Bioinformatics, Volume 27

Volume 27, Number 1, January 2011

Original Papers - Genome Analysis

• 
  Qianchuan He, Dan-Yu Lin:
  A variable selection method for genome-wide association studies. 1-8
• 
  Maria Elena Sana, Maria Iascone, Daniela Marchetti, Jeffrey J. T. Palatini, Marco Galasso, Stefano Volinia:
  GAMES identifies and annotates mutations in next-generation sequencing projects. 9-13
• 
  Dong Seon Kim, Yoonsoo Hahn:
  Identification of human-specific transcript variants induced by DNA insertions in the human genome. 14-21

Sequence Analysis

• 
  Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Nitin Kumar Singh, Sharmila S. Mande:
  SPHINX - an algorithm for taxonomic binning of metagenomic sequences. 22-30
• 
  Yuheng Li, Nicholas Chia, Mario Lauria, Ralf Bundschuh:
  A performance enhanced PSI-BLAST based on hybrid alignment. 31-37

Phylogenetics

• 
  Jaime Huerta-Cepas, Toni Gabaldón:
  Assigning duplication events to relative temporal scales in genome-wide studies. 38-45

Structural Bioinformatics

• 
  R. Dustin Schaeffer, Amanda L. Jonsson, Andrew M. Simms, Valerie Daggett:
  Generation of a consensus protein domain dictionary. 46-54
• 
  Chandrajit L. Bajaj, Rezaul Alam Chowdhury, Muhibur Rasheed:
  A dynamic data structure for flexible molecular maintenance and informatics. 55-62

Gene Expression

• 
  Haimao Zhan, Xin Chen, Shizhong Xu:
  A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes. 63-69
• 
  Johannes M. Freudenberg, Siva Sivaganesan, Mukta Phatak, Kaustubh Shinde, Mario Medvedovic:
  Generalized random set framework for functional enrichment analysis using primary genomics datasets. 70-77
• 
  Sunghee Oh, Dongwan D. Kang, Guy N. Brock, George C. Tseng:
  Biological impact of missing-value imputation on downstream analyses of gene expression profiles. 78-86
• 
  Vanya Van Belle, Kristiaan Pelckmans, Sabine Van Huffel, Johan A. K. Suykens:
  Improved performance on high-dimensional survival data by application of Survival-SVM. 87-94

Genetics and Population Analysis

• 
  Peilin Jia, Siyuan Zheng, Jirong Long, Wei Zheng, Zhongming Zhao:
  dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. 95-102

Systems Biology

• 
  Nidhal Bouaynaya, Roman Shterenberg, Dan Schonfeld:
  Inverse perturbation for optimal intervention in gene regulatory networks. 103-110
• 
  Guy Geva, Roded Sharan:
  Identification of protein complexes from co-immunoprecipitation data. 111-117

Data and Text Mining

• 
  Shi Yu, Xinhai Liu, Léon-Charles Tranchevent, Wolfgang Glänzel, Johan A. K. Suykens, Bart De Moor, Yves Moreau:
  Optimized data fusion for K-means Laplacian clustering. 118-126

Applications Note Genome Analysis

• 
  Gail L. Rosen, Erin R. Reichenberger, Aaron M. Rosenfeld:
  NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads. 127-129

Sequence Analysis

• 
  Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub:
  SAMStat: monitoring biases in next generation sequencing data. 130-131

Structural Bioinformatics

• 
  Jean-Christophe Gelly, Alexandre G. de Brevern:
  Protein Peeling 3D: new tools for analyzing protein structures. 132-133

Genetics and Population Analysis

• 
  Ryan Abo, Stacey Knight, Alun Thomas, Nicola J. Camp:
  Automated construction and testing of multi-locus gene-gene associations. 134-136

Systems Biology

• 
  Fernando García-Alcalde, Federico García-López, Joaquín Dopazo, Ana Conesa:
  Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. 137-139
• 
  Laurin A. J. Mueller, Karl G. Kugler, Andreas Dander, Armin Graber, Matthias Dehmer:
  QuACN: an R package for analyzing complex biological networks quantitatively. 140-141
• 
  Ronan M. T. Fleming, Ines Thiele:
  von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. 142-143

Data and Text Mining

• 
  Paul Martin, Anne Barton, Stephen Eyre:
  ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies. 144-146

Volume 27, Number 2, January 2011

Original Papers - Genome Analysis

• 
  Dong Dong, Xiaojian Shao, Zhaolei Zhang:
  Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective. 147-152
• 
  Giuseppe Narzisi, Bud Mishra:
  Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons. 153-160
• 
  Vito M. R. Muggeo, Giada Adelfio:
  Efficient change point detection for genomic sequences of continuous measurements. 161-166

Sequence Analysis

• 
  Pramila Nuwantha Ariyaratne, Wing-Kin Sung:
  PE-Assembler: de novo assembler using short paired-end reads. 167-174
• 
  Ahrim Youn, Richard Simon:
  Identifying cancer driver genes in tumor genome sequencing studies. 175-181
• 
  Panagiotis D. Vouzis, Nikolaos V. Sahinidis:
  GPU-BLAST: using graphics processors to accelerate protein sequence alignment. 182-188
• 
  Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok N. Choudhary:
  Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing. 189-195
• 
  Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, Elena Marchiori:
  MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. 196-203

Structural Bioinformatics

• 
  Tobias Hamp, Fabian Birzele, Fabian Buchwald, Stefan Kramer:
  Improving structure alignment-based prediction of SCOP families using Vorolign Kernels. 204-210
• 
  Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin:
  PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. 211-219

Gene Expression

• 
  Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, Howard A. Fine:
  Predicting in vitro drug sensitivity using Random Forests. 220-224
• 
  Hong-Qiang Wang, Lindsey K. Tuominen, Chung-Jui Tsai:
  SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures. 225-231

Systems Biology

• 
  Darong Lai, Xinyi Yang, Gang Wu, Yuanhua Liu, Christine Nardini:
  Inference of gene networks - application to Bifidobacterium. 232-237
• 
  Holger Fröhlich, Paurush Praveen, Achim Tresch:
  Fast and efficient dynamic nested effects models. 238-244
• 
  Tae-Hwan Kim, Junil Kim, Pat Heslop-Harrison, Kwang-Hyun Cho:
  Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. 245-251
• 
  Isabel A. Nepomuceno-Chamorro, Francisco Azuaje, Yvan Devaux, Petr V. Nazarov, Arnaud Muller, Jesús S. Aguilar-Ruiz, Daniel R. Wagner:
  Prognostic transcriptional association networks: a new supervised approach based on regression trees. 252-258

Data and Text Mining

• 
  Quoc-Chinh Bui, Sophia Katrenko, Peter M. A. Sloot:
  A hybrid approach to extract protein-protein interactions. 259-265

Applications Note - Genome Analysis

• 
  Qing Yu, Elizabeth M. Ryan, Todd M. Allen, Bruce W. Birren, Matthew R. Henn, Niall J. Lennon:
  PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes. 266-267
• 
  Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot:
  Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. 268-269
• 
  Simon J. van Heeringen, Gert Jan C. Veenstra:
  GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. 270-271
• 
  Ryan Koehler, Hadar Issac, Nicole Cloonan, Sean M. Grimmond:
  The uniqueome: a mappability resource for short-tag sequencing. 272-274

Sequence Analysis

• 
  Paulo C. Carvalho, Juliana S. G. Fischer, Jonas Perales, John R. Yates III, Valmir Carneiro Barbosa, Elias Bareinboim:
  Analyzing marginal cases in differential shotgun proteomics. 275-276
• 
  Emese Meglécz, Sylvain Piry, Erick Desmarais, Maxime Galan, André Gilles, Emmanuel Guivier, Nicolas Pech, Jean-François Martin:
  SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing. 277-278
• 
  Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer:
  PLEXY: efficient target prediction for box C/D snoRNAs. 279-280

Gene Expression

• 
  Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel S. Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein:
  RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. 281-283

Genetics and Population Analysis

• 
  Nicholas A. Davis, Ahwan Pandey, Brett A. McKinney:
  Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. 284-285
• 
  Rebecca Rooke, Guojun Yang:
  TE Displayer for post-genomic analysis of transposable elements. 286-287

Systems Biology

• 
  Matthias Vigelius, Aidan Lane, Bernd Meyer:
  Accelerating reaction-diffusion simulations with general-purpose graphics processing units. 288-290

Volume 27, Number 3, February 2011

Iscb

• 
  Lucian Ilie, Farideh Fazayeli, Silvana Ilie:
  HiTEC: accurate error correction in high-throughput sequencing data. 295-302
• 
  Lars Halvor Gidskehaug, Matthew Kent, Ben J. Hayes, Sigbjørn Lien:
  Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. 303-310
• 
  Haitao Jiang, Binhai Zhu, Daming Zhu:
  Algorithms for sorting unsigned linear genomes by the DCJ operations. 311-316

Sequence Analysis

• 
  Peter Menzel, Peter F. Stadler, Jan Gorodkin:
  maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. 317-325
• 
  Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin:
  Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. 326-333
• 
  Samuel V. Angiuoli, Steven L. Salzberg:
  Mugsy: fast multiple alignment of closely related whole genomes. 334-342

Structural Bioinformatics

• 
  Pascal Benkert, Marco Biasini, Torsten Schwede:
  Toward the estimation of the absolute quality of individual protein structure models. 343-350
• 
  Hongbo Zhu, M. Teresa Pisabarro:
  MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets. 351-358

Gene Expression

• 
  Vinícius Bonato, Veerabhadran Baladandayuthapani, Bradley M. Broom, Erik P. Sulman, Kenneth D. Aldape, Kim-Anh Do:
  Bayesian ensemble methods for survival prediction in gene expression data. 359-367
• 
  António dos Anjos, Anders L. B. Møller, Bjarne Kjær Ersbøll, Christine Finnie, Hamid Reza Shahbazkia:
  New approach for segmentation and quantification of two-dimensional gel electrophoresis images. 368-375

Systems Biology

• 
  Todd A. Gibson, Debra Goldberg:
  Improving evolutionary models of protein interaction networks. 376-382
• 
  Xiaojian Shao, Chris Soon Heng Tan, Courtney Voss, Shawn S. C. Li, Naiyang Deng, Gary D. Bader:
  A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. 383-390
• 
  Yongsoo Kim, Taek-Kyun Kim, Yungu Kim, Jiho Yoo, Sungyong You, Inyoul Y. Lee, George Carlson, Leroy Hood, Seungjin Choi, Daehee Hwang:
  Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. 391-398
• 
  Ming Zhou, Xiliang Zheng, Jin Wang, Shaojun Dong:
  'Non-destructive' biocomputing security system based on gas-controlled biofuel cell and potentially used for intelligent medical diagnostics. 399-404
• 
  Gábor Iván, Vince Grolmusz:
  When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks. 405-407

Data and Text Mining

• 
  Emily Doughty, Attila Kertész-Farkas, Olivier Bodenreider, Gary Thompson, Asa Adadey, Thomas A. Peterson, Maricel G. Kann:
  Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. 408-415

Applications Note - Genome Analysis

• 
  Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer:
  MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions. 416-418
• 
  Philippe Lamy, Carsten Wiuf, Torben F. Ørntoft, Claus L. Andersen:
  Rseg - an R package to optimize segmentation of SNP array data. 419-420

Sequence Analysis

• 
  Shao-Ke Lou, Bing Ni, Leung-Yau Lo, Stephen Kwok-Wing Tsui, Ting-Fung Chan, Kwong-Sak Leung:
  ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. 421-422

Structural Bioinformatics

• 
  Daniel Aioanei, Marco Brucale, Bruno Samorì:
  Open source platform for the execution and analysis of mechanical refolding experiments. 423-425
• 
  Per Larsson, Marcin J. Skwark, Björn Wallner, Arne Elofsson:
  Improved predictions by Pcons.net using multiple templates. 426-427

Gene Expression

• 
  Xun Lan, Russell Bonneville, Jeff Apostolos, Wangcheng Wu, Victor X. Jin:
  W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. 428-430

Systems Biology

• 
  Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker:
  Cytoscape 2.8: new features for data integration and network visualization. 431-432
• 
  Albert Gevorgyan, Michael E. Bushell, Claudio Avignone-Rossa, Andrzej M. Kierzek:
  SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks. 433-434

Databases and Ontologies

• 
  Miquel Miquel, I. López-Ribera, Miquel Ràmia, Sònia Casillas, Antonio Barbadilla, Carlos M. Vicient:
  MASISH: a database for gene expression in maize seeds. 435-436
• 
  Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia:
  WIST: toolkit for rapid, customized LIMS development. 437-438

Corrigendum - Databases and Ontologies

• 
  Daniel F. Schwarz, Inke R. König, Andreas Ziegler:
  On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data. 439

Volume 27, Number 4, February 2011

Review Genome Analysis

• 
  Melissa S. Cline, Rachel Karchin:
  Using bioinformatics to predict the functional impact of SNVs. 441-448

Original Papers - Genome Analysis

• 
  Bernhard Haubold, Floyd A. Reed, Peter Pfaffelhuber:
  Alignment-free estimation of nucleotide diversity. 449-455

Sequence Analysis

• 
  Andrew X. Li, Manja Marz, Jing Qin, Christian M. Reidys:
  RNA-RNA interaction prediction based on multiple sequence alignments. 456-463
• 
  Kana Shimizu, Koji Tsuda:
  SlideSort: all pairs similarity search for short reads. 464-470
• 
  Tak-Ming Chan, Ka-Chun Wong, Kin-Hong Lee, Man Hon Wong, Chi-Kong Lau, Stephen Kwok-Wing Tsui, Kwong-Sak Leung:
  Discovering approximate-associated sequence patterns for protein-DNA interactions. 471-478
• 
  Thomas C. Conway, Andrew J. Bromage:
  Succinct data structures for assembling large genomes. 479-486

Structural Bioinformatics

• 
  Teppei Ebina, Hiroyuki Toh, Yutaka Kuroda:
  DROP: an SVM domain linker predictor trained with optimal features selected by random forest. 487-494

Gene Expression

• 
  Francesco C. Stingo, Marina Vannucci:
  Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data. 495-501
• 
  Zhengpeng Wu, Xi Wang, Xuegong Zhang:
  Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. 502-508
• 
  Sangsoon Woo, Jeffrey T. Leek, John D. Storey:
  A computationally efficient modular optimal discovery procedure. 509-515

Genetics and Population Analysis

• 
  Jiahan Li, Kiranmoy Das, Guifang Fu, Runze Li, Rongling Wu:
  The Bayesian lasso for genome-wide association studies. 516-523

Systems Biology

• 
  Frank-Michael Schleif, T. Riemer, U. Börner, L. Schnapka-Hille, Michael Cross:
  Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications. 524-533
• 
  Alberto Rezola, Luis F. de Figueiredo, Matthias Brock, Jon Pey, Adam Podhorski, Christoph Wittmann, Stefan Schuster, Alexander Bockmayr, Francisco J. Planes:
  Exploring metabolic pathways in genome-scale networks via generating flux modes. 534-540
• 
  Paul A. Jensen, Jason A. Papin:
  Functional integration of a metabolic network model and expression data without arbitrary thresholding. 541-547
• 
  Ritwik Layek, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
  Cancer therapy design based on pathway logic. 548-555
• 
  Wessel N. van Wieringen, Aad van der Vaart:
  Statistical analysis of the cancer cell's molecular entropy using high-throughput data. 556-563

Data and Text Mining

• 
  Hang Xiao, Ying Li, Jiulin Du, Axel Mosig:
  Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach. 564-571
• 
  Jürgen Hartler, Martin Trötzmüller, Chandramohan Chitraju, Friedrich Spener, Harald C. Köfeler, Gerhard G. Thallinger:
  Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data. 572-577

Applications Note - Genome Analysis

• 
  Marten Boetzer, Christiaan V. Henkel, Hans J. Jansen, Derek Butler, Walter Pirovano:
  Scaffolding pre-assembled contigs using SSPACE. 578-579

Sequence Analysis

• 
  David L. A. Wood, Qinying Xu, John V. Pearson, Nicole Cloonan, Sean M. Grimmond:
  X-MATE: a flexible system for mapping short read data. 580-581

Structural Bioinformatics

• 
  Jose Ignacio Agulleiro Baldo, José-Jesús Fernández:
  Fast tomographic reconstruction on multicore computers. 582-583

Systems Biology

• 
  Clive G. Bowsher:
  Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA. 584-586

Data and Text Mining

• 
  Leonardo Bottolo, Marc Chadeau-Hyam, David I. Hastie, Sarah R. Langley, Enrico Petretto, Laurence Tiret, David Tregouet, Sylvia Richardson:
  ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration. 587-588

Databases and Ontologies

• 
  Mikhail Gostev, Julio Fernandez-Banet, Johan Rung, Joern Dietrich, Inga Prokopenko, Samuli Ripatti, Mark I. McCarthy, Alvis Brazma, Maria Krestyaninova:
  SAIL - a software system for sample and phenotype availability across biobanks and cohorts. 589-591

Phylogenetics

• 
  Klaus Peter Schliep:
  phangorn: phylogenetic analysis in R. 592-593

Volume 27, Number 5, March 2011

Original Papers - Genome Analysis

• 
  Alexej Abyzov, Mark Gerstein:
  AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. 595-603
• 
  Christopher Oldmeadow, Jonathan M. Keith:
  Model selection in Bayesian segmentation of multiple DNA alignments. 604-610

Sequence Analysis

• 
  Xiaolin Hao, Rui Jiang, Ting Chen:
  Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. 611-618

Structural Bioinformatics

• 
  Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker, Hans-Peter Lenhof, Andreas Hildebrandt:
  Automated bond order assignment as an optimization problem. 619-625
• 
  Zhenjiang Xu, David H. Mathews:
  Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. 626-632

Gene Expression

• 
  Ryung S. Kim, Juan Lin:
  Multi-level mixed effects models for bead arrays. 633-640
• 
  Eric Dugat-Bony, Mohieddine Missaoui, Eric Peyretaillade, Corinne Biderre-Petit, Ourdia Bouzid, Christophe Gouinaud, David R. C. Hill, Pierre Peyret:
  HiSpOD: probe design for functional DNA microarrays. 641-648
• 
  Xiujie Chen, Jiankai Xu, Bangqing Huang, Jin Li, Xin Wu, Ling Ma, Xiaodong Jia, Xiusen Bian, Fujian Tan, Lei Liu, Sheng Chen, Xia Li:
  A sub-pathway-based approach for identifying drug response principal network. 649-654
• 
  Yosef Prat, Menachem Fromer, Nathan Linial, Michal Linial:
  Recovering key biological constituents through sparse representation of gene expression. 655-661
• 
  Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui:
  Length bias correction for RNA-seq data in gene set analyses. 662-669

Genetics and Population Analysis

• 
  Xuexia Wang, Xiaofeng Zhu, Huaizhen Qin, Richard S. Cooper, Warren J. Ewens, Chun Li, Mingyao Li:
  Adjustment for local ancestry in genetic association analysis of admixed populations. 670-677
• 
  Vonn Walter, Andrew B. Nobel, Fred A. Wright:
  DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. 678-685
• 
  Lily Wang, Peilin Jia, Russell D. Wolfinger, Xi Chen, Britney L. Grayson, Thomas M. Aune, Zhongming Zhao:
  An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. 686-692

Systems Biology

• 
  Marco Grzegorczyk, Dirk Husmeier:
  Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes. 693-699
• 
  Hung Xuan Ta, Patrik Koskinen, Liisa Holm:
  A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees. 700-706

Data and Text Mining

• 
  Feng Feng, Ana Paula Sales, Thomas B. Kepler:
  A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays. 707-712

Applications Note - Genome Analysis

• 
  Jonathan M. Cairns, Christiana Spyrou, Rory Stark, Mike L. Smith, Andy G. Lynch, Simon Tavaré:
  BayesPeak - an R package for analysing ChIP-seq data. 713-714
• 
  Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L. Maskell, Kyungjoon Lee, Aibin He, William T. Pu, Sek Won Kong:
  CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. 715-717

Sequence Analysis

• 
  Heng Li:
  Tabix: fast retrieval of sequence features from generic TAB-delimited files. 718-719
• 
  Troy B. Hawkins, Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean D. Mooney, Kenneth Cornetta:
  Identifying viral integration sites using SeqMap 2.0. 720-722

Structural Bioinformatics

• 
  Kliment Olechnovic, Mindaugas Margelevicius, Ceslovas Venclovas:
  Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure. 723-724

Gene Expression

• 
  Daniel Baron, Audrey Bihouée, Raluca Teusan, Emeric Dubois, Frédérique Savagner, Marja Steenman, Rémi Houlgatte, Gérard Ramstein:
  MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. 725-726

Genetics and Population Analysis

• 
  Bevan Emma Huang, Andrew W. George:
  R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. 727-729

Systems Biology

• 
  Monica Chagoyen, Florencio Pazos:
  MBRole: enrichment analysis of metabolomic data. 730-731
• 
  Francois Ribalet, David M. Schruth, E. Virginia Armbrust:
  flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data. 732-733
• 
  Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano:
  MIRACH: efficient model checker for quantitative biological pathway models. 734-735

Data and Text Mining

• 
  Guoqiang Yu, Huai Li, Sook Shin Ha, Ie-Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Joseph Wang:
  PUGSVM: a caBIG^TM analytical tool for multiclass gene selection and predictive classification. 736-738
• 
  Ming Li, Shuo Chen, Joan Zhang, Heidi Chen, Yu Shyr:
  Wave-spec: a preprocessing package for mass spectrometry data. 739-740

Databases and Ontologies

• 
  Mark R. Southern, Patrick R. Griffin:
  A Java API for working with PubChem datasets. 741-742
• 
  Tommy Yu, Catherine M. Lloyd, David P. Nickerson, Mike T. Cooling, Andrew K. Miller, Alan Garny, Jonna R. Terkildsen, James R. Lawson, Randall Britten, Peter J. Hunter, Poul M. F. Nielsen:
  The Physiome Model Repository 2. 743-744

Volume 27, Number 6, March 2011

Discovery Note - Data and Text Mining

• 
  Wai-Ki Yip, Christoph Lange:
  Quantitative trait prediction based on genetic marker-array data, a simulation study. 745-748

Original Papers Genome Analysis

• 
  Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele:
  A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. 749-756
• 
  Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack:
  A novel hybrid gene prediction method employing protein multiple sequence alignments. 757-763

Sequence Analysis

• 
  Guillaume Marçais, Carl Kingsford:
  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. 764-770
• 
  Yi Zhang, Xianhui Wang, Le Kang:
  A k-mer scheme to predict piRNAs and characterize locust piRNAs. 771-776
• 
  Yejun Wang, Qing Zhang, Ming-an Sun, Dianjing Guo:
  High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. 777-784

Structural Bioinformatics

• 
  Yang Cao, Lin Song, Zhichao Miao, Yun Hu, Liqing Tian, Taijiao Jiang:
  Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation. 785-790
• 
  Guy Tsafnat, Jaron Schaeffer, Andrew Clayphan, Jonathan R. Iredell, Sally R. Partridge, Enrico W. Coiera:
  Computational inference of grammars for larger-than-gene structures from annotated gene sequences. 791-796

Gene Expression

• 
  Clement Chung, Jian Liu, Andrew Emili, Brendan J. Frey:
  Computational refinement of post-translational modifications predicted from tandem mass spectrometry. 797-806
• 
  Alexandra Posekany, K. Felsenstein, Peter Sykacek:
  Biological assessment of robust noise models in microarray data analysis. 807-814

Genetics and Population Analysis

• 
  Vanda M. Lourenço, Ana M. Pires, M. Kirst:
  Robust linear regression methods in association studies. 815-821
• 
  Rick Twee-Hee Ong, Xuanyao Liu, Wan-Ting Poh, Xueling Sim, Kee Seng Chia, Yik-Ying Teo:
  A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies. 822-828
• 
  Christian Rödelsperger, Peter M. Krawitz, Sebastian Bauer, Jochen Hecht, Abigail W. Bigham, Michael Bamshad, Birgit Jonske de Condor, Michal R. Schweiger, Peter N. Robinson:
  Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders. 829-836
• 
  Tianqi Zhu, Yucheng Hu, Zhiming Ma, De-Xing Zhang, Tiejun Li, Ziheng Yang:
  Efficient simulation under a population genetics model of carcinogenesis. 837-843

Systems Biology

• 
  Stuart R. Jefferys, Morgan C. Giddings:
  Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data. 844-852
• 
  Lin Hou, Lin Wang, Minping Qian, Dong Li, Chao Tang, Yunping Zhu, Minghua Deng, Fangting Li:
  Modular analysis of the probabilistic genetic interaction network. 853-859

Applications Note - Sequence Analysis

• 
  Sebastian Deorowicz, Szymon Grabowski:
  Compression of DNA sequence reads in FASTQ format. 860-862
• 
  Robert Schmieder, Robert A. Edwards:
  Quality control and preprocessing of metagenomic datasets. 863-864
• 
  Michael N. Edmonson, Jinghui Zhang, Chunhua Yan, Richard P. Finney, Daoud M. Meerzaman, Kenneth H. Buetow:
  Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. 865-866

Gene Expression

• 
  Ângela Gonçalves, Andrew Tikhonov, Alvis Brazma, Misha Kapushesky:
  A pipeline for RNA-seq data processing and quality assessment. 867-869
• 
  Qiang Song, Andrew D. Smith:
  Identifying dispersed epigenomic domains from ChIP-Seq data. 870-871
• 
  Andrew T. Magis, John C. Earls, Youn-Hee Ko, James A. Eddy, Nathan D. Price:
  Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. 872-873

Systems Biology

• 
  Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris P. Barnes:
  GPU accelerated biochemical network simulation. 874-876
• 
  Xuejian Xiong, Hongyan Song, Tuan On, Lucas Lochovsky, Nicholas J. Provart, John Parkinson:
  PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya. 877-878
• 
  Xin Wang, Camille Terfve, John C. Rose, Florian Markowetz:
  HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. 879-880
• 
  Matthieu Vignes, Juliette Blanchet, Damien Leroux, Florence Forbes:
  SpaCEM³: a software for biological module detection when data is incomplete, high dimensional and dependent. 881-882
• 
  Yanqi Hao, Anna Merkoulovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak:
  OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. 883-884

Data and Text Mining

• 
  Francesca Chignola, Silvia Mari, Tim J. Stevens, Rasmus H. Fogh, Valeria Mannella, Wayne Boucher, Giovanna Musco:
  The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR. 885-886
• 
  Riku Louhimo, Sampsa Hautaniemi:
  CNAmet: an R package for integrating copy number, methylation and expression data. 887-888

Databases and Ontologies

• 
  Thomas A. Down, Matias Piipari, Tim J. P. Hubbard:
  Dalliance: interactive genome viewing on the web. 889-890
• 
  Mark Y. Tong, Christopher A. Cassa, Isaac S. Kohane:
  Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. 891-893

Volume 27, Number 7, April 2011

Discovery Note - Genome Analysis

• 
  K. J. Siddle, Judith A. Goodship, Bernard D. Keavney, Mauro F. Santibanez-Koref:
  Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome. 895-898

Sequence Analysis

• 
  Katja Luck, Gilles Travé:
  Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions. 899-902

Original Papers - Genome Analysis

• 
  Burkhard Linke, Robert Giegerich, Alexander Goesmann:
  Conveyor: a workflow engine for bioinformatic analyses. 903-911
• 
  Grace S. Shieh, Shurong Zheng, Richard A. Johnson, Yi-Feng Chang, Kunio Shimizu, Chia-Chang Wang, Sen-Lin Tang:
  Modeling and comparing the organization of circular genomes. 912-918
• 
  Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa:
  B2G-FAR, a species-centered GO annotation repository. 919-924

Structural Bioinformatics

• 
  Ilona Kifer, Ruth Nussinov, Haim J. Wolfson:
  GOSSIP: a method for fast and accurate global alignment of protein structures. 925-932
• 
  James W. Shirley, Sereyvathana Ty, Shin-ichiro Takebayashi, Xiuwen Liu, David M. Gilbert:
  FISH Finder: a high-throughput tool for analyzing FISH images. 933-938
• 
  Francois Berenger, Yong Zhou, Rojan Shrestha, Kam Y. J. Zhang:
  Entropy-accelerated exact clustering of protein decoys. 939-945

Gene Expression

• 
  Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep:
  Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. 946-952
• 
  Florian Klinglmueller, Thomas Tuechler, Martin Posch:
  Cross-platform comparison of microarray data using order restricted inference. 953-960
• 
  Tomasz Konopka:
  Automated analysis of biological oscillator models using mode decomposition. 961-967

Genetics and Population Analysis

• 
  Alexander T. Dilthey, Loukas Moutsianas, Stephen Leslie, Gil McVean:
  HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes. 968-972

Systems Biology

• 
  Goksel Misirli, Jennifer Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne, Mike T. Cooling, Anil Wipat:
  Model annotation for synthetic biology: automating model to nucleotide sequence conversion. 973-979

Data and Text Mining

• 
  Maximilian Haeussler, Martin Gerner, Casey M. Bergman:
  Annotating genes and genomes with DNA sequences extracted from biomedical articles. 980-986
• 
  Björn Voss, Michael Hanselmann, Bernhard Y. Renard, Martin S. Lindner, Ullrich Köthe, Marc Kirchner, Fred A. Hamprecht:
  SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. 987-993
• 
  Sach Mukherjee, Steven M. Hill:
  Network clustering: probing biological heterogeneity by sparse graphical models. 994-1000

Databases and Ontologies

• 
  Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
  A common layer of interoperability for biomedical ontologies based on OWL EL. 1001-1008

Applications Note - Genome Analysis

• 
  Mitchell J. Sullivan, Nicola K. Petty, Scott A. Beatson:
  Easyfig: a genome comparison visualizer. 1009-1010
• 
  Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno:
  SHRiMP2: Sensitive yet Practical Short Read Mapping. 1011-1012
• 
  Francesco Strozzi, Jan Aerts:
  A Ruby API to query the Ensembl database for genomic features. 1013-1014
• 
  Brent S. Pedersen, Haibao Tang, Michael Freeling:
  Gobe: an interactive, web-based tool for comparative genomic visualization. 1015-1016

Sequence Analysis

• 
  Charles E. Grant, Timothy L. Bailey, William Stafford Noble:
  FIMO: scanning for occurrences of a given motif. 1017-1018
• 
  Zachary Dwight, Robert Palais, Carl T. Wittwer:
  uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. 1019-1020

Structural Bioinformatics

• 
  Gerd Neudert, Gerhard Klebe:
  fconv: format conversion, manipulation and feature computation of molecular data. 1021-1022

Gene Expression

• 
  Rendong Yang, Chen Zhang, Zhen Su:
  LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data. 1023-1025
• 
  Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray, Neil D. Lawrence:
  tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor. 1026-1027

Systems Biology

• 
  Zhike Zi:
  SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models. 1028-1029
• 
  Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere:
  PiNGO: a Cytoscape plugin to find candidate genes in biological networks. 1030-1031

Data and Text Mining

• 
  Minlie Huang, Jingchen Liu, Xiaoyan Zhu:
  GeneTUKit: a software for document-level gene normalization. 1032-1033
• 
  Annekathrin Bartsch, Boyke Bunk, Isam Haddad, Johannes Klein, Richard Münch, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, Ida Retter:
  GeneReporter - sequence-based document retrieval and annotation. 1034-1035
• 
  Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Joseph Wang:
  DDN: a caBIG^® analytical tool for differential network analysis. 1036-1038
• 
  Kamil Tamiola, Frans A. A. Mulder:
  ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. 1039-1040
• 
  Ketil Malde:
  Flower: extracting information from pyrosequencing data. 1041-1042

Databases and Ontologies

• 
  Andrew G. Winter, Jan Wildenhain, Mike Tyers:
  BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. 1043-1044

Volume 27, Number 8, April 2011

Original Papers - Genome Analysis

• 
  Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal:
  eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study. 1045-1051
• 
  Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert B. Scharpf, Chunfa Jie, Benilton S. 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. 1052-1060

Sequence Analysis

• 
  David Koslicki:
  Topological entropy of DNA sequences. 1061-1067
• 
  Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna:
  Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. 1068-1075

Structural Bioinformatics

• 
  Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel:
  Topology and prediction of RNA pseudoknots. 1076-1085
• 
  Emidio Capriotti, Tomás Norambuena, Marc A. Martí-Renom, Francisco Melo:
  All-atom knowledge-based potential for RNA structure prediction and assessment. 1086-1093

Gene Expression

• 
  Jessica Cara Mar, Christine A. Wells, John Quackenbush:
  Defining an informativeness metric for clustering gene expression data. 1094-1100
• 
  Liangxiu Han, Jano I. van Hemert, Richard A. Baldock:
  Automatically identifying and annotating mouse embryo gene expression patterns. 1101-1107

Systems Biology

• 
  Marie 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. 1108-1112
• 
  Duc-Hau Le, Yung-Keun Kwon:
  The effects of feedback loops on disease comorbidity in human signaling networks. 1113-1120
• 
  Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki:
  Interactive, multiscale navigation of large and complicated biological networks. 1121-1127
• 
  Victor 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. 1128-1134
• 
  Andrew D. Fox, Benjamin J. Hescott, Anselm Blumer, Donna K. Slonim:
  Connectedness of PPI network neighborhoods identifies regulatory hub proteins. 1135-1142

Data and Text Mining

• 
  Jung-Hsien Chiang, Heng-Hui Liu, Yi-Ting Huang:
  Condensing biomedical journal texts through paragraph ranking. 1143-1149

Applications Note - Genome Analysis

• 
  Marcela Dávila López, Tore Samuelsson:
  eGOB: eukaryotic Gene Order Browser. 1150-1151
• 
  Justin Jee, Joel S. Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert D. Bjornson, Guoneng Zhong, Zhengdong D. Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein:
  ACT: aggregation and correlation toolbox for analyses of genome tracks. 1152-1154
• 
  Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones:
  Human variation database: an open-source database template for genomic discovery. 1155-1156

Sequence Analysis

• 
  Heng Li:
  Improving SNP discovery by base alignment quality. 1157-1158
• 
  William 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. 1159-1161
• 
  Hans-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. 1162-1163

Phylogenetics

• 
  Diego Darriba, Guillermo L. Taboada, Ramon Doallo, David Posada:
  ProtTest 3: fast selection of best-fit models of protein evolution. 1164-1165

Gene Expression

• 
  Marc Kirchner, Buote Xu, Hanno Steen, Judith A. J. Steen:
  libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. 1166-1167
• 
  Haleh Yasrebi:
  SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data. 1168-1169

Systems Biology

• 
  Guido Klingbeil, Radek Erban, Mike B. Giles, Philip K. Maini:
  STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB. 1170-1171
• 
  Yoshinori 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. 1172-1173
• 
  George C. Linderman, Vishal N. Patel, Mark R. Chance, Gürkan Bebek:
  BiC: a web server for calculating bimodality of coexpression between gene and protein networks. 1174-1175
• 
  Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A. Swertz, Heorhiy Byelas, Martijn Dijkstra, Rob W. W. Hooft, Dmitry Katsubo, Bas van Breukelen, Rainer Bischoff, Peter Horvatovich:
  A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. 1176-1178
• 
  Lee 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. 1179-1180
• 
  Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan:
  FNV: light-weight flash-based network and pathway viewer. 1181-1182

Data and Text Mining

• 
  Michael Specht, Sebastian Kuhlgert, Christian Fufezan, Michael Hippler:
  Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows. 1183-1184
• 
  Simon 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. 1185-1186

Databases and Ontologies

• 
  Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, Sarah Cohen Boulakia:
  Gene List significance at-a-glance with GeneValorization. 1187-1189
• 
  Hongzhan 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. 1190-1191
• 
  Javed 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. 1192-1193

Letter to the Editor - Gene Expression

• 
  Meïli C. Baragatti, Denys Pommeret:
  Comments on 'Bayesian variable selection for disease classification using gene expression data'. 1194

Volume 27, Number 9, May 2011

Original Papers - Genome Analysis

• 
  Tomas W. Fitzgerald, Lee D. Larcombe, Solena Le Scouarnec, Stephen Clayton, Diana Rajan, Nigel P. Carter, Richard Redon:
  aCGH.Spline - an R package for aCGH dye bias normalization. 1195-1200
• 
  Jie Huang, Andrew D. Johnson, Christopher J. O'Donnell:
  PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies. 1201-1206
• 
  António C. M. Costa, José António Tenreiro Machado, Maria Dulce Quelhas:
  Histogram-based DNA analysis for the visualization of chromosome, genome and species information. 1207-1214
• 
  Christoph J. Thieme, Lydia Gramzow, Dajana Lobbes, Günter Theißen:
  SplamiR - prediction of spliced miRNAs in plants. 1215-1223

Sequence Analysis

• 
  Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio:
  MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. 1224-1230
• 
  Celine Vens, Marie-Noëlle Rosso, Etienne G. J. Danchin:
  Identifying discriminative classification-based motifs in biological sequences. 1231-1238
• 
  Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén:
  A probabilistic model of nuclear import of proteins. 1239-1246
• 
  Liisa Heikkinen, Mikko Kolehmainen, Garry Wong:
  Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map. 1247-1254

Phylogenetics

• 
  Jianfu Zhou, Xiaoguang Liu, Douglas S. Stones, Qiang Xie, Gang Wang:
  MrBayes on a Graphics Processing Unit. 1255-1261

Structural Bioinformatics

• 
  Wei Zhao, Meng Xu, Zhi Liang, Bo Ding, Liwen Niu, Haiyan Liu, Maikun Teng:
  Structure-based de novo prediction of zinc-binding sites in proteins of unknown function. 1262-1268

Gene Expression

• 
  Jangsun Baek, Geoffrey J. McLachlan:
  Mixtures of common t-factor analyzers for clustering high-dimensional microarray data. 1269-1276
• 
  Hafiz Muhammad Shahzad Asif, Guido Sanguinetti:
  Large-scale learning of combinatorial transcriptional dynamics from gene expression. 1277-1283
• 
  Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon:
  A wholly defined Agilent microarray spike-in dataset. 1284-1289
• 
  Haisu Ma, Eric E. Schadt, Lee M. Kaplan, Hongyu Zhao:
  COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. 1290-1298

Systems Biology

• 
  Jochen Weile, Matthew R. Pocock, Simon J. Cockell, Phillip W. Lord, James M. Dewar, Eva-Maria Holstein, Darren J. Wilkinson, David A. Lydall, Jennifer Hallinan, Anil Wipat:
  Customizable views on semantically integrated networks for systems biology. 1299-1306

Applications Note - Genome Analysis

• 
  Micha Bayer, Iain Milne, Gordon Stephen, Paul D. Shaw, Linda Cardle, Frank Wright, David F. Marshall:
  Comparative visualization of genetic and physical maps with Strudel. 1307-1308
• 
  Ling Sing Yung, Can Yang, Xiang Wan, Weichuan Yu:
  GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies. 1309-1310
• 
  Ernesto Picardi, Mattia D'Antonio, Danilo Carrabino, Tiziana Castrignanò, Graziano Pesole:
  ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments. 1311-1312
• 
  Matteo Cereda, Manuela Sironi, Matteo Cavalleri, Uberto Pozzoli:
  GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. 1313-1315

Sequence Analysis

• 
  Manuela Hummel, Sarah Bonnin, Ernesto Lowy-Gallego, Guglielmo Roma:
  TEQC: an R package for quality control in target capture experiments. 1316-1317
• 
  Andrzej Zielezinski, Wojciech M. Karlowski:
  Agos - a universal web tool for GW Argonaute-binding domain prediction. 1318-1319

Structural Bioinformatics

• 
  Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma, Mohd Shahir Shamsir:
  birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics. 1320-1321
• 
  Aron Hennerdal, Arne Elofsson:
  Rapid membrane protein topology prediction. 1322-1323
• 
  Jamel Meslamani, Didier Rognan, Esther Kellenberger:
  sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins. 1324-1326
• 
  David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan:
  Rigid substructure search. 1327-1329

Gene Expression

• 
  Amy L. Olex, Jacquelyn S. Fetrow:
  SC²ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data. 1330-1331

Genetics and Population Analysis

• 
  Laurent Excoffier, Matthieu Foll:
  fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. 1332-1334
• 
  Tiago Antao, Ian M. Hastings:
  ogaraK: a population genetics simulator for malaria. 1335-1336

Systems Biology

• 
  Asad Naeem, Andrew P. French, Darren M. Wells, Tony P. Pridmore:
  High-throughput feature counting and measurement of roots. 1337-1338
• 
  Arnald Alonso, Antonio Julià, Antoni Beltran, Maria Vinaixa, Marta Díaz, Lourdes Ibañez, Xavier Correig, Sara Marsal:
  AStream: an R package for annotating LC/MS metabolomic data. 1339-1340

Data and Text Mining

• 
  Björn A. Grüning, Christian Senger, Anika Erxleben, Stephan Flemming, Stefan Günther:
  Compounds In Literature (CIL): screening for compounds and relatives in PubMed. 1341-1342

Databases and Ontologies

• 
  Catherine A. Hayes, Niclas G. Karlsson, Weston B. Struwe, Frédérique Lisacek, Pauline M. Rudd, Nicolle H. Packer, Matthew P. Campbell:
  UniCarb-DB: a database resource for glycomic discovery. 1343-1344

Volume 27, Number 10, May 2011

Editorial

• 
  Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia:
  On the organization of bioinformatics core services in biology-based research institutes. 1345

Discovery Note - Sequence Analysis

• 
  Daniel C. Ellwanger, Florian A. Büttner, Hans-Werner Mewes, Volker Stümpflen:
  The sufficient minimal set of miRNA seed types. 1346-1350

Original Papers - Sequence Analysis

• 
  Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann:
  Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. 1351-1358

Phylogenetics

• 
  W. Timothy J. White, Barbara R. Holland:
  Faster exact maximum parsimony search with XMP. 1359-1367

Structural Bioinformatics

• 
  Ping Xuan, Maozu Guo, Xiaoyan Liu, Yangchao Huang, Wenbin Li, Yufei Huang:
  PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs. 1368-1376

Gene Expression

• 
  Klaus Jung, Benjamin Becker, Edgar Brunner, Tim Beißbarth:
  Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. 1377-1383

Genetics and Population Analysis

• 
  Erdal Cosgun, Nita A. Limdi, Christine W. Duarte:
  High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans. 1384-1389

Systems Biology

• 
  Oleksii Kuchaiev, Natasa Przulj:
  Integrative network alignment reveals large regions of global network similarity in yeast and human. 1390-1396
• 
  Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski:
  Mass-balanced randomization of metabolic networks. 1397-1403
• 
  Martial Sankar, Karen S. Osmont, Jakub Rolcik, Bojan Gujas, Danuse Tarkowska, Miroslav Strnad, Ioannis Xenarios, Christian S. Hardtke:
  A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. 1404-1412

Data and Text Mining

• 
  Christophe Bécavin, Nicolas Tchitchek, Colette Mintsa-Eya, Annick Lesne, Arndt Benecke:
  Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition. 1413-1421
• 
  Hei-Chia Wang, Yi-Hsiu Chen, Hung-Yu Kao, Shaw-Jenq Tsai:
  Inference of transcriptional regulatory network by bootstrapping patterns. 1422-1428

Databases and Ontologies

• 
  Lauren Becnel Boyd, Scott P. Hunicke-Smith, Grace A. Stafford, Elaine T. Freund, Michele Ehlman, Uma Chandran, Robert Dennis, Anna T. Fernandez, Stephen Goldstein, David Steffen, Benjamin Tycko, Juli D. Klemm:
  The caBIG® Life Science Business Architecture Model. 1429-1435

Applications Note - Sequence Analysis

• 
  Yuanwei Zhang, Yifan Yang, Huan Zhang, Xiaohua Jiang, Bo Xu, Yu Xue, Yunxia Cao, Qian Zhai, Yong Zhai, Mingqing Xu, Howard J. Cooke, Qinghua Shi:
  Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. 1436-1437

Structural Bioinformatics

• 
  Timothy Nugent, Sean Ward, David T. Jones:
  The MEMPACK alpha-helical transmembrane protein structure prediction server. 1438-1439

Gene Expression

• 
  Ola Larsson, Nahum Sonenberg, Robert Nadon:
  anota: analysis of differential translation in genome-wide studies. 1440-1441
• 
  Marc Johannes, Holger Fröhlich, Holger Sültmann, Tim Beißbarth:
  pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. 1442-1443

Databases and Ontologies

• 
  Xinan Yang, Jianrong Li, Younghee Lee, Yves A. Lussier:
  GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. 1444-1446
• 
  Li Chen, George Wu, Hongkai Ji:
  hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. 1447-1448

Volume 27, Number 11, June 2011

Review - Structural Bioinformatics

• 
  Ferenc Orosz, Judit Ovádi:
  Proteins without 3D structure: definition, detection and beyond. 1449-1454

Original Papers - Genome Analysis

• 
  Leena Salmela, Jan Schröder:
  Correcting errors in short reads by multiple alignments. 1455-1461
• 
  Gibran Hemani, Athanasios Theocharidis, Wenhua Wei, Chris S. Haley:
  EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. 1462-1465
• 
  Mirjana Domazet-Loso, Bernhard Haubold:
  Alignment-free detection of local similarity among viral and bacterial genomes. 1466-1472
• 
  Guoqiang Yu, Bai Zhang, G. Steven Bova, Jianfeng Xu, Ie-Ming Shih, Yue Joseph Wang:
  BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. 1473-1480

Sequence Analysis

• 
  Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
  Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. 1481-1488
• 
  Henry C. M. Leung, Siu-Ming Yiu, Bin Yang, Yu Peng, Yi Wang, Zhihua Liu, Jing-Chi Chen, Junjie Qin, Ruiqiang Li, Francis Y. L. Chin:
  A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. 1489-1495

Gene Expression

• 
  Andrew E. Teschendorff, Joanna Zhuang, Martin Widschwendter:
  Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. 1496-1505
• 
  Bin Wang, Xiao-Feng Wang, Yaguang Xi:
  Normalizing bead-based microRNA expression data: a measurement error model-based approach. 1506-1512

Genetics and Population Analysis

• 
  Dan He, Farhad Hormozdiari, Nicholas A. Furlotte, Eleazar Eskin:
  Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. 1513-1520

Systems Biology

• 
  Qianghu Wang, Jie Sun, Meng Zhou, Haixiu Yang, Yan Li, Xiang Li, Sali Lv, Xia Li, Yixue Li:
  A novel network-based method for measuring the functional relationship between gene sets. 1521-1528
• 
  Markus Maucher, Barbara Kracher, Michael Kühl, Hans A. Kestler:
  Inferring Boolean network structure via correlation. 1529-1536
• 
  Fangping Mu, Clifford J. Unkefer, Pat J. Unkefer, William S. Hlavacek:
  Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. 1537-1545

Data and Text Mining

• 
  Kai Christian Bader, Christian Grothoff, Harald Meier:
  Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. 1546-1554
• 
  Teo Shu Mei, Yudi Pawitan, Vikrant Kumar, Anbupalam Thalamuthu, Mark Seielstad, Kee Seng Chia, Agus Salim:
  Multi-platform segmentation for joint detection of copy number variants. 1555-1561

Databases and Ontologies

• 
  Ward Blondé, Vladimir Mironov, Aravind Venkatesan, Erick Antezana, Bernard De Baets, Martin Kuiper:
  Reasoning with bio-ontologies: using relational closure rules to enable practical querying. 1562-1568

Applications Note - Sequence Analysis

• 
  Cenny Taslim, Tim Hui-Ming Huang, Shili Lin:
  DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models. 1569-1570
• 
  Felix Krueger, Simon R. Andrews:
  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. 1571-1572

Structural Bioinformatics

• 
  Corinna Vehlow, Henning Stehr, Matthias Winkelmann, Jose M. Duarte, Lars Petzold, Juliane Dinse, Michael Lappe:
  CMView: Interactive contact map visualization and analysis. 1573-1574
• 
  Ahmet Bakan, Lidio M. C. Meireles, Ivet Bahar:
  ProDy: Protein Dynamics Inferred from Theory and Experiments. 1575-1577

Systems Biology

• 
  Tian Xia, John L. Van Hemert, Julie A. Dickerson:
  CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling. 1578-1580
• 
  Deguo Xia, Haoran Zheng, Zhiqiang Liu, Guisheng Li, Jinlong Li, Jiong Hong, Kai Zhao:
  MRSD: a web server for Metabolic Route Search and Design. 1581-1582
• 
  Ahmet Emre Aladag, Cesim Erten, Melih Sözdinler:
  Reliability-Oriented bioinformatic networks visualization. 1583-1584
• 
  Ambarish Biswas, Raghuraj Rao, Shivshankar Umashankar, Kalyan C. Mynampati, Sheela Reuben, Gauri Parab, Sanjay Swarup:
  datPAV - an online processing, analysis and visualization tool for exploratory investigation of experimental data. 1585-1586
• 
  Pieter Audenaert, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel:
  CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. 1587-1588

Data and Text Mining

• 
  Soumya Raychaudhuri:
  VIZ-GRAIL: visualizing functional connections across disease loci. 1589-1590

Databases and Ontologies

• 
  Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano:
  Systems biology model repository for macrophage pathway simulation. 1591-1593

Volume 27, Number 12, June 2011

Original Papers - Genome Analysis

• 
  Michael C. Wendl, John W. Wallis, Ling Lin, Cyriac Kandoth, Elaine R. Mardis, Richard K. Wilson, Li Ding:
  PathScan: a tool for discerning mutational significance in groups of putative cancer genes. 1595-1602
• 
  Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble, Uri Keich:
  Improved similarity scores for comparing motifs. 1603-1609
• 
  Justin Bedo, Adam Kowalczyk:
  Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data. 1610-1617

Sequence Analysis

• 
  Peter Meinicke, Kathrin Petra Aßhauer, Thomas Lingner:
  Mixture models for analysis of the taxonomic composition of metagenomes. 1618-1624

Structural Bioinformatics

• 
  Matteo Floris, Domenico Raimondo, Guido Leoni, Massimiliano Orsini, Paolo Marcatili, Anna Tramontano:
  MAISTAS: a tool for automatic structural evaluation of alternative splicing products. 1625-1629
• 
  Ali Abdul-Gader, Andrew John Miles, B. A. Wallace:
  A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy. 1630-1636

Gene Expression

• 
  Cheng Zheng, Shucha Zhang, Susanne Ragg, Daniel Raftery, Olga Vitek:
  Identification and quantification of metabolites in ¹H NMR spectra by Bayesian model selection. 1637-1644
• 
  Michael Seifert, Marc Strickert, Alexander Schliep, Ivo Grosse:
  Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models. 1645-1652
• 
  Timothy L. Bailey:
  DREME: motif discovery in transcription factor ChIP-seq data. 1653-1659

Systems Biology

• 
  Seongho Kim, Aiqin Fang, Bing Wang, Jaesik Jeong, Xiang Zhang:
  An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure. 1660-1666
• 
  Senol Isci, Cengizhan Ozturk, Jon Jones, Hasan H. Otu:
  Pathway analysis of high-throughput biological data within a Bayesian network framework. 1667-1674

Data and Text Mining

• 
  Mohammadmahdi R. Yousefi, Jianping Hua, Edward R. Dougherty:
  Multiple-rule bias in the comparison of classification rules. 1675-1683

Databases and Ontologies

• 
  Olga Ivchenko, Erfan Younesi, Mohammad Shahid, Antje Wolf, Bernd Müller, Martin Hofmann-Apitius:
  PLIO: an ontology for formal description of protein-ligand interactions. 1684-1690

Applications Note - Genome Analysis

• 
  Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael Strömberg, Gabor T. Marth:
  BamTools: a C++ API and toolkit for analyzing and managing BAM files. 1691-1692
• 
  Camille Sabbah, Gildas Mazo, Caroline Paccard, Fabien Reyal, Philippe Hupé:
  SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip. 1693-1695
• 
  Philip Machanick, Timothy L. Bailey:
  MEME-ChIP: motif analysis of large DNA datasets. 1696-1697
• 
  Irina Ostrovnaya, Venkatraman E. Seshan, Adam B. Olshen, Colin B. Begg:
  Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles. 1698-1699

Sequence Analysis

• 
  Daniel Beck, Matt Settles, James A. Foster:
  OTUbase: an R infrastructure package for operational taxonomic unit data. 1700-1701
• 
  Nanjiang Shu, Arne Elofsson:
  KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. 1702-1703
• 
  Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li:
  FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. 1704-1705
• 
  Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight:
  Boulder ALignment Editor (ALE): a web-based RNA alignment tool. 1706-1707
• 
  Yang Li, Jeremy Chien, David I. Smith, Jian Ma:
  FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. 1708-1710

Structural Bioinformatics

• 
  Joost J. J. van Durme, Javier Delgado Blanco, Francois Stricher, Luis Serrano, Joost Schymkowitz, Frederic Rousseau:
  A graphical interface for the FoldX forcefield. 1711-1712
• 
  Fabien Mareuil, Christophe Blanchet, Therese E. Malliavin, Michael Nilges:
  Grid computing for improving conformational sampling in NMR structure calculation. 1713-1714
• 
  Zheng Wang, Jesse Eickholt, Jianlin Cheng:
  APOLLO: a quality assessment service for single and multiple protein models. 1715-1716

Genetics and Population Analysis

• 
  Tiago Antao, Mark A. Beaumont:
  Mcheza: a workbench to detect selection using dominant markers. 1717-1718

Systems Biology

• 
  Ola Spjuth, Martin Eklund, Maris Lapins, Muhammad Junaid, Jarl E. S. Wikberg:
  Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre. 1719-1720
• 
  Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai:
  RuleBender: a visual interface for rule-based modeling. 1721-1722

Data and Text Mining

• 
  Shashank Agarwal, Hong Yu:
  Figure summarizer browser extensions for PubMed Central. 1723-1724
• 
  Joachim von Eichborn, Philip E. Bourne, Robert Preissner:
  Cobweb: a Java applet for network exploration and visualisation. 1725-1726
• 
  Woonghee Lee, Jin Hae Kim, William M. Westler, John L. Markley:
  PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. 1727-1728
• 
  Vlad Popovici, Eva Budinska, Mauro Delorenzi:
  Rgtsp: a generalized top scoring pairs package for class prediction. 1729-1730
• 
  Kangseok Kim, Wonil Kim, Sunshin Kim:
  ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms. 1731-1733

Databases and Ontologies

• 
  Dominic Sebastian Lütjohann, Asmi H. Shah, Michael P. Christen, Florian Richter, Karsten Knese, Urban Liebel:
  'Sciencenet' - towards a global search and share engine for all scientific knowledge. 1734-1735
• 
  Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam:
  Signaling gateway molecule pages - a data model perspective. 1736-1738
• 
  Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P. Mesirov:
  Molecular signatures database (MSigDB) 3.0. 1739-1740

Volume 27, Number 13, July 2011

ISMB/ECCB 2011 Proceedings

• 
  Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén:
  Sorting the nuclear proteome. 7-14
• 
  Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane:
  Environment specific substitution tables improve membrane protein alignment. 15-23
• 
  Marcin J. Mizianty, Lukasz A. Kurgan:
  Sequence-based prediction of protein crystallization, purification and production propensity. 24-33
• 
  Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger:
  A method for probing the mutational landscape of amyloid structure. 34-42
• 
  Arun Siddharth Konagurthu, Lloyd Allison, Peter J. Stuckey, Arthur M. Lesk:
  Piecewise linear approximation of protein structures using the principle of minimum message length. 43-51
• 
  Andrej J. Savol, Virginia M. Burger, Pratul K. Agarwal, Arvind Ramanathan, Chakra S. Chennubhotla:
  QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. 52-60
• 
  S. Shivashankar, S. Srivathsan, Balaraman Ravindran, Ashish V. Tendulkar:
  Multi-view methods for protein structure comparison using latent dirichlet allocation. 61-68
• 
  Min Xu, Martin Beck, Frank Alber:
  Template-free detection of macromolecular complexes in cryo electron tomograms. 69-76
• 
  André Altmann, Peter Weber, Carina Quast, Monika Rex-Haffner, Elisabeth B. Binder, Bertram Müller-Myhsok:
  vipR: variant identification in pooled DNA using R. 77-84
• 
  Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai:
  IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. 85-93
• 
  Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin:
  Meta-IDBA: a de Novo assembler for metagenomic data. 94-101
• 
  Zhiyong Wang, Jinbo Xu:
  A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. 102-110
• 
  Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun'ichi Tsujii, Sophia Ananiadou:
  Discovering and visualizing indirect associations between biomedical concepts. 111-119
• 
  Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan:
  MeSH: a window into full text for document summarization. 120-128
• 
  Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
  A folding algorithm for extended RNA secondary structures. 129-136
• 
  Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner:
  Error correction of high-throughput sequencing datasets with non-uniform coverage. 137-141
• 
  Regev Schweiger, Michal Linial, Nathan Linial:
  Generative probabilistic models for protein-protein interaction networks - the biclique perspective. 142-148
• 
  Günhan Gülsoy, Tamer Kahveci:
  RINQ: Reference-based Indexing for Network Queries. 149-158
• 
  Zhipeng Xie, Chee Keong Kwoh, Xiaoli Li, Min Wu:
  Construction of co-complex score matrix for protein complex prediction from AP-MS data. 159-166
• 
  Yong Chen, Tao Jiang, Rui Jiang:
  Uncover disease genes by maximizing information flow in the phenome-interactome network. 167-176
• 
  Noa Novershtern, Aviv Regev, Nir Friedman:
  Physical Module Networks: an integrative approach for reconstructing transcription regulation. 177-185
• 
  Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani:
  Identification of metabolic network models from incomplete high-throughput datasets. 186-195
• 
  Ankur P. Parikh, Wei Wu, Ross E. Curtis, Eric P. Xing:
  TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages. 196-204
• 
  Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp:
  Optimally discriminative subnetwork markers predict response to chemotherapy. 205-213
• 
  Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok, Karsten M. Borgwardt:
  Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs. 214-221
• 
  Jing Li, Benjamin Horstman, Yixuan Chen:
  Detecting epistatic effects in association studies at a genomic level based on an ensemble approach. 222-229
• 
  Theodore Alexandrov, Jan Hendrik Kobarg:
  Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering. 230-238
• 
  Hanchuan Peng, Fuhui Long, Gene Myers:
  Automatic 3D neuron tracing using all-path pruning. 239-247
• 
  Céline Scornavacca, Franziska Zickmann, Daniel H. Huson:
  Tanglegrams for rooted phylogenetic trees and networks. 248-256
• 
  Haris Gavranovic, Cédric Chauve, Jérôme Salse, Eric Tannier:
  Mapping ancestral genomes with massive gene loss: A matrix sandwich problem. 257-265
• 
  Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette:
  Predicting site-specific human selective pressure using evolutionary signatures. 266-274
• 
  Michael F. Lin, Irwin Jungreis, Manolis Kellis:
  PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. 275-282
• 
  Nicola Bonzanni, Nianshu Zhang, Stephen G. Oliver, Jasmin Fisher:
  The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae. 283-287
• 
  Nicholas A. Furlotte, Hyun Min Kang, Chun Ye, Eleazar Eskin:
  Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. 288-294
• 
  Michael B. Mayhew, Joshua W. Robinson, Boyoun Jung, Steven B. Haase, Alexander J. Hartemink:
  A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. 295-303
• 
  Susanne Balzer, Ketil Malde, Inge Jonassen:
  Systematic exploration of error sources in pyrosequencing flowgram data. 304-309
• 
  Guangxu Jin, Hong Zhao, Xiaobo Zhou, Stephen T. C. Wong:
  An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data. 310-316
• 
  David Golan, Saharon Rosset:
  Accurate estimation of heritability in genome wide studies using random effects models. 317-323
• 
  Suyash Shringarpure, Daegun Won, Eric P. Xing:
  StructHDP: automatic inference of number of clusters and population structure from admixed genotype data. 324-332
• 
  Sofia Kyriazopoulou-Panagiotopoulou, Dorna Kashef Haghighi, Sarah J. Aerni, Andreas Sundquist, Sivan Bercovici, Serafim Batzoglou:
  Reconstruction of genealogical relationships with applications to Phase III of HapMap. 333-341
• 
  Limin Li, Barbara Rakitsch, Karsten M. Borgwardt:
  ccSVM: correcting Support Vector Machines for confounding factors in biological data classification. 342-348
• 
  Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, Stefan Schulz:
  Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases. 349-356
• 
  Henning Redestig, Ivan G. Costa:
  Detection and interpretation of metabolite-transcript coresponses using combined profiling data. 357-365
• 
  Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer:
  From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. 366-373
• 
  Edoardo M. Airoldi, Katherine A. Heller, Ricardo Bezerra de Andrade e Silva:
  Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. 374-382
• 
  Pawel P. Labaj, Germán G. Leparc, Bryan E. Linggi, Lye Meng Markillie, H. Steven Wiley, David P. Kreil:
  Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. 383-391
• 
  Julia Sivriver, Naomi Habib, Nir Friedman:
  An integrative clustering and modeling algorithm for dynamical gene expression data. 392-400
• 
  Shi-Hua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou:
  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. 401-409
• 
  Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman:
  Genome Analysis. 1741-1748

Discovery Note

• 
  Yong E. Zhang, Maria D. Vibranovski, Benjamin H. Krinsky, Manyuan Long:
  A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. 1749-1753
• 
  Roberto Chignola, Vladislav Vyshemirsky, Marcello Farina, Alessio Del Fabbro, Edoardo Milotti:
  Modular model of TNFα cytotoxicity. 1754-1757

Original Papers

• 
  Zhiming Dai, Xianhua Dai, Qian Xiang:
  Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast. 1758-1764
• 
  Josue Samayoa, Fitnat H. Yildiz, Kevin Karplus:
  Identification of prokaryotic small proteins using a comparative genomic approach. 1765-1771
• 
  Qiwei Li, Xiaodan Fan, Tong Liang, Shuo-Yen Robert Li:
  An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences. 1772-1779
• 
  Tzong-Yi Lee, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, Cheng-Tsung Lu:
  Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. 1780-1787
• 
  Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai:
  A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. 1788-1797
• 
  Sungroh Yoon, Jinkyu Kim, Justine Hum, Hanjoo Kim, Seunghyun Park, Wipapat Kladwang, Rhiju Das:
  HiTRACE: high-throughput robust analysis for capillary electrophoresis. 1798-1805
• 
  Ferenc Zsila, Zsolt Bikádi, David Malik, Péter Hári, Imre Pechan, Attila Bérces, Eszter Hazai:
  Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking. 1806-1813
• 
  Tingjun Hou, Youyong Li, Wei Wang:
  Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. 1814-1821
• 
  Lori A. Dalton, Edward R. Dougherty:
  Application of the Bayesian MMSE estimator for classification error to gene expression microarray data. 1822-1831
• 
  Sushmita Roy, Margaret Werner-Washburne, Terran Lane:
  A multiple network learning approach to capture system-wide condition-specific responses. 1832-1838
• 
  Hendrik Rohn, Christian Klukas, Falk Schreiber:
  Creating views on integrated multidomain data. 1839-1845
• 
  Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park:
  Integrative gene network construction for predicting a set of complementary prostate cancer genes. 1846-1853
• 
  Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic:
  Model building and intelligent acquisition with application to protein subcellular location classification. 1854-1859
• 
  Jesse A. Gillis, Paul Pavlidis:
  The role of indirect connections in gene networks in predicting function. 1860-1866

Applications Note

• 
  Clifford A. Meyer, Housheng H. He, Myles Brown, Xiaole Shirley Liu:
  BINOCh: binding inference from nucleosome occupancy changes. 1867-1868
• 
  Brian Walenz, Liliana Florea:
  Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. 1869-1870
• 
  Fernando Muñiz-Fernandez, Angel Carreño-Torres, Carlos Morcillo-Suarez, Arcadi Navarro:
  Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management. 1871-1872
• 
  Hariklia Eleftherohorinou, Johanna C. Andersson-Assarsson, Robin G. Walters, Julia S. El-Sayed Moustafa, Lachlan J. M. Coin, Peter Jacobson, Lena M. S. Carlsson, Alexandra I. F. Blakemore, Philippe Froguel, Andrew J. Walley, Mario Falchi:
  famCNV: copy number variant association for quantitative traits in families. 1873-1875
• 
  Gabriele Sales, Chiara Romualdi:
  parmigene - a parallel R package for mutual information estimation and gene network reconstruction. 1876-1877
• 
  Matti Kankainen, Peddinti V. Gopalacharyulu, Liisa Holm, Matej Oresic:
  MPEA - metabolite pathway enrichment analysis. 1878-1879
• 
  Ross E. Curtis, Amos Yuen, Le Song, Anuj Goyal, Eric P. Xing:
  TVNViewer: An interactive visualization tool for exploring networks that change over time or space. 1880-1881
• 
  Sebastian Bauer, Peter N. Robinson, Julien Gagneur:
  Model-based gene set analysis for Bioconductor. 1882-1883

Volume 27, Number 14, July 2011

Discovery Note - Sequence Analysis

• 
  Luis Sánchez-Pulido, Chris P. Ponting:
  Cdc45: the missing RecJ ortholog in eukaryotes? 1885-1888

Original Paper - Genome Analysis

• 
  Julien Lajugie, Eric E. Bouhassira:
  GenPlay, a multipurpose genome analyzer and browser. 1889-1893
• 
  Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler:
  Computational discovery of human coding and non-coding transcripts with conserved splice sites. 1894-1900
• 
  Hieu Dinh, Sanguthevar Rajasekaran:
  A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly. 1901-1907

Sequence Analysis

• 
  Craig T. Armstrong, Thomas L. Vincent, Peter J. Green, Derek N. Woolfson:
  SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. 1908-1914
• 
  Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
  Sensitive and fast mapping of di-base encoded reads. 1915-1921
• 
  Huanying Ge, Kejun Liu, Todd Juan, Fang Fang, Matthew Newman, Wolfgang Hoeck:
  FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. 1922-1928
• 
  Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A. F. T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Henk Stunnenberg, Marc Strous, Mike S. M. Jetten, Huub J. M. Op den Camp, Martijn A. Huynen:
  FACIL: Fast and Accurate Genetic Code Inference and Logo. 1929-1933

Structural Bioinformatics

• 
  Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker:
  Fast accessibility-based prediction of RNA-RNA interactions. 1934-1940
• 
  Haim Ashkenazy, Ron Unger, Yossef Kliger:
  Hidden conformations in protein structures. 1941-1947

Gene Expression

• 
  Riet De Smet, Kathleen Marchal:
  An ensemble biclustering approach for querying gene expression compendia with experimental lists. 1948-1956

Systems Biology

• 
  Wanding Zhou, Luay Nakhleh:
  The strength of chemical linkage as a criterion for pruning metabolic graphs. 1957-1963
• 
  Gengjie Jia, Gregory Stephanopoulos, Rudiyanto Gunawan:
  Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method. 1964-1970
• 
  Ales Maver, Borut Peterlin:
  Positional integratomic approach in identification of genomic candidate regions for Parkinson's disease. 1971-1978

Data and Text Mining

• 
  Maurice Berk, Timothy M. D. Ebbels, Giovanni Montana:
  A statistical framework for biomarker discovery in metabolomic time course data. 1979-1985
• 
  Laura Tolosi, Thomas Lengauer:
  Classification with correlated features: unreliability of feature ranking and solutions. 1986-1994

Applications Note - Genome Analysis

• 
  Yufeng Shen, Ruijie Song, Itsik Pe'er:
  Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. 1995-1997
• 
  Dongliang Ge, Elizabeth K. Ruzzo, Kevin V. Shianna, Min He, Kimberly Pelak, Erin L. Heinzen, Anna C. Need, Elizabeth T. Cirulli, Jessica M. Maia, Samuel P. Dickson, Mingfu Zhu, Abanish Singh, Andrew S. Allen, David B. Goldstein:
  SVA: software for annotating and visualizing sequenced human genomes. 1998-2000

Sequence Analysis

• 
  Peter V. Troshin, James B. Procter, Geoffrey J. Barton:
  Java bioinformatics analysis web services for multiple sequence alignment - JABAWS: MSA. 2001-2002

Structural Bioinformatics

• 
  Alberto J. M. Martin, Michele Vidotto, Filippo Boscariol, Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto:
  RING: networking interacting residues, evolutionary information and energetics in protein structures. 2003-2005

Genetics and Population Analysis

• 
  Chunfa Tong, Zhong Wang, Bo Zhang, Jisen Shi, Rongling Wu:
  3FunMap: full-sib family functional mapping of dynamic traits. 2006-2008

Systems Biology

• 
  Stefan Gretar Thorleifsson, Ines Thiele:
  rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. 2009-2010
• 
  Alex T. Kalinka, Pavel Tomancak:
  linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. 2011-2012
• 
  Nicolas Rapin, Ole Lund, Filippo Castiglione:
  Immune system simulation online. 2013-2014

Data and Text Mining

• 
  Supawadee Ingsriswang, Sunai Yokwai, Duangdao Wichadakul:
  LinkinPath: from sequence to interconnected pathway. 2015-2017
• 
  David Lagorce, Julien Maupetit, Jonathan B. Baell, Olivier Sperandio, Pierre Tufféry, Maria A. Miteva, Hervé Galons, Bruno O. Villoutreix:
  The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. 2018-2020

Databases and Ontologies

• 
  Katy Wolstencroft, Stuart Owen, Matthew Horridge, Olga Krebs, Wolfgang Müller, Jacky L. Snoep, Franco B. du Preez, Carole A. Goble:
  RightField: embedding ontology annotation in spreadsheets. 2021-2022
• 
  Sudhir Kumar, S. Blair Hedges:
  TimeTree2: species divergence times on the iPhone. 2023-2024

Letter to the Editor - Data and Text Mining

• 
  Jonathan D. Wren:
  Question answering systems in biology and medicine - the time is now. 2025-2026

Volume 27, Number 15, August 2011

Discovery Note - Sequence Analysis

• 
  Ofer Isakov, Shira Modai, Noam Shomron:
  Pathogen detection using short-RNA deep sequencing subtraction and assembly. 2027-2030

Original Papers - Genome Analysis

• 
  Yong Lin, Jian Li, Hui Shen, Lei Zhang, Christopher J. Papasian, Hong-Wen Deng:
  Comparative studies of de novo assembly tools for next-generation sequencing technologies. 2031-2037
• 
  Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen, Venkatraman E. Seshan:
  Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. 2038-2046

Sequence Analysis

• 
  Vikas Bansal, Ondrej Libiger:
  A probabilistic method for the detection and genotyping of small indels from population-scale sequence data. 2047-2053
• 
  Rui Yan, Paul C. Boutros, Igor Jurisica:
  A tree-based approach for motif discovery and sequence classification. 2054-2061
• 
  Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha:
  Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. 2062-2067

Phylogenetics

• 
  Simon A. Berger, Alexandros Stamatakis:
  Aligning short reads to reference alignments and trees. 2068-2075

Structural Bioinformatics

• 
  Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou:
  Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. 2076-2082
• 
  Zengming Zhang, Yu Li, Biaoyang Lin, Michael Schroeder, Bingding Huang:
  Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. 2083-2088

Gene Expression

• 
  Martin Sill, Sebastian Kaiser, Axel Benner, Annette Kopp-Schneider:
  Robust biclustering by sparse singular value decomposition incorporating stability selection. 2089-2097
• 
  Stan Pounds, Cuilan Lani Gao, Robert A. Johnson, Karen D. Wright, Helen Poppleton, David Finkelstein, Sarah E. S. Leary, Richard J. Gilbertson:
  A procedure to statistically evaluate agreement of differential expression for cross-species genomics. 2098-2103

Genetics and Population Analysis

• 
  Harm-Jan Westra, Ritsert C. Jansen, Rudolf S. N. Fehrmann, Gerard J. te Meerman, David van Heel, Cisca Wijmenga, Lude Franke:
  MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. 2104-2111
• 
  Todd L. Edwards, Zhuo Song, Chun Li:
  Enriching targeted sequencing experiments for rare disease alleles. 2112-2118
• 
  Shujie Ma, Lijian Yang, Roberto Romero, Yuehua Cui:
  Varying coefficient model for gene-environment interaction: a non-linear look. 2119-2126

Systems Biology

• 
  Luca Beltrame, Enrica Calura, Razvan R. Popovici, Lisa Rizzetto, Damariz Rivero Guedez, Michele Donato, Chiara Romualdi, Sorin Draghici, Duccio Cavalieri:
  The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. 2127-2133
• 
  Oleg Paliy, Brent D. Foy:
  Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays. 2134-2140

Applications Note - Genome Analysis

• 
  Rong She, Jeffrey Shih-Chieh Chu, Bora Uyar, Jun Wang, Ke Wang, Nansheng Chen:
  genBlastG: using BLAST searches to build homologous gene models. 2141-2143
• 
  Joseph K. Pickrell, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard:
  False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. 2144-2146
• 
  Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin:
  CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. 2147-2148
• 
  Oscar Flores, Modesto Orozco:
  nucleR: a package for non-parametric nucleosome positioning. 2149-2150

Sequence Analysis

• 
  Thomas K. F. Wong, Kwok-Lung Wan, Bay-Yuan Hsu, Brenda W. Y. Cheung, Wing-Kai Hon, Tak Wah Lam, Siu-Ming Yiu:
  RNASAlign: RNA Structural Alignment System. 2151-2152
• 
  Aurelien Ginolhac, Morten Rasmussen, M. Thomas P. Gilbert, Eske Willerslev, Ludovic Orlando:
  mapDamage: testing for damage patterns in ancient DNA sequences. 2153-2155
• 
  Petr Danecek, Adam Auton, Gonçalo R. Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin:
  The variant call format and VCFtools. 2156-2158
• 
  Luca Pireddu, Simone Leo, Gianluigi Zanetti:
  SEAL: a distributed short read mapping and duplicate removal tool. 2159-2160

Structural Bioinformatics

• 
  Mark Moll, Drew H. Bryant, Lydia E. Kavraki:
  The LabelHash Server and Tools for substructure-based functional annotation. 2161-2162
• 
  Abdullah Kahraman, Lars Malmström, Ruedi Aebersold:
  Xwalk: computing and visualizing distances in cross-linking experiments. 2163-2164

Systems Biology

• 
  Augustin Luna, Margot Sunshine, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn:
  PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). 2165-2166
• 
  Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka:
  JSBML: a flexible Java library for working with SBML. 2167-2168

Letter to the Editor - Gene Expression

• 
  Xin-Yuan Song, Zhaohua Lu:
  Response to "Comments on 'Bayesian variable selection for disease classification using gene expression data'". 2169-2170

Corrigendum - Gene Expression

• 
  Susanne Balzer, Ketil Malde, Anders Lanzén, Animesh Sharma, Inge Jonassen:
  Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim. 2171

Volume 27, Number 16, August 2011

Original Papers - Genome Analysis

• 
  Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, David E. Salt, Olga Vitek:
  Noise reduction in genome-wide perturbation screens using linear mixed-effect models. 2173-2180
• 
  Lucy F. Stead, I. C. Wood, David R. Westhead:
  KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels. 2181-2186
• 
  Eva-Maria Willing, Margarete Hoffmann, Juliane Damaris Klein, Detlef Weigel, Christine Dreyer:
  Paired-end RAD-seq for de novo assembly and marker design without available reference. 2187-2193

Sequence Analysis

• 
  Robert C. Edgar, Brian J. Haas, José Carlos Clemente, Christopher Quince, Rob Knight:
  UCHIME improves sensitivity and speed of chimera detection. 2194-2200

Structural Bioinformatics

• 
  Yong-Min Lao, Lan Xiao, Zhi-Wei Ye, Jian-Guo Jiang, Shi-Shui Zhou:
  In silico analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis in Duanliella bardawil. 2201-2208
• 
  Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan:
  Gaia: automated quality assessment of protein structure models. 2209-2215
• 
  Seymour Knowles-Barley, Nancy J. Butcher, Ian A. Meinertzhagen, J. Douglas Armstrong:
  Biologically inspired EM image alignment and neural reconstruction. 2216-2223
• 
  Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio:
  Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. 2224-2230

Gene Expression

• 
  Matthias Maneck, Alexandra Schrader, Dieter Kube, Rainer Spang:
  Genomic data integration using guided clustering. 2231-2238
• 
  Tobias Bauer, Roland Eils, Rainer König:
  RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors. 2239-2247

Systems Biology

• 
  Stephan Symons, Kay Nieselt:
  MGV: a generic graph viewer for comparative omics data. 2248-2255
• 
  Siu Hung Joshua Chan, Ping Ji:
  Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. 2256-2262
• 
  Thomas Schaffter, Daniel Marbach, Dario Floreano:
  GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. 2263-2270

Data and Text Mining

• 
  Sanjay Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons:
  Enhancing the rate of scaffold discovery with diversity-oriented prioritization. 2271-2278
• 
  Timothy Driscoll, Joseph L. Gabbard, Chunhong Mao, Oral Dalay, Maulik Shukla, Clark C. Freifeld, Anne Gatewood Hoen, John S. Brownstein, Bruno W. S. Sobral:
  Integration and visualization of host-pathogen data related to infectious diseases. 2279-2287

Databases and Ontologies

• 
  Carissa G. Fonseca, Michael Backhaus, David A. Bluemke, Randall Britten, Jae Do Chung, Brett R. Cowan, Ivo D. Dinov, J. Paul Finn, Peter J. Hunter, Alan H. Kadish, Daniel C. Lee, Joao A. C. Lima, Pau Medrano-Gracia, Kalyanam Shivkumar, Avan Suinesiaputra, Wenchao Tao, Alistair A. Young:
  The Cardiac Atlas Project - an imaging database for computational modeling and statistical atlases of the heart. 2288-2295

Applications Note - Genome Analysis

• 
  Yurong Xin, Yongchao Ge, Fatemeh G. Haghighi:
  Methyl-Analyzer - whole genome DNA methylation profiling. 2296-2297
• 
  Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Sufeng Chiang, Jen-Hao Cheng, Francis C. Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai:
  MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering. 2298-2299

Sequence Analysis

• 
  Jason R. Grant, Adriano S. Arantes, Xiaoping Liao, Paul Stothard:
  In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. 2300-2301
• 
  Xinyi Liu, Xubo Su, Fei Wang, Zhimin Huang, Qi Wang, Zhen Li, Ruina Zhang, Lifang Wu, Yi Pan, Yingyi Chen, Hanyi Zhuang, Guoqiang Chen, Ting Shi, Jian Zhang:
  ODORactor: a web server for deciphering olfactory coding. 2302-2303

Genetics and Population Analysis

• 
  Zhan Su, Jonathan Marchini, Peter Donnelly:
  HAPGEN2: simulation of multiple disease SNPs. 2304-2305
• 
  Martin Konopac, Petra Dusatkova, Ondrej Cinek:
  SNPman: a program for genotype calling using run data from TaqMan allelic discrimination. 2306-2308

Systems Biology

• 
  Hamid Bolouri, Rajiv Dulepet, Michael Angerman:
  Menu-driven cloud computing and resource sharing for R and Bioconductor. 2309-2310
• 
  Eva Balsa-Canto, Julio R. Banga:
  AMIGO, a toolbox for advanced model identification in systems biology using global optimization. 2311-2313
• 
  Clemens Wrzodek, Andreas Dräger, Andreas Zell:
  KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. 2314-2315
• 
  Raphael B. M. Aggio, Silas Granato Villas-Bôas, Katya Ruggiero:
  Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. 2316-2318
• 
  Jialiang Huang, Yi Liu, Wei Zhang, Hong Yu, Jing-Dong J. Han:
  eResponseNet: a package prioritizing candidate disease genes through cellular pathways. 2319-2320

Data and Text Mining

• 
  Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman:
  CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. 2321-2322

Corrigendum - Data and Text Mining

• 
  Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman:
  Bioinformatics challenges for personalized medicine. 2323

Volume 27, Number 17, September 2011

Original Papers - Genome Analysis

• 
  Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter:
  Identification of novel transcripts in annotated genomes using RNA-Seq. 2325-2329
• 
  Fabian Menges, Giuseppe Narzisi, Bud Mishra:
  TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. 2330-2337
• 
  Catherine Stamoulis, Rebecca A. Betensky:
  A novel signal processing approach for the detection of copy number variations in the human genome. 2338-2345
• 
  Hisanori Kiryu:
  Sufficient statistics and expectation maximization algorithms in phylogenetic tree models. 2346-2353

Sequence Analysis

• 
  Robert C. McLeay, Chris J. Leat, Timothy L. Bailey:
  Tissue-specific prediction of directly regulated genes. 2354-2360
• 
  Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph:
  DECOD: fast and accurate discriminative DNA motif finding. 2361-2367

Structural Bioinformatics

• 
  Alexander Goncearenco, Igor N. Berezovsky:
  Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. 2368-2375
• 
  Miguel Rojas-Chertó, Piotr T. Kasper, Egon L. Willighagen, Rob J. Vreeken, Thomas Hankemeier, Theo H. Reijmers:
  Elemental composition determination based on MSⁿ. 2376-2383
• 
  Ivano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato:
  A Grid-enabled web portal for NMR structure refinement with AMBER. 2384-2390

Gene Expression

• 
  Mikhail Jiline, Stan Matwin, Marcel Turcotte:
  Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments. 2391-2398

Systems Biology

• 
  Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano:
  A rank-based statistical test for measuring synergistic effects between two gene sets. 2399-2405
• 
  Yiming Lu, Yang Zhou, Wubin Qu, Minghua Deng, Chenggang Zhang:
  A Lasso regression model for the construction of microRNA-target regulatory networks. 2406-2413

Databases and Ontologies

• 
  Tiago J. S. Lopes, Martin H. Schaefer, Jason E. Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Gabriele Neumann, Miguel A. Andrade-Navarro, Yoshihiro Kawaoka, Hiroaki Kitano:
  Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. 2414-2421
• 
  Alan Tan, Ben W. Tripp, Denise Daley:
  BRISK - research-oriented storage kit for biology-related data. 2422-2425

Applications Note - Genome Analysis

• 
  Daniel J. Blankenberg, James Taylor, Anton Nekrutenko:
  Making whole genome multiple alignments usable for biologists. 2426-2428
• 
  Mitchell J. Brittnacher, Christine Fong, H. S. Hayden, M. A. Jacobs, Matthew Radey, Laurence Rohmer:
  PGAT: a multistrain analysis resource for microbial genomes. 2429-2430
• 
  Matthew Z. DeMaere, Federico M. Lauro, Torsten Thomas, Sheree Yau, Ricardo Cavicchioli:
  Simple high-throughput annotation pipeline (SHAP). 2431-2432

Sequence Analysis

• 
  Lucian Ilie, Silvana Ilie, Anahita Mansouri Bigvand:
  SpEED: fast computation of sensitive spaced seeds. 2433-2434
• 
  Brent Pedersen, Tzung-Fu Hsieh, Christian Ibarra, Robert L. Fischer:
  MethylCoder: software pipeline for bisulfite-treated sequences. 2435-2436

Phylogenetics

• 
  Jonathan M. Eastman, C. E. Timothy Paine, Olivier J. Hardy:
  spacodiR: structuring of phylogenetic diversity in ecological communities. 2437-2438
• 
  Martin Ryberg, R. Henrik Nilsson, P. Brandon Matheny:
  DivBayes and SubT: exploring species diversification using Bayesian statistics. 2439-2440

Structural Bioinformatics

• 
  Magdalena Rother, Kaja Milanowska, Tomasz Puton, Jaroslaw Jeleniewicz, Kristian Rother, Janusz M. Bujnicki:
  ModeRNA server: an online tool for modeling RNA 3D structures. 2441-2442
• 
  J. Y. Semegni, Mark Wamalwa, R. Gaujoux, G. W. Harkins, A. Gray, D. P. Martin:
  NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. 2443-2445

Gene Expression

• 
  Francesco Ferrari, Aldo Solari, Cristina Battaglia, Silvio Bicciato:
  PREDA: an R-package to identify regional variations in genomic data. 2446-2447

Genetics and Population Analysis

• 
  Asif Javed, Marc Pybus, Marta Melé, Filippo Utro, Jaume Bertranpetit, Francesc Calafell, Laxmi Parida:
  IRiS: Construction of ARG networks at genomic scales. 2448-2450

Systems Biology

• 
  Jan Bot, Marcel J. T. Reinders:
  CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages. 2451-2452
• 
  Mark Longair, Dean A. Baker, J. Douglas Armstrong:
  Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. 2453-2454
• 
  Jianguo Xia, Igor Sinelnikov, David S. Wishart:
  MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. 2455-2456
• 
  Kevin R. Sanft, Sheng Wu, Min K. Roh, Jin Fu, Rone Kwei Lim, Linda R. Petzold:
  StochKit2: software for discrete stochastic simulation of biochemical systems with events. 2457-2458
• 
  Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente:
  Simulating systems genetics data with SysGenSIM. 2459-2462

Data and Text Mining

• 
  Ulrich Bodenhofer, Andreas Kothmeier, Sepp Hochreiter:
  APCluster: an R package for affinity propagation clustering. 2463-2464
• 
  Qian-Nan Hu, Zhe Deng, Huanan Hu, Dong-Sheng Cao, Yi-Zeng Liang:
  RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity. 2465-2467

Databases and Ontologies

• 
  Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris A. Swertz, Misha Kapushesky:
  ontoCAT: an R package for ontology traversal and search. 2468-2470
• 
  Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano:
  CSO validator: improving manual curation workflow for biological pathways. 2471-2472

Volume 27, Number 18, September 2011

Discovery Note - Genome Analysis

• 
  Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E. Thasler, Ulrich M. Zanger, Andreas Zell:
  Inferring statin-induced gene regulatory relationships in primary human hepatocytes. 2473-2477

Original Papers - Genome Analysis

• 
  Luciana Ferrer, Alexander Glennon Shearer, Peter D. Karp:
  Discovering novel subsystems using comparative genomics. 2478-2485

Sequence Analysis

• 
  Donglai Wei, Lauren V. Alpert, Charles E. Lawrence:
  RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. 2486-2493
• 
  Dong Seon Kim, Yoonsoo Hahn:
  Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence. 2494-2501
• 
  Ergude Bao, Tao Jiang, Isgouhi Kaloshian, Thomas Girke:
  SEED: efficient clustering of next-generation sequences. 2502-2509
• 
  Matej Lexa, Tomás Martínek, Ivana Burgetova, Daniel Kopecek, Marie Brázdová:
  A dynamic programming algorithm for identification of triplex-forming sequences. 2510-2517
• 
  Gregory R. Grant, Michael H. Farkas, Angel D. Pizarro, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert Jr., John B. Hogenesch, Eric A. Pierce:
  Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). 2518-2528

Structural Bioinformatics

• 
  Qian Liu, Steven C. H. Hoi, Chinh T. T. Su, Zhenhua Li, Chee Keong Kwoh, Limsoon Wong, Jinyan Li:
  Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding? 2529-2536
• 
  Sheng Wang, Jian Peng, Jinbo Xu:
  Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. 2537-2545

Gene Expression

• 
  Lan Zagar, Francesca Mulas, Silvia Garagna, Maurizio Zuccotti, Riccardo Bellazzi, Blaz Zupan:
  Stage prediction of embryonic stem cell differentiation from genome-wide expression data. 2546-2553
• 
  Hui Yuan Xiong, Yoseph Barash, Brendan J. Frey:
  Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. 2554-2562
• 
  Inka J. Appel, Wolfram Gronwald, Rainer Spang:
  Estimating classification probabilities in high-dimensional diagnostic studies. 2563-2570

Genetics and Population Analysis

• 
  Fan Xia, Ji-Yuan Zhou, Wing Kam Fung:
  A powerful approach for association analysis incorporating imprinting effects. 2571-2577
• 
  Can Yang, Xiaowei Zhou, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu:
  Identifying disease-associated SNP clusters via contiguous outlier detection. 2578-2585

Data and Text Mining

• 
  Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai, Wen-Lian Hsu:
  Integration of gene normalization stages and co-reference resolution using a Markov logic network. 2586-2594

Applications Note - Genome Analysis

• 
  Igor Lukashin, Pavel S. Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak:
  VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies. 2595-2597

Sequence Analysis

• 
  Ying Wang, Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew P. Clark, Hee Jae Yoon, Lin Wan, Oleg V. Evgrafov, James A. Knowles, Ewa Deelman, Ting Chen:
  RseqFlow: workflows for RNA-Seq data analysis. 2598-2600
• 
  Kristian Cibulskis, Aaron McKenna, Tim Fennell, Eric Banks, Mark A. DePristo, Gad Getz:
  ContEst: estimating cross-contamination of human samples in next-generation sequencing data. 2601-2602

Phylogenetics

• 
  Marc J. Lajeunesse:
  phyloMeta: a program for phylogenetic comparative analyses with meta-analysis. 2603-2604

Structural Bioinformatics

• 
  David Fournier, Miguel A. Andrade-Navarro:
  PDBpaint, a visualization webservice to tag protein structures with sequence annotations. 2605-2606

Systems Biology

• 
  Li Chen, Tsung-Han Chan, Peter L. Choyke, Elizabeth M. C. Hillman, Chong-Yung Chi, Zaver M. Bhujwalla, Ge Wang, Sean S. Wang, Zsolt Szabo, Yue Joseph Wang:
  CAM-CM: a signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues. 2607-2609
• 
  Oana Chis, Julio R. Banga, Eva Balsa-Canto:
  GenSSI: a software toolbox for structural identifiability analysis of biological models. 2610-2611
• 
  Florian Battke, Stephan Symons, Alexander Herbig, Kay Nieselt:
  GaggleBridge: collaborative data analysis. 2612-2613

Data and Text Mining

• 
  Xiaozeng Yang, Lei Li:
  miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. 2614-2615

Databases and Ontologies

• 
  Jose M. Villaveces, Rafael C. Jiménez, Leyla J. García, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob:
  Dasty3, a WEB framework for DAS. 2616-2617
• 
  Jacek Sroka, Lukasz Krupa, Andrzej M. Kierzek, Jerzy Tyszkiewicz:
  CalcTav - integration of a spreadsheet and Taverna workbench. 2618-2619

Volume 27, Number 19, October 2011

Discovery Note - Sequence Analysis

• 
  Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalia G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod J. Makeev:
  A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. 2621-2624

Original Papers - Sequence Analysis

• 
  Mengyuan Xu, Clarice R. Weinberg, David M. Umbach, Leping Li:
  coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data. 2625-2632
• 
  Darshan Singh, Christian F. Orellana, Yin Hu, Corbin D. Jones, Yufeng Liu, Derek Y. Chiang, Jinze Liu, Jan F. Prins:
  FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. 2633-2640
• 
  He Quan Sun, Malcolm Yoke Hean Low, Wen-Jing Hsu, Ching-Wai Tan, Jagath C. Rajapakse:
  Tree-structured algorithm for long weak motif discovery. 2641-2647
• 
  Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson:
  Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. 2648-2654
• 
  Daniel Gaston, Edward Susko, Andrew J. Roger:
  A phylogenetic mixture model for the identification of functionally divergent protein residues. 2655-2663

Phylogenetics

• 
  Aïda Ouangraoua, Eric Tannier, Cédric Chauve:
  Reconstructing the architecture of the ancestral amniote genome. 2664-2671

Gene Expression

• 
  Yi-Hui Zhou, Kai Xia, Fred A. Wright:
  A powerful and flexible approach to the analysis of RNA sequence count data. 2672-2678

Systems Biology

• 
  Yinyin Yuan, Oscar M. Rueda, Christina Curtis, Florian Markowetz:
  Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. 2679-2685
• 
  Zheng Li, Ping Li, Arun Krishnan, Jingdong Liu:
  Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis. 2686-2691
• 
  TaeHyun Hwang, Wei Zhang, Maoqiang Xie, Jinfeng Liu, Rui Kuang:
  Inferring disease and gene set associations with rank coherence in networks. 2692-2699
• 
  Chih-Hung Wu, Hsiao-Ching Lee, Bor-Sen Chen:
  Robust synthetic gene network design via library-based search method. 2700-2706
• 
  Orland R. Gonzalez, Ralf Zimmer:
  Contextual analysis of RNAi-based functional screens using interaction networks. 2707-2713
• 
  Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro:
  Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. 2714-2720

Data and Text Mining

• 
  Nona Naderi, Thomas Kappler, Christopher J. O. Baker, René Witte:
  OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents. 2721-2729
• 
  Xinglong Wang, Iain McKendrick, Ian Barrett, Ian Dix, Tim French, Jun'ichi Tsujii, Sophia Ananiadou:
  Automatic extraction of angiogenesis bioprocess from text. 2730-2737
• 
  Domingo S. Rodríguez-Baena, Antonio J. Pérez-Pulido, Jesús S. Aguilar-Ruiz:
  A biclustering algorithm for extracting bit-patterns from binary datasets. 2738-2745
• 
  Elizabeth Rossin, Tsung-I Lin, Hsiu J. Ho, Steven J. Mentzer, Saumyadipta Pyne:
  A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues. 2746-2753

Applications Note - Genome Analysis

• 
  Ricardo Ramirez-Gonzalez, Mario Cáccamo, Daniel MacLean:
  Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data. 2754-2755
• 
  Aaron E. Darling, Andrew J. Tritt, Jonathan A. Eisen, Marc T. Facciotti:
  Mauve Assembly Metrics. 2756-2757

Phylogenetics

• 
  Cuong Cao Dang, Vincent Lefort, Le Sy Vinh, Si Quang Le, Olivier Gascuel:
  ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices. 2758-2760

Systems Biology

• 
  Georg Basler, Zoran Nikoloski:
  JMassBalance: mass-balanced randomization and analysis of metabolic networks. 2761-2762
• 
  Christoph Gille, Katrin Hübner, Andreas Hoppe, Hermann-Georg Holzhütter:
  Metannogen: annotation of biological reaction networks. 2763-2764
• 
  Xuan Vinh Nguyen, Madhu Chetty, Ross L. Coppel, Pramod P. Wangikar:
  GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion. 2765-2766
• 
  Duc-Hau Le, Yung-Keun Kwon:
  NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks. 2767-2768

Data and Text Mining

• 
  Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman:
  The GNAT library for local and remote gene mention normalization. 2769-2771

Databases and Ontologies

• 
  Yoona Kim, Steven Bark, Vivian Hook, Nuno Bandeira:
  NeuroPedia: neuropeptide database and spectral library. 2772-2773

Volume 27, Number 20, October 2011

Original Papers - Genome Analysis

• 
  Xiaohua Douglas Zhang, Francesca Santini, Raul Lacson, Shane D. Marine, Qian Wu, Luca Benetti, Ruojing Yang, Alex McCampbell, Joel P. Berger, Dawn M. Toolan, Erica M. Stec, Daniel J. Holder, Keith A. Soper, Joseph F. Heyse, Marc Ferrer:
  cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens. 2775-2781

Sequence Analysis

• 
  Lucía Spangenberg, Florian Battke, Martí Graña, Kay Nieselt, Hugo Naya:
  Identifying associations between amino acid changes and meta information in alignments. 2782-2789
• 
  Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk:
  Comparative analysis of algorithms for next-generation sequencing read alignment. 2790-2796
• 
  Tilo Eißler, Christopher P. Hodges, Harald Meier:
  PTPan - overcoming memory limitations in oligonucleotide string matching for primer/probe design. 2797-2805
• 
  Eugen Fazius, Vladimir Shelest, Ekaterina Shelest:
  SiTaR: a novel tool for transcription factor binding site prediction. 2806-2811
• 
  Catherine Mooney, Yong-Hong Wang, Gianluca Pollastri:
  SCLpred: protein subcellular localization prediction by N-to-1 neural networks. 2812-2819

Structural Bioinformatics

• 
  Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie:
  Spatial clustering of protein binding sites for template based protein docking. 2820-2827
• 
  Ying Shen, Hau-San Wong, Shaohong Zhang, Zhiwen Yu:
  Feature-based 3D motif filtering for ribosomal RNA. 2828-2835
• 
  Elad Donsky, Haim J. Wolfson:
  PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors. 2836-2842
• 
  José Ramón López-Blanco, José Ignacio Garzón, Pablo Chacón:
  iMod: multipurpose normal mode analysis in internal coordinates. 2843-2850

Gene Expression

• 
  Zhengyu Ouyang, Mingzhou Song, Robert Güth, Thomas Ha, Matt Larouche, Daniel Goldowitz:
  Conserved and differential gene interactions in dynamical biological systems. 2851-2858
• 
  Pushpike Jayantha Thilakarathne, Lieven Clement, Dan Lin, Ziv Shkedy, Adetayo Kasim, Willem Talloen, Matthias Versele, Geert Verbeke:
  The use of semiparametric mixed models to analyze PamChip^® peptide array data: an application to an oncology experiment. 2859-2865
• 
  Melissa M. Matzke, Katrina M. Waters, Thomas O. Metz, Jon M. Jacobs, Amy C. Sims, Ralph S. Baric, Joel G. Pounds, Bobbie-Jo M. Webb-Robertson:
  Improved quality control processing of peptide-centric LC-MS proteomics data. 2866-2872
• 
  Andrea Ocone, Guido Sanguinetti:
  Reconstructing transcription factor activities in hierarchical transcription network motifs. 2873-2879

Genetics and Population Analysis

• 
  Barak Markus, Ohad S. Birk, Dan Geiger:
  Integration of SNP genotyping confidence scores in IBD inference. 2880-2887

Systems Biology

• 
  Anthony R. Soltis, Jeffrey J. Saucerman:
  Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty. 2888-2894

Data and Text Mining

• 
  Lei Qu, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers, Hanchuan Peng:
  Simultaneous recognition and segmentation of cells: application in C.elegans. 2895-2902

Applications Note - Genome Analysis

• 
  Matthew K. Iyer, Arul M. Chinnaiyan, Christopher A. Maher:
  ChimeraScan: a tool for identifying chimeric transcription in sequencing data. 2903-2904
• 
  Arnaud Despalins, Souhir Marsit, Jacques Oberto:
  Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters. 2905-2906

Sequence Analysis

• 
  Bernd Jagla, Bernd Wiswedel, Jean-Yves Coppée:
  Extending KNIME for next-generation sequencing data analysis. 2907-2909

Phylogenetics

• 
  Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey:
  SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. 2910-2912

Structural Bioinformatics

• 
  Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley:
  Fast and accurate prediction of protein side-chain conformations. 2913-2914
• 
  Anna Vangone, Raffaele Spinelli, Vittorio Scarano, Luigi Cavallo, Romina Oliva:
  COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes. 2915-2916

Systems Biology

• 
  Atanas Kamburov, Rachel Cavill, Timothy M. D. Ebbels, Ralf Herwig, Hector C. Keun:
  Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. 2917-2918

Data and Text Mining

• 
  Jike Cui, Todd F. DeLuca, Jae-Yoon Jung, Dennis P. Wall:
  Detecting biological network organization and functional gene orthologs. 2919-2920
• 
  Rui-Ru Ji, Nathan O. Siemers, Ming Lei, Liang Schweizer, Robert E. Bruccoleri:
  SDRS - an algorithm for analyzing large-scale dose-response data. 2921-2923

Databases and Ontologies

• 
  Christina M. Bergey:
  AluHunter: a database of potentially polymorphic Alu insertions for use in primate phylogeny and population genetics. 2924-2925

Volume 27, Number 21, November 2011

Reviews- Sequence Analysis

• 
  Brett Trost, Anthony J. Kusalik:
  Computational prediction of eukaryotic phosphorylation sites. 2927-2935

Genetics and Population Analysis

• 
  Yue Wang, Guimei Liu, Mengling Feng, Limsoon Wong:
  An empirical comparison of several recent epistatic interaction detection methods. 2936-2943

Discovery Note - Systems Biology

• 
  Chaitanya A. Athale, Hemangi Chaudhari:
  Population length variability and nucleoid numbers in Escherichia coli. 2944-2948

Original Papers - Genome Analysis

• 
  Sandro Morganella, Stefano Maria Pagnotta, Michele Ceccarelli:
  Finding recurrent copy number alterations preserving within-sample homogeneity. 2949-2956
• 
  Tanja Magoc, Steven L. Salzberg:
  FLASH: fast length adjustment of short reads to improve genome assemblies. 2957-2963
• 
  Sergey Koren, Todd J. Treangen, Mihai Pop:
  Bambus 2: scaffolding metagenomes. 2964-2971

Sequence Analysis

• 
  Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang:
  Correlated evolution of transcription factors and their binding sites. 2972-2978
• 
  Sebastian Deorowicz, Szymon Grabowski:
  Robust relative compression of genomes with random access. 2979-2986
• 
  Heng Li:
  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. 2987-2993

Structural Bioinformatics

• 
  Yuan Li, Shaojie Zhang:
  Finding stable local optimal RNA secondary structures. 2994-3001
• 
  Iain H. Moal, Rudi Agius, Paul A. Bates:
  Protein-protein binding affinity prediction on a diverse set of structures. 3002-3009

Gene Expression

• 
  Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang:
  SpliceTrap: a method to quantify alternative splicing under single cellular conditions. 3010-3016
• 
  Mingguang Shi, Bing Zhang:
  Semi-supervised learning improves gene expression-based prediction of cancer recurrence. 3017-3023

Systems Biology

• 
  Yungki Park, Edward M. Marcotte:
  Revisiting the negative example sampling problem for predicting protein-protein interactions. 3024-3028
• 
  Genevera I. Allen, Mirjana Maletic-Savatic:
  Sparse non-negative generalized PCA with applications to metabolomics. 3029-3035

Data and Text Mining

• 
  Twan van Laarhoven, Sander B. Nabuurs, Elena Marchiori:
  Gaussian interaction profile kernels for predicting drug-target interaction. 3036-3043
• 
  Bin Chen, Kevin J. McConnell, Nikil Wale, David J. Wild, Eric M. Gifford:
  Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology. 3044-3049
• 
  X. G. Zhao, W. Dai, Y. Li, Lu Tian:
  AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density. 3050-3055
• 
  Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty:
  High-dimensional bolstered error estimation. 3056-3064

Applications Note - Genetics and Population Analysis

• 
  Huat Chye Lim, Marcel E. Curlin, John E. Mittler:
  HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens. 3065-3066
• 
  Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight:
  TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. 3067-3069
• 
  Thibaut Jombart, Ismaïl Ahmed:
  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. 3070-3071

Systems Biology

• 
  Ananth Kalyanaraman, William R. Cannon, Benjamin Latt, Douglas J. Baxter:
  MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification. 3072-3073

Data and Text Mining

• 
  Simon Roux, Michaël Faubladier, Antoine Mahul, Nils Paulhe, Aurélien Bernard, Didier Debroas, François Enault:
  Metavir: a web server dedicated to virome analysis. 3074-3075

Databases and Ontologies

• 
  Wenming Zhao, Wanfei Liu, Dongmei Tian, Bixia Tang, Yanqing Wang, Caixia Yu, Rujiao Li, Yunchao Ling, Jiayan Wu, Shuhui Song, Songnian Hu:
  wapRNA: a web-based application for the processing of RNA sequences. 3076-3077

Volume 27, Number 22, November 2011

Discovery Note - Genome Analysis

• 
  Kai Wang, Rasmus Wernersson, Søren Brunak:
  The strength of intron donor splice sites in human genes displays a bell-shaped pattern. 3079-3084

Original Papers - Genome Analysis

• 
  Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai:
  Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. 3085-3092
• 
  Naama Elefant, Yael Altuvia, Hanah Margalit:
  A wide repertoire of miRNA binding sites: prediction and functional implications. 3093-3101

Sequence Analysis

• 
  Diana L. Kolbe, Sean R. Eddy:
  Fast filtering for RNA homology search. 3102-3109

Structural Bioinformatics

• 
  Ivan Kalev, Michael Habeck:
  HHfrag: HMM-based fragment detection using HHpred. 3110-3116
• 
  Zhichao Miao, Yang Cao, Taijiao Jiang:
  RASP: rapid modeling of protein side chain conformations. 3117-3122
• 
  Castrense Savojardo, Piero Fariselli, Rita Casadio:
  Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. 3123-3128

Gene Expression

• 
  Kevin K. Dobbin, Stephanie Cooke:
  Lower confidence bounds for prediction accuracy in high dimensions via AROHIL Monte Carlo. 3129-3134
• 
  Christopher Minas, Simon J. Waddell, Giovanni Montana:
  Distance-based differential analysis of gene curves. 3135-3141
• 
  Yu-Cheng Liu, Chun-Pei Cheng, Vincent S. Tseng:
  Discovering relational-based association rules with multiple minimum supports on microarray datasets. 3142-3148

Systems Biology

• 
  Joana P. Gonçalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira, Sara C. Madeira:
  TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. 3149-3157
• 
  Ruiqi Wang, Kaihui Liu, Luonan Chen, Kazuyuki Aihara:
  Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling. 3158-3165
• 
  Anna Goldenberg, Sara Mostafavi, Gerald T. Quon, Paul C. Boutros, Quaid Morris:
  Unsupervised detection of genes of influence in lung cancer using biological networks. 3166-3172
• 
  Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang:
  An efficient network querying method based on conditional random fields. 3173-3178

Data and Text Mining

• 
  Yufan Guo, Anna Korhonen, Ilona Silins, Ulla Stenius:
  Weakly supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine? 3179-3185
• 
  Solange Delagenière, Patrice Brenchereau, Ludovic Launer, Alun W. Ashton, Ricardo Leal, Stéphanie Veyrier, José Gabadinho, Elspeth J. Gordon, Samuel D. Jones, Karl Erik Levik, Seán M. McSweeney, Stéphanie Monaco, Max Nanao, Darren Spruce, Olof Svensson, Martin A. Walsh, Gordon A. Leonard:
  ISPyB: an information management system for synchrotron macromolecular crystallography. 3186-3192

Databases and Ontologies

• 
  Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig:
  PIDO: the primary immunodeficiency disease ontology. 3193-3199

Applications Note - Genome Analysis

• 
  Pierre Lindenbaum, Solena Le Scouarnec, Vincent Portero, Richard Redon:
  Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME. 3200-3201

Sequence Analysis

• 
  Lorena Pantano, Xavier Estivill, Eulalia Martí:
  A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. 3202-3203

Gene Expression

• 
  Jonatan Taminau, David Steenhoff, Alain Coletta, Stijn Meganck, Cosmin Lazar, Virginie de Schaetzen, Robin Duque, Colin Molter, Hugues Bersini, Ann Nowé, David Y. Weiss Solís:
  inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. 3204-3205
• 
  Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains:
  survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. 3206-3208
• 
  Eleanor Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush:
  RNA-Seq analysis in MeV. 3209-3210

Systems Biology

• 
  Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips:
  Visual DSD: a design and analysis tool for DNA strand displacement systems. 3211-3213

Data and Text Mining

• 
  Zeqiang Ma, David L. Tabb, Joseph Burden, Matthew Chambers, Matthew B. Cox, Michael J. Cantrell, Amy-Joan L. Ham, Michael D. Litton, Michael R. Oreto, William C. Schultz, Scott M. Sobecki, Tina Y. Tsui, Gregory R. Wernke, Daniel C. Liebler:
  Supporting tool suite for production proteomics. 3214-3215

Databases and Ontologies

• 
  Gustavo Glusman, Juan Caballero, Denise E. Mauldin, Leroy E. Hood, Jared C. Roach:
  Kaviar: an accessible system for testing SNV novelty. 3216-3217
• 
  Meng-Pin Weng, Ben-Yang Liao:
  DroPhEA: Drosophila phenotype enrichment analysis for insect functional genomics. 3218-3219

Volume 27, Number 23, December 2011

Original Papers - Genome Analysis

• 
  Chao Cheng, Renqiang Min, Mark Gerstein:
  TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. 3221-3227
• 
  Jin Zhang, Yufeng Wu:
  SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. 3228-3234
• 
  Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård:
  Sequential Monte Carlo multiple testing. 3235-3241

Sequence Analysis

• 
  Zhenqiu Liu, William Hsiao, Brandi L. Cantarel, Elliott Franco Drábek, Claire Fraser-Liggett:
  Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. 3242-3249
• 
  Siavash Mirarab, Tandy J. Warnow:
  FASTSP: linear time calculation of alignment accuracy. 3250-3258
• 
  Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen:
  Fast scaffolding with small independent mixed integer programs. 3259-3265
• 
  Minmei Hou, Ping Yao, Angela Antonou, Mitrick A. Johns:
  Pico-inplace-inversions between human and chimpanzee. 3266-3275

Structural Bioinformatics

• 
  Peter Schmidtke, Axel Bidon-Chanal, F. Javier Luque, Xavier Barril:
  MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. 3276-3285
• 
  Gilad Wainreb, Lior Wolf, Haim Ashkenazy, Yves Dehouck, Nir Ben-Tal:
  Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. 3286-3292

Gene Expression

• 
  Shuiwang Ji:
  Computational network analysis of the anatomical and genetic organizations in the mouse brain. 3293-3299
• 
  A. Sofia Silva, Shona H. Wood, Sipko van Dam, Sven Berres, Anne McArdle, João Pedro de Magalhães:
  Gathering insights on disease etiology from gene expression profiles of healthy tissues. 3300-3305

Data and Text Mining

• 
  Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
  Extraction of data deposition statements from the literature: a method for automatically tracking research results. 3306-3312

Applications Note - Genome Analysis

• 
  Michal Wozniak, Limsoon Wong, Jerzy Tiuryn:
  CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains. 3313-3314

Structural Bioinformatics

• 
  Alex D. Stivala, Michael Wybrow, Anthony Wirth, James C. Whisstock, Peter J. Stuckey:
  Automatic generation of protein structure cartoons with Pro-origami. 3315-3316

Gene Expression

• 
  Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel Dudley, Rohan Mallelwar, Atul J. Butte:
  ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. 3317-3318
• 
  Sudhir Kumar, Charlotte Konikoff, Bernard Van Emden, Christopher Busick, Kailah T. Davis, Shuiwang Ji, Lin-Wei Wu, Hector Ramos, Thomas Brody, Sethuraman Panchanathan, Jieping Ye, Timothy L. Karr, Kristyn Gerold, Michael McCutchan, Stuart J. Newfeld:
  FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. 3319-3320

Systems Biology

• 
  Donglin Huang, Yiling Huang, Youhuang Bai, Dijun Chen, Ralf Hofestädt, Christian Klukas, Ming Chen:
  MyBioNet: interactively visualize, edit and merge biological networks on the Web. 3321-3322
• 
  Jonathan Blakes, Jamie Twycross, Francisco José Romero-Campero, Natalio Krasnogor:
  The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. 3323-3324
• 
  Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin, Roded Sharan:
  PRINCIPLE: a tool for associating genes with diseases via network propagation. 3325-3326

Data and Text Mining

• 
  Nikolas Papanikolaou, Evangelos Pafilis, Stavros Nikolaou, Christos A. Ouzounis, Ioannis Iliopoulos, Vasilis J. Promponas:
  BioTextQuest: a web-based biomedical text mining suite for concept discovery. 3327-3328

Databases and Ontologies

• 
  Qingqing Yang, Chengxiang Qiu, Jie Yang, Qing Wu, Qinghua Cui:
  miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes. 3329-3330

Volume 27, Number 24, December 2011

Editorial

• 
  Lars Juhl Jensen, Alex Bateman:
  The rise and fall of supervised machine learning techniques. 3331-3332

Original Papers - Genome Analysis

• 
  Sonja Althammer, Juan González-Vallinas, Cecilia Ballaré, Miguel Beato, Eduardo Eyras:
  Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. 3333-3340
• 
  Tse-Yi Wang, Chien-Hao Su, Huai-Kuang Tsai:
  MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions. 3341-3347

Sequence Analysis

• 
  Scott Hazelhurst, Zsuzsanna Lipták:
  KABOOM! A new suffix array based algorithm for clustering expression data. 3348-3355
• 
  Xugang Ye, Guoli Wang, Stephen F. Altschul:
  An assessment of substitution scores for protein profile-profile comparison. 3356-3363

Structural Bioinformatics

• 
  Mahmoud ElHefnawi, Nafisa Hassan, Mona Kamar, Rania Siam, Anna Lisa Remoli, Iman El-Azab, Osama Alaidi, Giulia Marsili, Marco Sgarbanti:
  The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus. 3364-3370
• 
  Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin:
  An automatic method for CASP9 free modeling structure prediction assessment. 3371-3378
• 
  Yunqi Li, Yaping Fang, Jianwen Fang:
  Predicting residue-residue contacts using random forest models. 3379-3384
• 
  Carsten Kemena, Jean-François Taly, Jens Kleinjung, Cédric Notredame:
  STRIKE: evaluation of protein MSAs using a single 3D structure. 3385-3391
• 
  Robbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis:
  Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. 3392-3398

Gene Expression

• 
  Levi Waldron, Melania Pintilie, Ming-Sound Tsao, Frances A. Shepherd, Curtis Huttenhower, Igor Jurisica:
  Optimized application of penalized regression methods to diverse genomic data. 3399-3406

Systems Biology

• 
  Mattia Zampieri, Giuseppe Legname, Daniel Segrè, Claudio Altafini:
  A system-level approach for deciphering the transcriptional response to prion infection. 3407-3414

Data and Text Mining

• 
  Nicholas E. Newell:
  Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop. 3415-3422

Applications Note - Genome Analysis

• 
  Ryan K. Dale, Brent S. Pedersen, Aaron R. Quinlan:
  Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. 3423-3424
• 
  Oksana Riba-Grognuz, Laurent Keller, Laurent Falquet, Ioannis Xenarios, Yannick Wurm:
  Visualization and quality assessment of de novo genome assemblies. 3425-3426
• 
  Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong:
  Mapping personal functional data to personal genomes. 3427-3429

Sequence Analysis

• 
  Douglas M. Fowler, Carlos L. Araya, Wayne Gerard, Stanley Fields:
  Enrich: software for analysis of protein function by enrichment and depletion of variants. 3430-3431

Gene Expression

• 
  Yang Zhou, Wubin Qu, Yiming Lu, Yanchun Zhang, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang:
  VizPrimer: a web server for visualized PCR primer design based on known gene structure. 3432-3434

Genetics and Population Analysis

• 
  Robert Kofler, Ram Vinay Pandey, Christian Schlötterer:
  PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). 3435-3436

Systems Biology

• 
  Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas:
  BioPAX support in CellDesigner. 3437-3438

Data and Text Mining

• 
  Kamil Fijorek, Damian Fijorek, Barbara Wisniowska, Sebastian Polak:
  BDTcomparator: a program for comparing binary classifiers. 3439-3440