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BMC Bioinformatics, Volume 15 - Supplements
Volume 15, Number S-1, January 2014
- Paolo Romano
, Frédérique Lisacek, Marco Masseroli:
NETTAB 2012 on "Integrated Bio-Search". S1 - Marco Masseroli, Barend Mons
, Erik Bongcam-Rudloff, Stefano Ceri, Alexander E. Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
:
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. S2 - Marco Masseroli, Matteo Picozzi, Giorgio Ghisalberti, Stefano Ceri:
Explorative search of distributed bio-data to answer complex biomedical questions. S3 - Gianvito Pio
, Donato Malerba
, Domenica D'Elia
, Michelangelo Ceci
:
Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach. S4 - Víctor Martínez, Carlos Cano, Armando Blanco:
ProphNet: A generic prioritization method through propagation of information. S5 - Paolo Cremaschi
, Sergio Rovida, Lucia Sacchi
, Antonella Lisa
, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti
, Silvia Bione
, Gianni Sacchi:
CorrelaGenes: a new tool for the interpretation of the human transcriptome. S6 - Francesca Finotello
, Enrico Lavezzo
, Luca Bianco
, Luisa Barzon
, Paolo Mazzon, Paolo Fontana, Stefano Toppo
, Barbara Di Camillo:
Reducing bias in RNA sequencing data: a novel approach to compute counts. S7 - Luca Zammataro
, Rita DeMolfetta, Gabriele Bucci
, Arnaud Céol
, Heiko Müller
:
AnnotateGenomicRegions: a web application. S8 - Matthew P. Campbell
, René Ranzinger, Thomas Lütteke
, Julien Mariethoz
, Catherine A. Hayes
, Jingyu Zhang, Yukie Akune, Kiyoko F. Aoki-Kinoshita
, David Damerell, Giorgio Carta, William S. York, Stuart M. Haslam, Hisashi Narimatsu
, Pauline M. Rudd, Niclas G. Karlsson
, Nicolle H. Packer
, Frédérique Lisacek:
Toolboxes for a standardised and systematic study of glycans. S9 - Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi
:
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. S10 - Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone
, Philippe Rocca-Serra:
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. S11 - Sarah Cohen Boulakia
, Jiuqiang Chen, Paolo Missier
, Carole A. Goble
, Alan R. Williams, Christine Froidevaux:
Distilling structure in Taverna scientific workflows: a refactoring approach. S12 - Piergiorgio Palla, Gianfranco Frau, Laura Vargiu, Patricia Rodriguez-Tomé:
QTREDS: a Ruby on Rails-based platform for omics laboratories. S13 - Federica Viti
, Silvia Scaglione
, Alessandro Orro, Luciano Milanesi
:
Guidelines for managing data and processes in bone and cartilage tissue engineering. S14 - Emilie Pasche
, Julien Gobeill
, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis
, Patrick Ruch
:
Development and tuning of an original search engine for patent libraries in medicinal chemistry. S15
Volume 15, Number S-2, January 2014
- Daniel Asarnow, Rahul Singh:
Automatic classification of protein structures using low-dimensional structure space mappings. S1 - Pablo A. Jaskowiak
, Ricardo J. G. B. Campello
, Ivan G. Costa
:
On the selection of appropriate distances for gene expression data clustering. S2 - Bin Liu, Jinghao Xu, Quan Zou
, Ruifeng Xu, Xiaolong Wang, Qingcai Chen:
Using distances between Top-n-gram and residue pairs for protein remote homology detection. S3 - Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng, Jagath C. Rajapakse
:
Extracting rate changes in transcriptional regulation from MEDLINE abstracts. S4 - Jiajie Peng
, Yadong Wang, Jin Chen:
Towards integrative gene functional similarity measurement. S5 - Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
:
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. S6 - Dipan Lal Shaw, A. S. M. Shohidull Islam, M. Sohel Rahman
, Masud Hasan:
Protein folding in HP model on hexagonal lattices with diagonals. S7 - Qingyao Wu, Yunming Ye, Michael K. Ng, Shen-Shyang Ho
, Ruichao Shi:
Collective prediction of protein functions from protein-protein interaction networks. S9 - Denan Zhang, Guohua Wang, Yadong Wang:
Transcriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data. S10
Volume 15, Number S-3, February 2014
- Tomás Di Domenico
, Cynthia Prudence, Esmeralda Vicedo, Emre Guney
, Anupama Jigisha, Avinash Kumar Shanmugam:
Highlights from the ISCB Student Council Symposium 2013. A1 - Han Lie:
Towards breaking the curse of dimensionality in computational methods for the conformational analysis of molecules. A2 - Achchuthan Shanmugasundram, Faviel F. Gonzalez-Galarza, Jonathan M. Wastling, Olga Vasieva, Andrew R. Jones:
An integrated approach to understand apicomplexan metabolism from their genomes. A3 - Séverine Affeldt
, Param Priya Singh, Giulia Malaguti, Hervé Isambert:
On the expansion of "dangerous" gene families in vertebrates. A4 - Aya Narunsky
, Nir Ben-Tal
:
ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure. A5 - Nathan Medina-Rodríguez, Ángelo Santana
, Ana M. Wägner, José M. Quinteiro
:
alleHap: an efficient algorithm to reconstruct zero-recombinant haplotypes from parent-offspring pedigrees. A6 - Vipin T. Sreedharan, Sebastian J. Schultheiß
, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
:
Oqtans: a multifunctional workbench for RNA-seq data analysis. A7 - Maribel Hernandez-Rosales, Nicolas Wieseke, Marc Hellmuth
, Peter F. Stadler
:
Simulation of gene family histories. A8 - Nadezda Kryuchkova, Marc Robinson-Rechavi
:
Determinants of protein evolutionary rates in light of ENCODE functional genomics. A9
Volume 15, Number S-4, March 2014
- Anne S. De Groot, Phoebe De Groot, Yongqun He:
ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. I1 - Lu He, Anne S. De Groot
, Andres H. Gutiérrez
, William D. Martin, Lenny Moise
, Chris Bailey-Kellogg:
Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. S1 - Rebecca Racz
, Xinna Li, Mukti Patel, Zuoshuang Xiang, Yongqun He
:
DNAVaxDB: the first web-based DNA vaccine database and its data analysis. S2 - Peng Fu, Linlin Yang, Yi Sun, Li Ye, Zhiwei Cao, Kailin Tang
:
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. S3
Volume 15, Number S-5, May 2014
- Safwat Abdel-Azeim
, Edrisse Chermak, Anna Vangone
, Romina Oliva
, Luigi Cavallo
:
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. S1 - Gianni D'Angelo, Salvatore Rampone
:
Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications. S2 - Paolo G. V. Martini
, Gabriele Sales
, Enrica Calura
, Stefano Cagnin
, Monica Chiogna, Chiara Romualdi
:
timeClip: pathway analysis for time course data without replicates. S3 - Davide Cangelosi
, Marco Muselli, Stefano Parodi
, Fabiola Blengio, Pamela Becherini, Rogier Versteeg
, Massimo Conte
, Luigi Varesio:
Use of Attribute Driven Incremental Discretization and Logic Learning Machine to build a prognostic classifier for neuroblastoma patients. S4
Volume 15, Number S-6, May 2014
- Andreas Holzinger
, Matthias Dehmer, Igor Jurisica:
Knowledge Discovery and interactive Data Mining in Bioinformatics - State-of-the-Art, future challenges and research directions. I1 - Jun Sun, Vasile Palade, Yujie Cai, Wei Fang, Xiaojun Wu:
Biochemical systems identification by a random drift particle swarm optimization approach. S1 - Christopher C. Mayer, Martin Bachler
, Matthias Hörtenhuber
, Christof Stocker, Andreas Holzinger
, Siegfried Wassertheurer:
Selection of entropy-measure parameters for knowledge discovery in heart rate variability data. S2 - Rachel D. Melamed
, Hossein Khiabanian
, Raul Rabadan
:
Data-driven discovery of seasonally linked diseases from an Electronic Health Records system. S3 - Marc Streit
, Samuel Gratzl, Michael Gillhofer, Andreas Mayr, Andreas Mitterecker, Sepp Hochreiter
:
Furby: fuzzy force-directed bicluster visualization. S4 - Heimo Müller
, Robert Reihs, Kurt Zatloukal, Andreas Holzinger
:
Analysis of biomedical data with multilevel glyphs. S5 - Frank Emmert-Streib
, Ricardo de Matos Simoes
, Galina V. Glazko, Simon S. McDade
, Benjamin Haibe-Kains
, Andreas Holzinger
, Matthias Dehmer, Frederick Campbell
:
Functional and genetic analysis of the colon cancer network. S6 - Pinar Yildirim, Ljiljana Majnaric
, Ilyas Ozgur Ekmekci, Andreas Holzinger
:
Knowledge discovery of drug data on the example of adverse reaction prediction. S7
Volume 15, Number S-7, May 2014
- Nathan L. Clement, Lee Parnell Thompson, Daniel P. Miranker:
ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries. S1 - Cristian Coarfa, Christina Pichot, Andrew R. Jackson, Arpit Tandon, Viren Amin, Sriram Raghuraman, Sameer Paithankar, Adrian V. Lee, Sean E. McGuire, Aleksandar Milosavljevic:
Analysis of interactions between the epigenome and structural mutability of the genome using Genboree workbench tools. S2 - M. Stanley Fujimoto, Paul M. Bodily, Nozomu Okuda, Mark J. Clement, Quinn Snell:
Effects of error-correction of heterozygous next-generation sequencing data. S3 - Wenlong Xu, F. Anthony San Lucas, Zixing Wang, Yin Liu:
Identifying microRNA targets in different gene regions. S4 - Jung Hun Oh
, Joseph O. Deasy
:
Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm. S5 - Perry G. Ridge, Taylor J. Maxwell, Spencer J. Foutz, Matthew H. Bailey
, Christopher D. Corcoran, JoAnn T. Tschanz, Maria C. Norton, Ronald G. Munger, Elizabeth O'Brien, Richard A. Kerber, Richard M. Cawthon, John S. K. Kauwe:
Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging. S6 - Ahmadreza Ghaffarizadeh, Nicholas S. Flann, Gregory J. Podgorski:
Multistable switches and their role in cellular differentiation networks. S7 - Aaron R. Sharp, Perry G. Ridge, Matthew H. Bailey
, Kevin L. Boehme, Maria C. Norton, JoAnn T. Tschanz, Ronald G. Munger, Christopher D. Corcoran, John S. K. Kauwe:
Population substructure in Cache County, Utah: the Cache County study. S8 - Robert Smith, Andrew D. Mathis, Dan Ventura, John T. Prince:
Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. S9 - Swarup Roy, Dhruba K. Bhattacharyya
, Jugal K. Kalita:
Reconstruction of gene co-expression network from microarray data using local expression patterns. S10 - Jingran Wen, Daniel R. Scoles, Julio C. Facelli
:
Structure prediction of polyglutamine disease proteins: comparison of methods. S11 - Mark T. W. Ebbert, Mark E. Wadsworth, Kevin L. Boehme, Kaitlyn L. Hoyt, Aaron R. Sharp, Brendan D. O'Fallon, John S. K. Kauwe, Perry G. Ridge:
Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. S12 - Abhishek Majumdar, Stephen D. Scott
, Jitender S. Deogun, Steven Harris:
Yeast pheromone pathway modeling using Petri nets. S13
Volume 15, Number S-8, July 2014
- Junjie Li, Sanjay Ranka
, Sartaj Sahni:
Multicore and GPU algorithms for Nussinov RNA folding. S1 - Rittika Shamsuddin
, Milka Doktorova, Sheila Jaswal, Audrey Lee-St. John, Kathryn McMenimen:
Computational prediction of hinge axes in proteins. S2 - Ashraf Yaseen, Yaohang Li:
Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features. S3 - Kevin Molloy, M. Jennifer Van, Daniel Barbará, Amarda Shehu
:
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. S4 - James Lara, F. Xavier López-Labrador
, Fernando González-Candelas
, Marina Berenguer
, Yuri Khudyakov:
Computational models of liver fibrosis progression for hepatitis C virus chronic infection. S5
Volume 15, Number S-9, September 2014
- Matteo Comin
, Michele Schimd
:
Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns. S1 - Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng, Pavan Balaji:
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores. S2 - Yan Huang, Yin Hu, Jinze Liu:
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. S3 - Ka-Kit Lam, Asif Khalak, David Tse:
Near-optimal assembly for shotgun sequencing with noisy reads. S4 - Romeo Rizzi, Alexandru I. Tomescu
, Veli Mäkinen
:
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. S5 - Jinghua Gu, Xiao Wang, Leena Hilakivi-Clarke, Robert Clarke
, Jianhua Xuan:
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data. S6 - Roye Rozov, Ron Shamir
, Eran Halperin:
Fast lossless compression via cascading Bloom filters. S7 - Wazim Ismail, Yuzhen Ye, Haixu Tang:
Gene finding in metatranscriptomic sequences. S8 - James Lindsay, Hamed Salooti, Ion I. Mandoiu
, Alexander Zelikovsky
:
ILP-based maximum likelihood genome scaffolding. S9 - Sunyoung Kwon
, Byunghan Lee, Sungroh Yoon:
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing. S10 - Anton Polishko, Evelien M. Bunnik
, Karine G. Le Roch, Stefano Lonardi
:
PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. S11 - Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi
, Hamidreza Chitsaz, Mehdi Sadeghi:
ARYANA: Aligning Reads by Yet Another Approach. S12 - Zeinab Taghavi:
Ensemble analysis of adaptive compressed genome sequencing strategies. S13 - Stephen Johnson, Brett Trost
, Jeffrey R. Long, Vanessa Pittet, Anthony J. Kusalik:
A better sequence-read simulator program for metagenomics. S14 - Ping Ge, Cuncong Zhong, Shaojie Zhang
:
ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search. S15 - Noam D. Beckmann, Sashank Karri, Gang Fang, Ali Bashir:
Detecting epigenetic motifs in low coverage and metagenomics settings. S16
Volume 15, Number S-10, September 2014
- Eric C. Rouchka, Julia H. Chariker
:
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. I1 - Xue Zhong, Qi Liu, Yu Shyr
:
CLIP-EZ: a computational tool for HITS-CLIP data analysis. P1 - Neil Moore, Jerzy W. Jaromczyk, Christopher L. Schardl
, Joedocei Hill, Devin Wright:
Automating deployment of several GBrowse instances. P2 - Yue Huang, Xiaodong Zhu, Lishi Wang, Xiaoyun Liu, Robert W. Williams
, Lu Lu, Yan Jiao, Weikuan Gu:
Genome wide analysis of sex difference in gene expression profiles of bone formations. P3 - Meredith Ray, Xin Tong
, Hongmei Zhang, Wilfried Karmaus:
Screening genome-wide DNA methylation CpG sites via training and testing data utilizing surrogate variables. P4 - Yan Zhang, Michelle Barati, Ignacio Munoz, Ming Li, Danny Wilkey, Eric C. Rouchka, Michael Merchant:
Transcriptomic characterization of short duration endoplasmic reticulum stress on cultured human proximal tubule cells. P5 - Hossein Taghizad, Mohammed Yeasin, Tara Cherry, Vida Abedi
:
Obnet: Network of semantic associations for obesity. P6 - Xing Li, Almudena Martinez-Fernandez, Jeanne Theis, Jean-Pierre A. Kocher, Andre Terzic, Timothy Olson
, Timothy J. Nelson:
Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome. P7 - Vida Abedi
, Mohammed Yeasin, Ramin Zand
:
Context-sensitive use of bioinformatics tools with complementary functionalities for generation of relevant hypothesis. P8 - Shuqiu Sun, Yan Jiao, Wei Wei, Arnold E. Postlethwaite, Weikuan Gu, Dianjun Sun:
Comparing genetic pathways variation of immunoinhibitory receptor LAIR-1 in murine vs human internal organs. P9 - Yan Jiao, Xiaoyun Liu, Yanhong Cao, Nan Deng, Yonghui Ma, Karen A. Hasty, John M. Stuart, Weikuan Gu:
Analysis of effect of congenic mice on the gene expression under genomic background of BALB/c mice. P10 - Benjamin J. Harrison
, Robert M. Flight, Abdallah M. Eteleeb, Eric C. Rouchka, Jeffrey C. Petruska:
UTR extension and alternate polyadenylation in neuroplasticity: an emerging paradigm? P11 - Lishi Wang, Yan Jiao, Yue Huang, Beth Bennett, Robert W. Williams
, Dawei Li, Hongyu Zhao, Joel Gelernter
, Henry R. Kranzler, Lindsay A. Farrer, Weikuan Gu:
Ttn as a likely causal gene for QTL of alcohol preference on mouse chromosome 2. P12 - Shreyas Joshi, Bruce F. O'Hara:
Identifying candidate genes for variation in sleep-related quantitative traits. P13 - Behrouz Madahian, Lih-Yuan Deng, Ramin Homayouni:
Development of sparse Bayesian multinomial generalized linear model for multi-class prediction. P14 - Ferhan M. Atici, Mustafa Atici, Ngoc Nguyen:
Parameter estimations of sigmoidal models of cancer. P15 - Shilin Zhao, Yan Guo, Quanhu Sheng
, Yu Shyr
:
Heatmap3: an improved heatmap package with more powerful and convenient features. P16 - Naga Nagisetty, Eunice Y. Huang
, Grady Wade, Teeradache Viangteeravat:
Building a knowledge base to assist clinical decision-making using the Pediatric Research Database (PRD) and machine learning: a case study on pediatric asthma patients. P17 - Nataliya I. Lenchik, Hao Chen, Dorothy N. Kakoola, Ivan Gerling:
Differences in gene expression profiles between individual islets from case #6213. P18 - Nam S. Vo
, Vinhthuy Phan:
Exploiting the bootstrap method to analyze patterns of gene expression. P19 - Vinay Raj, Susan Kadlubar:
Identification of gene expression profiles associated with prognostic groups of patients with Merkel cell carcinoma. P20 - Shruti S. Sakhare, Gautam G. Rao, Sammed N. Mandape
, Siddharth Pratap
:
Transcriptome profile of OVCAR3 cisplatin-resistant ovarian cancer cell line. P21 - Shanshan Guo, Vinthuy Phan:
A distributed framework for aligning short reads to genomes. P22 - Quang Tran, Vinhthuy Phan:
Alignment of short reads to multiple genomes using hashing. P23 - Kevin L. O'kello, Vinhthuy Phan:
Determining gene response patterns of time series gene expression data using R. P24 - Mark L. Farman, Patrick Calie, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Daniel R. Harris
, Christopher L. Schardl
:
An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis. P25 - Hao Chen:
Evaluating statistical learning methods for cell type classification and feature selection using RNA-seq data. P26 - Hao Chen, Burt M. Sharp:
Establishing a protocol for single cell transcriptome sequencing of the rat brain. P27 - Irit Hochberg, Quynh T. Tran, Ariel R. Barkan, Alan R. Saltiel, William F. Chandler, Dave Bridges:
Gene expression signature in adipose tissue of acromegaly patients. P28 - Wenjian Bi, Guolian Kang, Yuehua Cui, Yun Li, Christine Hartford, Wing Leung, Ji-Feng Zhang:
A new set-valued system identification approach to identifying rare genetic variants for ordered categorical phenotype. P29 - Nam S. Vo
, Quang Tran, Vinhthuy Phan:
An integrated approach for SNP calling based on population of genomes. P30 - Sen Yao, Robert M. Flight, Hunter N. B. Moseley
:
Coordination characterization of zinc metalloproteins. P31 - Charles A. Phillips, Erich J. Baker, Elissa J. Chesler, Michael A. Langston:
Algorithmic tools for tripartite data analysis. P32 - Hui Yu, Zhongming Zhao:
Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses. P33 - Guolian Kang, Wei Liu, Cheng Cheng, Carmen L. Wilson, Geoffrey Neale, Jun J. Yang, Kirsten K. Ness, Leslie L. Robison, Melissa M. Hudson, Kumar Srivastava:
Evaluation of two-step iterative resampling procedure for internal validation of genome-wide association studies. P34 - Georgina Iyamu, Pamela D. Thompson, Victor Paramov, Siddharth Pratap
, Amos Sakwe
, Josiah Ochieng, Dana Marshall:
Shotgun proteomic analysis of human head and neck squamous cell carcinoma cell line SQ20B with diminished AHSG expression. P35 - Joshua M. Mitchell, Teresa W.-M. Fan, Andrew N. Lane, Hunter N. B. Moseley
:
Development of large-scale metabolite identification methods for metabolomics. P36
Volume 15, Number S-11, October 2014
- Jonathan D. Wren
, Mikhail G. Dozmorov
, Dennis Burian, Andy D. Perkins, Chaoyang Zhang, Peter Hoyt
, Rakesh Kaundal:
Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. I1 - Zongliang Yue
, Ping Wan, Hui Huang, Zhan Xie, Jake Yue Chen
:
SLDR: a computational technique to identify novel genetic regulatory relationships. S1 - Nam S. Vo
, Vinhthuy Phan:
Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response. S2 - Michael A. Bauer
, Shweta S. Chavan, Erich A. Peterson, Christoph J. Heuck, Donald J. Johann:
Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing. S3 - Hui Wen Ng, Wenqian Zhang, Mao Shu, Heng Luo
, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong
:
Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. S4 - Wenchao Zhang
, Patrick Xuechun Zhao:
Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data. S5 - Wenqian Zhang, Joe Meehan
, Zhenqiang Su, Hui Wen Ng, Mao Shu, Heng Luo
, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong
:
Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. S6 - Jason Hennessey, Constantin Georgescu, Jonathan D. Wren
:
Trends in the production of scientific data analysis resources. S7 - Inimary T. Toby, Jonah Widmer, David W. Dyer:
Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group. S8 - Erich A. Peterson, Shweta S. Chavan, Michael A. Bauer
, Christoph J. Heuck, Donald J. Johann:
Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis. S9 - Yan Peng, Andrew S. Maxwell, Natalie D. Barker, Jennifer G. Laird, Alan J. Kennedy, Nan Wang, Chaoyang Zhang, Ping Gong:
SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data. S10 - Weizhong Zhao, Wen Zou
, James J. Chen:
Topic modeling for cluster analysis of large biological and medical datasets. S11 - Stephen C. Grace, Stephen Embry, Heng Luo
:
Haystack, a web-based tool for metabolomics research. S12 - Sitanshu S. Sahu
, Tyler Weirick
, Rakesh Kaundal:
Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. S13 - Taeho Jo
, Jianlin Cheng
:
Improving protein fold recognition by random forest. S14 - Tyler Weirick
, Sitanshu S. Sahu
, Ramamurthy Mahalingam, Rakesh Kaundal:
LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches. S15 - Mihir Jaiswal, Nathaniel Crabtree, Michael A. Bauer
, Roger A. Hall, Kevin D. Raney, Boris L. Zybailov
:
XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry. S16
Volume 15, Number S-12, November 2014
- James Zijun Wang, Yuanyuan Zhang, Liang Dong, Lin Li, Pradip K. Srimani, Philip S. Yu:
G-Bean: an ontology-graph based web tool for biomedical literature retrieval. S1 - En-Shiun Annie Lee, Sanderz Fung, Ho-Yin Sze-To, Andrew K. C. Wong:
Discovering co-occurring patterns and their biological significance in protein families. S2 - Qianqian Wu, Kate Smith-Miles
, Tianhai Tian
:
Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. S3 - Wei Wang, Juan Liu, Xionghui Zhou:
Identification of single-stranded and double-stranded dna binding proteins based on protein structure. S4 - Lijun Quan, Qiang Lü, Haiou Li, Xiaoyan Xia, Hongjie Wu:
Improved packing of protein side chains with parallel ant colonies. S5 - Zijing Mao, Chifeng Ma, Tim Hui-Ming Huang, Yidong Chen, Yufei Huang:
BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data. S6 - Xianjun Shen, Yanli Zhao, Yanan Li, Tingting He, Jincai Yang, Xiaohua Hu:
An efficient protein complex mining algorithm based on Multistage Kernel Extension. S7 - Lizhi Cui, Josiah Poon, Simon K. Poon, Hao Chen, Junbin Gao
, Paul Wing Hing Kwan
, Kei Fan, Zhihao Ling:
An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm. S8 - Liangxi Cheng, Hongfei Lin, Feng Zhou, Zhihao Yang, Jian Wang:
Enhancing the accuracy of knowledge discovery: a supervised learning method. S9 - Yue Shang, Huihui Hao, Jiajin Wu, Hongfei Lin:
Learning to rank-based gene summary extraction. S10
Volume 15, Number S-13, November 2014
- Cynthia Gibas
, Zhipeng Cai
, Oliver Eulenstein:
Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications. S1 - Alex R. Gawronski, Marcel Turcotte
:
RiboFSM: Frequent subgraph mining for the discovery of RNA structures and interactions. S2 - Pawel Górecki
, Oliver Eulenstein:
Refining discordant gene trees. S3 - Edward Hemphill, James Lindsay, Chih Lee, Ion I. Mandoiu
, Craig E. Nelson:
Feature selection and classifier performance on diverse bio- logical datasets. S4 - Ke Liu, Xiangmiao Zeng, Lei Qiao, Xisheng Li, Yubo Yang, Cuihong Dai, Aiju Hou, Dechang Xu
:
The sensitivity and significance analysis of parameters in the model of pH regulation on lactic acid production by Lactobacillus bulgaricus. S5 - Tianwei Yu
, Yun Bai:
Network-based modular latent structure analysis. S6
Volume 15, Number S-14, November 2014
- Paolo Romano
, Nicola Cannata:
NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories. S1 - Maciej Rybinski
, José Francisco Aldana Montes:
Calculating semantic relatedness for biomedical use in a knowledge-poor environment. S2 - Francesco Venco, Yuriy Vaskin, Arnaud Céol
, Heiko Müller
:
SMITH: a LIMS for handling next-generation sequencing workflows. S3 - Alejandra N. González-Beltrán
, Eamonn Maguire, Susanna-Assunta Sansone
, Philippe Rocca-Serra:
linkedISA: semantic representation of ISA-Tab experimental metadata. S4 - Larisa N. Soldatova
, Daniel Nadis, Ross D. King, Piyali S. Basu, Emma Haddi, Véronique Baumlé, Nigel J. Saunders
, Wolfgang Marwan, Brian B. Rudkin
:
EXACT2: the semantics of biomedical protocols. S5 - Fabio Rinaldi
, Simon Clematide
, Hernani Marques, Tilia Ellendorff, Martin Romacker, Raul Rodriguez-Esteban
:
OntoGene web services for biomedical text mining. S6 - Steffen Möller
, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal
, Timothy Booth, John Chilton
, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland
, Matús Kalas
, László Kaján, Eri Kibukawa, David R. Powell
, Pjotr Prins
, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi
, Torsten Seemann
, Clare Sloggett
, Stian Soiland-Reyes
, William Spooner, Sascha Steinbiss
, Andreas Tille, Anthony J. Travis
, Roman Guimera, Toshiaki Katayama, Brad A. Chapman:
Community-driven development for computational biology at Sprints, Hackathons and Codefests. S7
Volume 15, Number S-15, December 2014
- Xiaoli Lin, Xiaolong Zhang, Fengli Zhou:
Protein structure prediction with local adjust tabu search algorithm. S1 - Shu-Lin Wang, Liuchao Sun, Jianwen Fang:
Molecular cancer classification using a meta-sample-based regularized robust coding method. S2 - Chun-Hou Zheng, Lin Yuan
, Wen Sha, Zhan-Li Sun:
Gene differential coexpression analysis based on biweight correlation and maximum clique. S3 - Peng Chen
, Jianhua Z. Huang, Xin Gao
:
LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone. S4 - Byungkyu Brian Park, Hyungchan Kim, Kyungsook Han:
DBBP: database of binding pairs in protein-nucleic acid interactions. S5 - Sheng-Lung Peng, Yu-Wei Tsay:
Adjusting protein graphs based on graph entropy. S6 - Vitoantonio Bevilacqua
, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa
, Domenico Simone
, Graziano Pesole, Ernesto Picardi
:
EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. S7 - Yu-Ting Hsiao, Wei-Po Lee:
Reverse engineering gene regulatory networks: Coupling an optimization algorithm with a parameter identification technique. S8 - Zhu-Hong You
, Lin Zhu, Chun-Hou Zheng, Hongjie Yu, Suping Deng, Zhen Ji:
Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set. S9 - Jiarui Zhou, Zhen Ji, Zexuan Zhu, Shan He:
Compression of next-generation sequencing quality scores using memetic algorithm. S10
Volume 15, Number S-16, December 2014
- Shoba Ranganathan
, Tin Wee Tan, Christian Schönbach
:
InCoB2014: bioinformatics to tackle the data to knowledge challenge. I1 - Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen, Tzong-Yi Lee:
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. S1 - Jinwoo Kim, Miyoung Shin:
An integrative model of multi-organ drug-induced toxicity prediction using gene-expression data. S2 - Qian Liu, Zhenhua Li
, Jinyan Li:
Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts. S3 - Yi-Fan Liou, Phasit Charoenkwan, Yerukala Sathipati Srinivasulu
, Tamara Vasylenko, Shih-Chung Lai, Hua-Chin Lee, Yi-Hsiung Chen, Hui-Ling Huang, Shinn-Ying Ho
:
SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides. S4 - Lingxiao Zhou
, Renate Griffith, Bruno Gaëta
:
Combining spatial and chemical information for clustering pharmacophores. S5 - Yadav Kuleesha, Wee Choo Puah, Feng Lin, Martin Wasser
:
FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis. S6 - Bhyravabhotla Jayaram
, Priyanka Dhingra, Avinash Mishra
, Rahul Kaushik
, Goutam Mukherjee
, Ankita Singh, Shashank Shekhar:
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. S7 - Maad Shatnawi
, Nazar Zaki, Paul D. Yoo
:
Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties. S8 - Chinh Tran To Su
, Thuy-Diem Nguyen, Jie Zheng, Chee Keong Kwoh:
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking. S9 - Tzu-Hsien Yang
, Hong-Tsun Chang, Eric S. L. Hsiao, Juo-Ling Sun, Chung-Ching Wang, Hsin-Yi Wu, Pao-Chi Liao, Wei-Sheng Wu:
iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. S10 - Piers Johnson, Luke Vandewater, William J. Wilson
, Paul Maruff
, Greg Savage
, Petra Graham
, Lance S. Macaulay, Kathryn A. Ellis
, Cassandra Szoeke
, Ralph N. Martins
, Christopher Rowe, Colin L. Masters, David Ames, Ping Zhang
:
Genetic algorithm with logistic regression for prediction of progression to Alzheimer's disease. S11 - Kuldip K. Paliwal, Alok Sharma
, James G. Lyons, Abdollah Dehzangi:
Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information. S12 - Sonam Grover, Jaspreet Kaur Dhanjal, Sukriti Goyal, Abhinav Grover, Durai Sundar
:
Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus. S13 - Benjamin Drinkwater, Michael A. Charleston
:
Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem. S14 - Eleni Giannoulatou
, Shin-Ho Park
, David T. Humphreys, Joshua Wing Kei Ho
:
Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. S15 - Ran Su, Yao Li, Daniele Zink, Lit-Hsin Loo
:
Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels. S16
Volume 15, Number S-17, December 2014
- Jack Y. Yang, A. Keith Dunker, Jun S. Liu
, Xiang Qin, Hamid R. Arabnia
, William Yang, Andrzej Niemierko, Zhongxue Chen
, Zuojie Luo, Liangjiang Wang, Yunlong Liu, Dong Xu, Youping Deng, Weida Tong, Mary Qu Yang:
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. I1 - Mary Qu Yang, Laura Elnitski
:
Orthology-driven mapping of bidirectional promoters in human and mouse genomes. S1 - William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu
, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen
, Liangjiang Wang, Dong Xu, Hamid R. Arabnia
, Weida Tong, Mary Qu Yang:
Identification of genes and pathways involved in kidney renal clear cell carcinoma. S2 - Zhongxue Chen
, William Yang, Qingzhong Liu
, Jack Y. Yang, Jing Li, Mary Yang:
A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study. S3 - Fei Huang, Christopher J. Oldfield, Bin Xue, Wei-Lun Hsu, Jingwei Meng, Xiaowen Liu
, Li Shen
, Pedro Romero, Vladimir N. Uversky, A. Keith Dunker:
Improving protein order-disorder classification using charge-hydropathy plots. S4 - Chang Liu, Lili Lu, Quan Kong, Yan Li, Haihua Wu, William Yang, Shandan Xu, Xinyu Yang, Xiaolei Song, Jack Y. Yang, Mary Qu Yang, Youping Deng:
Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. S5 - Ke Yu, Jie Zhang, Minjun Chen, Xiaowei Xu, Ayako Suzuki
, Katarina Ilic, Weida Tong:
Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study. S6
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