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Correspondence Survey-based naming conventions for use in OBO Foundry ontology development Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra, and Susanna-Assunta Sansone PMCID: PMC2684543 FuGEFlow: data model and markup language for flow cytometry Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R Jones, Frank J Manion, Richard H Scheuermann, Rafick-Pierre Sekaly, and Ryan R Brinkman PMCID: PMC2711079 An introduction to scripting in Ruby for biologists Jan Aerts and Andy Law PMCID: PMC2722653 Database The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, and Ernst Hafen PMCID: PMC2648944 Motivated Proteins: A web application for studying small three-dimensional protein motifs David P Leader and E James Milner-White PMCID: PMC2651126 The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases Michael Knoll, Thomas M Hamm, Florian Wagner, Virginia Martinez, and Jürgen Pleiss PMCID: PMC2666664 dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation Manoj Hariharan, Vinod Scaria, and Samir K Brahmachari PMCID: PMC2676258 ACID: annotation of cassette and integron data Michael J Joss, Jeremy E Koenig, Maurizio Labbate, Martin F Polz, Michael R Gillings, Harold W Stokes, W Ford Doolittle, and Yan Boucher PMCID: PMC2674596 FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao, and Xiaokun Li PMCID: PMC2680407 Infrastructure for the life sciences: design and implementation of the UniProt website Eric Jain, Amos Bairoch, Severine Duvaud, Isabelle Phan, Nicole Redaschi, Baris E Suzek, Maria J Martin, Peter McGarvey, and Elisabeth Gasteiger PMCID: PMC2686714 eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology Sebastian Schönherr, Hansi Weißensteiner, Stefan Coassin, Günther Specht, Florian Kronenberg, and Anita Brandstätter PMCID: PMC2685123 MIMAS 3.0 is a Multiomics Information Management and Annotation System Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, and Michael Primig PMCID: PMC2694794 Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett, III, Matthew Shaker, and David Pot PMCID: PMC2704210 OrthoClusterDB: an online platform for synteny blocks Man-Ping Ng, Ismael A Vergara, Christian Frech, Qingkang Chen, Xinghuo Zeng, Jian Pei, and Nansheng Chen PMCID: PMC2711082 The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families Riccardo Percudani and Alessio Peracchi PMCID: PMC2748086 MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs Ahmet Sacan, Nilgun Ferhatosmanoglu, and Hakan Ferhatosmanoglu PMCID: PMC2761410 GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs Robert Lawrence, Aaron G Day-Williams, Richard Mott, John Broxholme, Lon R Cardon, and Eleftheria Zeggini PMCID: PMC2777181 A biosegmentation benchmark for evaluation of bioimage analysis methods Elisa Drelie Gelasca, Boguslaw Obara, Dmitry Fedorov, Kristian Kvilekval, and BS Manjunath PMCID: PMC2777895 Research article RNA folding on the 3D triangular lattice Joel Gillespie, Martin Mayne, and Minghui Jiang PMCID: PMC2780420 Elucidation of functional consequences of signalling pathway interactions Adaoha EC Ihekwaba, Phuong T Nguyen, and Corrado Priami PMCID: PMC2778660 Linguistic feature analysis for protein interaction extraction Timur Fayruzov, Martine De Cock, Chris Cornelis, and Veronique Hoste PMCID: PMC2781821 A generic algorithm for layout of biological networks Falk Schreiber, Tim Dwyer, Kim Marriott, and Michael Wybrow PMCID: PMC2785797 Prediction of protein binding sites in protein structures using hidden Markov support vector machine Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qiwen Dong, and Xuan Wang PMCID: PMC2785799 Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods Valentín Ruano-Rubio, Olivier Poch, and Julie D Thompson PMCID: PMC2787529 Automated vocabulary discovery for geo-parsing online epidemic intelligence Mikaela Keller, Clark C Freifeld, and John S Brownstein PMCID: PMC2787530 Software GenomeGraphs: integrated genomic data visualization with R Steffen Durinck, James Bullard, Paul T Spellman, and Sandrine Dudoit PMCID: PMC2629762 ContDist: a tool for the analysis of quantitative gene and promoter properties Michael Hackenberg, Gorka Lasso, and Rune Matthiesen PMCID: PMC2631519 TCP: a tool for designing chimera proteins based on the tertiary structure information Takashi Yoneya and Reina Nishida PMCID: PMC2631521 PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data Victoria Martin-Requena, Antonio Muñoz-Merida, M Gonzalo Claros, and Oswaldo Trelles PMCID: PMC2657788 ArrayIDer: automated structural re-annotation pipeline for DNA microarrays Bart HJ van den Berg, Jay H Konieczka, Fiona M McCarthy, and Shane C Burgess PMCID: PMC2636773 Genome Projector: zoomable genome map with multiple views Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, and Masaru Tomita PMCID: PMC2636772 VASCo: computation and visualization of annotated protein surface contacts Georg Steinkellner, Robert Rader, Gerhard G Thallinger, Christoph Kratky, and Karl Gruber PMCID: PMC2649047 The Genome Reverse Compiler: an explorative annotation tool Andrew S Warren and João Carlos Setubal PMCID: PMC2640359 DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz, and Florentino Fdez-Riverola PMCID: PMC2637236 STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design Lars Kraemer, Bánk Beszteri, Steffi Gäbler-Schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, and Stephan Frickenhaus PMCID: PMC2644677 GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, and Zohar Yakhini PMCID: PMC2644678 "GenotypeColour™": colour visualisation of SNPs and CNVs Sergio Barlati, Sergio Chiesa, and Chiara Magri PMCID: PMC2640356 EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler, and Alexander Goesmann PMCID: PMC2645365 RankAggreg, an R package for weighted rank aggregation Vasyl Pihur, Susmita Datta, and Somnath Datta PMCID: PMC2669484 QSRA – a quality-value guided de novo short read assembler Douglas W Bryant, Jr, Weng-Keen Wong, and Todd C Mockler PMCID: PMC2653489 RGG: A general GUI Framework for R scripts Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhaeusel, Christa Noehammer, Friedrich Leisch, and Albert Kriegner PMCID: PMC2653488 GMFilter and SXTestPlate: software tools for improving the SNPlex™ genotyping system Markus Teuber, Michael H Wenz, Stefan Schreiber, and Andre Franke PMCID: PMC2661053 Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin, and Bin Xia PMCID: PMC2666662 Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data Navdeep Jaitly, Anoop Mayampurath, Kyle Littlefield, Joshua N Adkins, Gordon A Anderson, and Richard D Smith PMCID: PMC2666663 MarVis: a tool for clustering and visualization of metabolic biomarkers Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, and Peter Meinicke PMCID: PMC2666665 JNets: Exploring networks by integrating annotation Jamie I MacPherson, John W Pinney, and David L Robertson PMCID: PMC2674432 ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble Jorge Estrada, Pau Bernadó, Martin Blackledge, and Javier Sancho PMCID: PMC2674053 flowCore: a Bioconductor package for high throughput flow cytometry Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, and Robert Gentleman PMCID: PMC2684747 POINeT: protein interactome with sub-network analysis and hub prioritization Sheng-An Lee, Chen-Hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, and Chi-Ying F Huang PMCID: PMC2683814 SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, and Shoji Tsuji PMCID: PMC2680848 Automated FingerPrint Background removal: FPB Simone Scalabrin, Michele Morgante, and Alberto Policriti PMCID: PMC2689866 Willows: a memory efficient tree and forest construction package Heping Zhang, Minghui Wang, and Xiang Chen PMCID: PMC2683818 SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes Hideya Kawaji, Yoshihide Hayashizaki, and Carsten O Daub PMCID: PMC2689195 CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants Pufeng Du, Liyan Jia, and Yanda Li PMCID: PMC2688514 PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships Mario Huerta, Juan Cedano, Dario Peña, Antonio Rodriguez, and Enrique Querol PMCID: PMC2688515 PanGEA: Identification of allele specific gene expression using the 454 technology Robert Kofler, Tatiana Teixeira Torres, Tamas Lelley, and Christian Schlötterer PMCID: PMC2693439 flowClust: a Bioconductor package for automated gating of flow cytometry data Kenneth Lo, Florian Hahne, Ryan R Brinkman, and Raphael Gottardo PMCID: PMC2701419 The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words Szymon Kaczanowski, Pawel Siedlecki, and Piotr Zielenkiewicz PMCID: PMC2694793 EDGAR: A software framework for the comparative analysis of prokaryotic genomes Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, and Alexander Goesmann PMCID: PMC2696450 Orymold: ontology based gene expression data integration and analysis tool applied to rice Jaume Mercadé, Antonio Espinosa, José-Enrique Adsuara, Rosa Adrados, Jordi Segura, and Tamara Maes PMCID: PMC2696451 Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses Gordon W Slysz, Charles AH Baker, Benjamin M Bozsa, Anthony Dang, Andrew J Percy, Melissa Bennett, and David C Schriemer PMCID: PMC2696453 mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection Kosuke M Teshima and Hideki Innan PMCID: PMC2693440 Fpocket: An open source platform for ligand pocket detection Vincent Le Guilloux, Peter Schmidtke, and Pierre Tuffery PMCID: PMC2700099 A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling Daniel G Pinheiro, Pedro AF Galante, Sandro J de Souza, Marco A Zago, and Wilson A Silva, Jr PMCID: PMC2701951 T-REX: software for the processing and analysis of T-RFLP data Steven W Culman, Robert Bukowski, Hugh G Gauch, Hinsby Cadillo-Quiroz, and Daniel H Buckley PMCID: PMC2702334 "PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation Ursula K Frei, Bernd Wollenweber, and Thomas Lübberstedt PMCID: PMC2707369 TOMOBFLOW: feature-preserving noise filtering for electron tomography Jose-Jesus Fernandez PMCID: PMC2753846 Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design Helen I Field, Serena A Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M Dunning, Douglas F Easton, and Paul DP Pharoah PMCID: PMC2711078 Automated genome mining for natural products Michael HT Li, Peter MU Ung, James Zajkowski, Sylvie Garneau-Tsodikova, and David H Sherman PMCID: PMC2712472 geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research Daniel Glez-Peña, Fernando Díaz, Jesús M Hernández, Juan M Corchado, and Florentino Fdez-Riverola PMCID: PMC2703634 designGG: an R-package and web tool for the optimal design of genetical genomics experiments Yang Li, Morris A Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, and Ritsert C Jansen PMCID: PMC2706229 DOTcvpSB, a software toolbox for dynamic optimization in systems biology Tomáš Hirmajer, Eva Balsa-Canto, and Julio R Banga PMCID: PMC2717952 Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis Ming Yi, Uma Mudunuri, Anney Che, and Robert M Stephens PMCID: PMC2709625 A-MADMAN: Annotation-based microarray data meta-analysis tool Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, and Stefania Bortoluzzi PMCID: PMC2711946 puma: a Bioconductor package for propagating uncertainty in microarray analysis Richard D Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D Lawrence, and Magnus Rattray PMCID: PMC2714555 Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference Lusheng Wang, Zhanyong Wang, and Wanling Yang PMCID: PMC2723091 OrthoSelect: a protocol for selecting orthologous groups in phylogenomics Fabian Schreiber, Kerstin Pick, Dirk Erpenbeck, Gert Wörheide, and Burkhard Morgenstern PMCID: PMC2719630 Information management for high content live cell imaging Daniel Jameson, David A Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G Spiller, Stephen G Oliver, Michael RH White, Douglas B Kell, and Norman W Paton PMCID: PMC2723092 mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics Bernhard Thielen, Stephanie Heinen, and Dietmar Schomburg PMCID: PMC2731052 CSA: An efficient algorithm to improve circular DNA multiple alignment Francisco Fernandes, Luísa Pereira, and Ana T Freitas PMCID: PMC2722656 TableButler – a Windows based tool for processing large data tables generated with high-throughput methods Christian Schwager, Ute Wirkner, Amir Abdollahi, and Peter E Huber PMCID: PMC2731053 sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures Shu-Dong Zhang and Timothy W Gant PMCID: PMC2732627 Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis Roberto T Arrial, Roberto C Togawa, and Marcelo de M Brigido PMCID: PMC2731755 R/BHC: fast Bayesian hierarchical clustering for microarray data Richard S Savage, Katherine Heller, Yang Xu, Zoubin Ghahramani, William M Truman, Murray Grant, Katherine J Denby, and David L Wild PMCID: PMC2736174 EvoRSR: an integrated system for exploring evolution of RNA structural robustness Wenjie Shu, Ming Ni, Xiaochen Bo, Zhiqiang Zheng, and Shengqi Wang PMCID: PMC2731758 OnEX: Exploring changes in life science ontologies Michael Hartung, Toralf Kirsten, Anika Gross, and Erhard Rahm PMCID: PMC2746816 SNAD: sequence name annotation-based designer Igor A Sidorov, Denis A Reshetov, and Alexander E Gorbalenya PMCID: PMC2739203 p3d – Python module for structural bioinformatics Christian Fufezan and Michael Specht PMCID: PMC2744707 Computing power of quantitative trait locus association mapping for haploid loci Derek Gordon and Andrew R Zinn PMCID: PMC2738682 GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, and Yixue Li PMCID: PMC2745391 dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface Gregor Rot, Anup Parikh, Tomaz Curk, Adam Kuspa, Gad Shaulsky, and Blaz Zupan PMCID: PMC2738683 Genoviz Software Development Kit: Java tool kit for building genomics visualization applications Gregg A Helt, John W Nicol, Ed Erwin, Eric Blossom, Steven G Blanchard, Jr, Stephen A Chervitz, Cyrus Harmon, and Ann E Loraine PMCID: PMC2746221 QPCR: Application for real-time PCR data management and analysis Stephan Pabinger, Gerhard G Thallinger, René Snajder, Heiko Eichhorn, Robert Rader, and Zlatko Trajanoski PMCID: PMC2741456 MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction Torsten Blum, Sebastian Briesemeister, and Oliver Kohlbacher PMCID: PMC2745392 Genephony: a knowledge management tool for genome-wide research Angelo Nuzzo and Alberto Riva PMCID: PMC2744709 EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments Aaron L Vollrath, Adam A Smith, Mark Craven, and Christopher A Bradfield PMCID: PMC2746223 ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites Chao Li, Yuhua Li, Xiangmin Zhang, Phillip Stafford, and Valentin Dinu PMCID: PMC2746817 Epitopia: a web-server for predicting B-cell epitopes Nimrod D Rubinstein, Itay Mayrose, Eric Martz, and Tal Pupko PMCID: PMC2751785 Automated seeding of specialised wiki knowledgebases with BioKb Jonathan R Manning, Ann Hedley, John J Mullins, and Donald R Dunbar PMCID: PMC2753848 PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees Philippe Gouret, Julie D Thompson, and Pierre Pontarotti PMCID: PMC2759962 SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services Damian DG Gessler, Gary S Schiltz, Greg D May, Shulamit Avraham, Christopher D Town, David Grant, and Rex T Nelson PMCID: PMC2761904 KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, and Fragiskos N Kolisis PMCID: PMC2764712 VANLO - Interactive visual exploration of aligned biological networks Steffen Brasch, Lars Linsen, and Georg Fuellen PMCID: PMC2766391 miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, and Na-Sheng Lin PMCID: PMC2767369 PLAST: parallel local alignment search tool for database comparison Van Hoa Nguyen and Dominique Lavenier PMCID: PMC2770072 BASE - 2nd generation software for microarray data management and analysis Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen PMCID: PMC2768720 ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery Frank M You, Naxin Huo, Yong Q Gu, Gerard R Lazo, Jan Dvorak, and Olin D Anderson PMCID: PMC2765976 STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data Daniel Jupiter, Hailin Chen, and Vincent VanBuren PMCID: PMC2765977 Magallanes: a web services discovery and automatic workflow composition tool Javier Ríos, Johan Karlsson, and Oswaldo Trelles PMCID: PMC2771019 iQuantitator: A tool for protein expression inference using iTRAQ John H Schwacke, Elizabeth G Hill, Edward L Krug, Susana Comte-Walters, and Kevin L Schey PMCID: PMC2770557 TIde: a software for the systematic scanning of drug targets in kinetic network models Marvin Schulz, Barbara M Bakker, and Edda Klipp PMCID: PMC2773792 Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB Aristotelis Chatziioannou, Panagiotis Moulos, and Fragiskos N Kolisis PMCID: PMC2771024 phyloXML: XML for evolutionary biology and comparative genomics Mira V Han and Christian M Zmasek PMCID: PMC2774328 AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses Surendra Kumar, Åsmund Skjæveland, Russell JS Orr, Pål Enger, Torgeir Ruden, Bjørn-Helge Mevik, Fabien Burki, Andreas Botnen, and Kamran Shalchian-Tabrizi PMCID: PMC2777179 ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization Enrico Glaab, Jonathan M Garibaldi, and Natalio Krasnogor PMCID: PMC2776026 BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing Daniel N Frank PMCID: PMC2777893 A novel R-package graphic user interface for the analysis of metabonomic profiles Jose L Izquierdo-García, Ignacio Rodríguez, Angelos Kyriazis, Palmira Villa, Pilar Barreiro, Manuel Desco, and Jesús Ruiz-Cabello PMCID: PMC2774703 multiplierz: an extensible API based desktop environment for proteomics data analysis Jignesh R Parikh, Manor Askenazi, Scott B Ficarro, Tanya Cashorali, James T Webber, Nathaniel C Blank, Yi Zhang, and Jarrod A Marto PMCID: PMC2774704 SitesIdentify: a protein functional site prediction tool Tracey Bray, Pedro Chan, Salim Bougouffa, Richard Greaves, Andrew J Doig, and Jim Warwicker PMCID: PMC2783165 iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G McNally, and Zlatko Trajanoski PMCID: PMC2789074 JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes Chunguang Liang, Alexander Schmid, María José López-Sánchez, Andres Moya, Roy Gross, Jörg Bernhardt, and Thomas Dandekar PMCID: PMC2789075 Research Articles Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis Chao Yang, Zengyou He, and Weichuan Yu PMCID: PMC2631518 Automated Alphabet Reduction for Protein Datasets Jaume Bacardit, Michael Stout, Jonathan D Hirst, Alfonso Valencia, Robert E Smith, and Natalio Krasnogor PMCID: PMC2646702 Bayesian DNA copy number analysis Paola MV Rancoita, Marcus Hutter, Francesco Bertoni, and Ivo Kwee PMCID: PMC2674052 Filtering for increased power for microarray data analysis Amber J Hackstadt and Ann M Hess PMCID: PMC2661050 MBA: a literature mining system for extracting biomedical abbreviations Yun Xu, ZhiHao Wang, YiMing Lei, YuZhong Zhao, and Yu Xue PMCID: PMC2639376 Robust discovery of periodically expressed genes using the laplace periodogram Kuo-ching Liang, Xiaodong Wang, and Ta-Hsin Li PMCID: PMC2650682 Predicting genetic interactions with random walks on biological networks Kyle C Chipman and Ambuj K Singh PMCID: PMC2653491 BFL: a node and edge betweenness based fast layout algorithm for large scale networks Tatsunori B Hashimoto, Masao Nagasaki, Kaname Kojima, and Satoru Miyano PMCID: PMC2753844 Detecting intergene correlation changes in microarray analysis: a new approach to gene selection Rui Hu, Xing Qiu, Galina Glazko, Lev Klebanov, and Andrei Yakovlev PMCID: PMC2657217 Prediction of nuclear proteins using SVM and HMM models Manish Kumar and Gajendra PS Raghava PMCID: PMC2632991 Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology JB Brown and Tatsuya Akutsu PMCID: PMC2660303 Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, and Thomas Wächter PMCID: PMC2663782 Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring Nils Arrigo, Jarek W Tuszynski, Dorothee Ehrich, Tommy Gerdes, and Nadir Alvarez PMCID: PMC2656475 Sparse canonical methods for biological data integration: application to a cross-platform study Kim-Anh Lê Cao, Pascal GP Martin, Christèle Robert-Granié, and Philippe Besse PMCID: PMC2640358 Prediction of protein-protein interaction types using association rule based classification Sung Hee Park, José A Reyes, David R Gilbert, Ji Woong Kim, and Sangsoo Kim PMCID: PMC2667511 On reliable discovery of molecular signatures Roland Nilsson, Johan Björkegren, and Jesper Tegnér PMCID: PMC2646701 Protein domain organisation: adding order Sarah K Kummerfeld and Sarah A Teichmann PMCID: PMC2657131 Is searching full text more effective than searching abstracts? Jimmy Lin PMCID: PMC2695361 Improving the analysis of designed studies by combining statistical modelling with study design information Uwe Thissen, Suzan Wopereis, Sjoerd AA van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen, and Age K Smilde PMCID: PMC2657790 Outcome prediction based on microarray analysis: a critical perspective on methods Michalis Zervakis, Michalis E Blazadonakis, Georgia Tsiliki, Vasiliki Danilatou, Manolis Tsiknakis, and Dimitris Kafetzopoulos PMCID: PMC2667512 A reexamination of information theory-based methods for DNA-binding site identification Ivan Erill and Michael C O'Neill PMCID: PMC2680408 Inverse Langmuir method for oligonucleotide microarray analysis Geert CWM Mulders, Gerard T Barkema, and Enrico Carlon PMCID: PMC2661052 CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? Leng Han and Zhongming Zhao PMCID: PMC2652441 Sample entropy analysis of cervical neoplasia gene-expression signatures Shaleen K Botting, Jerome P Trzeciakowski, Michelle F Benoit, Salama A Salama, and Concepcion R Diaz-Arrastia PMCID: PMC2656476 An improved ontological representation of dendritic cells as a paradigm for all cell types Anna Maria Masci, Cecilia N Arighi, Alexander D Diehl, Anne E Lieberman, Chris Mungall, Richard H Scheuermann, Barry Smith, and Lindsay G Cowell PMCID: PMC2662812 Gene set-based module discovery in the breast cancer transcriptome Atsushi Niida, Andrew D Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q Zhang, and Tetsu Akiyama PMCID: PMC2674431 Disease candidate gene identification and prioritization using protein interaction networks Jing Chen, Bruce J Aronow, and Anil G Jegga PMCID: PMC2657789 Adaptable data management for systems biology investigations John Boyle, Hector Rovira, Chris Cavnor, David Burdick, Sarah Killcoyne, and Ilya Shmulevich PMCID: PMC2670281 Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, and Jerzy Tiuryn PMCID: PMC2669485 Statistical identification of gene association by CID in application of constructing ER regulatory network Li-Yu D Liu, Chien-Yu Chen, Mei-Ju M Chen, Ming-Shian Tsai, Cho-Han S Lee, Tzu L Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang, and Fon-Jou Hsieh PMCID: PMC2679734 In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles Frank PY Lin, Enrico Coiera, Ruiting Lan, and Vitali Sintchenko PMCID: PMC2669486 Analyses of domains and domain fusions in human proto-oncogenes Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, and Ying Xu PMCID: PMC2679021 Bayesian clustering and feature selection for cancer tissue samples Pekka Marttinen, Samuel Myllykangas, and Jukka Corander PMCID: PMC2679022 New scoring schema for finding motifs in DNA Sequences Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdei Sadeghi, Abbas Nowzari-Dalini, and Bahram Goliaei PMCID: PMC2679735 Identifying significant temporal variation in time course microarray data without replicates Stephen C Billups, Margaret C Neville, Michael Rudolph, Weston Porter, and Pepper Schedin PMCID: PMC2682797 Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display Arumay Pal, Ranjit Prasad Bahadur, Partha Sarathi Ray, and Pinak Chakrabarti PMCID: PMC2680847 Prediction of guide strand of microRNAs from its sequence and secondary structure Firoz Ahmed, Hifzur Rahman Ansari, and Gajendra PS Raghava PMCID: PMC2676257 Identifying set-wise differential co-expression in gene expression microarray data Sung Bum Cho, Jihun Kim, and Ju Han Kim PMCID: PMC2679020 The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes Todd Riley, Xin Yu, Eduardo Sontag, and Arnold Levine PMCID: PMC2685388 Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation Konstantinos P Exarchos, Themis P Exarchos, Costas Papaloukas, Anastassios N Troganis, and Dimitrios I Fotiadis PMCID: PMC2678097 Most parsimonious haplotype allele sharing determination Zhipeng Cai, Hadi Sabaa, Yining Wang, Randy Goebel, Zhiquan Wang, Jiaofen Xu, Paul Stothard, and Guohui Lin PMCID: PMC2691739 Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig, and Dirk Walther PMCID: PMC2683816 Granger causality vs. dynamic Bayesian network inference: a comparative study Cunlu Zou and Jianfeng Feng PMCID: PMC2691740 Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning Philippe Lemey, Martin Lott, Darren P Martin, and Vincent Moulton PMCID: PMC2684544 On validation and invalidation of biological models James Anderson and Antonis Papachristodoulou PMCID: PMC2704209 Validating subcellular localization prediction tools with mycobacterial proteins Daniel Restrepo-Montoya, Carolina Vizcaíno, Luis F Niño, Marisol Ocampo, Manuel E Patarroyo, and Manuel A Patarroyo PMCID: PMC2685389 On finding minimal absent words Armando J Pinho, Paulo JSG Ferreira, Sara P Garcia, and João MOS Rodrigues PMCID: PMC2698904 Estimating parameters for generalized mass action models with connectivity information Chih-Lung Ko, Eberhard O Voit, and Feng-Sheng Wang PMCID: PMC2694188 Application of multiple statistical tests to enhance mass spectrometry-based biomarker discovery Niclas C Tan, Wayne G Fisher, Kevin P Rosenblatt, and Harold R Garner PMCID: PMC2688007 Effects of sample size on robustness and prediction accuracy of a prognostic gene signature Seon-Young Kim PMCID: PMC2689196 Protein-protein interaction based on pairwise similarity Nazar Zaki, Sanja Lazarova-Molnar, Wassim El-Hajj, and Piers Campbell PMCID: PMC2701420 BRNI: Modular analysis of transcriptional regulatory programs Iftach Nachman and Aviv Regev PMCID: PMC2694189 Transmembrane protein topology prediction using support vector machines Timothy Nugent and David T Jones PMCID: PMC2700806 GAGE: generally applicable gene set enrichment for pathway analysis Weijun Luo, Michael S Friedman, Kerby Shedden, Kurt D Hankenson, and Peter J Woolf PMCID: PMC2696452 Combining specificity determining and conserved residues improves functional site prediction Olga V Kalinina, Mikhail S Gelfand, and Robert B Russell PMCID: PMC2709924 Local alignment of two-base encoded DNA sequence Nils Homer, Barry Merriman, and Stanley F Nelson PMCID: PMC2709925 Improved results in proteomics by use of local and peptide-class specific false discovery rates Lau Sennels, Jimi-Carlo Bukowski-Wills, and Juri Rappsilber PMCID: PMC2709624 The textual characteristics of traditional and Open Access scientific journals are similar Karin Verspoor, K Bretonnel Cohen, and Lawrence Hunter PMCID: PMC2714574 The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, and Joachim L Schultze PMCID: PMC2711080 Platform dependence of inference on gene-wise and gene-set involvement in human lung development Rose Du, Kelan Tantisira, Vincent Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T Kho, Barbara J Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J Mariani, J Steven Leeder, and Scott T Weiss PMCID: PMC2711081 Modeling the role of p53 pulses in DNA damage- induced cell death decision Tingzhe Sun, Chun Chen, Yuanyuan Wu, Shuai Zhang, Jun Cui, and Pingping Shen PMCID: PMC2713228 Unsupervised assessment of microarray data quality using a Gaussian mixture model Brian E Howard, Beate Sick, and Steffen Heber PMCID: PMC2717951 Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis Otávio JB Brustolini, Luciano G Fietto, Cosme D Cruz, and Flávia ML Passos PMCID: PMC2711083 Ab initio and homology based prediction of protein domains by recursive neural networks Ian Walsh, Alberto JM Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, and Gianluca Pollastri PMCID: PMC2711945 Triangle network motifs predict complexes by complementing high-error interactomes with structural information Bill Andreopoulos, Christof Winter, Dirk Labudde, and Michael Schroeder PMCID: PMC2714575 A Bayesian approach to efficient differential allocation for resampling-based significance testing Shane T Jensen, Sameer Soi, and Li-San Wang PMCID: PMC2718927 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction Alex N Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, and Alan M Moses PMCID: PMC2711084 Integrated analysis of DNA copy number and gene expression microarray data using gene sets Renée X Menezes, Marten Boetzer, Melle Sieswerda, Gert-Jan B van Ommen, and Judith M Boer PMCID: PMC2753845 Clique-based data mining for related genes in a biomedical database Tsutomu Matsunaga, Chikara Yonemori, Etsuji Tomita, and Masaaki Muramatsu PMCID: PMC2721841 Representative transcript sets for evaluating a translational initiation sites predictor Jia Zeng, Reda Alhajj, and Douglas J Demetrick PMCID: PMC2712473 Ensemble approach to predict specificity determinants: benchmarking and validation Saikat Chakrabarti and Anna R Panchenko PMCID: PMC2716344 OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif Amar Drawid, Nupur Gupta, Vijayalakshmi H Nagaraj, Céline Gélinas, and Anirvan M Sengupta PMCID: PMC2718928 Iterative refinement of structure-based sequence alignments by Seed Extension Changhoon Kim, Chin-Hsien Tai, and Byungkook Lee PMCID: PMC2753854 A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data Bjoern H Menze, B Michael Kelm, Ralf Masuch, Uwe Himmelreich, Peter Bachert, Wolfgang Petrich, and Fred A Hamprecht PMCID: PMC2724423 Transcriptional programs: Modelling higher order structure in transcriptional control John E Reid, Sascha Ott, and Lorenz Wernisch PMCID: PMC2725141 PCI-SS: MISO dynamic nonlinear protein secondary structure prediction James R Green, Michael J Korenberg, and Mohammed O Aboul-Magd PMCID: PMC2720391 Incorporating rich background knowledge for gene named entity classification and recognition Yanpeng Li, Hongfei Lin, and Zhihao Yang PMCID: PMC2725142 FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral Fernando Garcia, Francisco J Lopez, Carlos Cano, and Armando Blanco PMCID: PMC2722654 Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules' John Draper, David P Enot, David Parker, Manfred Beckmann, Stuart Snowdon, Wanchang Lin, and Hassan Zubair PMCID: PMC2721842 Enzyme classification with peptide programs: a comparative study Daniel Faria, António EN Ferreira, and André O Falcão PMCID: PMC2724424 A realistic assessment of methods for extracting gene/protein interactions from free text Renata Kabiljo, Andrew B Clegg, and Adrian J Shepherd PMCID: PMC2723093 Resolving deconvolution ambiguity in gene alternative splicing Yiyuan She, Earl Hubbell, and Hui Wang PMCID: PMC2739860 Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures Chris Thachuk, José Crossa, Jorge Franco, Susanne Dreisigacker, Marilyn Warburton, and Guy F Davenport PMCID: PMC2734557 A structured overview of simultaneous component based data integration Katrijn Van Deun, Age K Smilde, Mariët J van der Werf, Henk AL Kiers, and Iven Van Mechelen PMCID: PMC2752463 A fast and efficient gene-network reconstruction method from multiple over-expression experiments Dejan Stokić, Rudolf Hanel, and Stefan Thurner PMCID: PMC2755483 The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations Xue Lin, Bahman Afsari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Naiman, and Donald Geman PMCID: PMC2745389 Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines Wei Guan, Manshui Zhou, Christina Y Hampton, Benedict B Benigno, L DeEtte Walker, Alexander Gray, John F McDonald, and Facundo M Fernández PMCID: PMC2741455 Assessing the druggability of protein-protein interactions by a supervised machine-learning method Nobuyoshi Sugaya and Kazuyoshi Ikeda PMCID: PMC2739204 Enhanced protein fold recognition through a novel data integration approach Yiming Ying, Kaizhu Huang, and Colin Campbell PMCID: PMC2761901 An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis σ66 promoters Ronna R Mallios, David M Ojcius, and David H Ardell PMCID: PMC2743672 Correlating gene and protein expression data using Correlated Factor Analysis Chuen Seng Tan, Agus Salim, Alexander Ploner, Janne Lehtiö, Kee Seng Chia, and Yudi Pawitan PMCID: PMC2744708 Comparative study of gene set enrichment methods Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Maria Creanza, Sayan Mukherjee, and Nicola Ancona PMCID: PMC2746222 Regression applied to protein binding site prediction and comparison with classification Joachim Giard, Jérôme Ambroise, Jean-Luc Gala, and Benoît Macq PMCID: PMC2749839 Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan, and Fengzhu Sun PMCID: PMC2755484 RRW: repeated random walks on genome-scale protein networks for local cluster discovery Kathy Macropol, Tolga Can, and Ambuj K Singh PMCID: PMC2748087 CASSIOPE: An expert system for conserved regions searches Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, Etienne GJ Danchin, and Pierre Pontarotti PMCID: PMC2756280 Accurate microRNA target prediction correlates with protein repression levels Manolis Maragkakis, Panagiotis Alexiou, Giorgio L Papadopoulos, Martin Reczko, Theodore Dalamagas, George Giannopoulos, George Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A Simossis, Praveen Sethupathy, Thanasis Vergoulis, Nectarios Koziris, Timos Sellis, Panagiotis Tsanakas, and Artemis G Hatzigeorgiou PMCID: PMC2752464 BayesPeak: Bayesian analysis of ChIP-seq data Christiana Spyrou, Rory Stark, Andy G Lynch, and Simon Tavaré PMCID: PMC2760534 Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum Scott Bringans, James K Hane, Tammy Casey, Kar-Chun Tan, Richard Lipscombe, Peter S Solomon, and Richard P Oliver PMCID: PMC2753851 Prediction of antigenic epitopes on protein surfaces by consensus scoring Shide Liang, Dandan Zheng, Chi Zhang, and Martin Zacharias PMCID: PMC2761409 The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature Anna Korhonen, Ilona Silins, Lin Sun, and Ulla Stenius PMCID: PMC2759963 A methodology for the analysis of differential coexpression across the human lifespan Jesse Gillis and Paul Pavlidis PMCID: PMC2761903 Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function Petri Törönen, Pauli J Ojala, Pekka Marttinen, and Liisa Holm PMCID: PMC2761411 Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays Peter Tiňo PMCID: PMC2761412 Challenges for automatically extracting molecular interactions from full-text articles Tara McIntosh and James R Curran PMCID: PMC2761905 Predicting protein-protein binding sites in membrane proteins Andrew J Bordner PMCID: PMC2761413 Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics Benjamin M Good, Joseph T Tennis, and Mark D Wilkinson PMCID: PMC2760536 Enhancing navigation in biomedical databases by community voting and database-driven text classification Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer, and Ralph Weissleder PMCID: PMC2768718 Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions Holger Fröhlich, Özgür Sahin, Dorit Arlt, Christian Bender, and Tim Beißbarth PMCID: PMC2770070 A stochastic context free grammar based framework for analysis of protein sequences Witold Dyrka and Jean-Christophe Nebel PMCID: PMC2765975 Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD) Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman, and Carolyn J Mattingly PMCID: PMC2768719 Clustering of protein domains for functional and evolutionary studies Pavle Goldstein, Jurica Zucko, Dušica Vujaklija, Anita Kriško, Daslav Hranueli, Paul F Long, Catherine Etchebest, Bojan Basrak, and John Cullum PMCID: PMC2770074 Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks Glennie Helles and Rasmus Fonseca PMCID: PMC2771020 Transcription factor site dependencies in human, mouse and rat genomes Andrija Tomovic, Michael Stadler, and Edward J Oakeley PMCID: PMC2770556 Integrating functional genomics data using maximum likelihood based simultaneous component analysis Robert A van den Berg, Iven Van Mechelen, Tom F Wilderjans, Katrijn Van Deun, Henk AL Kiers, and Age K Smilde PMCID: PMC2771021 Exploiting structural and topological information to improve prediction of RNA-protein binding sites Stefan R Maetschke and Zheng Yuan PMCID: PMC2774325 Arabidopsis gene co-expression network and its functional modules Linyong Mao, John L Van Hemert, Sudhansu Dash, and Julie A Dickerson PMCID: PMC2772859 GIFtS: annotation landscape analysis with GeneCards Arye Harel, Aron Inger, Gil Stelzer, Liora Strichman-Almashanu, Irina Dalah, Marilyn Safran, and Doron Lancet PMCID: PMC2774327 Construction of an annotated corpus to support biomedical information extraction Paul Thompson, Syed A Iqbal, John McNaught, and Sophia Ananiadou PMCID: PMC2774701 Time warping of evolutionary distant temporal gene expression data based on noise suppression Yury Goltsev and Dmitri Papatsenko PMCID: PMC2771023 Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy Zheng Rong Yang PMCID: PMC2777180 Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods Stefano Lise, Cedric Archambeau, Massimiliano Pontil, and David T Jones PMCID: PMC2777894 Methodology Articles Regularized gene selection in cancer microarray meta-analysis Shuangge Ma and Jian Huang PMCID: PMC2631520 Thermodynamic scaling behavior in genechips Alessandro Ferrantini, Joke Allemeersch, Paul Van Hummelen, and Enrico Carlon PMCID: PMC2628882 Bayesian optimal discovery procedure for simultaneous significance testing Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, and Michael A White PMCID: PMC2628883 Large-scale prediction of long disordered regions in proteins using random forests Pengfei Han, Xiuzhen Zhang, Raymond S Norton, and Zhi-Ping Feng PMCID: PMC2637845 Estimation of tumor heterogeneity using CGH array data Kai Wang, Jian Li, Shengting Li, Lars Bolund, and Carsten Wiuf PMCID: PMC2640360 MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson LS Tang, and Weichuan Yu PMCID: PMC2642772 Incorporating pathway information into boosting estimation of high-dimensional risk prediction models Harald Binder and Martin Schumacher PMCID: PMC2647532 Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis Christian Frech, Michael Kommenda, Viktoria Dorfer, Thomas Kern, Helmut Hintner, Johann W Bauer, and Kamil Önder PMCID: PMC2637843 Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data Debayan Datta and Hongyu Zhao PMCID: PMC2637844 An innovative approach for testing bioinformatics programs using metamorphic testing Tsong Yueh Chen, Joshua WK Ho, Huai Liu, and Xiaoyuan Xie PMCID: PMC2657898 Identifying differential exon splicing using linear models and correlation coefficients Sonia H Shah and Jacqueline A Pallas PMCID: PMC2636774 Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes Ujjwal Maulik, Anirban Mukhopadhyay, and Sanghamitra Bandyopadhyay PMCID: PMC2657792 Using least median of squares for structural superposition of flexible proteins Yu-Shen Liu, Yi Fang, and Karthik Ramani PMCID: PMC2639377 NIFTI: An evolutionary approach for finding number of clusters in microarray data Sudhakar Jonnalagadda and Rajagopalan Srinivasan PMCID: PMC2669482 Selecting control genes for RT-QPCR using public microarray data Vlad Popovici, Darlene R Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi, and Pratyaksha Wirapati PMCID: PMC2640357 An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters Qingbo Li and Bryan AP Roxas PMCID: PMC2645366 A new regularized least squares support vector regression for gene selection Pei-Chun Chen, Su-Yun Huang, Wei J Chen, and Chuhsing K Hsiao PMCID: PMC2669483 Comparison of small n statistical tests of differential expression applied to microarrays Carl Murie, Owen Woody, Anna Y Lee, and Robert Nadon PMCID: PMC2674054 A general modular framework for gene set enrichment analysis Marit Ackermann and Korbinian Strimmer PMCID: PMC2661051 Optimized ancestral state reconstruction using Sankoff parsimony José C Clemente, Kazuho Ikeo, Gabriel Valiente, and Takashi Gojobori PMCID: PMC2677398 TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner, and Rainer Merkl PMCID: PMC2667513 Assessing and selecting gene expression signals based upon the quality of the measured dynamics Eric Yang and Ioannis P Androulakis PMCID: PMC2653486 TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach Naryttza N Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus, and Tim W Nattkemper PMCID: PMC2653487 An effective docking strategy for virtual screening based on multi-objective optimization algorithm Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, and Hualiang Jiang PMCID: PMC2753843 A comparison on effects of normalisations in the detection of differentially expressed genes Monica Chiogna, Maria Sofia Massa, Davide Risso, and Chiara Romualdi PMCID: PMC2680204 Genotype determination for polymorphisms in linkage disequilibrium Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver, and Daniel J Schaid PMCID: PMC2753842 Quantitative measures for the management and comparison of annotated genomes Karen Eilbeck, Barry Moore, Carson Holt, and Mark Yandell PMCID: PMC2653490 Genotyping and inflated type I error rate in genome-wide association case/control studies Joshua N Sampson and Hongyu Zhao PMCID: PMC2679732 Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data Amalia Annest, Roger E Bumgarner, Adrian E Raftery, and Ka Yee Yeung PMCID: PMC2657791 Edge detection in microscopy images using curvelets Tobias Gebäck and Petros Koumoutsakos PMCID: PMC2663783 RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, and Ron Unger PMCID: PMC2682796 Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, and Joseph G Hacia PMCID: PMC2660304 Performance of random forest when SNPs are in linkage disequilibrium Yan A Meng, Yi Yu, L Adrienne Cupples, Lindsay A Farrer, and Kathryn L Lunetta PMCID: PMC2666661 CNV-seq, a new method to detect copy number variation using high-throughput sequencing Chao Xie and Martti T Tammi PMCID: PMC2667514 Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation Mickael Guedj, Stephane Robin, Alain Celisse, and Gregory Nuel PMCID: PMC2679733 Improved analysis of bacterial CGH data beyond the log-ratio paradigm Lars Snipen, Otto L Nyquist, Margrete Solheim, Ågot Aakra, and Ingolf F Nes PMCID: PMC2679023 Statistical and visual differentiation of subcellular imaging Nicholas A Hamilton, Jack TH Wang, Markus C Kerr, and Rohan D Teasdale PMCID: PMC2676259 Modeling genomic data with type attributes, balancing stability and maintainability Norbert Busch and Gero Wedemann PMCID: PMC2676260 Characterisation and correction of signal fluctuations in successive acquisitions of microarray images Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck, and Marie-Hélène Mucchielli-Giorgi PMCID: PMC2681461 Markov clustering versus affinity propagation for the partitioning of protein interaction graphs James Vlasblom and Shoshana J Wodak PMCID: PMC2682798 Biological sequences as pictures – a generic two dimensional solution for iterated maps Jonas S Almeida and Susana Vinga PMCID: PMC2678093 Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, and Hualiang Jiang PMCID: PMC2678094 GLOSSI: a method to assess the association of genetic loci-sets with complex diseases High-Seng Chai, Hugues Sicotte, Kent R Bailey, Stephen T Turner, Yan W Asmann, and Jean-Pierre A Kocher PMCID: PMC2678095 EFICAz2: enzyme function inference by a combined approach enhanced by machine learning Adrian K Arakaki, Ying Huang, and Jeffrey Skolnick PMCID: PMC2670841 Data-driven normalization strategies for high-throughput quantitative RT-PCR Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, and John Quackenbush PMCID: PMC2680405 Island method for estimating the statistical significance of profile-profile alignment scores Aleksandar Poleksic PMCID: PMC2678096 Profile analysis and prediction of tissue-specific CpG island methylation classes Christopher Previti, Oscar Harari, Igor Zwir, and Coral del Val PMCID: PMC2683815 A bag-of-words approach for Drosophila gene expression pattern annotation Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, and Jieping Ye PMCID: PMC2680406 Multichromosomal median and halving problems under different genomic distances Eric Tannier, Chunfang Zheng, and David Sankoff PMCID: PMC2683817 Marker-free image registration of electron tomography tilt-series Carlos Oscar Sanchez Sorzano, Cédric Messaoudi, Matthias Eibauer, JR Bilbao-Castro, R Hegerl, S Nickell, S Marco, and JM Carazo PMCID: PMC2694187 Identification of differentially expressed subnetworks based on multivariate ANOVA Taeyoung Hwang and Taesung Park PMCID: PMC2696448 Improving classification in protein structure databases using text mining Antonis Koussounadis, Oliver C Redfern, and David T Jones PMCID: PMC2688513 SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi, and Nori Kurata PMCID: PMC2706822 Robust MS quantification method for phospho-peptides using 18O/16O labeling Claus A Andersen, Stefano Gotta, Letizia Magnoni, Roberto Raggiaschi, Andreas Kremer, and Georg C Terstappen PMCID: PMC2693437 Incorporating functional inter-relationships into protein function prediction algorithms Gaurav Pandey, Chad L Myers, and Vipin Kumar PMCID: PMC2693438 Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments Tianqing Liu, Nan Lin, Ningzhong Shi, and Baoxue Zhang PMCID: PMC2696449 How to find simple and accurate rules for viral protease cleavage specificities Thorsteinn Rögnvaldsson, Terence A Etchells, Liwen You, Daniel Garwicz, Ian Jarman, and Paulo JG Lisboa PMCID: PMC2698905 Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach Alexandre P Francisco, Miguel Bugalho, Mário Ramirez, and João A Carriço PMCID: PMC2705362 Tableau-based protein substructure search using quadratic programming Alex Stivala, Anthony Wirth, and Peter J Stuckey PMCID: PMC2705363 Differential splicing using whole-transcript microarrays Mark D Robinson and Terence P Speed PMCID: PMC2703633 IDSS: deformation invariant signatures for molecular shape comparison Yu-Shen Liu, Yi Fang, and Karthik Ramani PMCID: PMC2694795 IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico Tzong-Yuan Wu, Chi-Chun Hsieh, Jun-Jie Hong, Chung-Yung Chen, and Yuh-Show Tsai PMCID: PMC2698906 Analyzing miRNA co-expression networks to explore TF-miRNA regulation Sanghamitra Bandyopadhyay and Malay Bhattacharyya PMCID: PMC2707367 Sample size calculation for microarray experiments with blocked one-way design Sin-Ho Jung, Insuk Sohn, Stephen L George, Liping Feng, and Phyllis C Leppert PMCID: PMC2702333 A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja, and Harri Lähdesmäki PMCID: PMC2717092 Measure of synonymous codon usage diversity among genes in bacteria Haruo Suzuki, Rintaro Saito, and Masaru Tomita PMCID: PMC2697163 A core-attachment based method to detect protein complexes in PPI networks Min Wu, Xiaoli Li, Chee-Keong Kwoh, and See-Kiong Ng PMCID: PMC2701950 Accounting for uncertainty when assessing association between copy number and disease: a latent class model Juan R González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier Estivill, and Lluís Armengol PMCID: PMC2707368 Improved ChIP-chip analysis by a mixture model approach Wei Sun, Michael J Buck, Mukund Patel, and Ian J Davis PMCID: PMC2700807 Computing paths and cycles in biological interaction graphs Steffen Klamt and Axel von Kamp PMCID: PMC2708159 Structural motifs recurring in different folds recognize the same ligand fragments Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, and Manuela Helmer-Citterich PMCID: PMC2704211 Filtering Genes for Cluster and Network Analysis David Tritchler, Elena Parkhomenko, and Joseph Beyene PMCID: PMC2708160 ResBoost: characterizing and predicting catalytic residues in enzymes Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, and Kimmen Sjölander PMCID: PMC2713229 Comparison of sequence-dependent tiling array normalization approaches Ho-Ryun Chung and Martin Vingron PMCID: PMC2753852 A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests Antonio Carvajal-Rodríguez, Jacobo de Uña-Alvarez, and Emilio Rolán-Alvarez PMCID: PMC2719628 Error statistics of hidden Markov model and hidden Boltzmann model results Lee A Newberg PMCID: PMC2722652 Construction and use of gene expression covariation matrix Jérôme Hennetin, Petri Pehkonen, and Michel Bellis PMCID: PMC2720390 Regression based predictor for p53 transactivation Sivakumar Gowrisankar and Anil G Jegga PMCID: PMC2719629 A compartmentalized approach to the assembly of physical maps Serdar Bozdag, Timothy J Close, and Stefano Lonardi PMCID: PMC2717093 A statistical framework to evaluate virtual screening Wei Zhao, Kirk E Hevener, Stephen W White, Richard E Lee, and James M Boyett PMCID: PMC2722655 Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael Müller, and Paul W Sternberg PMCID: PMC2719631 BSMAP: whole genome bisulfite sequence MAPping program Yuanxin Xi and Wei Li PMCID: PMC2724425 CLEAN: CLustering Enrichment ANalysis Johannes M Freudenberg, Vineet K Joshi, Zhen Hu, and Mario Medvedovic PMCID: PMC2734555 Generating rate equations for complex enzyme systems by a computer-assisted systematic method Feng Qi, Ranjan K Dash, Yu Han, and Daniel A Beard PMCID: PMC2729780 Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology Tao Xu, JianLei Gu, Yan Zhou, and LinFang Du PMCID: PMC2731756 Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels Kevin Y Yip, Philip M Kim, Drew McDermott, and Mark Gerstein PMCID: PMC2734556 ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics Jason WH Wong, Alexander B Schwahn, and Kevin M Downard PMCID: PMC2731054 Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity Flavien Quintus, Olivier Sperandio, Julien Grynberg, Michel Petitjean, and Pierre Tuffery PMCID: PMC2739202 Accurate and fast methods to estimate the population mutation rate from error prone sequences Bjarne Knudsen and Michael M Miyamoto PMCID: PMC2746815 Supervised learning for the automated transcription of spacer classification from spoligotype films David J Jeffries, Neil Abernethy, and Bouke C de Jong PMCID: PMC2731757 An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow Trevor Paterson and Andy Law PMCID: PMC2743669 Ultra-Structure database design methodology for managing systems biology data and analyses Christopher W Maier, Jeffrey G Long, Bradley M Hemminger, and Morgan C Giddings PMCID: PMC2748085 Extracting biologically significant patterns from short time series gene expression data Alain B Tchagang, Kevin V Bui, Thomas McGinnis, and Panayiotis V Benos PMCID: PMC2743670 Structure-based substrate screening for an enzyme Tao Xu, Lujia Zhang, Xuedong Wang, Dongzhi Wei, and Tianbi Li PMCID: PMC2745390 MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering Eun-Youn Kim, Seon-Young Kim, Daniel Ashlock, and Dougu Nam PMCID: PMC2743671 Integrative modeling of transcriptional regulation in response to antirheumatic therapy Michael Hecker, Robert Hermann Goertsches, Robby Engelmann, Hans-Juergen Thiesen, and Reinhard Guthke PMCID: PMC2757030 Global haplotype partitioning for maximal associated SNP pairs Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk, and Elahe Elahi PMCID: PMC2749056 A reliable measure of similarity based on dependency for short time series: an application to gene expression networks Mônica G Campiteli, Frederico M Soriani, Iran Malavazi, Osame Kinouchi, Carlos AB Pereira, and Gustavo H Goldman PMCID: PMC2757031 XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services Johannes Wagener, Ola Spjuth, Egon L Willighagen, and Jarl ES Wikberg PMCID: PMC2755485 Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics Matteo Rè, Graziano Pesole, and David S Horner PMCID: PMC2758873 Exploratory and inferential analysis of gene cluster neighborhood graphs Theresa Scharl, Ingo Voglhuber, and Friedrich Leisch PMCID: PMC2761902 In Silico screening for functional candidates amongst hypothetical proteins Claus Desler, Prashanth Suravajhala, May Sanderhoff, Merete Rasmussen, and Lene Juel Rasmussen PMCID: PMC2758874 Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information Marcio L Acencio and Ney Lemke PMCID: PMC2753850 A first principles approach to differential expression in microarray data analysis Robert A Rubin PMCID: PMC2749840 Efficient oligonucleotide probe selection for pan-genomic tiling arrays Adam M Phillippy, Xiangyu Deng, Wei Zhang, and Steven L Salzberg PMCID: PMC2753849 Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse, and Nachol Chaiyaratana PMCID: PMC2759961 NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction Morten Nielsen and Ole Lund PMCID: PMC2753847 Finding local communities in protein networks Konstantin Voevodski, Shang-Hua Teng, and Yu Xia PMCID: PMC2755114 Strategies for analyzing highly enriched IP-chip datasets Simon RV Knott, Christopher J Viggiani, Oscar M Aparicio, and Simon Tavaré PMCID: PMC2759964 Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously Oscar M Rueda and Ramon Diaz-Uriarte PMCID: PMC2760535 MetaTM - a consensus method for transmembrane protein topology prediction Martin Klammer, David N Messina, Thomas Schmitt, and Erik LL Sonnhammer PMCID: PMC2761906 Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks Sandra Waaijenborg and Aeilko H Zwinderman PMCID: PMC2760886 Unsupervised statistical clustering of environmental shotgun sequences Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, and Joshua S Weitz PMCID: PMC2765972 Kavosh: a new algorithm for finding network motifs Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, and Ali Masoudi-Nejad PMCID: PMC2765973 Generation of Gene Ontology benchmark datasets with various types of positive signal Petri Törönen, Petri Pehkonen, and Liisa Holm PMCID: PMC2762998 BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature Guillermo de la Calle, Miguel García-Remesal, Stefano Chiesa, Diana de la Iglesia, and Victor Maojo PMCID: PMC2765974 Discovering multiple realistic TFBS motifs based on a generalized model Tak-Ming Chan, Gang Li, Kwong-Sak Leung, and Kin-Hong Lee PMCID: PMC2770069 Riboswitch Detection Using Profile Hidden Markov Models Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, A Krishnamachari, and Supratim Sengupta PMCID: PMC2770071 Phylogenetic analysis of modularity in protein interaction networks Sinan Erten, Xin Li, Gurkan Bebek, Jing Li, and Mehmet Koyutürk PMCID: PMC2770073 A permutation-based multiple testing method for time-course microarray experiments Insuk Sohn, Kouros Owzar, Stephen L George, Sujong Kim, and Sin-Ho Jung PMCID: PMC2772858 Classification and biomarker identification using gene network modules and support vector machines Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise C Showe, and Michael K Showe PMCID: PMC2774324 Bayesian inference of biochemical kinetic parameters using the linear noise approximation Michał Komorowski, Bärbel Finkenstädt, Claire V Harper, and David A Rand PMCID: PMC2774326 BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors Junbai Wang and Morigen PMCID: PMC2771022 Direct calibration of PICKY-designed microarrays Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C Hsing, Pamela C Ronald, and Patrick S Schnable PMCID: PMC2773793 A structure filter for the Eukaryotic Linear Motif Resource Allegra Via, Cathryn M Gould, Christine Gemünd, Toby J Gibson, and Manuela Helmer-Citterich PMCID: PMC2774702 Bayesian modeling of ChIP-chip data using latent variables Mingqi Wu, Faming Liang, and Yanan Tian PMCID: PMC2779819 Stratification of co-evolving genomic groups using ranked phylogenetic profiles Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, and Christos A Ouzounis PMCID: PMC2775751 Analysis and comparison of very large metagenomes with fast clustering and functional annotation Weizhong Li PMCID: PMC2774329 Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA Naoki Hasegawa, Wataru Sugiura, Junko Shibata, Masakazu Matsuda, Fengrong Ren, and Hiroshi Tanaka PMCID: PMC2776027 (PS)2-v2: template-based protein structure prediction server Chih-Chieh Chen, Jenn-Kang Hwang, and Jinn-Moon Yang PMCID: PMC2775752 An empirical Bayesian approach for model-based inference of cellular signaling networks David J Klinke, II PMCID: PMC2781012 Illumina WG-6 BeadChip strips should be normalized separately Wei Shi, Ashish Banerjee, Matthew E Ritchie, Steve Gerondakis, and Gordon K Smyth PMCID: PMC2780421 A theoretical approach to spot active regions in antimicrobial proteins Marc Torrent, Victòria M Nogués, and Ester Boix PMCID: PMC2780422 Algorithms for effective querying of compound graph-based pathway databases Ugur Dogrusoz, Ahmet Cetintas, Emek Demir, and Ozgun Babur PMCID: PMC2784781 The ontology of biological sequences Robert Hoehndorf, Janet Kelso, and Heinrich Herre PMCID: PMC2785798 DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices Isabelle da Piedade, Man-Hung Eric Tang, and Olivier Elemento PMCID: PMC2788558 Corrections Algorithm of OMA for large-scale orthology inference Alexander CJ Roth, Gaston H Gonnet, and Christophe Dessimoz PMCID: PMC2729779 Corrects: Alexander CJ Roth, et al. Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics. 2008; 9: 518. Feature selection environment for genomic applications Fabrício Martins Lopes, David Corrêa Martins, Jr, and Roberto M Cesar, Jr PMCID: PMC2753853 Corrects: Ana C Fierro, et al. Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinformatics. 2008; 9: 1. Other Issues: Journal List
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