in biological
data},
journal = {Bioinform.},
volume = {32},
number = {18},
pages = {2800--2808},
year = {2016}
}
@article{DBLP:journals/bioinformatics/TohsatoHKO16,
author = {Yukako Tohsato and
Kenneth H. L. Ho and
Koji Kyoda and
Shuichi Onami},
title = {{SSBD:} a database of quantitative data of spatiotemporal dynamics
of biological phenomena},
journal = {Bioinform.},
volume = {32},
number = {22},
pages = {3471--3479},
year = {2016}
}
@article{DBLP:journals/bioinformatics/YangPGR16,
author = {Jing Yang and
Christopher A. Penfold and
Murray R. Grant and
Magnus Rattray},
title = {Inferring the perturbation time from biological time course data},
journal = {Bioinform.},
volume = {32},
number = {19},
pages = {2956--2964},
year = {2016}
}
@article{DBLP:journals/bmcbi/BaiDBBRJWJS16,
author = {Yongsheng Bai and
Lizhong Ding and
Steve Baker and
Jenny M. Bai and
Ethan Rath and
Feng Jiang and
Jianghong Wu and
Hui Jiang and
Gary W. Stuart},
title = {Dissecting the biological relationship between {TCGA} miRNA and mRNA
sequencing data using \emph{MMiRNA-Viewer}},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-13}},
pages = {336},
year = {2016}
}
@article{DBLP:journals/bmcbi/CaoCDLP16,
author = {Xueyuan Cao and
Kristine R. Crews and
James R. Downing and
Jatinder Lamba and
Stanley Pounds},
title = {{CC-PROMISE} effectively integrates two forms of molecular data with
multiple biologically related endpoints},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-13}},
pages = {382},
year = {2016}
}
@article{DBLP:journals/bmcbi/JaffeHKWCMLC16,
author = {Andrew E. Jaffe and
Thomas Hyde and
Joel Kleinman and
Daniel R. Weinberger and
Joshua Chenoweth and
Ronald McKay and
Jeffrey T. Leek and
Carlo Colantuoni},
title = {Erratum to: Practical impacts of genomic data "cleaning" on biological
discovery using surrogate variable analysis},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {302},
year = {2016}
}
@article{DBLP:journals/bmcbi/LeeJLKK16,
author = {Jusang Lee and
Kyuri Jo and
Sunwon Lee and
Jaewoo Kang and
Sun Kim},
title = {Prioritizing biological pathways by recognizing context in time-series
gene expression data},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-17}},
pages = {257--268},
year = {2016}
}
@article{DBLP:journals/bmcbi/ToureMWBSHPA16,
author = {Vasundra Tour{\'{e}} and
Alexander Mazein and
Dagmar Waltemath and
Irina Balaur and
Mansoor A. S. Saqi and
Ron Henkel and
Johann Pellet and
Charles Auffray},
title = {{STON:} exploring biological pathways using the {SBGN} standard and
graph databases},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {494:1--494:9},
year = {2016}
}
@article{DBLP:journals/bmcbi/VinciottiWJGPBH16,
author = {Veronica Vinciotti and
Ernst C. Wit and
Rick Jansen and
Eco J. C. de Geus and
Brenda W. J. H. Penninx and
Dorret I. Boomsma and
Peter A. C. 't Hoen},
title = {Consistency of biological networks inferred from microarray and sequencing
data},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {254},
year = {2016}
}
@article{DBLP:journals/bmcsb/BuddenC16,
author = {David M. Budden and
Edmund J. Crampin},
title = {Information theoretic approaches for inference of biological networks
from continuous-valued data},
journal = {{BMC} Syst. Biol.},
volume = {10},
pages = {89},
year = {2016}
}
@article{DBLP:journals/cmmm/MahapatraAKP16,
author = {Dwarikanath Mahapatra and
Krishna Agarwal and
Reza Khosrowabadi and
Dilip K. Prasad},
title = {Recent Advances in Statistical Data and Signal Analysis: Application
to Real World Diagnostics from Medical and Biological Signals},
journal = {Comput. Math. Methods Medicine},
volume = {2016},
pages = {1643687:1},
year = {2016}
}
@article{DBLP:journals/cmpb/HanifHSRBI16,
author = {Madiha Hanif and
Abdul Hafeez and
Yusuf Suleman and
M. Mustafa Rafique and
Ali Raza Butt and
Samir M. Iqbal},
title = {An accelerated framework for the classification of biological targets
from solid-state micropore data},
journal = {Comput. Methods Programs Biomed.},
volume = {134},
pages = {53--67},
year = {2016}
}
@article{DBLP:journals/csda/HasegawaNMSYMAI16,
author = {Takanori Hasegawa and
Atsushi Niida and
Tomoya Mori and
Teppei Shimamura and
Rui Yamaguchi and
Satoru Miyano and
Tatsuya Akutsu and
Seiya Imoto},
title = {A likelihood-free filtering method via approximate Bayesian computation
in evaluating biological simulation models},
journal = {Comput. Stat. Data Anal.},
volume = {94},
pages = {63--74},
year = {2016}
}
@article{DBLP:journals/ejes/WangD16,
author = {Haichao Wang and
Zeng Dong},
title = {Big data services drive mobile crowd embedded opportunistic control
mechanism for biological engineering},
journal = {{EURASIP} J. Embed. Syst.},
volume = {2016},
pages = {13},
year = {2016}
}
@article{DBLP:journals/eswa/FaridMMN16,
author = {Dewan Md. Farid and
M. Abdulla Al Mamun and
Bernard Manderick and
Ann Now{\'{e}}},
title = {An adaptive rule-based classifier for mining big biological data},
journal = {Expert Syst. Appl.},
volume = {64},
pages = {305--316},
year = {2016}
}
@article{DBLP:journals/gpb/ZhangDZZYQF16,
author = {Qian Zhang and
Nan Ding and
Lu Zhang and
Xuetong Zhao and
Yadong Yang and
Hongzhu Qu and
Xiangdong Fang},
title = {Biological Databases for Hematology Research},
journal = {Genom. Proteom. Bioinform.},
volume = {14},
number = {6},
pages = {333--337},
year = {2016}
}
@article{DBLP:journals/ijbidm/GopalanD16,
author = {Sindhuja Gopalan and
Sobha Lalitha Devi},
title = {BNEMiner: mining biomedical literature for extraction of biological
target, disease and chemical entities},
journal = {Int. J. Bus. Intell. Data Min.},
volume = {11},
number = {2},
pages = {190--204},
year = {2016}
}
@article{DBLP:journals/ijdmb/WangZLX16,
author = {Xi Wang and
Peiyan Zhu and
Tao Liu and
Ke Xu},
title = {BioTopic: a topic-driven biological literature mining system},
journal = {Int. J. Data Min. Bioinform.},
volume = {14},
number = {4},
pages = {373--386},
year = {2016}
}
@article{DBLP:journals/information/HosseiniPP16,
author = {Seyed Morteza Hosseini and
Diogo Pratas and
Armando J. Pinho},
title = {A Survey on Data Compression Methods for Biological Sequences},
journal = {Inf.},
volume = {7},
number = {4},
pages = {56},
year = {2016}
}
@article{DBLP:journals/jib/LiZJZBTYSHC16,
author = {Qilin Li and
Yincong Zhou and
Yingmin Jiao and
Zhao Zhang and
Lin Bai and
Li Tong and
Xiong Yang and
Bj{\"{o}}rn Sommer and
Ralf Hofest{\"{a}}dt and
Ming Chen},
title = {DaTo: an atlas of biological databases and tools},
journal = {J. Integr. Bioinform.},
volume = {13},
number = {4},
year = {2016}
}
@article{DBLP:journals/jib/Rottger16,
author = {Richard R{\"{o}}ttger},
title = {Clustering of Biological Datasets in the Era of Big Data},
journal = {J. Integr. Bioinform.},
volume = {13},
number = {1},
year = {2016}
}
@article{DBLP:journals/jis/KimB16,
author = {Youngseek Kim and
Christopher Sean Burns},
title = {Norms of data sharing in biological sciences: The roles of metadata,
data repository, and journal and funding requirements},
journal = {J. Inf. Sci.},
volume = {42},
number = {2},
pages = {230--245},
year = {2016}
}
@article{DBLP:journals/nar/PerfettoBCPILLM16,
author = {Livia Perfetto and
Leonardo Briganti and
Alberto Calderone and
Andrea Cerquone Perpetuini and
Marta Iannuccelli and
Francesca Langone and
Luana Licata and
Milica Marinkovic and
Anna Mattioni and
Theodora Pavlidou and
Daniele Peluso and
Lucia Lisa Petrilli and
Stefano Pirr{\`{o}} and
Daniela Posca and
Elena Santonico and
Alessandra Silvestri and
Filomena Spada and
Luisa Castagnoli and
Gianni Cesareni},
title = {{SIGNOR:} a database of causal relationships between biological entities},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {548--554},
year = {2016}
}
@article{DBLP:journals/nar/ShenWLLLCSYGHHC16,
author = {Qiancheng Shen and
Guanqiao Wang and
Shuai Li and
Xinyi Liu and
Shaoyong Lu and
Zhongjie Chen and
Kun Song and
Junhao Yan and
Lv Geng and
Zhimin Huang and
Wenkang Huang and
Guoqiang Chen and
Jian Zhang},
title = {{ASD} v3.0: unraveling allosteric regulation with structural mechanisms
and biological networks},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {527--535},
year = {2016}
}
@article{DBLP:journals/ploscb/BagleySCBA16,
author = {Steven C. Bagley and
Marina Sirota and
Richard O. Chen and
Atul J. Butte and
Russ B. Altman},
title = {Constraints on Biological Mechanism from Disease Comorbidity Using
Electronic Medical Records and Database of Genetic Variants},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {4},
year = {2016}
}
@article{DBLP:journals/ploscb/HelmyCB16,
author = {Mohamed Helmy and
Alexander Crits{-}Christoph and
Gary D. Bader},
title = {Ten Simple Rules for Developing Public Biological Databases},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {11},
year = {2016}
}
@article{DBLP:journals/ploscb/PasolliTMWS16,
author = {Edoardo Pasolli and
Duy Tin Truong and
Faizan Malik and
Levi Waldron and
Nicola Segata},
title = {Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools
and Biological Insights},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {7},
year = {2016}
}
@article{DBLP:journals/ploscb/WaagmeesterKRMW16,
author = {Andra Waagmeester and
Martina Kutmon and
Anders Riutta and
Ryan A. Miller and
Egon L. Willighagen and
Chris T. A. Evelo and
Alexander R. Pico},
title = {Using the Semantic Web for Rapid Integration of WikiPathways with
Other Biological Online Data Resources},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {6},
year = {2016}
}
@article{DBLP:journals/rjour/DeveauBBZB16,
author = {Paul Deveau and
Emmanuel Barillot and
Valentina Boeva and
Andrei Yu. Zinovyev and
Eric Bonnet},
title = {Calculating Biological Module Enrichment or Depletion and Visualizing
Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages},
journal = {R J.},
volume = {8},
number = {2},
pages = {293},
year = {2016}
}
@article{DBLP:journals/rjour/Wright16,
author = {Erik Scott Wright},
title = {Using {DECIPHER} v2.0 to Analyze Big Biological Sequence Data in {R}},
journal = {R J.},
volume = {8},
number = {1},
pages = {352},
year = {2016}
}
@article{DBLP:journals/tcbb/GuzziM16,
author = {Pietro Hiram Guzzi and
Marco Mina},
title = {Guest Editorial for Special Section on Semantic-Based Approaches for
Analysis of Biological Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {13},
number = {2},
pages = {196},
year = {2016}
}
@article{DBLP:journals/tcbb/MooreB16,
author = {Erin J. Moore and
Thirimachos Bourlai},
title = {Expectation Maximization of Frequent Patterns, a Specific, Local,
Pattern-Based Biclustering Algorithm for Biological Datasets},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {13},
number = {5},
pages = {812--824},
year = {2016}
}
@article{DBLP:journals/tjs/LiFMF16,
author = {Jinyan Li and
Simon Fong and
Sabah Mohammed and
Jinan Fiaidhi},
title = {Improving the classification performance of biological imbalanced
datasets by swarm optimization algorithms},
journal = {J. Supercomput.},
volume = {72},
number = {10},
pages = {3708--3728},
year = {2016}
}
@inproceedings{DBLP:conf/3dui/LagesALSB16,
author = {Wallace Santos Lages and
Gustavo A. Arango and
David H. Laidlaw and
John J. Socha and
Doug A. Bowman},
title = {Designing capsule, an input device to support the manipulation of
biological datasets},
booktitle = {3DUI},
pages = {255--256},
publisher = {{IEEE} Computer Society},
year = {2016}
}
@inproceedings{DBLP:conf/aaaiss/HaradaUKTKMT16,
author = {Tomohiro Harada and
Fumito Uwano and
Takahiro Komine and
Yusuke Tajima and
Takahiro Kawashima and
Morito Morishima and
Keiki Takadama},
title = {Real-Time Sleep Stage Estimation from Biological Data with Trigonometric
Function Regression Model},
booktitle = {{AAAI} Spring Symposia},
publisher = {{AAAI} Press},
year = {2016}
}
@inproceedings{DBLP:conf/amcc/AchantaMV16,
author = {Hema Kumari Achanta and
Burook Misganaw and
M. Vidyasagar},
title = {A transfer learning approach for integrating biological data across
platforms},
booktitle = {{ACC}},
pages = {6695--6697},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/besc/LiYCS16,
author = {Qian Li and
Zhenglu Yang and
Wei Cao and
Kentaro Shimizu},
title = {An effective system for managing biological data},
booktitle = {{BESC}},
pages = {1--2},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/clei/Parraga-AlavaI16,
author = {Jorge Parraga{-}Alava and
Mario Inostroza{-}Ponta},
title = {A bi-objective model for gene clustering combining expression data
and external biological knowledge},
booktitle = {{CLEI}},
pages = {1--12},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/cmsb/AbdallahRMRI16,
author = {Emna Ben Abdallah and
Tony Ribeiro and
Morgan Magnin and
Olivier F. Roux and
Katsumi Inoue},
title = {Inference of Delayed Biological Regulatory Networks from Time Series
Data},
booktitle = {{CMSB}},
series = {Lecture Notes in Computer Science},
volume = {9859},
pages = {30--48},
publisher = {Springer},
year = {2016}
}
@inproceedings{DBLP:conf/cods/VatsaAS16,
author = {Deepika Vatsa and
Sumeet Agarwal and
Ashwin Srinivasan},
title = {Learning transition models of biological regulatory and signaling
networks from noisy data},
booktitle = {{CODS}},
pages = {9:1--9:6},
publisher = {{ACM}},
year = {2016}
}
@inproceedings{DBLP:conf/eScience/AlzuruMTF16,
author = {Icaro Alzuru and
Andr{\'{e}}a M. Matsunaga and
Maur{\'{\i}}cio O. Tsugawa and
Jos{\'{e}} A. B. Fortes},
title = {Cooperative human-machine data extraction from biological collections},
booktitle = {eScience},
pages = {41--50},
publisher = {{IEEE} Computer Society},
year = {2016}
}
@inproceedings{DBLP:conf/embc/NowakLDC16,
author = {Michael R. Nowak and
Alexander Lozovskiy and
Dimitri Dobroskok and
Yoonsuck Choe},
title = {Knife-edge scanning microscopy for in silico study of cerebral blood
flow: From biological imaging data to flow simulations},
booktitle = {{EMBC}},
pages = {5957--5960},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/embc/PahujaLM16,
author = {Vardaan Pahuja and
Ritwik Kumar Layek and
Pabitra Mitra},
title = {Learning a Probabilistic Boolean Network model from biological pathways
and time-series expression data},
booktitle = {{EMBC}},
pages = {1471--1475},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/euspn/CaninoSCMTGCV16,
author = {Giovanni Canino and
Mariagrazia Scarpino and
Francesca Cristiano and
Domenico Mirarchi and
Giuseppe Tradigo and
Pietro Hiram Guzzi and
Giovanni Cuda and
Pierangelo Veltri},
title = {Geoblood: {A} Web Based Tool for Geo-analysis of Biological Data},
booktitle = {{EUSPN/ICTH}},
series = {Procedia Computer Science},
volume = {98},
pages = {473--478},
publisher = {Elsevier},
year = {2016}
}
@inproceedings{DBLP:conf/icbo/Raghuvanshi16,
author = {Saurabh Raghuvanshi},
title = {Semantic Digitization of Experimental Data in Biological Sciences},
booktitle = {ICBO/BioCreative},
series = {{CEUR} Workshop Proceedings},
volume = {1747},
publisher = {CEUR-WS.org},
year = {2016}
}
@inproceedings{DBLP:conf/icra/ShahriariRBDM16,
author = {Navid Shahriari and
Roy J. Roesthuis and
Nick J. van de Berg and
John van den Dobbelsteen and
Sarthak Misra},
title = {Steering an actuated-tip needle in biological tissue: Fusing FBG-sensor
data and ultrasound images},
booktitle = {{ICRA}},
pages = {4443--4449},
publisher = {{IEEE}},
year = {2016}
}
@inproceedings{DBLP:conf/isbra/EshlemanS16,
author = {Ryan Eshleman and
Rahul Singh},
title = {Progression Reconstruction from Unsynchronized Biological Data using
Cluster Spanning Trees},
booktitle = {{ISBRA}},
series = {Lecture Notes in Computer Science},
volume = {9683},
pages = {136--147},
publisher = {Springer},
year = {2016}
}
@inproceedings{DBLP:conf/sebd/CaninoGSTV16,
author = {Giovanni Canino and
Pietro Hiram Guzzi and
Mariagrazia Scarpino and
Giuseppe Tradigo and
Pierangelo Veltri},
title = {Patient wellness: geoanalysis of biological and environmental data},
booktitle = {{SEBD}},
pages = {278--285},
publisher = {Matematicamente.it},
year = {2016}
}
@inproceedings{DBLP:conf/semweb/ParkKKYLLJHK16,
author = {Junho Park and
Min{-}Ji Kim and
Eung{-}Hee Kim and
Sung{-}Kwon Yang and
Sungin Lee and
Jin{-}Muk Lim and
Hyunwhan Joe and
Kyung{-}Sik Ha and
Hong{-}Gee Kim},
title = {BiDIP: a Biological Data Integration Platform for Transcriptome Analysis},
booktitle = {BMDID@ISWC},
series = {{CEUR} Workshop Proceedings},
volume = {1709},
publisher = {CEUR-WS.org},
year = {2016}
}
@inproceedings{DBLP:conf/semweb/TakatsukiSKTOOL16,
author = {Terue Takatsuki and
Mikako Saito and
Sadahiro Kumagai and
Eiki Takayama and
Kazuya Ohshima and
Nozomu Ohshiro and
Kai Lenz and
Nobuhiko Tanaka and
Norio Kobayashi and
Hiroshi Masuya},
title = {A {RDF} based Portal of Biological Phenotype Data produced in Japan},
booktitle = {{ISWC} (Posters {\&} Demos)},
series = {{CEUR} Workshop Proceedings},
volume = {1690},
publisher = {CEUR-WS.org},
year = {2016}
}
@inproceedings{DBLP:conf/swat4ls/DeraspeBBCCCCCH16,
author = {Maxime D{\'{e}}raspe and
Gail Binkley and
Daniela Butano and
Matthew Chadwick and
J. Michael Cherry and
Justin Clark{-}Casey and
Sergio Contrino and
Jacques Corbeil and
Joshua Heimbach and
Kalpana Karra and
Rachel Lyne and
Julie M. Sullivan and
Yo Yehudi and
Gos Micklem and
Michel Dumontier},
title = {Making Linked Data {SPARQL} with the InterMine Biological Data Warehouse},
booktitle = {{SWAT4LS}},
series = {{CEUR} Workshop Proceedings},
volume = {1795},
publisher = {CEUR-WS.org},
year = {2016}
}
@inproceedings{DBLP:conf/tpcg/VogogiasKASC16,
author = {Athanasios Vogogias and
Jessie Kennedy and
Daniel Archambault and
V. Anne Smith and
Hannah Currant},
title = {MLCut: Exploring Multi-Level Cuts in Dendrograms for Biological Data},
booktitle = {{CGVC}},
pages = {1--8},
publisher = {Eurographics Association},
year = {2016}
}
@incollection{DBLP:books/cu/p/AcharyaZ16,
author = {Lipi R. Acharya and
Dongxiao Zhu},
title = {Gene-set-based inference of biological network topologies from big
molecular profiling data},
booktitle = {Big Data over Networks},
pages = {391--408},
publisher = {Cambridge University Press},
year = {2016}
}
@incollection{DBLP:books/sp/16/LongL16,
author = {Tran Van Long and
Lars Linsen},
title = {Efficient Reordering of Parallel Coordinates and Its Application to
Multidimensional Biological Data Visualization},
booktitle = {Visualization in Medicine and Life Sciences {III}},
series = {Mathematics and Visualization},
pages = {309--328},
publisher = {Springer},
year = {2016}
}
@incollection{DBLP:series/ccn/PedersenB16,
author = {Edvard Pedersen and
Lars Ailo Bongo},
title = {Big Biological Data Management},
booktitle = {Resource Management for Big Data Platforms},
series = {Computer Communications and Networks},
pages = {265--277},
publisher = {Springer},
year = {2016}
}
@article{DBLP:journals/corr/GrinblatBMGS16,
author = {Guillermo L. Grinblat and
Ariel E. Bay{\'{a}} and
Diego H. Milone and
Pablo M. Granitto and
Georgina Stegmayer},
title = {Inferring unknown biological function by integration of {GO} annotations
and gene expression data},
journal = {CoRR},
volume = {abs/1608.03672},
year = {2016}
}
@phdthesis{DBLP:phd/basesearch/Charpilloz15,
author = {Christophe Charpilloz},
title = {Analysis of large biological data: metabolic network modularization
and prediction of N-terminal acetylation},
school = {University of Geneva, Switzerland},
year = {2015}
}
@phdthesis{DBLP:phd/basesearch/Woods15,
author = {Tonya M. Woods},
title = {Extracting meaningful statistics for the characterization and classification
of biological, medical, and financial data},
school = {Georgia Institute of Technology, Atlanta, GA, {USA}},
year = {2015}
}
@phdthesis{DBLP:phd/dnb/Barghash15,
author = {Ahmad Barghash},
title = {Identifying biological associations from high-throughput datasets},
school = {Saarland University},
year = {2015}
}
@phdthesis{DBLP:phd/hal/Brancotte15,
author = {Bryan Brancotte},
title = {Agr{\'{e}}gation de classements avec {\'{e}}galit{\'{e}}s
: algorithmes, guides {\`{a}} l'utilisateur et applications aux donn{\'{e}}es
biologiques. (Rank aggregation with ties : algorithms, user guidance
et applications to biologicals data)},
school = {University of Paris-Sud, Orsay, France},
year = {2015}
}
@phdthesis{DBLP:phd/jp/Hasegawa15,
author = {Takanori Hasegawa},
title = {Reconstructing Biological Systems Incorporating Multi-Source Biological
Data via Data Assimilation Techniques},
school = {Kyoto University, Japan},
year = {2015}
}
@phdthesis{DBLP:phd/us/Dhulekar15,
author = {Nimit Dhulekar},
title = {Data analytics of time-series for complex (biological) systems},
school = {Rensselaer Polytechnic Institute, {USA}},
year = {2015}
}
@phdthesis{DBLP:phd/us/Iyer15,
author = {Sowmya Iyer},
title = {Analysis of genomic data to derive biological conclusions on {(1)}
transcriptional regulation in the human genome and {(2)} antibody
resistance in hepatitis {C} virus},
school = {Boston University, {USA}},
year = {2015}
}
@article{DBLP:journals/alr/MatsumaeIMIOT15,
author = {Hiromi Matsumae and
Ryosuke R. Ishiwata and
Toshifumi Minamoto and
Norio Ishida and
Soichi Ogishima and
Hiroshi Tanaka},
title = {Detection of periodic patterns in microarray data reveals novel oscillating
transcripts of biological rhythms in Ciona intestinalis},
journal = {Artif. Life Robotics},
volume = {20},
number = {4},
pages = {347--352},
year = {2015}
}
@article{DBLP:journals/bigdata/BierutC15,
author = {Laura J. Bierut and
David Cesarini},
title = {How Genetic and Other Biological Factors Interact with Smoking Decisions},
journal = {Big Data},
volume = {3},
number = {3},
pages = {198--202},
year = {2015}
}
@article{DBLP:journals/biodatamining/WeissZHDSSM15,
author = {Talia Weiss and
Amanda L. Zieselman and
Douglas P. Hill and
Solomon Gilbert Diamond and
Li Shen and
Andrew J. Saykin and
Jason H. Moore},
title = {The role of visualization and 3-D printing in biological data mining},
journal = {BioData Min.},
volume = {8},
pages = {22},
year = {2015}
}
@article{DBLP:journals/biodatamining/WilliamsM15,
author = {Scott M. Williams and
Jason H. Moore},
title = {Lumping versus splitting: the need for biological data mining in precision
medicine},
journal = {BioData Min.},
volume = {8},
pages = {16},
year = {2015}
}
@article{DBLP:journals/biodb/BelinkyNSZSSL15,
author = {Frida Belinky and
Noam Nativ and
Gil Stelzer and
Shahar Zimmerman and
Tsippi Iny Stein and
Marilyn Safran and
Doron Lancet},
title = {PathCards: multi-source consolidation of human biological pathways},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015}
}
@article{DBLP:journals/biodb/BoueTWHFPSSFAMV15,
author = {St{\'{e}}phanie Bou{\'{e}} and
Marja Talikka and
Jurjen Willem Westra and
William Hayes and
Anselmo Di Fabio and
Jennifer Park and
Walter K. Schlage and
Alain Sewer and
Brett Fields and
Sam Ansari and
Florian Martin and
Emilija Veljkovic and
Ren{\'{e}}e Kenney and
Manuel C. Peitsch and
Julia Hoeng},
title = {Causal biological network database: a comprehensive platform of causal
biological network models focused on the pulmonary and vascular systems},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015}
}
@article{DBLP:journals/biodb/SzostakAMFTILHP15,
author = {Justyna Szostak and
Sam Ansari and
Sumit Madan and
Juliane Fluck and
Marja Talikka and
Anita Iskandar and
Hector De Leon and
Martin Hofmann{-}Apitius and
Manuel C. Peitsch and
Julia Hoeng},
title = {Construction of biological networks from unstructured information
based on a semi-automated curation workflow},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015}
}
@article{DBLP:journals/bioinformatics/KyodaTHO15,
author = {Koji Kyoda and
Yukako Tohsato and
Kenneth H. L. Ho and
Shuichi Onami},
title = {Biological Dynamics Markup Language {(BDML):} an open format for representing
quantitative biological dynamics data},
journal = {Bioinform.},
volume = {31},
number = {7},
pages = {1044--1052},
year = {2015}
}
@article{DBLP:journals/bioinformatics/TsoiEA15,
author = {Lam C. Tsoi and
James T. Elder and
Gon{\c{c}}alo R. Abecasis},
title = {Graphical algorithm for integration of genetic and biological data:
proof of principle using psoriasis as a model},
journal = {Bioinform.},
volume = {31},
number = {8},
pages = {1243--1249},
year = {2015}
}
@article{DBLP:journals/bioinformatics/ZhangAWLGPTWSB15,
author = {Qunyuan Zhang and
Haley Abel and
Alan Wells and
Petra Lenzini and
Felicia Gomez and
Michael A. Province and
Alan A. Templeton and
George M. Weinstock and
Nita H. Salzman and
Ingrid B. Borecki},
title = {Selection of models for the analysis of risk-factor trees: leveraging
biological knowledge to mine large sets of risk factors with application
to microbiome data},
journal = {Bioinform.},
volume = {31},
number = {10},
pages = {1607--1613},
year = {2015}
}
@article{DBLP:journals/bmcbi/AertsMNNSW15,
author = {Jan Aerts and
G. Elisabeta Marai and
Kay Nieselt and
Cydney B. Nielsen and
Marc Streit and
Daniel Weiskopf},
title = {Highlights from the 5th Symposium on Biological Data Visualization:
Part 1},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S11}},
pages = {S1},
year = {2015}
}
@article{DBLP:journals/bmcbi/BharH0W15,
author = {Anirban Bhar and
Martin Haubrock and
Anirban Mukhopadhyay and
Edgar Wingender},
title = {Multiobjective triclustering of time-series transcriptome data reveals
key genes of biological processes},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {200:1--200:19},
year = {2015}
}
@article{DBLP:journals/bmcbi/JaffeHKWCMLC15,
author = {Andrew E. Jaffe and
Thomas Hyde and
Joel Kleinman and
Daniel Weinbergern and
Joshua Chenoweth and
Ronald McKay and
Jeffrey T. Leek and
Carlo Colantuoni},
title = {Practical impacts of genomic data "cleaning" on biological discovery
using surrogate variable analysis},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {372:1--372:10},
year = {2015}
}
@article{DBLP:journals/bmcbi/KimNSJAMK15,
author = {Sa Kim and
Tuong Nguyen and
Na Seo and
Seunghup Jung and
Hyun An and
David A. Mills and
Jae Kim},
title = {Comparative proteomics: assessment of biological variability and dataset
comparability},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {121:1--121:10},
year = {2015}
}
@article{DBLP:journals/bmcbi/VehlowKBHWG15,
author = {Corinna Vehlow and
David P. Kao and
Michael R. Bristow and
Lawrence E. Hunter and
Daniel Weiskopf and
Carsten G{\"{o}}rg},
title = {Visual analysis of biological data-knowledge networks},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {135:1--135:15},
year = {2015}
}
@article{DBLP:journals/bmcbi/ZhuSGSFC15,
author = {Yongnan Zhu and
Liang Sun and
Alexander Garbarino and
Carl J. Schmidt and
Jinglong Fang and
Jian Chen},
title = {PathRings: a web-based tool for exploration of ortholog and expression
data in biological pathways},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {165:1--165:7},
year = {2015}
}
@article{DBLP:journals/bmcsb/YinGMGS15,
author = {Weiwei Yin and
Swetha Garimalla and
Alberto Moreno and
Mary R. Galinski and
Mark P. Styczynski},
title = {A tree-like Bayesian structure learning algorithm for small-sample
datasets from complex biological model systems},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {49},
year = {2015}
}
@article{DBLP:journals/cbm/PirimEP15,
author = {Harun Pirim and
Burak Eksioglu and
Andy D. Perkins},
title = {Clustering high throughput biological data with B-MST, a minimum spanning
tree based heuristic},
journal = {Comput. Biol. Medicine},
volume = {62},
pages = {94--102},
year = {2015}
}
@article{DBLP:journals/cea/TijskensSKJ15,
author = {L. M. M. Tijskens and
R. E. Schouten and
Pawel Konopacki and
Geurt Jongbloed},
title = {Basic principles of analysing biological and technical variation in
non-destructive data},
journal = {Comput. Electron. Agric.},
volume = {111},
pages = {121--126},
year = {2015}
}
@article{DBLP:journals/cmpb/NepomucenoLNA15,
author = {Juan A. Nepomuceno and
Alicia Troncoso Lora and
Isabel A. Nepomuceno{-}Chamorro and
Jes{\'{u}}s S. Aguilar{-}Ruiz},
title = {Integrating biological knowledge based on functional annotations for
biclustering of gene expression data},
journal = {Comput. Methods Programs Biomed.},
volume = {119},
number = {3},
pages = {163--180},
year = {2015}
}
@article{DBLP:journals/gpb/ZouMYZ15,
author = {Dong Zou and
Lina Ma and
Jun Yu and
Zhang Zhang},
title = {Biological Databases for Human Research},
journal = {Genom. Proteom. Bioinform.},
volume = {13},
number = {1},
pages = {55--63},
year = {2015}
}
@article{DBLP:journals/ijait/KouzinopoulosAPM15,
author = {Charalampos S. Kouzinopoulos and
John{-}Alexander M. Assael and
Themistoklis K. Pyrgiotis and
Konstantinos G. Margaritis},
title = {A Hybrid Parallel Implementation of the Aho-Corasick and Wu-Manber
Algorithms Using {NVIDIA} {CUDA} and {MPI} Evaluated on a Biological
Sequence Database},
journal = {Int. J. Artif. Intell. Tools},
volume = {24},
number = {1},
pages = {1540001:1--1540001:32},
year = {2015}
}
@article{DBLP:journals/ijdmb/BernaboMB15,
author = {Nicola Bernab{\`{o}} and
Mauro Mattioli and
Barbara Barboni},
title = {Signal transduction in the activation of spermatozoa compared to other
signalling pathways: a biological networks study},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {1},
pages = {59--69},
year = {2015}
}
@article{DBLP:journals/ijdmb/ChenGLM15,
author = {Yifei Chen and
Hongjian Guo and
Feng Liu and
Bernard Manderick},
title = {Improving protein-protein interaction article classification using
biological domain knowledge},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {2},
pages = {144--166},
year = {2015}
}
@article{DBLP:journals/ijdmb/FaroGM15,
author = {Alberto Faro and
Daniela Giordano and
Francesco Maiorana},
title = {Mining literatures to discover novel multiple biological associations
in a disease context},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {2},
pages = {224--256},
year = {2015}
}
@article{DBLP:journals/ijdmb/KimSTH15,
author = {Sunghan Kim and
Fabien Scalzo and
Donatello Telesca and
Xiao Hu},
title = {Ensemble of sparse classifiers for high-dimensional biological data},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {2},
pages = {167--183},
year = {2015}
}
@article{DBLP:journals/ijdmb/KuttiyapillaiR15,
author = {Dhanasekaran Kuttiyapillai and
R. Rajeswari},
title = {A method for extracting task-oriented information from biological
text sources},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {4},
pages = {387--399},
year = {2015}
}
@article{DBLP:journals/ijdmb/LiZ15,
author = {Limin Li and
Shuqin Zhang},
title = {Orthogonal projection correction for confounders in biological data
classification},
journal = {Int. J. Data Min. Bioinform.},
volume = {13},
number = {2},
pages = {181--196},
year = {2015}
}
@article{DBLP:journals/ijdmb/ReddyA15,
author = {Chandan K. Reddy and
Mohammad S. Aziz},
title = {Predicting gene functions from multiple biological sources using novel
ensemble methods},
journal = {Int. J. Data Min. Bioinform.},
volume = {12},
number = {2},
pages = {184--206},
year = {2015}
}
@article{DBLP:journals/ijdmb/WangZ15,
author = {Shuliang Wang and
Yiping Zhao},
title = {Analysing large biological data sets with an improved algorithm for
{MIC}},
journal = {Int. J. Data Min. Bioinform.},
volume = {13},
number = {2},
pages = {158--170},
year = {2015}
}
@article{DBLP:journals/ijhis/Soncco-AlvarezABA15,
author = {Jos{\'{e}} Luis Soncco{-}{\'{A}}lvarez and
Gabriel Marchesan Almeida and
J{\"{u}}rgen Becker and
Mauricio Ayala{-}Rinc{\'{o}}n},
title = {Parallelization of genetic algorithms for sorting permutations by
reversals over biological data},
journal = {Int. J. Hybrid Intell. Syst.},
volume = {12},
number = {1},
pages = {53--64},
year = {2015}
}
@article{DBLP:journals/it/GeraschKNS0KL15,
author = {Andreas Gerasch and
Jan K{\"{u}}ntzer and
Peter Niermann and
Daniel St{\"{o}}ckel and
Michael Kaufmann and
Oliver Kohlbacher and
Hans{-}Peter Lenhof},
title = {Network-based interactive navigation and analysis of large biological
datasets},
journal = {it Inf. Technol.},
volume = {57},
number = {1},
pages = {37--48},
year = {2015}
}
@article{DBLP:journals/jbi/KimKYP15,
author = {Jeongwoo Kim and
Hyunjin Kim and
Youngmi Yoon and
Sanghyun Park},
title = {LGscore: {A} method to identify disease-related genes using biological
literature and Google data},
journal = {J. Biomed. Informatics},
volume = {54},
pages = {270--282},
year = {2015}
}
@article{DBLP:journals/jcb/BaurB15,
author = {Brittany A. Baur and
Serdar Bozdag},
title = {A Canonical Correlation Analysis-Based Dynamic Bayesian Network Prior
to Infer Gene Regulatory Networks from Multiple Types of Biological
Data},
journal = {J. Comput. Biol.},
volume = {22},
number = {4},
pages = {289--299},
year = {2015}
}
@article{DBLP:journals/jcb/SakhanenkoG15,
author = {Nikita A. Sakhanenko and
David J. Galas},
title = {Biological Data Analysis as an Information Theory Problem: Multivariable
Dependence Measures and the Shadows Algorithm},
journal = {J. Comput. Biol.},
volume = {22},
number = {11},
pages = {1005--1024},
year = {2015}
}
@article{DBLP:journals/jossac/JiangQCC15,
author = {Hao Jiang and
Yushan Qiu and
Xiaoqing Cheng and
Wai{-}Ki Ching},
title = {On Eigen-matrix translation method for classification of biological
data},
journal = {J. Syst. Sci. Complex.},
volume = {28},
number = {5},
pages = {1212--1230},
year = {2015}
}
@article{DBLP:journals/nar/SquizzatoPBGCLU15,
author = {Silvano Squizzato and
Young Mi Park and
Nicola Buso and
Tamer Gur and
Andrew Peter Cowley and
Weizhong Li and
Mahmut Uludag and
Sangya Pundir and
Jennifer A. Cham and
Hamish McWilliam and
Rodrigo Lopez},
title = {The {EBI} Search engine: providing search and retrieval functionality
for biological data from {EMBL-EBI}},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Webserver-Issue},
pages = {W585--W588},
year = {2015}
}
@article{DBLP:journals/nar/ValentiniKPJS15,
author = {Erica Valentini and
Alexey G. Kikhney and
Gianpietro Previtali and
Cy M. Jeffries and
Dmitri I. Svergun},
title = {SASBDB, a repository for biological small-angle scattering data},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {357--363},
year = {2015}
}
@article{DBLP:journals/ploscb/KingDESLP15,
author = {Zachary A. King and
Andreas Dr{\"{a}}ger and
Ali Ebrahim and
Nikolaus Sonnenschein and
Nathan E. Lewis and
Bernhard O. Palsson},
title = {Escher: {A} Web Application for Building, Sharing, and Embedding Data-Rich
Visualizations of Biological Pathways},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {8},
year = {2015}
}
@article{DBLP:journals/ploscb/SteinMS15,
author = {Richard R. Stein and
Debora S. Marks and
Chris Sander},
title = {Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy
Probability Models},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {7},
year = {2015}
}
@article{DBLP:journals/ploscb/ZhanCECACL15,
author = {Mei Zhan and
Matthew M. Crane and
Eugeni V. Entchev and
Antonio Caballero and
Diana Andrea Fernandes de Abreu and
QueeLim Ch'ng and
Hang Lu},
title = {Automated Processing of Imaging Data through Multi-tiered Classification
of Biological Structures Illustrated Using \emph{Caenorhabditis elegans}},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {4},
year = {2015}
}
@article{DBLP:journals/polibits/RinaldiLLGBSC15,
author = {Fabio Rinaldi and
Oscar Lithgow{-}Serrano and
Alejandra L{\'{o}}pez{-}Fuentes and
Socorro Gama{-}Castro and
Yalbi I. Balderas{-}Mart{\'{\i}}nez and
Hilda Solano{-}Lira and
Julio Collado{-}Vides},
title = {An Approach towards Semi-automated Biomedical Literature Curation
and Enrichment for a Major Biological Database},
journal = {Polibits},
volume = {52},
pages = {25--31},
year = {2015}
}
@article{DBLP:journals/quanbio/DengDS15,
author = {Chao Deng and
Timothy Daley and
Andrew D. Smith},
title = {Applications of species accumulation curves in large-scale biological
data analysis},
journal = {Quant. Biol.},
volume = {3},
number = {3},
pages = {135--144},
year = {2015}
}
@article{DBLP:journals/tcbb/BordonMZM15,
author = {Jure Bordon and
Miha Moskon and
Nikolaj Zimic and
Miha Mraz},
title = {Fuzzy Logic as a Computational Tool for Quantitative Modelling of
Biological Systems with Uncertain Kinetic Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {12},
number = {5},
pages = {1199--1205},
year = {2015}
}
@article{DBLP:journals/titb/Taha15,
author = {Kamal Taha},
title = {Extracting Various Classes of Data From Biological Text Using the
Concept of Existence Dependency},
journal = {{IEEE} J. Biomed. Health Informatics},
volume = {19},
number = {6},
pages = {1918--1928},
year = {2015}
}
@article{DBLP:journals/vlsisp/Abu-JamousFRN15,
author = {Basel Abu{-}Jamous and
Rui Fa and
David Roberts and
Asoke K. Nandi},
title = {Application of the Bi-CoPaM Method to Five Escherichia Coli Datasets
Generated under Various Biological Conditions},
journal = {J. Signal Process. Syst.},
volume = {79},
number = {2},
pages = {159--166},
year = {2015}
}
@inproceedings{DBLP:conf/IEEEcloud/ToniniS15,
author = {Gustavo Tonini and
Frank Siqueira},
title = {Improving the Performance of Biological Data Analysis in Cloud Computing
Platforms},
booktitle = {{CLOUD}},
pages = {766--772},
publisher = {{IEEE} Computer Society},
year = {2015}
}
@inproceedings{DBLP:conf/bibm/LanLSW15,
author = {Haidong Lan and
Weiguo Liu and
Bertil Schmidt and
Bingqiang Wang},
title = {Accelerating large-scale biological database search on Xeon Phi-based
neo-heterogeneous architectures},
booktitle = {{BIBM}},
pages = {503--510},
publisher = {{IEEE} Computer Society},
year = {2015}
}
@inproceedings{DBLP:conf/birthday/PapageorgiouV15,
author = {Haralambos Papageorgiou and
Maria Vardaki},
title = {Classical and Symbolic metadata setting for biological datasets},
booktitle = {Symbolic Data Analysis and Visualization},
series = {{RNTI}},
volume = {{E-29}},
pages = {49--58},
publisher = {Hermann-{\'{E}}ditions},
year = {2015}
}
@inproceedings{DBLP:conf/ciarp/VicenteMROL15,
author = {F{\'{a}}bio Fernandes da Rocha Vicente and
Euler Menezes and
Gabriel Rubino and
Juliana de Oliveira and
Fabr{\'{\i}}cio Martins Lopes},
title = {A Feature Selection Approach for Evaluate the Inference of GRNs Through
Biological Data Integration - {A} Case Study on A. Thaliana},
booktitle = {{CIARP}},
series = {Lecture Notes in Computer Science},
volume = {9423},
pages = {667--675},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/cibcb/SoylevA15,
author = {Arda Soylev and
Osman Abul},
title = {{REFBSS:} Reference based similarity search in biological network
databases},
booktitle = {{CIBCB}},
pages = {1--8},
publisher = {{IEEE}},
year = {2015}
}
@inproceedings{DBLP:conf/ciss/JalaliMC15,
author = {Bahram Jalali and
Ata Mahjoubfar and
Claire L. Chen},
title = {High-throughput biological cell classification featuring real-time
optical data compression},
booktitle = {{CISS}},
pages = {1--3},
publisher = {{IEEE}},
year = {2015}
}
@inproceedings{DBLP:conf/eva/Stadon15,
author = {Julian Stadon},
title = {Data Body Banking: Understanding Post Biological Identity through
Embodied Mixed Reality Art},
booktitle = {{EVA}},
series = {Workshops in Computing},
publisher = {{BCS}},
year = {2015}
}
@inproceedings{DBLP:conf/gbrpr/CarlettiFVJ15,
author = {Vincenzo Carletti and
Pasquale Foggia and
Mario Vento and
Xiaoyi Jiang},
title = {Report on the First Contest on Graph Matching Algorithms for Pattern
Search in Biological Databases},
booktitle = {GbRPR},
series = {Lecture Notes in Computer Science},
volume = {9069},
pages = {178--187},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/hci/WinklerPJ15,
author = {Manuel H. Winkler and
Herbert Plischke and
Werner Jensch},
title = {Subjective Ratings of Biological Effective Light in Seminar Rooms
and How to Handle Small Sample Sizes of Ordinal Data},
booktitle = {{HCI} {(8)}},
series = {Lecture Notes in Computer Science},
volume = {9176},
pages = {594--603},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/icdm/BhardwajDB15,
author = {Manju Bhardwaj and
Debasis Dash and
Vasudha Bhatnagar},
title = {Accurate Classification of Biological Data Using Ensembles},
booktitle = {{ICDM} Workshops},
pages = {1486--1493},
publisher = {{IEEE} Computer Society},
year = {2015}
}
@inproceedings{DBLP:conf/iclp/AngelopoulosG15,
author = {Nicos Angelopoulos and
Georgios Giamas},
title = {A Logical Approach to Working with Biological Databases},
booktitle = {{ICLP} (Technical Communications)},
series = {{CEUR} Workshop Proceedings},
volume = {1433},
publisher = {CEUR-WS.org},
year = {2015}
}
@inproceedings{DBLP:conf/isbi/KrasowskiBKKHK15,
author = {Nikola Krasowski and
Thorsten Beier and
Graham W. Knott and
Ullrich K{\"{o}}the and
Fred A. Hamprecht and
Anna Kreshuk},
title = {Improving 3D {EM} data segmentation by joint optimization over boundary
evidence and biological priors},
booktitle = {{ISBI}},
pages = {536--539},
publisher = {{IEEE}},
year = {2015}
}
@inproceedings{DBLP:conf/isbi/PrestonJW15,
author = {J. Samuel Preston and
Sarang C. Joshi and
Ross T. Whitaker},
title = {Multiscale {MRF} optimization for robust registration of 2D biological
data},
booktitle = {{ISBI}},
pages = {302--305},
publisher = {{IEEE}},
year = {2015}
}
@inproceedings{DBLP:conf/macis/BouaguelMM15,
author = {Waad Bouaguel and
Emna Mouelhi and
Ghazi Bel Mufti},
title = {New Method for Instance Feature Selection Using Redundant Features
for Biological Data},
booktitle = {{MACIS}},
series = {Lecture Notes in Computer Science},
volume = {9582},
pages = {398--405},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/mda/Ciufudean15,
author = {Calin Ciufudean},
title = {Basic Support of Fuzzy Filters of Biological Data},
booktitle = {{MDA}},
pages = {17--28},
publisher = {ibai Publishing},
year = {2015}
}
@inproceedings{DBLP:conf/mike/MouelhiBM15,
author = {Emna Mouelhi and
Waad Bouaguel and
Ghazi Bel Mufti},
title = {A Redundancy Study for Feature Selection in Biological Data},
booktitle = {{MIKE}},
series = {Lecture Notes in Computer Science},
volume = {9468},
pages = {22--28},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/pdp/PedersenREB15,
author = {Edvard Pedersen and
Inge Alexander Raknes and
Martin Ernstsen and
Lars Ailo Bongo},
title = {Integrating Data-Intensive Computing Systems with Biological Data
Analysis Frameworks},
booktitle = {{PDP}},
pages = {733--740},
publisher = {{IEEE} Computer Society},
year = {2015}
}
@article{DBLP:journals/corr/GesingCT15,
author = {Sandra Gesing and
Thomas Richard Connor and
Ian J. Taylor},
title = {Genomics and Biological Big Data: Facing Current and Future Challenges
around Data and Software Sharing and Reproducibility},
journal = {CoRR},
volume = {abs/1511.02689},
year = {2015}
}
@article{DBLP:journals/corr/PedersenB15,
author = {Edvard Pedersen and
Lars Ailo Bongo},
title = {Large-scale Biological Meta-Database Management},
journal = {CoRR},
volume = {abs/1503.07759},
year = {2015}
}
@article{DBLP:journals/corr/Raza15,
author = {Khalid Raza},
title = {Formal Concept Analysis for Knowledge Discovery from Biological Data},
journal = {CoRR},
volume = {abs/1506.00366},
year = {2015}
}
@article{DBLP:journals/corr/YuDDB15,
author = {Yun William Yu and
Noah M. Daniels and
David Christian Danko and
Bonnie Berger},
title = {Entropy-scaling search of massive biological data},
journal = {CoRR},
volume = {abs/1503.05638},
year = {2015}
}
@book{DBLP:books/hal/SmailTabbone14,
author = {Malika Sma{\"{\i}}l{-}Tabbone},
title = {Contributions {\`{a}} l'extraction de connaissances {\`{a}} partir
de donn{\'{e}}es biologiques. (Contribution to knowledge extraction
from biological data)},
year = {2014}
}
@phdthesis{DBLP:phd/basesearch/Adhikari14,
author = {Prem Raj Adhikari},
title = {Probabilistic Modelling of Multiresolution Biological Data},
school = {Aalto University, Helsinki, Finland},
year = {2014}
}
@phdthesis{DBLP:phd/basesearch/Farhangmehr14,
author = {Farzaneh Farhangmehr},
title = {Statistical Approaches for Big Data Analytics and Machine Learning
: Data-Driven Network Reconstruction and Predictive Modeling of Time
Series Biological Systems},
school = {University of California, San Diego, {USA}},
year = {2014}
}
@phdthesis{DBLP:phd/basesearch/PatelRajesh14,
author = {Vishal Patel Rajesh},
title = {Large Scale Integration, Analysis, and Visualization of Biological
Data},
school = {University of California, Irvine, {USA}},
year = {2014}
}
@phdthesis{DBLP:phd/dnb/Kratsch14,
author = {Christina Kratsch},
title = {Computational methods to study phenotype evolution and feature selection
techniques for biological data under evolutionary constraints},
school = {Heinrich Heine University D{\"{u}}sseldorf},
year = {2014}
}
@phdthesis{DBLP:phd/dnb/Praveen14,
author = {Paurush Praveen},
title = {Reverse engineering of biological signaling networks via integration
of data and knowledge using probabilistic graphical models},
school = {University of Bonn},
year = {2014}
}
@phdthesis{DBLP:phd/es/Moreno14,
author = {Bernat Gel Moreno},
title = {Dissemination and visualisation of biological data},
school = {Polytechnic University of Catalonia, Spain},
year = {2014}
}
@phdthesis{DBLP:phd/gr/Koumakis14,
author = {Lefteris Koumakis},
title = {Computational methods for knowledge discovery from heterogeneous data
sources: methodology and implementation on biological and molecular
sources},
school = {Technical University of Crete, Greece},
year = {2014}
}
@phdthesis{DBLP:phd/hal/Yang14a,
author = {Bo Yang},
title = {Bioinformatics analysis and consensus ranking for biological high
throughput data. (Analyses bioinformatiques et classements consensus
pour les donn{\'{e}}es biologiques {\`{a}} haut d{\'{e}}bit)},
school = {University of Paris-Sud, Orsay, France},
year = {2014}
}
@phdthesis{DBLP:phd/hu/Alvarez14,
author = {Roberto Vera},
title = {Large scale annotation of biological data using integrated database
managament tools},
school = {P{\'{a}}zm{\'{a}}ny P{\'{e}}ter Catholic University,
Hungary},
year = {2014}
}
@phdthesis{DBLP:phd/it/Rehman14,
author = {Hafeez Ur Rehman},
title = {Integration and Analysis of Heterogeneous Biological Data},
school = {Polytechnic University of Turin, Italy},
year = {2014}
}
@article{DBLP:journals/bib/KouskoumvekakiSB14,
author = {Irene Kouskoumvekaki and
Nour Shublaq and
S{\o}ren Brunak},
title = {Facilitating the use of large-scale biological data and tools in the
era of translational bioinformatics},
journal = {Briefings Bioinform.},
volume = {15},
number = {6},
pages = {942--952},
year = {2014}
}
@article{DBLP:journals/bib/KurataMOT14,
author = {Hiroyuki Kurata and
Kazuhiro Maeda and
Toshikazu Onaka and
Takenori Takata},
title = {BioFNet: biological functional network database for analysis and synthesis
of biological systems},
journal = {Briefings Bioinform.},
volume = {15},
number = {5},
pages = {699--709},
year = {2014}
}
@article{DBLP:journals/biodatamining/SalemO14,
author = {Saeed Salem and
Cagri Ozcaglar},
title = {Hybrid coexpression link similarity graph clustering for mining biological
modules from multiple gene expression datasets},
journal = {BioData Min.},
volume = {7},
pages = {16},
year = {2014}
}
@article{DBLP:journals/biodb/RakBCRA14,
author = {Rafal Rak and
Riza Theresa Batista{-}Navarro and
Jacob Carter and
Andrew Rowley and
Sophia Ananiadou},
title = {Processing biological literature with customizable Web services supporting
interoperable formats},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014}
}
@article{DBLP:journals/bioinformatics/GuneyGO14,
author = {Emre Guney and
Javier Garc{\'{\i}}a{-}Garc{\'{\i}}a and
Baldo Oliva},
title = {GUILDify: a web server for phenotypic characterization of genes through
biological data integration and network-based prioritization algorithms},
journal = {Bioinform.},
volume = {30},
number = {12},
pages = {1789--1790},
year = {2014}
}
@article{DBLP:journals/bioinformatics/HauswedellSR14,
author = {Hannes Hauswedell and
Jochen Singer and
Knut Reinert},
title = {Lambda: the local aligner for massive biological data},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {349--355},
year = {2014}
}
@article{DBLP:journals/bioinformatics/IsciDOO14,
author = {Senol Isci and
Haluk Dogan and
Cengizhan Ozturk and
Hasan H. Otu},
title = {Bayesian network prior: network analysis of biological data using
external knowledge},
journal = {Bioinform.},
volume = {30},
number = {6},
pages = {860--867},
year = {2014}
}
@article{DBLP:journals/bioinformatics/UlrichZ14,
author = {Luke E. Ulrich and
Igor B. Zhulin},
title = {SeqDepot: streamlined database of biological sequences and precomputed
features},
journal = {Bioinform.},
volume = {30},
number = {2},
pages = {295--297},
year = {2014}
}
@article{DBLP:journals/biomedsem/WuFYBY14,
author = {Hongyan Wu and
Toyofumi Fujiwara and
Yasunori Yamamoto and
Jerven T. Bolleman and
Atsuko Yamaguchi},
title = {BioBenchmark Toyama 2012: an evaluation of the performance of triple
stores on biological data},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {32},
year = {2014}
}
@article{DBLP:journals/biosystems/HasegawaNYIM14,
author = {Takanori Hasegawa and
Masao Nagasaki and
Rui Yamaguchi and
Seiya Imoto and
Satoru Miyano},
title = {An efficient method of exploring simulation models by assimilating
literature and biological observational data},
journal = {Biosyst.},
volume = {121},
pages = {54--66},
year = {2014}
}
@article{DBLP:journals/bmcbi/RayWCDLLMB14,
author = {William C. Ray and
Samuel L. Wolock and
Nicholas W. Callahan and
Min Dong and
Qingshun Quinn Li and
Chun Liang and
Thomas J. Magliery and
Christopher W. Bartlett},
title = {Addressing the unmet need for visualizing conditional random fields
in biological data},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {202},
year = {2014}
}
@article{DBLP:journals/bmcbi/Reboiro-JatoAOF14,
author = {Miguel Reboiro{-}Jato and
Joel Arrais and
Jos{\'{e}} Lu{\'{\i}}s Oliveira and
Florentino Fdez{-}Riverola},
title = {geneCommittee: a web-based tool for extensively testing the discriminatory
power of biologically relevant gene sets in microarray data classification},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {31},
year = {2014}
}
@article{DBLP:journals/bmcbi/SchweigerTP14,
author = {Dominik Schweiger and
Zlatko Trajanoski and
Stephan Pabinger},
title = {SPARQLGraph: a web-based platform for graphically querying biological
Semantic Web databases},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {279},
year = {2014}
}
@article{DBLP:journals/bmcbi/ZhangPRBCL14,
author = {Yun Zhang and
Charles A. Phillips and
Gary L. Rogers and
Erich J. Baker and
Elissa J. Chesler and
Michael A. Langston},
title = {On finding bicliques in bipartite graphs: a novel algorithm and its
application to the integration of diverse biological data types},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {110},
year = {2014}
}
@article{DBLP:journals/bmcbi/ZhaoZC14,
author = {Weizhong Zhao and
Wen Zou and
James J. Chen},
title = {Topic modeling for cluster analysis of large biological and medical
datasets},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-11}},
pages = {S11},
year = {2014}
}
@article{DBLP:journals/bmcsb/CostaVV14,
author = {Rafael S. Costa and
Andr{\'{e}} Ver{\'{\i}}ssimo and
Susana Vinga},
title = {KiMoSys: a web-based repository of experimental data for KInetic MOdels
of biological SYStems},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {85},
year = {2014}
}
@article{DBLP:journals/cbm/ShigemitsuYOKGYIS14,
author = {Ryuji Shigemitsu and
Nobuhiro Yoda and
Toru Ogawa and
Tetsuo Kawata and
Yoshinori Gunji and
Yuki Yamakawa and
Kiyohiro Ikeda and
Keiichi Sasaki},
title = {Biological-data-based finite-element stress analysis of mandibular
bone with implant-supported overdenture},
journal = {Comput. Biol. Medicine},
volume = {54},
pages = {44--52},
year = {2014}
}
@article{DBLP:journals/cga/CarpendaleCEGGHRSS14,
author = {Sheelagh Carpendale and
Min Chen and
Daniel Evanko and
Nils Gehlenborg and
Carsten G{\"{o}}rg and
Lawrence Hunter and
Francis Rowland and
Margaret{-}Anne D. Storey and
Hendrik Strobelt},
title = {Ontologies in Biological Data Visualization},
journal = {{IEEE} Computer Graphics and Applications},
volume = {34},
number = {2},
pages = {8--15},
year = {2014}
}
@article{DBLP:journals/cga/MachirajuGO14,
author = {Raghu Machiraju and
Carsten G{\"{o}}rg and
Arthur J. Olson},
title = {Visual Analytics for Biological Data},
journal = {{IEEE} Computer Graphics and Applications},
volume = {34},
number = {2},
pages = {24--25},
year = {2014}
}
@article{DBLP:journals/cogcom/MalikHW14,
author = {Zeeshan Khawar Malik and
Amir Hussain and
Q. M. Jonathan Wu},
title = {Novel Biologically Inspired Approaches to Extracting Online Information
from Temporal Data},
journal = {Cogn. Comput.},
volume = {6},
number = {3},
pages = {595--607},
year = {2014}
}
@article{DBLP:journals/concurrency/SpampinatoKAPGF14,
author = {Concetto Spampinato and
Isaak Kavasidis and
Marco Aldinucci and
Carmelo Pino and
Daniela Giordano and
Alberto Faro},
title = {Discovering biological knowledge by integrating high-throughput data
and scientific literature on the cloud},
journal = {Concurr. Comput. Pract. Exp.},
volume = {26},
number = {10},
pages = {1771--1786},
year = {2014}
}
@article{DBLP:journals/evi/ThomasJ14,
author = {Spencer Angus Thomas and
Yaochu Jin},
title = {Reconstructing biological gene regulatory networks: where optimization
meets big data},
journal = {Evol. Intell.},
volume = {7},
number = {1},
pages = {29--47},
year = {2014}
}
@article{DBLP:journals/gpb/LiC14,
author = {Yixue Li and
Luonan Chen},
title = {Big Biological Data: Challenges and Opportunities},
journal = {Genom. Proteom. Bioinform.},
volume = {12},
number = {5},
pages = {187--189},
year = {2014}
}
@article{DBLP:journals/gpb/LiaoZGZ14,
author = {Ruiqi Liao and
Yifan Zhang and
Jihong Guan and
Shuigeng Zhou},
title = {CloudNMF: {A} MapReduce Implementation of Nonnegative Matrix Factorization
for Large-scale Biological Datasets},
journal = {Genom. Proteom. Bioinform.},
volume = {12},
number = {1},
pages = {48--51},
year = {2014}
}
@article{DBLP:journals/ibmrd/NguyenMTP14,
author = {Hoan Nguyen and
L. Michel and
Julie Dawn Thompson and
Olivier Poch},
title = {Heterogeneous biological data integration with declarative query language},
journal = {{IBM} J. Res. Dev.},
volume = {58},
number = {2/3},
year = {2014}
}
@article{DBLP:journals/ijkdb/Tzanis14,
author = {George Tzanis},
title = {Biological and Medical Big Data Mining},
journal = {Int. J. Knowl. Discov. Bioinform.},
volume = {4},
number = {1},
pages = {42--56},
year = {2014}
}
@article{DBLP:journals/ijon/FanCSW14,
author = {Weiwei Fan and
Bolin Chen and
Gopalan Selvaraj and
Fang{-}Xiang Wu},
title = {Discovering biological patterns from short time-series gene expression
profiles with integrating {PPI} data},
journal = {Neurocomputing},
volume = {145},
pages = {3--13},
year = {2014}
}
@article{DBLP:journals/jbi/BaenaUCFJ14,
author = {Rafael Marcos Luque Baena and
Daniel Urda and
M. Gonzalo Claros and
Leonardo Franco and
Jos{\'{e}} M. Jerez},
title = {Robust gene signatures from microarray data using genetic algorithms
enriched with biological pathway keywords},
journal = {J. Biomed. Informatics},
volume = {49},
pages = {32--44},
year = {2014}
}
@article{DBLP:journals/jcheminf/FiannacaRFGRU14,
author = {Antonino Fiannaca and
Massimo La Rosa and
Giuseppe Di Fatta and
Salvatore Gaglio and
Riccardo Rizzo and
Alfonso Urso},
title = {The BioDICE Taverna plugin for clustering and visualization of biological
data: a workflow for molecular compounds exploration},
journal = {J. Cheminformatics},
volume = {6},
number = {1},
pages = {24},
year = {2014}
}
@article{DBLP:journals/jcheminf/KleinKKMS14,
author = {Karsten Klein and
Oliver Koch and
Nils M. Kriege and
Petra Mutzel and
Till Sch{\"{a}}fer},
title = {Scaffold hunter: visual analysis of biological activity data},
journal = {J. Cheminformatics},
volume = {6},
number = {{S-1}},
pages = {33},
year = {2014}
}
@article{DBLP:journals/jcheminf/QabajaAAA14,
author = {Ala Qabaja and
Mohammed Alshalalfa and
Eisa Alanazi and
Reda Alhajj},
title = {Prediction of novel drug indications using network driven biological
data prioritization and integration},
journal = {J. Cheminformatics},
volume = {6},
number = {1},
pages = {1},
year = {2014}
}
@article{DBLP:journals/jcp/FardoosJF14,
author = {Asma Fardoos and
Jamshaid Iqbal Janjua and
Amjad Farooq},
title = {Ontology Engineering Techniques for Biological Data},
journal = {J. Comput.},
volume = {9},
number = {9},
pages = {2151--2158},
year = {2014}
}
@article{DBLP:journals/nar/BhattacharyaZC14,
author = {Anindya Bhattacharya and
Jesse D. Ziebarth and
Yan Cui},
title = {PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their
target sites with human diseases and biological pathways},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {86--91},
year = {2014}
}
@article{DBLP:journals/nar/BrekerGMS14,
author = {Michal Breker and
Melissa Gymrek and
Ofer Moldavski and
Maya Schuldiner},
title = {LoQAtE - Localization and Quantitation ATlas of the yeast proteomE.
{A} new tool for multiparametric dissection of single-protein behavior
in response to biological perturbations in yeast},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {726--730},
year = {2014}
}
@article{DBLP:journals/nar/MaiettaLCPLVT14,
author = {Paolo Maietta and
Gonzalo L{\'{o}}pez and
Angel Carro and
Benjamin J. Pingilley and
Leticia G. Leon and
Alfonso Valencia and
Michael L. Tress},
title = {FireDB: a compendium of biological and pharmacologically relevant
ligands},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {267--272},
year = {2014}
}
@article{DBLP:journals/nar/SeilerPSHSSFAPSTFL14,
author = {Catherine Y. Seiler and
Jin G. Park and
Amit Sharma and
Preston Hunter and
Padmini Surapaneni and
Casey Sedillo and
James Field and
Rhys Algar and
Andrea Price and
Jason Steel and
Andrea Throop and
Michael Fiacco and
Joshua LaBaer},
title = {{DNASU} plasmid and {PSI:} Biology-Materials repositories: resources
to accelerate biological research},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {1253--1260},
year = {2014}
}
@article{DBLP:journals/nar/TurkarslanWWJBFRNB14,
author = {Serdar Turkarslan and
Elisabeth J. Wurtmann and
Wei{-}Ju Wu and
Ning Jiang and
J. Christopher Bare and
Karen Foley and
David J. Reiss and
Pavel S. Novichkov and
Nitin S. Baliga},
title = {Network portal: a database for storage, analysis and visualization
of biological networks},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {184--190},
year = {2014}
}
@article{DBLP:journals/netmahib/BegumA14,
author = {Salma Begum and
Ramazan Savas Ayg{\"{u}}n},
title = {Greedy hierarchical binary classifiers for multi-class classification
of biological data},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {3},
number = {1},
year = {2014}
}
@article{DBLP:journals/netmahib/NagiB14,
author = {Sajid Nagi and
Dhruba K. Bhattacharyya},
title = {Cluster analysis of cancer data using semantic similarity, sequence
similarity and biological measures},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {3},
number = {1},
year = {2014}
}
@article{DBLP:journals/staeors/QiMHL14,
author = {Lin Qi and
Ronghua Ma and
Weiping Hu and
Steven Arthur Loiselle},
title = {Assimilation of {MODIS} Chlorophyll-a Data Into a Coupled Hydrodynamic-Biological
Model of Taihu Lake},
journal = {{IEEE} J. Sel. Top. Appl. Earth Obs. Remote. Sens.},
volume = {7},
number = {5},
pages = {1623--1631},
year = {2014}
}
@inproceedings{DBLP:conf/amcc/LinT14,
author = {Xiao Lin and
Gabriel Terejanu},
title = {Model-driven data collection for biological systems},
booktitle = {{ACC}},
pages = {2524--2529},
publisher = {{IEEE}},
year = {2014}
}
@inproceedings{DBLP:conf/apn/BordonMM14,
author = {Jure Bordon and
Miha Moskon and
Miha Mraz},
title = {Overcoming unknown kinetic data for quantitative modelling of biological
systems using fuzzy logic and Petri nets},
booktitle = {BioPPN@Petri Nets},
series = {{CEUR} Workshop Proceedings},
volume = {1159},
pages = {3--14},
publisher = {CEUR-WS.org},
year = {2014}
}
@inproceedings{DBLP:conf/bcb/McDermott14,
author = {Jason E. McDermott},
title = {Promises and challenges in analysis of biological big data},
booktitle = {{BCB}},
pages = {680},
publisher = {{ACM}},
year = {2014}
}
@inproceedings{DBLP:conf/bcb/WestA14,
author = {Sean West and
Hesham H. Ali},
title = {On the impact of data integration and edge enrichment in mining significant
signals from biological networks},
booktitle = {{BCB}},
pages = {760--767},
publisher = {{ACM}},
year = {2014}
}
@inproceedings{DBLP:conf/bibm/KimHZ14,
author = {Chang Sik Kim and
Seungwoo Hwang and
Shu{-}Dong Zhang},
title = {{RMA} with quantile normalization mixes biological signals between
different sample groups in microarray data analysis},
booktitle = {{BIBM}},
pages = {139--143},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/bigdataconf/ShahGRL14,
author = {Asmi H. Shah and
Gayathri Gopalakrishnan and
Adithya Rajendran and
Urban Liebel},
title = {Data mining and sharing tool for high content screening large scale
biological image data},
booktitle = {{IEEE} BigData},
pages = {1068--1076},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/cbms/GaterS14,
author = {Ahmed Gater and
Rahul Singh},
title = {Biological Image Indexing for Content-Based Retrieval of Drug Effects
in Phenotypic Screening Data of Macroparasites},
booktitle = {{CBMS}},
pages = {300--303},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/cbms/OrtunoPRV14,
author = {Francisco M. Ortu{\~{n}}o Guzman and
H{\'{e}}ctor Pomares and
Ignacio Rojas Ruiz and
Olga Valenzuela},
title = {Creation of a Database Including a Set of Biological Features Related
to Protein Sequences and Their Corresponding Alignment},
booktitle = {{CBMS}},
pages = {557--558},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/cibb/BongoPE14,
author = {Lars Ailo Bongo and
Edvard Pedersen and
Martin Ernstsen},
title = {Data-Intensive Computing Infrastructure Systems for Unmodified Biological
Data Analysis Pipelines},
booktitle = {{CIBB}},
series = {Lecture Notes in Computer Science},
volume = {8623},
pages = {259--272},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/cibcb/AndonieFS14,
author = {Razvan Andonie and
Levente Fabry{-}Asztalos and
Lucian Mircea Sasu},
title = {Bayesian {ARTMAP} prediction of biological activities for potential
{HIV-1} protease inhibitors using a small molecular dataset},
booktitle = {{CIBCB}},
pages = {1--8},
publisher = {{IEEE}},
year = {2014}
}
@inproceedings{DBLP:conf/data/CuomoMPP14,
author = {Salvatore Cuomo and
Pasquale De Michele and
Giovanni Ponti and
Maria Rosaria Posteraro},
title = {A Clustering-based Approach for a Finest Biological Model Generation
Describing Visitor Behaviours in a Cultural Heritage Scenario},
booktitle = {{DATA}},
pages = {427--433},
publisher = {SciTePress},
year = {2014}
}
@inproceedings{DBLP:conf/data/CuomoMPP14a,
author = {Salvatore Cuomo and
Pasquale De Michele and
Giovanni Ponti and
Maria Rosaria Posteraro},
title = {Validation Approaches for a Biological Model Generation Describing
Visitor Behaviours in a Cultural Heritage Scenario},
booktitle = {{DATA} (Revised Selected Papers)},
series = {Communications in Computer and Information Science},
volume = {178},
pages = {154--168},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/dexaw/MhamdiM14,
author = {Hanen Mhamdi and
Faouzi Mhamdi},
title = {Feature Selection Methods on Biological Knowledge Discovery and Data
Mining: {A} Survey},
booktitle = {{DEXA} Workshops},
pages = {46--50},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/dils/BrancotteRDB14,
author = {Bryan Brancotte and
Bastien Rance and
Alain Denise and
Sarah Cohen Boulakia},
title = {ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological
Data},
booktitle = {{DILS}},
series = {Lecture Notes in Computer Science},
volume = {8574},
pages = {128--142},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/gi/DiepenbroekGGGHKKNSTT14,
author = {Michael Diepenbroek and
Frank Oliver Gl{\"{o}}ckner and
Peter Grobe and
Anton G{\"{u}}ntsch and
Robert Huber and
Birgitta K{\"{o}}nig{-}Ries and
Ivaylo Kostadinov and
Jens Nieschulze and
Bernhard Seeger and
Robert Tolksdorf and
Dagmar Triebel},
title = {Towards an Integrated Biodiversity and Ecological Research Data Management
and Archiving Platform: The German Federation for the Curation of
Biological Data (GFBio)},
booktitle = {GI-Jahrestagung},
series = {{LNI}},
volume = {{P-232}},
pages = {1711--1721},
publisher = {{GI}},
year = {2014}
}
@inproceedings{DBLP:conf/hci/HondaH14,
author = {Kaoru Honda and
Fukuyo Honda},
title = {Changes in Biological Data during Prolonged Use of a Learning Support
System and the Effects of a Rest Break},
booktitle = {{HCI} {(27)}},
series = {Communications in Computer and Information Science},
volume = {435},
pages = {455--460},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/icdse/ArunanandNPP14,
author = {T. A. Arunanand and
K. A. Abdul Nazeer and
Mathew J. Palakal and
Meeta Pradhan},
title = {A nature-inspired hybrid Fuzzy C-means algorithm for better clustering
of biological data sets},
booktitle = {{ICDSE}},
pages = {76--82},
publisher = {{IEEE}},
year = {2014}
}
@inproceedings{DBLP:conf/icisp/SakamotoDFKGPOHOKH14,
author = {Joji Sakamoto and
Jennifer Dumont and
Laure Fauch and
Sarita Keski{-}Saari and
Lars Granlund and
Ilkka Porali and
Joni Orava and
Jouni Hiltunen and
Elina Oksanen and
Markku Kein{\"{a}}nen and
Markku Hauta{-}Kasari},
title = {Natural Vision Data File Format as a New Spectral Image Format for
Biological Applications},
booktitle = {{ICISP}},
series = {Lecture Notes in Computer Science},
volume = {8509},
pages = {124--132},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/ifip12/IoannouNSTT14,
author = {Zafeiria{-}Marina Ioannou and
Nikolaos Nodarakis and
Spyros Sioutas and
Athanasios K. Tsakalidis and
Giannis Tzimas},
title = {Mining Biological Data on the Cloud - {A} MapReduce Approach},
booktitle = {{AIAI} Workshops},
series = {{IFIP} Advances in Information and Communication Technology},
volume = {437},
pages = {96--105},
publisher = {Springer},
year = {2014}
}
@inproceedings{DBLP:conf/ipps/WangCDLML14,
author = {Lipeng Wang and
Yuandong Chan and
Xiaohui Duan and
Haidong Lan and
Xiangxu Meng and
Weiguo Liu},
title = {{XSW:} Accelerating Biological Database Search on Xeon Phi},
booktitle = {{IPDPS} Workshops},
pages = {950--957},
publisher = {{IEEE} Computer Society},
year = {2014}
}
@inproceedings{DBLP:conf/iwbbio/NakhlaN14,
author = {Zina Nakhla and
Kaouther Nouira},
title = {Automatically building database from biological ontology},
booktitle = {{IWBBIO}},
pages = {1403--1411},
publisher = {Copicentro Editorial},
year = {2014}
}
@inproceedings{DBLP:conf/robio/StelzerMS14,
author = {Annett Stelzer and
Elmar Mair and
Michael Suppa},
title = {Trail-Map: {A} scalable landmark data structure for biologically inspired
range-free navigation},
booktitle = {{ROBIO}},
pages = {2138--2145},
publisher = {{IEEE}},
year = {2014}
}
@inproceedings{DBLP:conf/sebd/CaninoCGTV14,
author = {Giovanni Canino and
Mario Cannataro and
Pietro Hiram Guzzi and
Giuseppe Tradigo and
Pierangelo Veltri},
title = {Geoanalysis of Clinical Diagnoses and Biological Analytes Data},
booktitle = {{SEBD}},
pages = {53--60},
year = {2014}
}
@inproceedings{DBLP:conf/semcco/JenaDM14,
author = {Manaswini Jena and
Rasmita Dash and
Bijan Bihari Misra},
title = {Biological Data Analysis Using Hybrid Functional Link Artificial Neural
Network},
booktitle = {{SEMCCO}},
series = {Lecture Notes in Computer Science},
volume = {8947},
pages = {88--97},
publisher = {Springer},
year = {2014}
}
@incollection{DBLP:series/lncs/HuppertzH14,
author = {Berthold Huppertz and
Andreas Holzinger},
title = {Biobanks - {A} Source of Large Biological Data Sets: Open Problems
and Future Challenges},
booktitle = {Interactive Knowledge Discovery and Data Mining in Biomedical Informatics},
series = {Lecture Notes in Computer Science},
volume = {8401},
pages = {317--330},
publisher = {Springer},
year = {2014}
}
@incollection{DBLP:series/lncs/OtasekPHJ14,
author = {David Otasek and
Chiara Pastrello and
Andreas Holzinger and
Igor Jurisica},
title = {Visual Data Mining: Effective Exploration of the Biological Universe},
booktitle = {Interactive Knowledge Discovery and Data Mining in Biomedical Informatics},
series = {Lecture Notes in Computer Science},
volume = {8401},
pages = {19--33},
publisher = {Springer},
year = {2014}
}
@incollection{DBLP:reference/cn/ChelliahJLHN14,
author = {Vijayalakshmi Chelliah and
Nick S. Juty and
Camille Laibe and
Henning Hermjakob and
Nicolas Le Nov{\`{e}}re},
title = {BioModels Database: a public repository for sharing models of biological
processes},
booktitle = {Encyclopedia of Computational Neuroscience},
publisher = {Springer},
year = {2014}
}
@article{DBLP:journals/corr/Calderone14,
author = {Alberto Calderone},
title = {Assembling biological boolean networks using manually curated databases
and prediction algorithms},
journal = {CoRR},
volume = {abs/1412.1013},
year = {2014}
}
@article{DBLP:journals/corr/KouzinopoulosAPM14,
author = {Charalampos S. Kouzinopoulos and
John{-}Alexander M. Assael and
Themistoklis K. Pyrgiotis and
Konstantinos G. Margaritis},
title = {A Hybrid Parallel Implementation of the Aho-Corasick and Wu-Manber
Algorithms Using {NVIDIA} {CUDA} and {MPI} Evaluated on a Biological
Sequence Database},
journal = {CoRR},
volume = {abs/1407.2889},
year = {2014}
}
@article{DBLP:journals/corr/RayWCDLLMB14,
author = {William C. Ray and
Samuel L. Wolock and
Nicholas W. Callahan and
Min Dong and
Qingshun Quinn Li and
Chun Liang and
Thomas J. Magliery and
Christopher W. Bartlett},
title = {Addressing the unmet need for visualizing Conditional Random Fields
in Biological Data},
journal = {CoRR},
volume = {abs/1407.2110},
year = {2014}
}
@article{DBLP:journals/corr/Tsourakakis14b,
author = {Charalampos E. Tsourakakis},
title = {Mathematical and Algorithmic Analysis of Network and Biological Data},
journal = {CoRR},
volume = {abs/1407.0375},
year = {2014}
}
@article{DBLP:journals/corr/WangZ14a,
author = {Shuliang Wang and
Yiping Zhao},
title = {Analyzing Large Biological Datasets with an Improved Algorithm for
{MIC}},
journal = {CoRR},
volume = {abs/1403.3495},
year = {2014}
}
@article{DBLP:journals/f1000research/Corpas14,
author = {Manuel Corpas},
title = {The BioJS article collection of open source components for biological
data visualisation},
journal = {F1000Research},
volume = {3},
pages = {56},
year = {2014}
}
@article{DBLP:journals/f1000research/ScardoniTFSFL14,
author = {Giovanni Scardoni and
Gabriele Tosadori and
Mohammed Faizan and
Fausto Spoto and
Franco Fabbri and
Carlo Laudanna},
title = {Biological network analysis with CentiScaPe: centralities and experimental
dataset integration},
journal = {F1000Research},
volume = {3},
pages = {139},
year = {2014}
}
@phdthesis{DBLP:phd/basesearch/Jeong13,
author = {Kyowon Jeong},
title = {Statistical Algorithms for High-throughput Biological Data /},
school = {University of California, San Diego, {USA}},
year = {2013}
}
@phdthesis{DBLP:phd/basesearch/Kruczyk13,
author = {Marcin Kruczyk},
title = {Rule-Based Approaches for Large Biological Datasets Analysis : {A}
Suite of Tools and Methods},
school = {Uppsala University, Sweden},
year = {2013}
}
@phdthesis{DBLP:phd/basesearch/Rashid13,
author = {Naim U. Rashid},
title = {Model-based approaches for the detection of biologically active genomic
regions from next generation sequencing data},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2013}
}
@phdthesis{DBLP:phd/basesearch/Yuan13a,
author = {Lei Yuan},
title = {Structured Sparse Learning and Its Applications to Biomedical and
Biological Data},
school = {Arizona State University, Tempe, {USA}},
year = {2013}
}
@phdthesis{DBLP:phd/basesearch/Zhang13,
author = {Yuji Zhang},
title = {Module{\_}based Analysis of Biological Data for Network Inference
and Biomarker Discovery},
school = {Virginia Tech, Blacksburg, VA, {USA}},
year = {2013}
}
@phdthesis{DBLP:phd/hal/AravenaDuarte13,
author = {Andr{\'{e}}s Octavio Aravena Duarte},
title = {Probabilistic and constraint based modelling to determine regulation
events from heterogeneous biological data. (Mod{\'{e}}lisation
probabiliste ou {\`{a}} base de contraintes pour d{\'{e}}terminer
des r{\'{e}}gulations {\`{a}} partir de donn{\'{e}}es biologiques
h{\'{e}}t{\'{e}}rog{\`{e}}nes)},
school = {University of Rennes 1, France},
year = {2013}
}
@article{DBLP:journals/bib/SloutskyJSN13,
author = {Roman Sloutsky and
Nicolas Jimenez and
S. Joshua Swamidass and
Kristen M. Naegle},
title = {Accounting for noise when clustering biological data},
journal = {Briefings Bioinform.},
volume = {14},
number = {4},
pages = {423--436},
year = {2013}
}
@article{DBLP:journals/bigdata/Swan13,
author = {Melanie Swan},
title = {The Quantified Self: Fundamental Disruption in Big Data Science and
Biological Discovery},
journal = {Big Data},
volume = {1},
number = {2},
pages = {85--99},
year = {2013}
}
@article{DBLP:journals/biodatamining/MalleyDM13,
author = {James D. Malley and
Abhijit Dasgupta and
Jason H. Moore},
title = {The limits of p-values for biological data mining},
journal = {BioData Min.},
volume = {6},
pages = {10},
year = {2013}
}
@article{DBLP:journals/biodatamining/MalleyM13,
author = {James D. Malley and
Jason H. Moore},
title = {The disconnect between classical biostatistics and the biological
data mining community},
journal = {BioData Min.},
volume = {6},
pages = {12},
year = {2013}
}
@article{DBLP:journals/biodatamining/MooreR13,
author = {Jason H. Moore and
Marylyn D. Ritchie},
title = {The central role of biological data mining in connecting diverse disciplines},
journal = {BioData Min.},
volume = {6},
pages = {14},
year = {2013}
}
@article{DBLP:journals/biodb/GaudetMRABCKOY13,
author = {Pascale Gaudet and
Monica C. Munoz{-}Torres and
Marc Robinson{-}Rechavi and
Teresa K. Attwood and
Alex Bateman and
J. Michael Cherry and
Renate Kania and
Claire O'Donovan and
Chisato Yamasaki},
title = {DATABASE, \emph{The Journal of Biological Databases and Curation},
is now the official journal of the International Society for Biocuration},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013}
}
@article{DBLP:journals/biodb/OberlinJBF13,
author = {Andrew Oberlin and
Dominika A. Jurkovic and
Mitchell F. Balish and
Iddo Friedberg},
title = {Biological Database of Images and Genomes: tools for community annotations
linking image and genomic information},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013}
}
@article{DBLP:journals/biodb/PercudaniCP13,
author = {Riccardo Percudani and
Davide Carnevali and
Vincenzo Puggioni},
title = {Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological
databases are incorporated in scientific papers and vice versa},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013}
}
@article{DBLP:journals/bioinformatics/CamiloBAFCML13,
author = {Esther Camilo and
Luiz A. Bovolenta and
Marcio Luis Acencio and
Jos{\'{e}} L. Rybarczyk Filho and
Mauro A. A. Castro and
Jos{\'{e}} C. F. Moreira and
Ney Lemke},
title = {{GALANT:} a Cytoscape plugin for visualizing data as functional landscapes
projected onto biological networks},
journal = {Bioinform.},
volume = {29},
number = {19},
pages = {2505--2506},
year = {2013}
}
@article{DBLP:journals/bioinformatics/DeckardAHHH13,
author = {Anastasia Deckard and
Ron C. Anafi and
John B. Hogenesch and
Steven B. Haase and
John Harer},
title = {Design and analysis of large-scale biological rhythm studies: a comparison
of algorithms for detecting periodic signals in biological data},
journal = {Bioinform.},
volume = {29},
number = {24},
pages = {3174--3180},
year = {2013}
}
@article{DBLP:journals/bioinformatics/GomezGSVGGMLAdDOVHZPCJ13,
author = {John G{\'{o}}mez and
Leyla J. Garc{\'{\i}}a and
Gustavo A. Salazar and
Jose M. Villaveces and
Swanand P. Gore and
Alexander Garc{\'{\i}}a Castro and
Maria Jesus Martin and
Guillaume Launay and
Rafael Alc{\'{a}}ntara and
Noemi del{-}Toro and
Marine Dumousseau and
Sandra E. Orchard and
Sameer Velankar and
Henning Hermjakob and
Chenggong Zong and
Peipei Ping and
Manuel Corpas and
Rafael C. Jim{\'{e}}nez},
title = {BioJS: an open source JavaScript framework for biological data visualization},
journal = {Bioinform.},
volume = {29},
number = {8},
pages = {1103--1104},
year = {2013}
}
@article{DBLP:journals/bioinformatics/McClellanMSS13,
author = {Elizabeth A. McClellan and
Perry D. Moerland and
Peter J. van der Spek and
Andrew Stubbs},
title = {NetWeAvers: an \emph{R} package for integrative biological network
analysis with mass spectrometry data},
journal = {Bioinform.},
volume = {29},
number = {22},
pages = {2946--2947},
year = {2013}
}
@article{DBLP:journals/biosystems/LonesSTAJ13,
author = {Michael A. Lones and
Stephen L. Smith and
Andy M. Tyrrell and
Jane E. Alty and
D. R. Stuart Jamieson},
title = {Characterising neurological time series data using biologically motivated
networks of coupled discrete maps},
journal = {Biosyst.},
volume = {112},
number = {2},
pages = {94--101},
year = {2013}
}
@article{DBLP:journals/bmcbi/HaughtonB13,
author = {David Haughton and
F{\'{e}}lix Balado},
title = {BioCode: Two biologically compatible Algorithms for embedding data
in non-coding and coding regions of {DNA}},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {121},
year = {2013}
}
@article{DBLP:journals/bmcbi/MoulosKJSBS13,
author = {Panagiotis Moulos and
Julie Klein and
Simon Jupp and
Robert Stevens and
Jean{-}Loup Bascands and
Joost P. Schanstra},
title = {The KUPNetViz: a biological network viewer for multiple -omics datasets
in kidney diseases},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {235},
year = {2013}
}
@article{DBLP:journals/bmcbi/PartlLSKKS13,
author = {Christian Partl and
Alexander Lex and
Marc Streit and
Denis Kalkofen and
Karl Kashofer and
Dieter Schmalstieg},
title = {enRoute: dynamic path extraction from biological pathway maps for
exploring heterogeneous experimental datasets},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-19}},
pages = {S3},
year = {2013}
}
@article{DBLP:journals/bmcbi/SinghYDAMFGSF13,
author = {Rahul Singh and
Hui Yang and
Ben Dalziel and
Daniel Asarnow and
William Murad and
David Foote and
Matthew Gormley and
Jonathan Stillman and
Susan Fisher},
title = {Towards human-computer synergetic analysis of large-scale biological
data},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-14}},
pages = {S10},
year = {2013}
}
@article{DBLP:journals/bmcbi/VerbanckLP13,
author = {Marie Verbanck and
S{\'{e}}bastien L{\^{e}} and
J{\'{e}}r{\^{o}}me Pag{\`{e}}s},
title = {A new unsupervised gene clustering algorithm based on the integration
of biological knowledge into expression data},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {42},
year = {2013}
}
@article{DBLP:journals/bmcbi/WollbrettLLR13,
author = {Julien Wollbrett and
Pierre Larmande and
Fr{\'{e}}d{\'{e}}ric de Lamotte and
Manuel Ruiz},
title = {Clever generation of rich {SPARQL} queries from annotated relational
schema: application to Semantic Web Service creation for biological
databases},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {126},
year = {2013}
}
@article{DBLP:journals/bmcsb/LiN13,
author = {Yifeng Li and
Alioune Ngom},
title = {Sparse representation approaches for the classification of high-dimensional
biological data},
journal = {{BMC} Syst. Biol.},
volume = {7},
number = {{S-4}},
pages = {S6},
year = {2013}
}
@article{DBLP:journals/cbm/Huang13a,
author = {Yao{-}Huei Huang},
title = {A note on hyper ellipse method for classifying biological and medical
data},
journal = {Comput. Biol. Medicine},
volume = {43},
number = {11},
pages = {1978--1986},
year = {2013}
}
@article{DBLP:journals/cbm/ZhuLS13,
author = {Xiangyuan Zhu and
Kenli Li and
Ahmad Salah},
title = {A data parallel strategy for aligning multiple biological sequences
on multi-core computers},
journal = {Comput. Biol. Medicine},
volume = {43},
number = {4},
pages = {350--361},
year = {2013}
}
@article{DBLP:journals/concurrency/GreenfieldR13,
author = {Paul Greenfield and
Uwe R{\"{o}}hm},
title = {Answering biological questions by querying k-mer databases},
journal = {Concurr. Comput. Pract. Exp.},
volume = {25},
number = {4},
pages = {497--509},
year = {2013}
}
@article{DBLP:journals/dke/SymeonidisIMM13,
author = {Panagiotis Symeonidis and
Nantia D. Iakovidou and
Nikolaos Mantas and
Yannis Manolopoulos},
title = {From biological to social networks: Link prediction based on multi-way
spectral clustering},
journal = {Data Knowl. Eng.},
volume = {87},
pages = {226--242},
year = {2013}
}
@article{DBLP:journals/envsoft/HaimiMCV13,
author = {Henri Haimi and
Michela Mulas and
Francesco Corona and
Riku Vahala},
title = {Data-derived soft-sensors for biological wastewater treatment plants:
An overview},
journal = {Environ. Model. Softw.},
volume = {47},
pages = {88--107},
year = {2013}
}
@article{DBLP:journals/eswa/MiloneSKLC13,
author = {Diego H. Milone and
Georgina Stegmayer and
Laura Kamenetzky and
Mariana G. Lopez and
Fernando Carrari},
title = {Clustering biological data with SOMs: On topology preservation in
non-linear dimensional reduction},
journal = {Expert Syst. Appl.},
volume = {40},
number = {9},
pages = {3841--3845},
year = {2013}
}
@article{DBLP:journals/eswa/Reboiro-JatoLLGDF13,
author = {Miguel Reboiro{-}Jato and
Rosal{\'{\i}}a Laza and
Hugo L{\'{o}}pez{-}Fern{\'{a}}ndez and
Daniel Glez{-}Pe{\~{n}}a and
Fernando D{\'{\i}}az and
Florentino Fdez{-}Riverola},
title = {genEnsemble: {A} new model for the combination of classifiers and
integration of biological knowledge applied to genomic data},
journal = {Expert Syst. Appl.},
volume = {40},
number = {1},
pages = {52--63},
year = {2013}
}
@article{DBLP:journals/hisas/Gong13,
author = {Peng Gong},
title = {Dynamic integration of biological data sources using the data concierge},
journal = {Health Inf. Sci. Syst.},
volume = {1},
number = {1},
pages = {7},
year = {2013}
}
@article{DBLP:journals/ijdmb/Iam-onBGP13,
author = {Natthakan Iam{-}on and
Tossapon Boongoen and
Simon M. Garrett and
Chris J. Price},
title = {New cluster ensemble approach to integrative biological data analysis},
journal = {Int. J. Data Min. Bioinform.},
volume = {8},
number = {2},
pages = {150--168},
year = {2013}
}
@article{DBLP:journals/ijdmb/LiuLY13,
author = {I{-}Hsin Liu and
Yu{-}Shu Lo and
Jinn{-}Moon Yang},
title = {Template-based scoring functions for visualising biological insights
of H-2K\({}^{\mbox{b}}\)-peptide-TCR complexes},
journal = {Int. J. Data Min. Bioinform.},
volume = {8},
number = {3},
pages = {326--337},
year = {2013}
}
@article{DBLP:journals/ijdmb/YuWLSW13,
author = {Yang Yu and
Xiaolong Wang and
Lei Lin and
Chengjie Sun and
Xuan Wang},
title = {A supervised approach to detect protein complex by combining biological
and topological properties},
journal = {Int. J. Data Min. Bioinform.},
volume = {8},
number = {1},
pages = {105--121},
year = {2013}
}
@article{DBLP:journals/ijitn/Saedy13,
author = {Mahdy Saedy},
title = {Biologically Inspired Networks: On Energy Efficient Event-Driven Data
Collection for Wireless Sensor Networks},
journal = {Int. J. Interdiscip. Telecommun. Netw.},
volume = {5},
number = {1},
pages = {14--25},
year = {2013}
}
@article{DBLP:journals/ivs/JusufiKS13,
author = {Ilir Jusufi and
Andreas Kerren and
Falk Schreiber},
title = {Exploring biological data: Mappings between ontology- and cluster-based
representations},
journal = {Inf. Vis.},
volume = {12},
number = {3-4},
pages = {291--307},
year = {2013}
}
@article{DBLP:journals/jaciii/HashikamiTHHSN13,
author = {Hidenobu Hashikami and
Takanari Tanabata and
Fumiaki Hirose and
Nur Hasanah and
Kazuhito Sawase and
Hajime Nobuhara},
title = {An Algorithm for Recomputing Concepts in Microarray Data Analysis
by Biological Lattice},
journal = {J. Adv. Comput. Intell. Intell. Informatics},
volume = {17},
number = {5},
pages = {761--771},
year = {2013}
}
@article{DBLP:journals/jcb/WangHDN13,
author = {Hua Wang and
Heng Huang and
Chris H. Q. Ding and
Feiping Nie},
title = {Predicting Protein-Protein Interactions from Multimodal Biological
Data Sources via Nonnegative Matrix Tri-Factorization},
journal = {J. Comput. Biol.},
volume = {20},
number = {4},
pages = {344--358},
year = {2013}
}
@article{DBLP:journals/jclinbioinf/SilvestreZBBMM13,
author = {Dario Silvestre and
Italo Zoppis and
Francesca Brambilla and
Valeria Bellettato and
Giancarlo Mauri and
Pierluigi Mauri},
title = {Availability of MudPIT data for classification of biological samples},
journal = {J. Clin. Bioinform.},
volume = {3},
pages = {1},
year = {2013}
}
@article{DBLP:journals/kybernetes/BaridamA13,
author = {Barile{\'{e}} B. Baridam and
M. Montaz Ali},
title = {An investigation of K-means clustering to high and multi-dimensional
biological data},
journal = {Kybernetes},
volume = {42},
number = {4},
pages = {614--627},
year = {2013}
}
@article{DBLP:journals/nar/AndreiniCLR13,
author = {Claudia Andreini and
Gabriele Cavallaro and
Serena Lorenzini and
Antonio Rosato},
title = {MetalPDB: a database of metal sites in biological macromolecular structures},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {312--319},
year = {2013}
}
@article{DBLP:journals/nar/HastingsMDEHKMOTWS13,
author = {Janna Hastings and
Paula de Matos and
Adriano Dekker and
Marcus Ennis and
Bhavana Harsha and
Namrata Kale and
Venkatesh Muthukrishnan and
Gareth I. Owen and
Steve Turner and
Mark Williams and
Christoph Steinbeck},
title = {The ChEBI reference database and ontology for biologically relevant
chemistry: enhancements for 2013},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {456--463},
year = {2013}
}
@article{DBLP:journals/nar/YangRZ13,
author = {Jianyi Yang and
Ambrish Roy and
Yang Zhang},
title = {BioLiP: a semi-manually curated database for biologically relevant
ligand-protein interactions},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {1096--1103},
year = {2013}
}
@article{DBLP:journals/ploscb/DemirBRAFGSBS13,
author = {Emek Demir and
{\"{O}}zg{\"{u}}n Babur and
Igor V. Rodchenkov and
B{\"{u}}lent Arman Aksoy and
Ken I. Fukuda and
Benjamin E. Gross and
Sel{\c{c}}uk Onur S{\"{u}}mer and
Gary D. Bader and
Chris Sander},
title = {Using Biological Pathway Data with Paxtools},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {9},
year = {2013}
}
@article{DBLP:journals/ploscb/PastrelloOFACSJ13,
author = {Chiara Pastrello and
David Otasek and
Kristen Fortney and
Giuseppe Agapito and
Mario Cannataro and
Elize Shirdel and
Igor Jurisica},
title = {Visual Data Mining of Biological Networks: One Size Does Not Fit All},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {1},
year = {2013}
}
@article{DBLP:journals/scfbm/LiN13,
author = {Yifeng Li and
Alioune Ngom},
title = {The non-negative matrix factorization toolbox for biological data
mining},
journal = {Source Code Biol. Medicine},
volume = {8},
pages = {10},
year = {2013}
}
@article{DBLP:journals/tbe/HsuL13,
author = {Ying Hsu and
Andreas A. Linninger},
title = {Quantitative Integration of Biological, Pharmacokinetic, and Medical
Imaging Data for Organ-Wide Dose-Response Predictions},
journal = {{IEEE} Trans. Biomed. Eng.},
volume = {60},
number = {3},
pages = {625--632},
year = {2013}
}
@article{DBLP:journals/tbe/PapoutsoglouB13,
author = {George S. Papoutsoglou and
Costas Balas},
title = {Estimation of Neoplasia-Related Biological Parameters Through Modeling
and Sensitivity Analysis of Optical Molecular Imaging Data},
journal = {{IEEE} Trans. Biomed. Eng.},
volume = {60},
number = {5},
pages = {1241--1249},
year = {2013}
}
@article{DBLP:journals/tcbb/LiN13,
author = {Yifeng Li and
Alioune Ngom},
title = {Nonnegative Least-Squares Methods for the Classification of High-Dimensional
Biological Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {2},
pages = {447--456},
year = {2013}
}
@article{DBLP:journals/tmi/Humeau-HeurtierAM13,
author = {Anne Humeau{-}Heurtier and
Pierre Abraham and
Guillaume Mah{\'{e}}},
title = {Linguistic Analysis of Laser Speckle Contrast Images Recorded at Rest
and During Biological Zero: Comparison With Laser Doppler Flowmetry
Data},
journal = {{IEEE} Trans. Medical Imaging},
volume = {32},
number = {12},
pages = {2311--2321},
year = {2013}
}
@inproceedings{DBLP:conf/aina/DemongeotHGT13,
author = {Jacques Demongeot and
Ali Hamie and
Antonio Glar{\'{\i}}a and
Carla Taramasco},
title = {Dynalets: {A} New Representation of Periodic Biological Signals and
Spectral Data},
booktitle = {{AINA} Workshops},
pages = {1525--1532},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/amcc/LiZ13,
author = {Xiaobo Li and
Mingjun Zhang},
title = {Hybrid time-data-driven control for biological cellular systems},
booktitle = {{ACC}},
pages = {1507--1512},
publisher = {{IEEE}},
year = {2013}
}
@inproceedings{DBLP:conf/ant/RezaeiMCS13,
author = {Navid Rezaei and
Deyasini Majumdar and
Bruce F. Cockburn and
Christian Schlegel},
title = {Electromagnetic Energy and Data Transfer in Biological Tissues Using
Loop Antennas},
booktitle = {{ANT/SEIT}},
series = {Procedia Computer Science},
volume = {19},
pages = {908--913},
publisher = {Elsevier},
year = {2013}
}
@inproceedings{DBLP:conf/bibe/MingaGVSHSMC13,
author = {Evangelia Minga and
Athanasios Gkoufas and
Anna Vardi and
Evangelia Stalika and
Anastasia Hadzidimitriou and
Kostas Stamatopoulos and
Nicos Maglaveras and
Ioanna Chouvarda},
title = {Towards an integrated framework for clinico-biological data management
and analysis: The case of Chronic Lymphocytic Leukemia},
booktitle = {{BIBE}},
pages = {1--4},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/bibm/LiuDPDMCW13,
author = {Sheng Liu and
Shamitha Dissanayake and
Sanjay Patel and
Xin Dang and
Todd Mlsna and
Yixin Chen and
Dawn Wilkins},
title = {Rule based regression and feature selection for biological data},
booktitle = {{BIBM}},
pages = {446--451},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/bibm/PodpecanMPSGML13,
author = {Vid Podpecan and
Dragana Miljkovic and
Marko Petek and
Tjasa Stare and
Kristina Gruden and
Igor Mozetic and
Nada Lavrac},
title = {Integrating semantic transcriptomic data analysis and knowledge extraction
from biological literature},
booktitle = {{BIBM}},
pages = {477--480},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/cec/SilvaRA13,
author = {Reslley Gabriel Oliveira Silva and
Marcos Wagner de Souza Ribeiro and
Laurence Rodrigues do Amaral},
title = {Building high level knowledge from high dimensionality biological
dataset {(NCI60)} using Genetic Algorithms and feature selection strategies},
booktitle = {{IEEE} Congress on Evolutionary Computation},
pages = {578--583},
publisher = {{IEEE}},
year = {2013}
}
@inproceedings{DBLP:conf/cibb/DessiPMP13,
author = {Nicoletta Dess{\`{\i}} and
Emanuele Pascariello and
Gabriele Milia and
Barbara Pes},
title = {BioCloud Search EnGene: Surfing Biological Data on the Cloud},
booktitle = {{CIBB}},
series = {Lecture Notes in Computer Science},
volume = {8452},
pages = {33--48},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/cse/ToniniS13,
author = {Gustavo Tonini and
Frank Siqueira},
title = {A Distributed Data Allocation Algorithm for Biological Databases},
booktitle = {{CSE}},
pages = {531--537},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/dexaw/BakhtinaFJ13,
author = {Uliana Bakhtina and
Dirk Fleischer and
Kai Jannaschk},
title = {Application of Systematic Data Mining for Prediction of Biological
Quality Indices},
booktitle = {{DEXA} Workshops},
pages = {95--99},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/eScience/CuglerMST13,
author = {Daniel Cintra Cugler and
Claudia Bauzer Medeiros and
Shashi Shekhar and
Lu{\'{\i}}s Felipe Toledo},
title = {A Geographical Approach for Metadata Quality Improvement in Biological
Observation Databases},
booktitle = {e-Science},
pages = {212--220},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/embc/BosioSBO13,
author = {Mattia Bosio and
Philippe Salembier and
Pau Bellot and
Albert Oliveras{-}Verg{\'{e}}s},
title = {Hierarchical clustering combining numerical and biological similarities
for gene expression data classification},
booktitle = {{EMBC}},
pages = {584--587},
publisher = {{IEEE}},
year = {2013}
}
@inproceedings{DBLP:conf/eucc/GonzalezUSCBF13,
author = {Andres M. Gonzalez and
Jannis Uhlendorf and
Joe Schaul and
Eugenio Cinquemani and
Gr{\'{e}}gory Batt and
Giancarlo Ferrari{-}Trecate},
title = {Identification of biological models from single-cell data: {A} comparison
between mixed-effects and moment-based inference},
booktitle = {{ECC}},
pages = {3652--3657},
publisher = {{IEEE}},
year = {2013}
}
@inproceedings{DBLP:conf/hci/RychlikSM13,
author = {Michal Rychlik and
Witold Stankiewicz and
Marek Morzynski},
title = {Biological Objects Data Registration Algorithm for Modal (Low Dimensional)
Analysis},
booktitle = {{HCI} {(28)}},
series = {Communications in Computer and Information Science},
volume = {373},
pages = {655--659},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/iccabs/Altintas13,
author = {Ilkay Altintas},
title = {Workflow-driven programming paradigms for distributed analysis of
biological big data},
booktitle = {{ICCABS}},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@inproceedings{DBLP:conf/iciap/CarlettiFV13,
author = {Vincenzo Carletti and
Pasquale Foggia and
Mario Vento},
title = {Performance Comparison of Five Exact Graph Matching Algorithms on
Biological Databases},
booktitle = {{ICIAP} Workshops},
series = {Lecture Notes in Computer Science},
volume = {8158},
pages = {409--417},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/icmla/WaldKSN13,
author = {Randall Wald and
Taghi M. Khoshgoftaar and
Ahmad Abu Shanab and
Amri Napolitano},
title = {Comparative Analysis on the Stability of Feature Selection Techniques
Using Three Frameworks on Biological Datasets},
booktitle = {{ICMLA} {(1)}},
pages = {418--423},
publisher = {{IEEE}},
year = {2013}
}
@inproceedings{DBLP:conf/iimss/MaekawaMKK13,
author = {Yasuko Maekawa and
Yukie Majima and
Tsuneo Kawano and
Mako Katagiri},
title = {Characteristics of Practical Nursing Knowledge from Biological Data},
booktitle = {{IIMSS}},
series = {Frontiers in Artificial Intelligence and Applications},
volume = {254},
pages = {251--260},
publisher = {{IOS} Press},
year = {2013}
}
@inproceedings{DBLP:conf/iwbbio/Pareja-TobesPMPT13,
author = {Pablo Pareja{-}Tobes and
Eduardo Pareja{-}Tobes and
Marina Manrique and
Eduardo Pareja and
Raquel Tobes},
title = {Bio4J: An Open source biological data integration platform},
booktitle = {{IWBBIO}},
pages = {281},
publisher = {Copicentro Editorial},
year = {2013}
}
@inproceedings{DBLP:conf/miwai/AhmadY13,
author = {Farzana Kabir Ahmad and
Nooraini Yusoff},
title = {Reconstructing Gene Regulatory Network Using Heterogeneous Biological
Data},
booktitle = {{MIWAI}},
series = {Lecture Notes in Computer Science},
volume = {8271},
pages = {97--107},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/prib/LiN13,
author = {Yifeng Li and
Alioune Ngom},
title = {Versatile Sparse Matrix Factorization and Its Applications in High-Dimensional
Biological Data Analysis},
booktitle = {{PRIB}},
series = {Lecture Notes in Computer Science},
volume = {7986},
pages = {91--101},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/recomb/TranCZ13,
author = {Ngoc Hieu Tran and
Kwok Pui Choi and
Louxin Zhang},
title = {Counting Motifs in the Entire Biological Network from Noisy and Incomplete
Data - (Extended Abstract)},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {7821},
pages = {269--270},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/sac/TripletB13,
author = {Thomas Triplet and
Gregory Butler},
title = {BenchDW: a generic framework for biological data warehouse benchmarking},
booktitle = {{SAC}},
pages = {1328--1334},
publisher = {{ACM}},
year = {2013}
}
@inproceedings{DBLP:conf/vmls-ws/LeittePRSW13,
author = {Heike Leitte and
Julia Portl and
Ira V. R{\"{o}}der and
Rasmus R. Schr{\"{o}}der and
Irene U. Wacker},
title = {Towards a Structured Analysis of Quantitative Descriptors from Segmented
Biological Image Data},
booktitle = {VMLS@EuroVis (Short Papers)},
publisher = {Eurographics Association},
year = {2013}
}
@inproceedings{DBLP:conf/wob/NiidaTIM13,
author = {Atsushi Niida and
Georg Tremmel and
Seiya Imoto and
Satoru Miyano},
title = {Multilayer Cluster Heat Map Visualizing Biological Tensor Data},
booktitle = {{BSB}},
series = {Lecture Notes in Computer Science},
volume = {8213},
pages = {116--125},
publisher = {Springer},
year = {2013}
}
@incollection{DBLP:books/crc/aggarwal13/ReddyHZ13,
author = {Chandan K. Reddy and
Mohammad Al Hasan and
Mohammed J. Zaki},
title = {Clustering Biological Data},
booktitle = {Data Clustering: Algorithms and Applications},
pages = {381--414},
publisher = {{CRC} Press},
year = {2013}
}
@proceedings{DBLP:conf/biovis/2013,
title = {{IEEE} Symposium on Biological Data Visualization, BioVis 2013, Atlanta,
GA, USA, October 13-14, 2013},
publisher = {{IEEE} Computer Society},
year = {2013}
}
@phdthesis{DBLP:phd/basesearch/Gaire12,
author = {Raj K. Gaire},
title = {Effective integration of diverse biological datasets for better understanding
of cancer},
school = {University of Melbourne, Australia},
year = {2012}
}
@phdthesis{DBLP:phd/basesearch/Wirth12,
author = {Henry Wirth},
title = {Analysis of large-scale molecular biological data using self-organizing
maps},
school = {Leipzig University, Germany},
year = {2012}
}
@phdthesis{DBLP:phd/dnb/Blank12,
author = {Sebastian Blank},
title = {A Biological Inspired Approach for Sensor Data Management in Modular
Agricultural Machines},
school = {University of Kaiserslautern},
year = {2012}
}
@phdthesis{DBLP:phd/tr/Korkmaz12,
author = {G{\"{u}}lberal Kir{\c{c}}i{\c{c}}egi Yoksul Korkmaz},
title = {Mining microarray data for biologically important gene sets (Biyolojik
{\"{o}}nem ta{\c{s}}{\i}yan gen listelerinin bulunmas{\i} i{\c{c}}in
mikrodizi veri madencili{\u{g}}i)},
school = {Middle East Technical University, Turkey},
year = {2012}
}
@article{DBLP:journals/abi/Al-ShalalfaBA12,
author = {Mohammed Al{-}Shalalfa and
Tarek A. Bismar and
Reda Alhajj},
title = {Detecting Cancer Outlier Genes with Potential Rearrangement Using
Gene Expression Data and Biological Networks},
journal = {Adv. Bioinformatics},
volume = {2012},
pages = {373506:1--373506:13},
year = {2012}
}
@article{DBLP:journals/almob/VingaCFRA12,
author = {Susana Vinga and
Alexandra M. Carvalho and
Alexandre P. Francisco and
Lu{\'{\i}}s M. S. Russo and
Jonas S. Almeida},
title = {Pattern matching through Chaos Game Representation: bridging numerical
and discrete data structures for biological sequence analysis},
journal = {Algorithms Mol. Biol.},
volume = {7},
pages = {10},
year = {2012}
}
@article{DBLP:journals/bib/BebekKPC12,
author = {G{\"{u}}rkan Bebek and
Mehmet Koyut{\"{u}}rk and
Nathan D. Price and
Mark R. Chance},
title = {Network biology methods integrating biological data for translational
science},
journal = {Briefings Bioinform.},
volume = {13},
number = {4},
pages = {446--459},
year = {2012}
}
@article{DBLP:journals/bib/GuzziMGC12,
author = {Pietro Hiram Guzzi and
Marco Mina and
Concettina Guerra and
Mario Cannataro},
title = {Semantic similarity analysis of protein data: assessment with biological
features and issues},
journal = {Briefings Bioinform.},
volume = {13},
number = {5},
pages = {569--585},
year = {2012}
}
@article{DBLP:journals/biodb/NeveolWL12,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
W. John Wilbur and
Zhiyong Lu},
title = {Improving links between literature and biological data with text mining:
a case study with GEO, {PDB} and {MEDLINE}},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012}
}
@article{DBLP:journals/bioinformatics/ChangKLC12,
author = {Darby Tien{-}Hao Chang and
Chao{-}Hsuan Ke and
Jung{-}Hsin Lin and
Jung{-}Hsien Chiang},
title = {AutoBind: automatic extraction of protein-ligand-binding affinity
data from biological literature},
journal = {Bioinform.},
volume = {28},
number = {16},
pages = {2162--2168},
year = {2012}
}
@article{DBLP:journals/bioinformatics/GlausHR12,
author = {Peter Glaus and
Antti Honkela and
Magnus Rattray},
title = {Identifying differentially expressed transcripts from RNA-seq data
with biological variation},
journal = {Bioinform.},
volume = {28},
number = {13},
pages = {1721--1728},
year = {2012}
}
@article{DBLP:journals/bioinformatics/SmithABCCHLLKRSSWWM12,
author = {Richard N. Smith and
Jelena Aleksic and
Daniela Butano and
Adrian Carr and
Sergio Contrino and
Fengyuan Hu and
Mike Lyne and
Rachel Lyne and
Alex Kalderimis and
Kim Rutherford and
Radek Stepan and
Julie M. Sullivan and
Matthew Wakeling and
Xavier Watkins and
Gos Micklem},
title = {InterMine: a flexible data warehouse system for the integration and
analysis of heterogeneous biological data},
journal = {Bioinform.},
volume = {28},
number = {23},
pages = {3163--3165},
year = {2012}
}
@article{DBLP:journals/bioinformatics/WangLZH12,
author = {Haitian Wang and
Shaw{-}Hwa Lo and
Tian Zheng and
Inchi Hu},
title = {Interaction-based feature selection and classification for high-dimensional
biological data},
journal = {Bioinform.},
volume = {28},
number = {21},
pages = {2834--2842},
year = {2012}
}
@article{DBLP:journals/biomedsem/SamadianMW12,
author = {Soroush Samadian and
Bruce McManus and
Mark D. Wilkinson},
title = {Extending and encoding existing biological terminologies and datasets
for use in the reasoned semantic web},
journal = {J. Biomed. Semant.},
volume = {3},
pages = {6},
year = {2012}
}
@article{DBLP:journals/bmcbi/BartlettCHPLJBVHNSAR12,
author = {Christopher W. Bartlett and
Soo Yeon Cheong and
Liping Hou and
Jesse Paquette and
Pek Yee Lum and
G{\"{u}}nter J{\"{a}}ger and
Florian Battke and
Corinna Vehlow and
Julian Heinrich and
Kay Nieselt and
Ryo Sakai and
Jan Aerts and
William C. Ray},
title = {An eQTL biological data visualization challenge and approaches from
the visualization community},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-8}},
pages = {S8},
year = {2012}
}
@article{DBLP:journals/bmcbi/DibC12,
author = {Linda Dib and
Alessandra Carbone},
title = {{CLAG:} an unsupervised non hierarchical clustering algorithm handling
biological data},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {194},
year = {2012}
}
@article{DBLP:journals/bmcbi/EronenT12,
author = {Lauri Eronen and
Hannu Toivonen},
title = {Biomine: predicting links between biological entities using network
models of heterogeneous databases},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {119},
year = {2012}
}
@article{DBLP:journals/bmcbi/HolfordMCK12,
author = {Matthew Holford and
Jamie P. McCusker and
Kei{-}Hoi Cheung and
Michael Krauthammer},
title = {A semantic web framework to integrate cancer omics data with biological
knowledge},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-1}},
pages = {S10},
year = {2012}
}
@article{DBLP:journals/bmcbi/KennedyR12,
author = {Jessie Kennedy and
Jos B. T. M. Roerdink},
title = {Highlights of the 1st {IEEE} Symposium on Biological Data Visualization},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-8}},
pages = {S1},
year = {2012}
}
@article{DBLP:journals/bmcbi/KhanFMPKPKWK12,
author = {Suleiman A. Khan and
Ali Faisal and
John Mpindi and
Juuso A. Parkkinen and
Tuomo Kalliokoski and
Antti Poso and
Olli{-}P. Kallioniemi and
Krister Wennerberg and
Samuel Kaski},
title = {Comprehensive data-driven analysis of the impact of chemoinformatic
structure on the genome-wide biological response profiles of cancer
cells to 1159 drugs},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {112},
year = {2012}
}
@article{DBLP:journals/bmcbi/MironovSBASK12,
author = {Vladimir Mironov and
Nirmala Seethappan and
Ward Blond{\'{e}} and
Erick Antezana and
Andrea Splendiani and
Martin Kuiper},
title = {Gauging triple stores with actual biological data},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-1}},
pages = {S3},
year = {2012}
}
@article{DBLP:journals/bmcbi/SallouBR12,
author = {Olivier Sallou and
Anthony Bretaudeau and
Aurelien Roult},
title = {Seqcrawler: biological data indexing and browsing platform},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {175},
year = {2012}
}
@article{DBLP:journals/bmcbi/SchonbachTCBTR12,
author = {Christian Sch{\"{o}}nbach and
Sissades Tongsima and
Jonathan H. Chan and
Vladimir Brusic and
Tin Wee Tan and
Shoba Ranganathan},
title = {InCoB2012 Conference: from biological data to knowledge to technological
breakthroughs},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-17}},
pages = {S1},
year = {2012}
}
@article{DBLP:journals/bmcbi/TchagangPFSFHZHCLP12,
author = {Alain B. Tchagang and
Sieu Phan and
Fazel Famili and
Heather Shearer and
Pierre R. Fobert and
Yi Huang and
Jitao Zou and
Daiqing Huang and
Adrian Cutler and
Ziying Liu and
Youlian Pan},
title = {Mining biological information from 3D short time-series gene expression
data: the OPTricluster algorithm},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {54},
year = {2012}
}
@article{DBLP:journals/bmcbi/YaoCC12,
author = {Fangzhou Yao and
Jeff Coquery and
Kim{-}Anh L{\^{e}} Cao},
title = {Independent Principal Component Analysis for biologically meaningful
dimension reduction of large biological data sets},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {24},
year = {2012}
}
@article{DBLP:journals/bmcsb/LoRDZSBY12,
author = {Kenneth Lo and
Adrian E. Raftery and
Kenneth M. Dombek and
Jun Zhu and
Eric E. Schadt and
Roger Eugene Bumgarner and
Ka Yee Yeung},
title = {Integrating external biological knowledge in the construction of regulatory
networks from time-series expression data},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {101},
year = {2012}
}
@article{DBLP:journals/bmcsb/MartinTSDMWPHP12,
author = {Florian Martin and
Ty M. Thomson and
Alain Sewer and
David A. Drubin and
Carole Mathis and
Dirk Weisensee and
Dexter Pratt and
Julia Hoeng and
Manuel C. Peitsch},
title = {Assessment of network perturbation amplitudes by applying high-throughput
data to causal biological networks},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {54},
year = {2012}
}
@article{DBLP:journals/bmcsb/YangW12,
author = {Tzu{-}Hsien Yang and
Wei{-}Sheng Wu},
title = {Identifying biologically interpretable transcription factor knockout
targets by jointly analyzing the transcription factor knockout microarray
and the ChIP-chip data},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {102},
year = {2012}
}
@article{DBLP:journals/cim/StegmayerGM12,
author = {Georgina Stegmayer and
Matias Gerard and
Diego H. Milone},
title = {Data Mining Over Biological Datasets: An Integrated Approach Based
on Computational Intelligence},
journal = {{IEEE} Comput. Intell. Mag.},
volume = {7},
number = {4},
pages = {22--34},
year = {2012}
}
@article{DBLP:journals/cmmm/LiL12a,
author = {Hui Li and
Chunmei Liu},
title = {A Dynamic Data-Driven Framework for Biological Data Using 2D Barcodes},
journal = {Comput. Math. Methods Medicine},
volume = {2012},
pages = {892098:1--892098:5},
year = {2012}
}
@article{DBLP:journals/cmpb/LambertMMB12,
author = {Ronald J. W. Lambert and
Ioannis Mytilinaios and
Luke Maitland and
Angus M. Brown},
title = {Monte Carlo simulation of parameter confidence intervals for non-linear
regression analysis of biological data using Microsoft Excel},
journal = {Comput. Methods Programs Biomed.},
volume = {107},
number = {2},
pages = {155--163},
year = {2012}
}
@article{DBLP:journals/datamine/LiHDK12,
author = {Zhenhui Li and
Jiawei Han and
Bolin Ding and
Roland Kays},
title = {Mining periodic behaviors of object movements for animal and biological
sustainability studies},
journal = {Data Min. Knowl. Discov.},
volume = {24},
number = {2},
pages = {355--386},
year = {2012}
}
@article{DBLP:journals/ecoi/MichenerABCDFKKTV12,
author = {William K. Michener and
Suzie Allard and
Amber E. Budden and
Robert B. Cook and
Kimberly Douglass and
Mike Frame and
Steve Kelling and
Rebecca Koskela and
Carol Tenopir and
David Vieglais},
title = {Participatory design of DataONE - Enabling cyberinfrastructure for
the biological and environmental sciences},
journal = {Ecol. Informatics},
volume = {11},
pages = {5--15},
year = {2012}
}
@article{DBLP:journals/hac/HastonCH12,
author = {Elspeth Haston and
Robert Cubey and
David J. Harris},
title = {Data concepts and their relevance for data capture in large scale
digitisation of biological collections},
journal = {Int. J. Humanit. Arts Comput.},
volume = {6},
number = {1-2},
pages = {111--119},
year = {2012}
}
@article{DBLP:journals/ijdmb/QinG12,
author = {Guimin Qin and
Lin Gao},
title = {An algorithm for network motif discovery in biological networks},
journal = {Int. J. Data Min. Bioinform.},
volume = {6},
number = {1},
pages = {1--16},
year = {2012}
}
@article{DBLP:journals/ijdmb/Reboiro-JatoGDF12,
author = {Miguel Reboiro{-}Jato and
Daniel Glez{-}Pe{\~{n}}a and
Fernando D{\'{\i}}az and
Florentino Fdez{-}Riverola},
title = {A novel ensemble approach for multicategory classification of {DNA}
microarray data using biological relevant gene sets},
journal = {Int. J. Data Min. Bioinform.},
volume = {6},
number = {6},
pages = {602--616},
year = {2012}
}
@article{DBLP:journals/nar/BolserCPGJASBGSHREBESPCRBB12,
author = {Dan M. Bolser and
Pierre{-}Yves Chibon and
Nicolas Palopoli and
Sungsam Gong and
Daniel Jacob and
Victoria Dominguez Del Angel and
Daniel Swan and
Sebastian Bassi and
Virginia Gonz{\'{a}}lez and
Prashanth Suravajhala and
Seungwoo Hwang and
Paolo Romano and
Rob Edwards and
Bryan Bishop and
John Eargle and
Timur Shtatland and
Nicholas J. Provart and
Dave Clements and
Daniel P. Renfro and
Daeui Park and
Jong Bhak},
title = {MetaBase - the wiki-database of biological databases},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {1250--1254},
year = {2012}
}
@article{DBLP:journals/nar/KelderIHKCEP12,
author = {Thomas Kelder and
Martijn P. van Iersel and
Kristina Hanspers and
Martina Kutmon and
Bruce R. Conklin and
Chris T. A. Evelo and
Alexander R. Pico},
title = {WikiPathways: building research communities on biological pathways},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {1301--1307},
year = {2012}
}
@article{DBLP:journals/ploscb/SchneiderJ12,
author = {Maria Victoria Schneider and
Rafael C. Jim{\'{e}}nez},
title = {Teaching the Fundamentals of Biological Data Integration Using Classroom
Games},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {12},
year = {2012}
}
@article{DBLP:journals/sadm/ZhuWJL12,
author = {Xiangxin Zhu and
Max Welling and
Fang Jin and
John S. Lowengrub},
title = {Predicting simulation parameters of biological systems using a Gaussian
process model},
journal = {Stat. Anal. Data Min.},
volume = {5},
number = {6},
pages = {509--522},
year = {2012}
}
@article{DBLP:journals/siamam/KimF12,
author = {Jae Kyoung Kim and
Daniel B. Forger},
title = {On the Existence and Uniqueness of Biological Clock Models Matching
Experimental Data},
journal = {{SIAM} J. Appl. Math.},
volume = {72},
number = {6},
pages = {1842--1855},
year = {2012}
}
@article{DBLP:journals/sighit/CeciGMCMMFMP12,
author = {Michelangelo Ceci and
Pietro Hiram Guzzi and
Elio Masciari and
Mauro Coluccia and
Federica Mandreoli and
Massimo Mecella and
Fabio Fumarola and
Riccardo Martoglia and
Wilma Penzo},
title = {The IS-BioBank project: a framework for biological data normalization,
interoperability, and mining for cancer microenvironment analysis},
journal = {{SIGHIT} Rec.},
volume = {2},
number = {2},
pages = {16--21},
year = {2012}
}
@article{DBLP:journals/sp/HasanHCZ12,
author = {Mohammad Al Hasan and
Jun Huan and
Jake Yue Chen and
Mohammed J. Zaki},
title = {Biological knowledge discovery and data mining},
journal = {Sci. Program.},
volume = {20},
number = {1},
pages = {1--2},
year = {2012}
}
@article{DBLP:journals/tcbb/AnsariBVD12,
author = {Nadeem Ansari and
Riyue Bao and
Calin Voichita and
Sorin Draghici},
title = {Detecting Phenotype-Specific Interactions between Biological Processes
from Microarray Data and Annotations},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {5},
pages = {1399--1409},
year = {2012}
}
@article{DBLP:journals/tcbb/CampelloMS12,
author = {Ricardo J. G. B. Campello and
Davoud Moulavi and
J{\"{o}}rg Sander},
title = {A Simpler and More Accurate {AUTO-HDS} Framework for Clustering and
Visualization of Biological Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {6},
pages = {1850--1852},
year = {2012}
}
@article{DBLP:journals/tcbb/NounouNMDD12,
author = {Mohamed N. Nounou and
Hazem N. Nounou and
Nader Meskin and
Aniruddha Datta and
Edward R. Dougherty},
title = {Multiscale Denoising of Biological Data: {A} Comparative Analysis},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {5},
pages = {1539--1545},
year = {2012}
}
@article{DBLP:journals/tcbb/StegmayerMKLC12,
author = {Georgina Stegmayer and
Diego H. Milone and
Laura Kamenetzky and
Mariana G. Lopez and
Fernando Carrari},
title = {A Biologically Inspired Validity Measure for Comparison of Clustering
Methods over Metabolic Data Sets},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {3},
pages = {706--716},
year = {2012}
}
@article{DBLP:journals/widm/LiuWZ12,
author = {Li{-}Zhi Liu and
Fang{-}Xiang Wu and
Wen{-}Jun Zhang},
title = {Reverse engineering of gene regulatory networks from biological data},
journal = {WIREs Data Mining Knowl. Discov.},
volume = {2},
number = {5},
pages = {365--385},
year = {2012}
}
@article{DBLP:journals/widm/Vital-LopezMD12,
author = {Francisco G. Vital{-}Lopez and
Vesna Memisevic and
Bhaskar Dutta},
title = {Tutorial on biological networks},
journal = {WIREs Data Mining Knowl. Discov.},
volume = {2},
number = {4},
pages = {298--325},
year = {2012}
}
@inproceedings{DBLP:conf/bcb/HillSS12,
author = {Steven Hill and
Bismita Srichandan and
Rajshekhar Sunderraman},
title = {An iterative MapReduce approach to frequent subgraph mining in biological
datasets},
booktitle = {{BCB}},
pages = {661--666},
publisher = {{ACM}},
year = {2012}
}
@inproceedings{DBLP:conf/bibm/JiangC12,
author = {Hao Jiang and
Wai{-}Ki Ching},
title = {The role of Eigen-matrix translation in classification of biological
datasets},
booktitle = {{BIBM}},
pages = {1--4},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/bibm/LeeS12a,
author = {Hyokyeong Lee and
Rahul Singh},
title = {Unsupervised kernel parameter estimation by constrained nonlinear
optimization for clustering nonlinear biological data},
booktitle = {{BIBM}},
pages = {1--6},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/bibm/LiN12,
author = {Yifeng Li and
Alioune Ngom},
title = {Fast sparse representation approaches for the classification of high-dimensional
biological data},
booktitle = {{BIBM}},
pages = {1--6},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/bibm/MesaVK12,
author = {Liliana Marcela Olarte Mesa and
Luis Fernando Ni{\~{n}}o Vasquez and
Liliana L{\'{o}}pez Kleine},
title = {Identification and analysis of gene clusters in biological data},
booktitle = {{BIBM} Workshops},
pages = {551--557},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/biovis/PartlKLKSS12,
author = {Christian Partl and
Denis Kalkofen and
Alexander Lex and
Karl Kashofer and
Marc Streit and
Dieter Schmalstieg},
title = {enRoute: Dynamic path extraction from biological pathway maps for
in-depth experimental data analysis},
booktitle = {BioVis},
pages = {107--114},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/cbms/SpampinatoGKM12,
author = {Concetto Spampinato and
Daniela Giordano and
Isaak Kavasidis and
Sebastiano Milardo},
title = {BioWizard: Discovering and validating associations between biological
entities by integrated analysis of scientific literature and experimental
data},
booktitle = {{CBMS}},
pages = {1--6},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/cikm/Song12,
author = {Min Song},
title = {Session details: Mining biological data and text},
booktitle = {DTMBIO@CIKM},
pages = {1},
publisher = {{ACM}},
year = {2012}
}
@inproceedings{DBLP:conf/colognetwente/PhillipsJBCL12,
author = {Charles A. Phillips and
Jeremy J. Jay and
Erich J. Baker and
Elissa J. Chesler and
Michael A. Langston},
title = {On Bipartite Graph Decomposition in the Presence of Noise, with Applications
to Biological Data Clustering},
booktitle = {{CTW}},
pages = {215--219},
year = {2012}
}
@inproceedings{DBLP:conf/edbt/AltintasWCL12,
author = {Ilkay Altintas and
Jianwu Wang and
Daniel Crawl and
Weizhong Li},
title = {Challenges and approaches for distributed workflow-driven analysis
of large-scale biological data: vision paper},
booktitle = {{EDBT/ICDT} Workshops},
pages = {73--78},
publisher = {{ACM}},
year = {2012}
}
@inproceedings{DBLP:conf/embc/Dimitrakopoulos12,
author = {Georgios N. Dimitrakopoulos and
Kyriakos N. Sgarbas and
Konstantina Dimitrakopoulou and
Andrei Dragomir and
Anastasios Bezerianos and
Ioannis A. Maraziotis},
title = {Multi-scale modeling of gene regulatory networks via integration of
temporal and topological biological data},
booktitle = {{EMBC}},
pages = {1242--1245},
publisher = {{IEEE}},
year = {2012}
}
@inproceedings{DBLP:conf/evoW/HolzingerDFFCR12,
author = {Emily Rose Holzinger and
Scott M. Dudek and
Alex T. Frase and
Brooke L. Fridley and
Prabhakar Chalise and
Marylyn D. Ritchie},
title = {Comparison of Methods for Meta-dimensional Data Analysis Using in
Silico and Biological Data Sets},
booktitle = {EvoBIO},
series = {Lecture Notes in Computer Science},
volume = {7246},
pages = {134--143},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/gcb/RottgerKVWB12,
author = {Richard R{\"{o}}ttger and
Christoph Kreutzer and
Thuy Duong Vu and
Tobias Wittkop and
Jan Baumbach},
title = {Online Transitivity Clustering of Biological Data with Missing Values},
booktitle = {{GCB}},
series = {OASIcs},
volume = {26},
pages = {57--68},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2012}
}
@inproceedings{DBLP:conf/iberamia/SkrobanekUWMD12,
author = {Pawel Skrobanek and
Olgierd Unold and
Ewa Walkowicz and
Henryk Maciejewski and
Maciej Dobrowolski},
title = {Study on the Impact of Affinity on the Results of Data Mining in Biological
Populations},
booktitle = {{IBERAMIA}},
series = {Lecture Notes in Computer Science},
volume = {7637},
pages = {111--119},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/icaisc/MaciejewskiWUS12,
author = {Henryk Maciejewski and
Ewa Walkowicz and
Olgierd Unold and
Pawel Skrobanek},
title = {Enhancing Recognition of a Weak Class - Comparative Study Based on
Biological Population Data Mining},
booktitle = {{ICAISC} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {7268},
pages = {136--143},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/icmla/BegumA12,
author = {Salma Begum and
Ramazan Savas Ayg{\"{u}}n},
title = {Analyzing the Performance of Hierarchical Binary Classifiers for Multi-class
Classification Problem Using Biological Data},
booktitle = {{ICMLA} {(2)}},
pages = {145--150},
publisher = {{IEEE}},
year = {2012}
}
@inproceedings{DBLP:conf/ida/KlawonnABJ12,
author = {Frank Klawonn and
Nada Abidi and
Evelin Berger and
Lothar J{\"{a}}nsch},
title = {Curve Fitting for Short Time Series Data from High Throughput Experiments
with Correction for Biological Variation},
booktitle = {{IDA}},
series = {Lecture Notes in Computer Science},
volume = {7619},
pages = {150--160},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/imis/Ogiela12,
author = {Lidia Ogiela},
title = {Biological Modelling in Semantic Data Analysis Systems},
booktitle = {{IMIS}},
pages = {99--102},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@inproceedings{DBLP:conf/incdm/GasparovicaKA12,
author = {Madara Gasparovica and
Gita Krievina and
Ludmila Aleksejeva},
title = {Biological Interpretation of Metabolic Syndrome Data Missing Value
Imputation and Classification},
booktitle = {{ICDM} (Workshops)},
pages = {167--176},
publisher = {ibai Publishing},
year = {2012}
}
@inproceedings{DBLP:conf/iri/ShanabKWN12,
author = {Ahmad Abu Shanab and
Taghi M. Khoshgoftaar and
Randall Wald and
Amri Napolitano},
title = {Impact of noise and data sampling on stability of feature ranking
techniques for biological datasets},
booktitle = {{IRI}},
pages = {415--422},
publisher = {{IEEE}},
year = {2012}
}
@inproceedings{DBLP:conf/isvc/RosenkranzXZYS12,
author = {Joshua Rosenkranz and
Yuan Xu and
Xing Zhang and
Lijun Yin and
William Stein},
title = {Panorama Image Construction Using Multiple-Photos Stitching from Biological
Data},
booktitle = {{ISVC} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {7432},
pages = {242--252},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/iti/ZhangKL12,
author = {Leishi Zhang and
Jasna Kuljis and
Xiaohui Liu},
title = {Visualization of high throughput biological data},
booktitle = {{ITI}},
pages = {163--168},
publisher = {{IEEE}},
year = {2012}
}
@inproceedings{DBLP:conf/recomb/WangHDN12,
author = {Hua Wang and
Heng Huang and
Chris H. Q. Ding and
Feiping Nie},
title = {Predicting Protein-Protein Interactions from Multimodal Biological
Data Sources via Nonnegative Matrix Tri-Factorization},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {7262},
pages = {314--325},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/sac/ChhelLGS12,
author = {Fabien Chhel and
Fr{\'{e}}d{\'{e}}ric Lardeux and
Adrien Go{\"{e}}ffon and
Fr{\'{e}}d{\'{e}}ric Saubion},
title = {Minimum multiple characterization of biological data using partially
defined boolean formulas},
booktitle = {{SAC}},
pages = {1399--1405},
publisher = {{ACM}},
year = {2012}
}
@inproceedings{DBLP:conf/scisisis/TaniiKNKTH12,
author = {Hideaki Tanii and
Kei Kuramoto and
Hiroshi Nakajima and
Syoji Kobashi and
Naoki Tsuchiya and
Yutaka Hata},
title = {A Fuzzy time-series prediction model with multi-biological data for
health management},
booktitle = {SCIS{\&}ISIS},
pages = {1259--1264},
publisher = {{IEEE}},
year = {2012}
}
@inproceedings{DBLP:conf/sebd/CeciCFGMMMMP12,
author = {Michelangelo Ceci and
Mauro Coluccia and
Fabio Fumarola and
Pietro Hiram Guzzi and
Federica Mandreoli and
Riccardo Martoglia and
Elio Masciari and
Massimo Mecella and
Wilma Penzo},
title = {A Framework for Biological Data Normalization, Interoperability, and
Mining for Cancer Microenvironment Analysis},
booktitle = {{SEBD}},
pages = {67--74},
publisher = {Edizioni Libreria Progetto, Padova, Italy},
year = {2012}
}
@inproceedings{DBLP:conf/swat4ls/JulienLR12,
author = {Julien Wollbrett and
Pierre Larmande and
Manuel Ruiz},
title = {Semi-automatic Generation of Semantic Web Services for Relational
Biological Databases},
booktitle = {{SWAT4LS}},
series = {{CEUR} Workshop Proceedings},
volume = {952},
publisher = {CEUR-WS.org},
year = {2012}
}
@inproceedings{DBLP:conf/swat4ls/JuppPM12,
author = {Simon Jupp and
Helen E. Parkinson and
James Malone},
title = {Semantic Web Atlas: Putting Gene Expression Data into Biological Context},
booktitle = {{SWAT4LS}},
series = {{CEUR} Workshop Proceedings},
volume = {952},
publisher = {CEUR-WS.org},
year = {2012}
}
@inproceedings{DBLP:conf/vda/HolzhuterLSSSS12,
author = {Clemens Holzh{\"{u}}ter and
Alexander Lex and
Dieter Schmalstieg and
Hans{-}J{\"{o}}rg Schulz and
Heidrun Schumann and
Marc Streit},
title = {Visualizing uncertainty in biological expression data},
booktitle = {Visualization and Data Analysis},
series = {{SPIE} Proceedings},
volume = {8294},
pages = {82940O},
publisher = {{SPIE}},
year = {2012}
}
@incollection{DBLP:books/daglib/p/KnollWH12,
author = {Aaron Knoll and
Rolf Westerteiger and
Hans Hagen},
title = {An Evaluation of Peak Finding for {DVR} Classification of Biological
Data},
booktitle = {Visualization in Medicine and Life Sciences {II}},
series = {Mathematics and visualization},
pages = {91--106},
publisher = {Springer},
year = {2012}
}
@incollection{DBLP:books/igi/12/GomezML12,
author = {Karina Mabell Gomez and
Daniele Miorandi and
David B. Lowe},
title = {Data Highways},
booktitle = {Biologically Inspired Networking and Sensing},
pages = {223--241},
publisher = {{IGI} Global},
year = {2012}
}
@proceedings{DBLP:conf/biovis/2012,
title = {2012 {IEEE} Symposium on Biological Data Visualization, BioVis 2011,
Seattle, WA, USA, October 14-15, 2012},
publisher = {{IEEE} Computer Society},
year = {2012}
}
@article{DBLP:journals/dagstuhl-reports/GorgHKOW12,
author = {Carsten G{\"{o}}rg and
Lawrence Hunter and
Jessie Kennedy and
Se{\'{a}}n I. O'Donoghue and
Jarke J. van Wijk},
title = {Biological Data Visualization (Dagstuhl Seminar 12372)},
journal = {Dagstuhl Reports},
volume = {2},
number = {9},
pages = {131--164},
year = {2012}
}
@phdthesis{DBLP:phd/basesearch/Garcia11,
author = {Wandaliz Torres{-}Garc{\'{\i}}a},
title = {Integrative Analyses of Diverse Biological Data Sources},
school = {Arizona State University, Tempe, {USA}},
year = {2011}
}
@phdthesis{DBLP:phd/basesearch/Guner11,
author = {Ugur Guner},
title = {Identification of topological and dynamic properties of biological
networks through diverse types of data},
school = {Georgia Institute of Technology, Atlanta, GA, {USA}},
year = {2011}
}
@phdthesis{DBLP:phd/basesearch/Luo11a,
author = {Man Luo},
title = {Cheminformatics Modeling of Diverse and Disparate Biological Data
and the Use of Models to Discover Novel Bioactive Molecules},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2011}
}
@phdthesis{DBLP:phd/ca/Min11,
author = {Renqiang Min},
title = {Machine Learning Approaches to Biological Sequence and Phenotype Data
Analysis},
school = {University of Toronto, Canada},
year = {2011}
}
@phdthesis{DBLP:phd/de/Uhlmann2011,
author = {Johannes Uhlmann},
title = {Multivariate Algorithmics in Biological Data Analysis},
school = {Berlin Institute of Technology},
year = {2011}
}
@article{DBLP:journals/abi/Iber11,
author = {Dagmar Iber},
title = {Inferring Biological Mechanisms by Data-Based Mathematical Modelling:
Compartment-Specific Gene Activation during Sporulation in \emph{Bacillus
subtilis} as a Test Case},
journal = {Adv. Bioinformatics},
volume = {2011},
pages = {124062:1--124062:12},
year = {2011}
}
@article{DBLP:journals/aicom/Schietgat11,
author = {Leander Schietgat},
title = {Graph-based data mining for biological applications},
journal = {{AI} Commun.},
volume = {24},
number = {1},
pages = {95--96},
year = {2011}
}
@article{DBLP:journals/bc/TwickelBP11,
author = {Arndt von Twickel and
Ansgar B{\"{u}}schges and
Frank Pasemann},
title = {Deriving neural network controllers from neuro-biological data: implementation
of a single-leg stick insect controller},
journal = {Biol. Cybern.},
volume = {104},
number = {1-2},
pages = {95--119},
year = {2011}
}
@article{DBLP:journals/bib/MansmannJ11,
author = {Ulrich Mansmann and
Vindi Jurinovic},
title = {Biological feature validation of estimated gene interaction networks
from microarray data: a case study on {MYC} in lymphomas},
journal = {Briefings Bioinform.},
volume = {12},
number = {3},
pages = {230--244},
year = {2011}
}
@article{DBLP:journals/biodatamining/UrbachM11,
author = {Davnah Urbach and
Jason H. Moore},
title = {The spatial dimension in biological data mining},
journal = {BioData Min.},
volume = {4},
pages = {6},
year = {2011}
}
@article{DBLP:journals/biodatamining/UrbachM11a,
author = {Davnah Urbach and
Jason H. Moore},
title = {Data mining and the evolution of biological complexity},
journal = {BioData Min.},
volume = {4},
pages = {7},
year = {2011}
}
@article{DBLP:journals/biodatamining/ZhengJHZGCZL11,
author = {Guang Zheng and
Miao Jiang and
Xiaojuan He and
Jing Zhao and
Hongtao Guo and
Gao Chen and
Qinglin Zha and
Aiping Lu},
title = {Discrete derivative: a data slicing algorithm for exploration of sharing
biological networks between rheumatoid arthritis and coronary heart
disease},
journal = {BioData Min.},
volume = {4},
pages = {18},
year = {2011}
}
@article{DBLP:journals/biodb/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11,
author = {Pascale Gaudet and
Amos Bairoch and
Dawn Field and
Susanna{-}Assunta Sansone and
Chris F. Taylor and
Teresa K. Attwood and
Alex Bateman and
Judith A. Blake and
Carol J. Bult and
J. Michael Cherry and
Rex L. Chisholm and
Guy Cochrane and
Charles E. Cook and
Janan T. Eppig and
Michael Y. Galperin and
Robert Gentleman and
Carole A. Goble and
Takashi Gojobori and
John M. Hancock and
Douglas G. Howe and
Tadashi Imanishi and
Janet Kelso and
David Landsman and
Suzanna E. Lewis and
Ilene Karsch{-}Mizrachi and
Sandra E. Orchard and
B. F. Francis Ouellette and
Shoba Ranganathan and
Lorna J. Richardson and
Philippe Rocca{-}Serra and
Paul N. Schofield and
Damian Smedley and
Christopher Southan and
Tin Wee Tan and
Tatiana A. Tatusova and
Patricia L. Whetzel and
Owen White and
Chisato Yamasaki},
title = {Towards BioDBcore: a community-defined information specification for
biological databases},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011}
}
@article{DBLP:journals/biodb/GubermanAA11,
author = {Jonathan M. Guberman and
Jiye Ai and
Olivier Arnaiz and
Joachim Baran and
Andrew Blake and
Richard A. Baldock and
Claude Chelala and
David Croft and
Anthony Cros and
Rosalind J. Cutts and
Alex Di G{\'{e}}nova and
Simon A. Forbes and
Takatomo Fujisawa and
Emanuela Gadaleta and
David M. Goodstein and
Gunes Gundem and
Bernard Haggarty and
Syed Haider and
Matthew Hall and
Todd W. Harris and
Robin Haw and
Shen Hu and
Simon J. Hubbard and
Jack Hsu and
Vivek Iyer and
Philip Jones and
Toshiaki Katayama and
Rhoda Kinsella and
Lei Kong and
Daniel Lawson and
Yong Liang and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Jie Luo and
Michael J. Lush and
Jeremy C. Mason and
Fran{\c{c}}ois Moreews and
Nelson Ndegwa and
Darren J. Oakley and
Christian Perez{-}Llamas and
Michael Primig and
Elena Rivkin and
Steven Rosanoff and
Rebecca Shepherd and
Reinhard Simon and
William C. Skarnes and
Damian Smedley and
Linda Sperling and
William Spooner and
Peter Stevenson and
Kevin R. Stone and
Jon W. Teague and
Jun Wang and
Jianxin Wang and
Brett Whitty and
David Tai Wai Wong and
Marie Wong{-}Erasmus and
Long Yao and
Ken Youens{-}Clark and
Christina K. Yung and
Junjun Zhang and
Arek Kasprzyk},
title = {BioMart Central Portal: an open database network for the biological
community},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011}
}
@article{DBLP:journals/biodb/Kasprzyk11,
author = {Arek Kasprzyk},
title = {BioMart: driving a paradigm change in biological data management},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011}
}
@article{DBLP:journals/biodb/LaulederkindSHLNPSWPKLRMDTJ11,
author = {Stanley J. F. Laulederkind and
Mary Shimoyama and
G. Thomas Hayman and
Timothy Lowry and
Rajni Nigam and
Victoria Petri and
Jennifer R. Smith and
Shur{-}Jen Wang and
Jeff de Pons and
George Kowalski and
Weisong Liu and
Wes Rood and
Diane H. Munzenmaier and
Melinda R. Dwinell and
Simon N. Twigger and
Howard J. Jacob},
title = {The Rat Genome Database curation tool suite: a set of optimized software
tools enabling efficient acquisition, organization, and presentation
of biological data},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011}
}
@article{DBLP:journals/bioinformatics/IsciOJO11,
author = {Senol Isci and
Cengizhan Ozturk and
Jon Jones and
Hasan H. Otu},
title = {Pathway analysis of high-throughput biological data within a Bayesian
network framework},
journal = {Bioinform.},
volume = {27},
number = {12},
pages = {1667--1674},
year = {2011}
}
@article{DBLP:journals/bioinformatics/LiRB11,
author = {Limin Li and
Barbara Rakitsch and
Karsten M. Borgwardt},
title = {ccSVM: correcting Support Vector Machines for confounding factors
in biological data classification},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {342--348},
year = {2011}
}
@article{DBLP:journals/bioinformatics/PosekanyFS11,
author = {Alexandra Posekany and
K. Felsenstein and
Peter Sykacek},
title = {Biological assessment of robust noise models in microarray data analysis},
journal = {Bioinform.},
volume = {27},
number = {6},
pages = {807--814},
year = {2011}
}
@article{DBLP:journals/bioinformatics/VignesBLF11,
author = {Matthieu Vignes and
Juliette Blanchet and
Damien Leroux and
Florence Forbes},
title = {SpaCEM\({}^{\mbox{3}}\): a software for biological module detection
when data is incomplete, high dimensional and dependent},
journal = {Bioinform.},
volume = {27},
number = {6},
pages = {881--882},
year = {2011}
}
@article{DBLP:journals/bmcbi/GaoW11,
author = {Shouguo Gao and
Xujing Wang},
title = {Quantitative utilization of prior biological knowledge in the Bayesian
network modeling of gene expression data},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {359},
year = {2011}
}
@article{DBLP:journals/bmcbi/JeongNUM11,
author = {Euna Jeong and
Masao Nagasaki and
Kazuko Ueno and
Satoru Miyano},
title = {Ontology-based instance data validation for high-quality curated biological
pathways},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-1}},
pages = {S8},
year = {2011}
}
@article{DBLP:journals/bmcbi/RangarajanSYCHOFDISCSM11,
author = {Arun Rangarajan and
Tim Schedl and
Karen Yook and
Juancarlos Chan and
Stephen Haenel and
Lolly Otis and
Sharon Faelten and
Tracey DePellegrin{-}Connelly and
Ruth Isaacson and
Marek S. Skrzypek and
J. Michael Cherry and
Paul W. Sternberg and
Hans{-}Michael M{\"{u}}ller},
title = {Toward an interactive article: integrating journals and biological
databases},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {175},
year = {2011}
}
@article{DBLP:journals/bmcbi/SongPCSKK11,
author = {Young Soo Song and
Chan Hee Park and
Hee{-}Joon Chung and
Hyunjung Shin and
Jihun Kim and
Ju Han Kim},
title = {Semantically enabled and statistically supported biological hypothesis
testing with tissue microarray databases},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-1}},
pages = {S51},
year = {2011}
}
@article{DBLP:journals/bmcsb/KozhenkovSDGRPB11,
author = {Sergey Kozhenkov and
Mayya Sedova and
Yulia Dubinina and
Amarnath Gupta and
Animesh Ray and
Julia V. Ponomarenko and
Michael Baitaluk},
title = {BiologicalNetworks - tools enabling the integration of multi-scale
data for the host-pathogen studies},
journal = {{BMC} Syst. Biol.},
volume = {5},
pages = {7},
year = {2011}
}
@article{DBLP:journals/bmcsb/NdukumFSVD11,
author = {Juliet Ndukum and
Lu{\'{\i}}s L. Fonseca and
Helena Santos and
Eberhard O. Voit and
Susmita Datta},
title = {Statistical Inference Methods for Sparse Biological Time Series Data},
journal = {{BMC} Syst. Biol.},
volume = {5},
pages = {57},
year = {2011}
}
@article{DBLP:journals/cbm/LiH11,
author = {Han{-}Lin Li and
Yao{-}Huei Huang},
title = {A {DIAMOND} method of inducing classification rules for biological
data},
journal = {Comput. Biol. Medicine},
volume = {41},
number = {8},
pages = {587--599},
year = {2011}
}
@article{DBLP:journals/ci/CohenVJROBWTH11,
author = {K. Bretonnel Cohen and
Karin Verspoor and
Helen L. Johnson and
Christophe Roeder and
Philip V. Ogren and
William A. Baumgartner Jr. and
Elizabeth K. White and
Hannah J. Tipney and
Lawrence Hunter},
title = {High-Precision Biological Event Extraction: Effects of System and
of Data},
journal = {Comput. Intell.},
volume = {27},
number = {4},
pages = {681--701},
year = {2011}
}
@article{DBLP:journals/csda/LiuTSH11,
author = {Rui{-}Yin Liu and
Jian Tao and
Ning{-}Zhong Shi and
Xuming He},
title = {Bayesian analysis of the patterns of biological susceptibility via
reversible jump {MCMC} sampling},
journal = {Comput. Stat. Data Anal.},
volume = {55},
number = {3},
pages = {1498--1508},
year = {2011}
}
@article{DBLP:journals/csda/Wu11,
author = {Han{-}Ming Wu},
title = {On biological validity indices for soft clustering algorithms for
gene expression data},
journal = {Comput. Stat. Data Anal.},
volume = {55},
number = {5},
pages = {1969--1979},
year = {2011}
}
@article{DBLP:journals/dke/GuptaCQ11,
author = {Amarnath Gupta and
Christopher Condit and
Xufei Qian},
title = {Corrigendum to "BioDB: An ontology-enhanced information system for
heterogeneous biological information" [Data {\&} Knowledge Engineering
69 {(11)} {(2010)} 1084-1102]},
journal = {Data Knowl. Eng.},
volume = {70},
number = {1},
pages = {165},
year = {2011}
}
@article{DBLP:journals/dlib/MichenerVVKCJ11,
author = {William Michener and
David Vieglais and
Todd J. Vision and
John A. Kunze and
Patricia Cruse and
Greg Jan{\'{e}}e},
title = {DataONE: Data Observation Network for Earth - Preserving Data and
Enabling Innovation in the Biological and Environmental Sciences},
journal = {D Lib Mag.},
volume = {17},
number = {1/2},
year = {2011}
}
@article{DBLP:journals/ejasp/PiconGRIW11,
author = {Artzai Pic{\'{o}}n and
Ovidiu Ghita and
Sergio Rodr{\'{\i}}guez{-}Vaamonde and
Pedro M. Iriondo and
Paul F. Whelan},
title = {Biologically-inspired data decorrelation for hyper-spectral imaging},
journal = {{EURASIP} J. Adv. Signal Process.},
volume = {2011},
pages = {66},
year = {2011}
}
@article{DBLP:journals/ijdmb/NingNL11,
author = {Kang Ning and
Hoong Kee Ng and
Hon Wai Leong},
title = {Analysis of the relationships among Longest Common Subsequences, Shortest
Common Supersequences and patterns and its application on pattern
discovery in biological sequences},
journal = {Int. J. Data Min. Bioinform.},
volume = {5},
number = {6},
pages = {611--625},
year = {2011}
}
@article{DBLP:journals/ijiids/SaleemFAA11,
author = {Kashif Saleem and
Norsheila Fisal and
Muhammad Sharil Abdullah and
Sharifah Hafizah Syed Ariffin},
title = {Biological inspired secure autonomous routing mechanism for wireless
sensor networks},
journal = {Int. J. Intell. Inf. Database Syst.},
volume = {5},
number = {4},
pages = {313--337},
year = {2011}
}
@article{DBLP:journals/ijkdb/SrinivasanABGKLMMMRSSST11,
author = {Narayanaswamy Srinivasan and
Garima Agarwal and
Ramachandra M. Bhaskara and
Rupali A. Gadkari and
Oruganty Krishnadev and
B. Lakshmi and
Swapnil Mahajan and
Smita Mohanty and
Richa Mudgal and
R. Rakshambikai and
Sankaran Sandhya and
G. Sudha and
L. S. Swapna and
N. Tyagi},
title = {Influence of Genomic and Other Biological Data Sets in the Understanding
of Protein Structures, Functions and Interactions},
journal = {Int. J. Knowl. Discov. Bioinform.},
volume = {2},
number = {1},
pages = {24--44},
year = {2011}
}
@article{DBLP:journals/im/AlcarazKWWB11,
author = {Nicolas Alcaraz and
Hande K{\"{u}}c{\"{u}}k and
Jochen Weile and
Anil Wipat and
Jan Baumbach},
title = {KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using
Expression Data},
journal = {Internet Math.},
volume = {7},
number = {4},
pages = {299--313},
year = {2011}
}
@article{DBLP:journals/it/KormeierHH11,
author = {Benjamin Kormeier and
Klaus Hippe and
Ralf Hofest{\"{a}}dt},
title = {Data Warehouses in Bioinformatics: Integration of Molecular Biological
Data},
journal = {it Inf. Technol.},
volume = {53},
number = {5},
pages = {241--249},
year = {2011}
}
@article{DBLP:journals/jcheminf/KhannaR11,
author = {Varun Khanna and
Shoba Ranganathan},
title = {Structural diversity of biologically interesting datasets: a scaffold
analysis approach},
journal = {J. Cheminformatics},
volume = {3},
pages = {30},
year = {2011}
}
@article{DBLP:journals/jcp/LiuC11a,
author = {Wei Liu and
Ling Chen},
title = {An Efficient Way of Frequent Embedded Subtree Mining on Biological
Data},
journal = {J. Comput.},
volume = {6},
number = {12},
pages = {2574--2581},
year = {2011}
}
@article{DBLP:journals/jib/TahaE11,
author = {Kamal Taha and
Ramez Elmasri},
title = {{GMB:} An Efficient Query Processor for Biological Data},
journal = {J. Integr. Bioinform.},
volume = {8},
number = {2},
year = {2011}
}
@article{DBLP:journals/jms/LuKH11,
author = {Ying{-}Hao Lu and
Chen{-}Chun Kuo and
Yaw{-}Bin Huang},
title = {WebBio, a Web-Based Management and Analysis System for Patient Data
of Biological Products in Hospital},
journal = {J. Medical Syst.},
volume = {35},
number = {4},
pages = {579--584},
year = {2011}
}
@article{DBLP:journals/nar/CeramiGDRBASBS11,
author = {Ethan G. Cerami and
Benjamin E. Gross and
Emek Demir and
Igor V. Rodchenkov and
{\"{O}}zg{\"{u}}n Babur and
Nadia Anwar and
Nikolaus Schultz and
Gary D. Bader and
Chris Sander},
title = {Pathway Commons, a web resource for biological pathway data},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {685--690},
year = {2011}
}
@article{DBLP:journals/nar/CroftOWHGMCGGJJKMMNSSYBHDS11,
author = {David Croft and
Gavin O'Kelly and
Guanming Wu and
Robin Haw and
Marc Gillespie and
Lisa Matthews and
Michael Caudy and
Phani V. Garapati and
Gopal Gopinath and
Bijay Jassal and
Steven Jupe and
Irina Kalatskaya and
Shahana Mahajan and
Bruce May and
Nelson Ndegwa and
Esther Schmidt and
Veronica Shamovsky and
Christina K. Yung and
Ewan Birney and
Henning Hermjakob and
Peter D'Eustachio and
Lincoln Stein},
title = {Reactome: a database of reactions, pathways and biological processes},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {691--697},
year = {2011}
}
@article{DBLP:journals/nar/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11,
author = {Pascale Gaudet and
Amos Bairoch and
Dawn Field and
Susanna{-}Assunta Sansone and
Chris F. Taylor and
Teresa K. Attwood and
Alex Bateman and
Judith A. Blake and
Carol J. Bult and
J. Michael Cherry and
Rex L. Chisholm and
Guy Cochrane and
Charles E. Cook and
Janan T. Eppig and
Michael Y. Galperin and
Robert Gentleman and
Carole A. Goble and
Takashi Gojobori and
John M. Hancock and
Douglas G. Howe and
Tadashi Imanishi and
Janet Kelso and
David Landsman and
Suzanna E. Lewis and
Ilene Karsch{-}Mizrachi and
Sandra E. Orchard and
B. F. Francis Ouellette and
Shoba Ranganathan and
Lorna J. Richardson and
Philippe Rocca{-}Serra and
Paul N. Schofield and
Damian Smedley and
Christopher Southan and
Tin Wee Tan and
Tatiana A. Tatusova and
Patricia L. Whetzel and
Owen White and
Chisato Yamasaki},
title = {Towards BioDBcore: a community-defined information specification for
biological databases},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {7--10},
year = {2011}
}
@article{DBLP:journals/tcbb/AndonieFAABM11,
author = {Razvan Andonie and
Levente Fabry{-}Asztalos and
Christopher B. Abdul{-}Wahid and
Sarah Abdul{-}Wahid and
Grant I. Barker and
Lukas Magill},
title = {Fuzzy {ARTMAP} Prediction of Biological Activities for Potential {HIV-1}
Protease Inhibitors Using a Small Molecular Data Set},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {1},
pages = {80--93},
year = {2011}
}
@article{DBLP:journals/tcbb/SehgalDNSE11,
author = {Aditya Kumar Sehgal and
Sanmay Das and
Keith Noto and
Milton H. Saier Jr. and
Charles Elkan},
title = {Identifying Relevant Data for a Biological Database: Handcrafted Rules
versus Machine Learning},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {3},
pages = {851--857},
year = {2011}
}
@article{DBLP:journals/titb/ChatziioannouKDMKM11,
author = {Aristotelis A. Chatziioannou and
Ioannis Kanaris and
Charalampos Doukas and
Panagiotis Moulos and
Fragiskos N. Kolisis and
Ilias Maglogiannis},
title = {{GRISSOM} Platform: Enabling Distributed Processing and Management
of Biological Data Through Fusion of Grid and Web Technologies},
journal = {{IEEE} Trans. Inf. Technol. Biomed.},
volume = {15},
number = {1},
pages = {83--92},
year = {2011}
}
@article{DBLP:journals/tmi/MiwakeichiOOKTI11,
author = {Fumikazu Miwakeichi and
Yoshitaka Oku and
Yasumasa Okada and
Shigeharu Kawai and
Yoshiyasu Tamura and
Makio Ishiguro},
title = {Detection and Visualization Method of Dynamic State Transition for
Biological Spatio-Temporal Imaging Data},
journal = {{IEEE} Trans. Medical Imaging},
volume = {30},
number = {3},
pages = {859--866},
year = {2011}
}
@article{DBLP:journals/tsp/TriganoIR11,
author = {Thomas Trigano and
Uri Isserles and
Yaacov Ritov},
title = {Semiparametric Curve Alignment and Shift Density Estimation for Biological
Data},
journal = {{IEEE} Trans. Signal Process.},
volume = {59},
number = {5},
pages = {1970--1984},
year = {2011}
}
@article{DBLP:journals/widm/ArshadiJ11,
author = {Niloofar Arshadi and
Igor Jurisica},
title = {Ensembles of case-based reasoning classifiers in high-dimensional
biological domains},
journal = {WIREs Data Mining Knowl. Discov.},
volume = {1},
number = {2},
pages = {164--171},
year = {2011}
}
@inproceedings{DBLP:conf/adcons/EdlaJ11,
author = {Damodar Reddy Edla and
Prasanta K. Jana},
title = {Clustering Biological Data Using Voronoi Diagram},
booktitle = {{ADCONS}},
series = {Lecture Notes in Computer Science},
volume = {7135},
pages = {188--197},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/bcb/ShihP11,
author = {Yu{-}Keng Shih and
Srinivasan Parthasarathy},
title = {Scalable multiple global network alignment for biological data},
booktitle = {{BCB}},
pages = {96--105},
publisher = {{ACM}},
year = {2011}
}
@inproceedings{DBLP:conf/bibm/DittmanKWW11,
author = {David J. Dittman and
Taghi M. Khoshgoftaar and
Randall Wald and
Huanjing Wang},
title = {Stability Analysis of Feature Ranking Techniques on Biological Datasets},
booktitle = {{BIBM}},
pages = {252--256},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/bibm/Jamil11,
author = {Hasan M. Jamil},
title = {Toward a Cooperative Natural Language Query Interface for Biological
Databases},
booktitle = {{BIBM}},
pages = {556--561},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/bibm/LiuPDLFDCW11,
author = {Sheng Liu and
Ronak Y. Patel and
Pankaj R. Daga and
Haining Liu and
Gang Fu and
Robert J. Doerksen and
Yixin Chen and
Dawn Wilkins},
title = {Multi-class Joint Rule Extraction and Feature Selection for Biological
Data},
booktitle = {{BIBM}},
pages = {476--481},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/biostec/AbateAFM11,
author = {Francesco Abate and
Andrea Acquaviva and
Elisa Ficarra and
Enrico Macii},
title = {A New Latent Semantic Analysis based Methodology for Knowledge Extraction
from Biomedical Literature and Biological Pathways Databases},
booktitle = {{BIOINFORMATICS}},
pages = {66--74},
publisher = {SciTePress},
year = {2011}
}
@inproceedings{DBLP:conf/biostec/CoutoSS11a,
author = {Br{\'{a}}ulio Roberto Gon{\c{c}}alves Marinho Couto and
Marcelo Matos Santoro and
Marcos Augusto dos Santos},
title = {Unrevealing Biological Process with Linear Algebra - Extracting Patterns
from Noisy Data},
booktitle = {{BIOINFORMATICS}},
pages = {313--317},
publisher = {SciTePress},
year = {2011}
}
@inproceedings{DBLP:conf/cdc/MontefuscoCAB11,
author = {Francesco Montefusco and
Carlo Cosentino and
Francesco Amato and
Declan G. Bates},
title = {Reverse-engineering biological interaction networks from noisy data
using Regularized Least Squares and Instrumental Variables},
booktitle = {{CDC/ECC}},
pages = {4395--4400},
publisher = {{IEEE}},
year = {2011}
}
@inproceedings{DBLP:conf/chinagrid/ZhuLL11,
author = {Xiangyuan Zhu and
Kenli Li and
Renfa Li},
title = {A Data Parallel Strategy for Aligning Multiple Biological Sequences
on Homogeneous Multiprocessor Platform},
booktitle = {ChinaGrid},
pages = {188--195},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/ciss/PorterIBE11,
author = {Joshua R. Porter and
Pablo A. Iglesias and
John S. Burg and
Peter J. Espenshade},
title = {Overcoming data limitations to identify a static nonlinearity in a
biological signaling cascade},
booktitle = {{CISS}},
pages = {1--6},
publisher = {{IEEE}},
year = {2011}
}
@inproceedings{DBLP:conf/cw/Stadon11,
author = {Julian Stadon},
title = {Post-Biological Hypersurfacing: Embodied Mixed Reality Data Transfer},
booktitle = {{CW}},
pages = {264--268},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/dexaw/HanczarN11,
author = {Blaise Hanczar and
Mohamed Nadif},
title = {Improving the Biological Relevance of Biclustering for Microarray
Data in Using Ensemble Methods},
booktitle = {{DEXA} Workshops},
pages = {413--417},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/dsrt/StadonG11,
author = {Julian Stadon and
Rapha{\"{e}}l Grasset},
title = {Syncretic Post-Biological Digital Identity: Hybridizing Mixed Reality
Data Transfer Systems},
booktitle = {{DS-RT}},
pages = {120--125},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@inproceedings{DBLP:conf/esann/Lapuyade-LahorgueM11,
author = {J{\'{e}}r{\^{o}}me Lapuyade{-}Lahorgue and
Ali Mohammad{-}Djafari},
title = {Nearest neighbors and correlation dimension for dimensionality estimation.
Application to factor analysis of real biological time series data},
booktitle = {{ESANN}},
year = {2011}
}
@inproceedings{DBLP:conf/gensips/VicenteLH11,
author = {F{\'{a}}bio Fernandes da Rocha Vicente and
Fabr{\'{\i}}cio Martins Lopes and
Ronaldo Fumio Hashimoto},
title = {Improvement of GNs inference through biological data integration},
booktitle = {GENSiPS},
pages = {70--73},
publisher = {{IEEE}},
year = {2011}
}
@inproceedings{DBLP:conf/haicta/DachBPK11,
author = {Jacek Dach and
Piotr Boniecki and
Krzysztof Pilarski and
Adam Krysztofiak},
title = {Data Acquisition During Composting Experiments with Usage of 4-chamber
Bioreactor for Modeling of Biological Processes},
booktitle = {{HAICTA}},
series = {{CEUR} Workshop Proceedings},
volume = {1152},
pages = {737--742},
publisher = {CEUR-WS.org},
year = {2011}
}
@inproceedings{DBLP:conf/hci/RychlikSM11,
author = {Michal Rychlik and
Witold Stankiewicz and
Marek Morzynski},
title = {Numerical Analysis of Geometrical Features of 3D Biological Objects,
for Three-Dimensional Biometric and Anthropometric Database},
booktitle = {{HCI} {(6)}},
series = {Lecture Notes in Computer Science},
volume = {6766},
pages = {108--117},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/hic/NguyenSC11,
author = {Quang Vinh Nguyen and
Simeon J. Simoff and
Daniel R. Catchpoole},
title = {Interactive Visualisation with User Perspective for Biological Data
Analysis},
booktitle = {{HIC}},
series = {Studies in Health Technology and Informatics},
volume = {168},
pages = {125--132},
publisher = {{IOS} Press},
year = {2011}
}
@inproceedings{DBLP:conf/hvei/NagelLBSU11,
author = {Axel Nagel and
Marc Lohse and
Anthony M. Bolger and
Mark Stitt and
Bj{\"{o}}rn Usadel},
title = {Visualizing large, high-throughput datasets based on the cognitive
representation of biological pathways},
booktitle = {Human Vision and Electronic Imaging},
series = {{SPIE} Proceedings},
volume = {7865},
pages = {78650H},
publisher = {SPIE/IS{\&}T},
year = {2011}
}
@inproceedings{DBLP:conf/icbo/MasuyaGTWOKKDKHWTM11,
author = {Hiroshi Masuya and
Georgios V. Gkoutos and
Nobuhiko Tanaka and
Kazunori Waki and
Yoshihiro Okuda and
Tatsuya Kushida and
Norio Kobayashi and
Koji Doi and
Kouji Kozaki and
Robert Hoehndorf and
Shigeharu Wakana and
Tetsuro Toyoda and
Riichiro Mizoguchi},
title = {An Advanced Strategy for Integration of Biological Measurement Data},
booktitle = {{ICBO}},
series = {{CEUR} Workshop Proceedings},
volume = {833},
publisher = {CEUR-WS.org},
year = {2011}
}
@inproceedings{DBLP:conf/imagapp/RohnKS11,
author = {Hendrik Rohn and
Christian Klukas and
Falk Schreiber},
title = {Visual Analytics of Multimodal Biological Data},
booktitle = {{IMAGAPP/IVAPP}},
pages = {256--261},
publisher = {SciTePress},
year = {2011}
}
@inproceedings{DBLP:conf/kes/BoukiYIN11,
author = {Yoshihiko Bouki and
Takuya Yoshihiro and
Etsuko Inoue and
Masaru Nakagawa},
title = {Normalization of Biological Expression Data Based on Selection of
a Stable Element Set},
booktitle = {{KES} {(3)}},
series = {Lecture Notes in Computer Science},
volume = {6883},
pages = {153--166},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/pakdd/YangZZZ11,
author = {Pengyi Yang and
Zili Zhang and
Bing Bing Zhou and
Albert Y. Zomaya},
title = {Sample Subset Optimization for Classifying Imbalanced Biological Data},
booktitle = {{PAKDD} {(2)}},
series = {Lecture Notes in Computer Science},
volume = {6635},
pages = {333--344},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/recomb/PengL11,
author = {Hanchuan Peng and
Fuhui Long},
title = {Seeing More Is Knowing More: {V3D} Enables Real-Time 3D Visualization
and Quantitative Analysis of Large-Scale Biological Image Data Sets},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {336},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/sebd/AtzeniPT11,
author = {Paolo Atzeni and
Fabio Polticelli and
Daniele Toti},
title = {Automatic Discovery and Resolution of Protein Abbreviations from Full-Text
Scientific Papers: {A} Light-Weight Approach Towards Data Extraction
from Unstructured Biological Sources (Extended Abstract)},
booktitle = {{SEBD}},
pages = {318--325},
year = {2011}
}
@inproceedings{DBLP:conf/siggrapha/LiBPZSLZL011,
author = {Guangxia Li and
Andrew Bragdon and
Zhigeng Pan and
Mingmin Zhang and
Sharon M. Swartz and
David H. Laidlaw and
Chaoyang Zhang and
Hanyu Liu and
Jian Chen},
title = {VisBubbles: a workflow-driven framework for scientific data analysis
of time-varying biological datasets},
booktitle = {{SIGGRAPH} Asia Posters},
pages = {27:1},
publisher = {{ACM}},
year = {2011}
}
@inproceedings{DBLP:conf/ssdbm/BoulakiaDH11,
author = {Sarah Cohen Boulakia and
Alain Denise and
Sylvie Hamel},
title = {Using Medians to Generate Consensus Rankings for Biological Data},
booktitle = {{SSDBM}},
series = {Lecture Notes in Computer Science},
volume = {6809},
pages = {73--90},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/swat4ls/Garcia-GodoyDM11,
author = {Mar{\'{\i}}a Jes{\'{u}}s Garc{\'{\i}}a{-}Godoy and
Ismael Navas{-}Delgado and
Jos{\'{e}} Francisco Aldana Montes},
title = {Bioqueries: a social community sharing experiences while querying
biological linked data},
booktitle = {{SWAT4LS}},
pages = {24--31},
publisher = {{ACM}},
year = {2011}
}
@inproceedings{DBLP:conf/swat4ls/KobayashiT11,
author = {Norio Kobayashi and
Tetsuro Toyoda},
title = {BioSPARQL: ontology-based smart building of {SPARQL} queries for biological
linked open data},
booktitle = {{SWAT4LS}},
pages = {47--49},
publisher = {{ACM}},
year = {2011}
}
@inproceedings{DBLP:conf/swat4ls/NishikataT11,
author = {Koro Nishikata and
Tetsuro Toyoda},
title = {BioLOD.org: ontology-based integration of biological linked open data},
booktitle = {{SWAT4LS}},
pages = {92--93},
publisher = {{ACM}},
year = {2011}
}
@inproceedings{DBLP:conf/swis/BellaachiaB11,
author = {Abdelghani Bellaachia and
Anasse Bari},
title = {{SFLOSCAN:} {A} biologically-inspired data mining framework for community
identification in dynamic social networks},
booktitle = {{SWIS}},
pages = {156--163},
publisher = {{IEEE}},
year = {2011}
}
@inproceedings{DBLP:conf/wea/FrinhaniSMFR11,
author = {Rafael M. D. Frinhani and
Ricardo M. A. Silva and
Geraldo R. Mateus and
Paola Festa and
Mauricio G. C. Resende},
title = {{GRASP} with Path-Relinking for Data Clustering: {A} Case Study for
Biological Data},
booktitle = {{SEA}},
series = {Lecture Notes in Computer Science},
volume = {6630},
pages = {410--420},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/wims/VenkatesanBASMBMK11,
author = {Aravind Venkatesan and
Ward Blond{\'{e}} and
Erick Antezana and
Mats Skillingstad and
M. Scott Marshall and
Bernard De Baets and
Vladimir Mironov and
Martin Kuiper},
title = {The {RDF} foundry: call for an initiative to build enhanced {RDF}
resources for biological data integration},
booktitle = {{WIMS}},
pages = {59},
publisher = {{ACM}},
year = {2011}
}
@proceedings{DBLP:conf/biovis/2011,
editor = {Jessie Kennedy and
Jos B. T. M. Roerdink},
title = {2011 {IEEE} Symposium on Biological Data Visualization, BioVis 2011,
Providence, RI, USA, October 23-24, 2011},
publisher = {{IEEE} Computer Society},
year = {2011}
}
@book{DBLP:books/daglib/0023942,
author = {Mitchell L. Model},
title = {Bioinformatics Programming Using Python - Practical Programming for
Biological Data: Covers Python 3},
publisher = {O'Reilly},
year = {2010}
}
@phdthesis{DBLP:phd/basesearch/Chen12c,
author = {Li Chen},
title = {Integrative Modeling and Analysis of High-throughput Biological Data},
school = {Virginia Tech, Blacksburg, VA, {USA}},
year = {2010}
}
@phdthesis{DBLP:phd/basesearch/Dost10,
author = {Banu Dost},
title = {Optimization algorithms for biological data},
school = {University of California, San Diego, {USA}},
year = {2010}
}
@phdthesis{DBLP:phd/basesearch/Kircher10,
author = {Amy L. Kircher},
title = {Use of early biological detection data by decision makers to minimize
the consequences of no-notice infectious disease outbreaks},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2010}
}
@phdthesis{DBLP:phd/basesearch/Li10c,
author = {Yunlei Li},
title = {Exploiting noisy and incomplete biological data for prediction and
knowledge discovery},
school = {Delft University of Technology, Netherlands},
year = {2010}
}
@phdthesis{DBLP:phd/basesearch/Shabalin10,
author = {Andrey A. Shabalin},
title = {Detection of Low Rank Signals in Noise and Fast Correlation Mining
with Applications to Large Biological Data},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2010}
}
a service of 
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
retrieved on 2024-06-18 10:07 CEST from data curated by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
