Journal: Bioinformatics

Volume 27, Issue 8

1045 -- 1051Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. ::::eCEO::::: an efficient Cloud Epistasis cOmputing model in genome-wide association study
1052 -- 1060Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert B. Scharpf, Chunfa Jie, Benilton Carvalho, Haiping Hao, Kurt N. Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, Rafael A. Irizarry. Performance assessment of copy number microarray platforms using a spike-in experiment
1061 -- 1067David Koslicki. Topological entropy of DNA sequences
1068 -- 1075Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
1076 -- 1085Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel. Topology and prediction of RNA pseudoknots
1086 -- 1093Emidio Capriotti, Tomás Norambuena, Marc A. Martí-Renom, Francisco Melo. All-atom knowledge-based potential for RNA structure prediction and assessment
1094 -- 1100Jessica C. Mar, Christine A. Wells, John Quackenbush. Defining an informativeness metric for clustering gene expression data
1101 -- 1107Liangxiu Han, Jano I. van Hemert, Richard A. Baldock. Automatically identifying and annotating mouse embryo gene expression patterns
1108 -- 1112Marie Brown, David C. Wedge, Royston Goodacre, Douglas B. Kell, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas, Ludwig Neyses, Warwick B. Dunn. Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets
1113 -- 1120Duc-Hau Le, Yung-Keun Kwon. The effects of feedback loops on disease comorbidity in human signaling networks
1121 -- 1127Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki. Interactive, multiscale navigation of large and complicated biological networks
1128 -- 1134Victor Spirin, Alexander Shpunt, Jan Seebacher, Marc Gentzel, Andrej Shevchenko, Steven Gygi, Shamil R. Sunyaev. Assigning spectrum-specific ::::P::::-values to protein identifications by mass spectrometry
1135 -- 1142Andrew D. Fox, Benjamin J. Hescott, Anselm Blumer, Donna K. Slonim. Connectedness of PPI network neighborhoods identifies regulatory hub proteins
1143 -- 1149Jung-Hsien Chiang, Heng-Hui Liu, Yi-Ting Huang. Condensing biomedical journal texts through paragraph ranking
1150 -- 1151Marcela Dávila López, Tore Samuelsson. eGOB: eukaryotic Gene Order Browser
1152 -- 1154Justin Jee, Joel S. Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong D. Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein. ACT: aggregation and correlation toolbox for analyses of genome tracks
1155 -- 1156Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones. Human variation database: an open-source database template for genomic discovery
1157 -- 1158Heng Li. Improving SNP discovery by base alignment quality
1159 -- 1161William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight. PrimerProspector: ::::de novo:::: design and taxonomic analysis of barcoded polymerase chain reaction primers
1162 -- 1163Hans-Ulrich Klein, Christoph Bartenhagen, Alexander Kohlmann, Vera Grossmann, Christian Ruckert, Torsten Haferlach, Martin Dugas. R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data
1164 -- 1165Diego Darriba, Guillermo L. Taboada, Ramon Doallo, David Posada. ProtTest 3: fast selection of best-fit models of protein evolution
1166 -- 1167Marc Kirchner, Buote Xu, Hanno Steen, Judith A. J. Steen. libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data
1168 -- 1169Haleh Yasrebi. SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data
1170 -- 1171Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB
1172 -- 1173Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano. SiGN-SSM: open source parallel software for estimating gene networks with state space models
1174 -- 1175George C. Linderman, Vishal N. Patel, Mark R. Chance, Gürkan Bebek. BiC: a web server for calculating bimodality of coexpression between gene and protein networks
1176 -- 1178Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A. Swertz, Heorhiy Byelas, Martijn Dijkstra, Rob W. W. Hooft, Dmitry Katsubo, Bas van Breukelen, Rainer Bischoff 0003, Peter Horvatovich. A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
1179 -- 1180Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
1181 -- 1182Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma ayan. FNV: light-weight flash-based network and pathway viewer
1183 -- 1184Michael Specht, Sebastian Kuhlgert, Christian Fufezan, Michael Hippler. Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
1185 -- 1186Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun-ichi Tsujii. AGRA: analysis of gene ranking algorithms
1187 -- 1189Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, Sarah Cohen Boulakia. Gene List significance at-a-glance with GeneValorization
1190 -- 1191Hongzhan Huang, Peter B. McGarvey, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu. A comprehensive protein-centric ID mapping service for molecular data integration
1192 -- 1193Javed Mohammed Khan, Harish Reddy Cheruku, Joo Chuan Tong, Shoba Ranganathan. MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures
1194 -- 0Meïli C. Baragatti, Denys Pommeret. Comments on 'Bayesian variable selection for disease classification using gene expression data'