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ORCIDBMC Bioinformatics, Volume 19 - Supplements
Volume 19-S, Number 1, February 2018
- Maryam Etemadi, Mehri Bagherian, Zhi-Zhong Chen, Lusheng Wang:
Better ILP models for haplotype assembly. 11-21 - Seowon Choi, Jin-Wu Nam:
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association. 23-31 - Hajime Suzuki, Masahiro Kasahara
:
Introducing difference recurrence relations for faster semi-global alignment of long sequences. 33-47 - In Seok Yang, Sangwoo Kim:
Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients. 40:1-40:10 - Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min, Sungroh Yoon:
HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment. 49-61 - Inyoung Kim, Saemi Choi, Sun Kim:
BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. 63-72 - Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert:
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. 73-84 - Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai:
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. 85-95 - Gunhwan Ko, Pan-Gyu Kim, Jongcheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byungwook Lee:
Closha: bioinformatics workflow system for the analysis of massive sequencing data. 97-104
Volume 19-S, Number 2, March 2018
- Lokmane Chebouba, Bertrand Miannay, Dalila Boughaci, Carito Guziolowski:
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. 15-26 - Kumar Parijat Tripathi, Marina Piccirillo, Mario Rosario Guarracino:
An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways. 27-40 - Maurizio Giordano, Kumar Parijat Tripathi, Mario Rosario Guarracino:
Ensemble of rankers for efficient gene signature extraction in smoke exposure classification. 41-54 - Diego Fioravanti, Ylenia Giarratano, Valerio Maggio, Claudio Agostinelli, Marco Chierici, Giuseppe Jurman, Cesare Furlanello:
Phylogenetic convolutional neural networks in metagenomics. 49:1-49:13
Volume 19-S, Number 3, March 2018
- Ali Foroughi Pour, Lori A. Dalton:
Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure. 5-19 - Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, Ranadip Pal:
Investigation of model stacking for drug sensitivity prediction. 21-33 - Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta:
Simulating variance heterogeneity in quantitative genome wide association studies. 35-44 - Ashish Katiyar, Anwoy Kumar Mohanty, Jianping Hua, Chao Sima, Rosana Lopes, Aniruddha Datta, Michael L. Bittner:
A Bayesian approach to determine the composition of heterogeneous cancer tissue. 45-58 - Yang Ni, Peter Müller, Lin Wei, Yuan Ji:
Bayesian graphical models for computational network biology. 59-69 - Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal:
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 69:1-69:4
Volume 19-S, Number 4, May 2018
- Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin:
A gene profiling deconvolution approach to estimating immune cell composition from complex tissues. 15-23 - Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Jin-Young Jang, Taesung Park:
Hierarchical structural component modeling of microRNA-mRNA integration analysis. 25-34 - Shunyun Yang, Runxin Guo, Rui Liu, Xiangke Liao, Quan Zou, Benyun Shi, Shaoliang Peng:
cmFSM: a scalable CPU-MIC coordinated drug-finding tool by frequent subgraph mining. 35-47 - Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda:
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. 49-59 - Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. 61-72 - Yujuan Gao, Sheng Wang, Minghua Deng, Jinbo Xu:
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. 73-84 - Sungyoung Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang, Taesung Park:
Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes. 85-97 - Jiyun Zhou, Hongpeng Wang, Zhishan Zhao, Ruifeng Xu, Qin Lu:
CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway. 99-109 - Y-h. Taguchi:
Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes. 99:1-99:13 - Xiaofeng Gong, Jianping Jiang, Zhongqu Duan, Hui Lu:
A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. 111-119
Volume 19-S, Number 5, April 2018
- Zhenxing Wang, Xiaoliang Wu, Yadong Wang:
A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. 15-22 - Xiaotian Hao, Jianye Hao, Wang Li, Hanxu Hou:
Effective norm emergence in cell systems under limited communication. 23-35 - Yang Hu, Tianyi Zhao, Ningyi Zhang, Tianyi Zang, Jun Zhang, Liang Cheng:
Identifying diseases-related metabolites using random walk. 37-46 - Shiquan Sun, Xifang Sun, Yan Zheng:
Higher-order partial least squares for predicting gene expression levels from chromatin states. 47-54 - Huaixiao Tou, Lu Yao, Zhongyu Wei, Xiahai Zhuang, Bo Zhang:
Automatic infection detection based on electronic medical records. 55-63 - Jiajie Peng, Weiwei Hui, Xuequn Shang:
Measuring phenotype-phenotype similarity through the interactome. 65-77 - Yan-Shuo Chu, Mingxiang Teng, Yadong Wang:
Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring. 79-87 - Yang Guo, Shuhui Liu, Zhanhuai Li, Xuequn Shang:
BCDForest: a boosting cascade deep forest model towards the classification of cancer subtypes based on gene expression data. 118:1-118:13
Volume 19-S, Number 6, May 2018
- Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab:
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. 15-30 - Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez:
Computing the family-free DCJ similarity. 31-42 - Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidanis:
On the rank-distance median of 3 permutations. 43-62 - Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller:
Generation and comparative genomics of synthetic dengue viruses. 140:1-140:14
Volume 19-S, Number 7, July 2018
- Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre:
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. 3-12 - Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli, Carlo Berzuini:
Mendelian randomisation analysis of clustered causal effects of body mass on cardiometabolic biomarkers. 13-22 - Marco Fornili, Patrizia Boracchi, Federico Ambrogi, Elia Biganzoli:
Modeling the covariates effects on the hazard function by piecewise exponential artificial neural networks: an application to a controlled clinical trial on renal carcinoma. 23-29 - Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti, Clelia Di Serio:
Effect of the number of removed lymph nodes on prostate cancer recurrence and survival: evidence from an observational study. 31-44 - Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini:
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. 45-59 - Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosuè Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio, Alfonso Urso:
Deep learning models for bacteria taxonomic classification of metagenomic data. 61-76 - Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
INBIA: a boosting methodology for proteomic network inference. 77-88 - Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi, Bassam AlKindy:
Comparison of metaheuristics to measure gene effects on phylogenetic supports and topologies. 89-107 - Kirsty L. Hassall, Andrew Mead:
Beyond the one-way ANOVA for 'omics data. 109-126 - Igor Saggese, Elisa Bona, Maxwell Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini, Flavio Mignone:
STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow. 127-137 - Francesco Bardozzo, Pietro Liò, Roberto Tagliaferri:
A study on multi-omic oscillations in Escherichia coli metabolic networks. 139-154 - Claudia Angelini, Andrea Bracciali, David Gilbert, Riccardo Rizzo:
Preface to the BMC-CIBB 2015-16 special issue. 201:1-201:2
Volume 19-S, Number 8, June 2018
- Ingoo Lee, Hojung Nam:
Identification of drug-target interaction by a random walk with restart method on an interactome network. 9-18 - Yousang Jo, Sanghyeon Kim, Doheon Lee:
Identification of common coexpression modules based on quantitative network comparison. 19-28 - Myeong-Sang Yu, Hyang-Mi Lee, Aaron Park, Chungoo Park, Hyithaek Ceong, Ki-Hyeong Rhee, Dokyun Na:
In silico prediction of potential chemical reactions mediated by human enzymes. 29-37 - Víctor Suárez-Paniagua, Isabel Segura-Bedmar:
Evaluation of pooling operations in convolutional architectures for drug-drug interaction extraction. 39-47 - Kyungrin Noh, Sunyong Yoo, Doheon Lee:
A systematic approach to identify therapeutic effects of natural products based on human metabolite information. 49-55 - Reilly Grant, David Kucher, Ana M. Leon, Jonathan Gemmell, Daniela Stan Raicu, Samah J. Fodeh:
Automatic extraction of informal topics from online suicidal ideation. 57-66 - Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta, Gordon R. Bernard:
Identifying tweets of personal health experience through word embedding and LSTM neural network. 67-74 - Munui Kim, Seung Han Baek, Min Song:
Relation extraction for biological pathway construction using node2vec. 75-84 - Shashank Gupta, Sachin Pawar, Nitin Ramrakhiyani, Girish Keshav Palshikar, Vasudeva Varma:
Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction mention extraction. 212:1-212:7
Volume 19-S, Number 9, August 2018
- Balaji Veeramani, John W. Raymond, Pritam Chanda:
DeepSort: deep convolutional networks for sorting haploid maize seeds. 85-93 - Dan Wang, Lusheng Wang:
GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences. 95-103 - Soumya Kundu, Mukul S. Bansal:
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation. 105-115 - Sungtae Kim, Sungkyoung Choi, Jung-Hwan Yoon, Youngsoo Kim, Seungyeoun Lee, Taesung Park:
Drug response prediction model using a hierarchical structural component modeling method. 117-128 - Jianliang Gao, Bo Song, Xiaohua Hu, Fengxia Yan, Jianxin Wang:
ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species. 129-135 - Tun-Wen Pai, Kuan-Hung Li, Cing-Han Yang, Chin-Hwa Hu, Han-Jia Lin, Wen-Der Wang, Yet-Ran Chen:
Multiple model species selection for transcriptomics analysis of non-model organisms. 137-150 - Shengling Wang, Chenyu Wang, Shenling Wang, Liran Ma:
Big data analysis for evaluating bioinvasion risk. 151-159 - Kaiyuan Zhu, Xiaowen Liu:
A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra. 161-168 - Jianyu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao, Siu-Ming Yiu:
BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion. 169-176 - Lishuang Li, Jia Wan, Jieqiong Zheng, Jian Wang:
Biomedical event extraction based on GRU integrating attention mechanism. 177-184 - Shaoliang Peng, Minxia Cheng, Kaiwen Huang, Yingbo Cui, Zhiqiang Zhang, Runxin Guo, Xiaoyu Zhang, Shunyun Yang, Xiangke Liao, Yutong Lu, Quan Zou, Benyun Shi:
Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture. 185-194 - Hsin-Yi Tsao, Pei-Ying S. Chan, Emily Chia-Yu Su:
Predicting diabetic retinopathy and identifying interpretable biomedical features using machine learning algorithms. 195-205
Volume 19-S, Number 10, October 2018
- Giuliano Armano, Giorgio Fotia, Andrea Manconi:
BITS 2017: the annual meeting of the Italian Society of Bioinformatics. 207-210 - Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A. Calogero:
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. 211-219 - Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno:
cuRnet: an R package for graph traversing on GPU. 221-230 - Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D'Elia, Nicola Bombieri, Flavio Licciulli, Rosalba Giugno:
Arena-Idb: a platform to build human non-coding RNA interaction networks. 231-244 - Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi, Giovanni Felici:
CamurWeb: a classification software and a large knowledge base for gene expression data of cancer. 245-256 - Marco Moscatelli, Andrea Manconi, Mauro Pessina, Giovanni Fellegara, Stefano Rampoldi, Luciano Milanesi, Andrea Casasco, Matteo Gnocchi:
An infrastructure for precision medicine through analysis of big data. 257-267 - Marco Frasca, Giuliano Grossi, Jessica Gliozzo, Marco Mesiti, Marco Notaro, Paolo Perlasca, Alessandro Petrini, Giorgio Valentini:
A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks. 269-280 - Elena Casiraghi, Veronica Huber, Marco Frasca, Mara Cossa, Matteo Tozzi, Licia Rivoltini, Biagio Eugenio Leone, Antonello Villa, Barbara Vergani:
A novel computational method for automatic segmentation, quantification and comparative analysis of immunohistochemically labeled tissue sections. 281-297 - A. Merlotti, Ìtalo Faria do Valle, Gastone C. Castellani, Daniel Remondini:
Statistical modelling of CG interdistance across multiple organisms. 299-306
Volume 19-S, Number 11, October 2018
- Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky, Yury Khudyakov:
Automated quality control for a molecular surveillance system. 358:1-358:15 - Blake Camp, Jaya Krishna Mandivarapu, Nagashayana Ramamurthy, James Wingo, Anu G. Bourgeois, Xiaojun Cao, Rajshekhar Sunderraman:
A new cross-platform architecture for epi-info software suite. 359:1-359:8 - Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums:
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. 360:1-360:10 - Fatima Zare, Abdelrahman Hosny, Sheida Nabavi:
Noise cancellation using total variation for copy number variation detection. 361:1-361:12 - Shrikant D. Pawar, Christopher Freas, Irene T. Weber, Robert W. Harrison:
Analysis of drug resistance in HIV protease. 362:1-362:6 - Finlay Campbell, Xavier Didelot, Richard G. FitzJohn, Neil M. Ferguson, Anne Cori, Thibaut Jombart:
outbreaker2: a modular platform for outbreak reconstruction. 363:1-363:8 - Kun Zhao, Elizabeth Henderson, Kelley Bullard, M. Steven Oberste, Cara Burns, Jaume Jorba:
PoSE: visualization of patterns of sequence evolution using PAML and MATLAB. 364:1-364:7
Volume 19-S, Number 12, October 2018
- Mehedi Hassan, Aishwarya Alex Namasivayam, Dan F. DeBlasio, Nazeefa Fatima, Benjamin Siranosian, R. Gonzalo Parra, Bart Cuypers, Sayane Shome, Alexander Miguel Monzon, Julien Fumey, Farzana Rahman:
Reflections on a journey: a retrospective of the ISCB Student Council symposium series. 347:1-347:8
Volume 19-S, Number 13, February 2019
- Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng, Tzong-Yi Lee:
Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. 13-25 - Yoshihiro Taguchi:
Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data. 27-42 - Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra, Francesco Pappalardo:
EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation. 43-53 - Hamendra Manhar Reddy, Alok Sharma, Abdollah Dehzangi, Daichi Shigemizu, Abel Avitesh Chandra, Tatsuhiko Tsunoda:
GlyStruct: glycation prediction using structural properties of amino acid residues. 55-64 - Arpah Abu, Chee Guan Ngo, Nur Idayu Adira Abu-Hassan, Siti Adibah Othman:
Automated craniofacial landmarks detection on 3D image using geometry characteristics information. 65-80 - Wajdi Dhifli, Júlia Puig, Aurélien Dispot, Mohamed Elati:
Latent network-based representations for large-scale gene expression data analysis. 81-90 - Yi Zheng, Hui Peng, Shameek Ghosh, Chaowang Lan, Jinyan Li:
Inverse similarity and reliable negative samples for drug side-effect prediction. 91-104 - Piyush Agrawal, Harinder Singh, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore, Gajendra P. S. Raghava:
Benchmarking of different molecular docking methods for protein-peptide docking. 105-124 - Rama Kaalia, Jagath C. Rajapakse:
Functional homogeneity and specificity of topological modules in human proteome. 125-138 - Nurul Aqilah Mohd Nor, Nur Aishah Taib, Marniza Saad, Hana Salwani Zaini, Zahir Ahmad, Yamin Ahmad, Sarinder Kaur Dhillon:
Development of electronic medical records for clinical and research purposes: the breast cancer module using an implementation framework in a middle income country- Malaysia. 139-154 - Ronesh Sharma, Alok Sharma, Ashwini Patil, Tatsuhiko Tsunoda:
Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions. 155-163 - Christian Simon, Kristian Davidsen, Christina Hansen, Emily Seymour, Mike Bogetofte Barnkob, Lars Rønn Olsen:
BioReader: a text mining tool for performing classification of biomedical literature. 165-170 - Shuhaila Mat-Sharani, Mohd Firdaus Raih:
Computational discovery and annotation of conserved small open reading frames in fungal genomes. 171-185 - Ari Hardianto, Varun Khanna, Fei Liu, Shoba Ranganathan:
Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. 187-197 - Deepak R. Bharti, Anmol Hemrom, Andrew M. Lynn:
GCAC: galaxy workflow system for predictive model building for virtual screening. 199-206 - Sapna M. Borah, Anupam Nath Jha:
Identification and analysis of structurally critical fragments in HopS2. 207-218 - Manisha Pritam, Garima Singh, Suchit Swaroop, Akhilesh Kumar Singh, Satarudra Prakash Singh:
Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum. 219-230 - Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik, Krishnananda Chattopadhyay:
Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis. 231-242 - Duleepa Jayasundara, Damayanthi Herath, Damith A. Senanayake, Isaam Saeed, Cheng-Yu Yang, Yuan Sun, Bill C. Chang, Sen-Lin Tang, Saman K. Halgamuge:
ENVirT: inference of ecological characteristics of viruses from metagenomic data. 377:1-377:12