| | Other Issues: previous | next | latest | archiveCorrespondence Extended Newick: it is time for a standard representation of phylogenetic networks Gabriel Cardona, Francesc Rosselló, and Gabriel Valiente PMCID: PMC2621367 Database A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis, and Stephen C Ekker PMCID: PMC2221974 SCOWLP classification: Structural comparison and analysis of protein binding regions Joan Teyra, Maciej Paszkowski-Rogacz, Gerd Anders, and M Teresa Pisabarro PMCID: PMC2259299 MeInfoText: associated gene methylation and cancer information from text mining Yu-Ching Fang, Hsuan-Cheng Huang, and Hsueh-Fen Juan PMCID: PMC2258285 Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee, and Jong Bhak PMCID: PMC2246157 TOBFAC: the database of tobacco transcription factors Paul J Rushton, Marta T Bokowiec, Thomas W Laudeman, Jennifer F Brannock, Xianfeng Chen, and Michael P Timko PMCID: PMC2246155 The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences Mathieu Fourment and Mark J Gibbs PMCID: PMC2263024 PDTD: a web-accessible protein database for drug target identification Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, and Hualiang Jiang PMCID: PMC2265675 DBMLoc: a Database of proteins with multiple subcellular localizations Song Zhang, Xuefeng Xia, Jincheng Shen, Yun Zhou, and Zhirong Sun PMCID: PMC2292141 GMDD: a database of GMO detection methods Wei Dong, Litao Yang, Kailin Shen, Banghyun Kim, Gijs A Kleter, Hans JP Marvin, Rong Guo, Wanqi Liang, and Dabing Zhang PMCID: PMC2430717 TiGER: A database for tissue-specific gene expression and regulation Xiong Liu, Xueping Yu, Donald J Zack, Heng Zhu, and Jiang Qian PMCID: PMC2438328 AMYPdb: A database dedicated to amyloid precursor proteins Sandrine Pawlicki, Antony Le Béchec, and Christian Delamarche PMCID: PMC2442844 Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins Michael Hsing and Artem Cherkasov PMCID: PMC2459192 SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland, Ari B Kahn, Hongfang Liu, and John N Weinstein PMCID: PMC2491637 RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database Mirela Andronescu, Vera Bereg, Holger H Hoos, and Anne Condon PMCID: PMC2536673 SQUAT: A web tool to mine human, murine and avian SAGE data Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, Jean-François Boulicaut, Jérémy Besson, Ruggero G Pensa, and Olivier Gandrillon PMCID: PMC2567996 MiMiR – an integrated platform for microarray data sharing, mining and analysis Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, and Laurence Game PMCID: PMC2572073 GlycomeDB – integration of open-access carbohydrate structure databases René Ranzinger, Stephan Herget, Thomas Wetter, and Claus-Wilhelm von der Lieth PMCID: PMC2567997 Automatically extracting functionally equivalent proteins from SwissProt Lisa EM McMillan and Andrew CR Martin PMCID: PMC2576269 A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm Sheila Podell, Terry Gaasterland, and Eric E Allen PMCID: PMC2573894 FUNYBASE: a FUNgal phYlogenomic dataBASE Sylvain Marthey, Gabriela Aguileta, François Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angélique Gautier, Marc-Henri Lebrun, and Hélène Chiapello PMCID: PMC2600828 Extension of the COG and arCOG databases by amino acid and nucleotide sequences Florian Meereis and Michael Kaufmann PMCID: PMC2588464 Structural descriptor database: a new tool for sequence-based functional site prediction Juliana S Bernardes, Jorge H Fernandez, and Ana Tereza R Vasconcelos PMCID: PMC2612011 MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit, and Meriem El Karoui PMCID: PMC2607288 Software EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration Javier Forment, Francisco Gilabert, Antonio Robles, Vicente Conejero, Fernando Nuez, and Jose M Blanca PMCID: PMC2258287 SeqAn An efficient, generic C++ library for sequence analysis Andreas Döring, David Weese, Tobias Rausch, and Knut Reinert PMCID: PMC2246154 FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification Paolo Verderio, Sara Pizzamiglio, Fabio Gallo, and Simon C Ramsden PMCID: PMC2245902 LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons David Ellinghaus, Stefan Kurtz, and Ute Willhoeft PMCID: PMC2253517 LeARN: a platform for detecting, clustering and annotating non-coding RNAs Céline Noirot, Christine Gaspin, Thomas Schiex, and Jérôme Gouzy PMCID: PMC2241582 Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools' Alexandre Kuhn, Ruth Luthi-Carter, and Mauro Delorenzi PMCID: PMC2267709 The XBabelPhish MAGE-ML and XML Translator Don Maier, Farrell Wymore, Gavin Sherlock, and Catherine A Ball PMCID: PMC2233607 SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data Ramon Diaz-Uriarte PMCID: PMC2265264 miRNAminer: A tool for homologous microRNA gene search Shay Artzi, Adam Kiezun, and Noam Shomron PMCID: PMC2258288 I-TASSER server for protein 3D structure prediction Yang Zhang PMCID: PMC2245901 Generating samples for association studies based on HapMap data Jing Li and Yixuan Chen PMCID: PMC2375120 EzArray: A web-based highly automated Affymetrix expression array data management and analysis system Yuerong Zhu, Yuelin Zhu, and Wei Xu PMCID: PMC2265266 Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures Chih-Hung Jen, Tsun-Po Yang, Chien-Yi Tung, Shu-Han Su, Chi-Hung Lin, Ming-Ta Hsu, and Hsei-Wei Wang PMCID: PMC2248562 E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI) Pere Puigbò, Ignacio G Bravo, and Santiago Garcia-Vallvé PMCID: PMC2246156 GraphCrunch: A tool for large network analyses Tijana Milenković, Jason Lai, and Nataša Pržulj PMCID: PMC2275247 AWclust: point-and-click software for non-parametric population structure analysis Xiaoyi Gao and Joshua D Starmer PMCID: PMC2253519 OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Jr, Helen L Johnson, Philip V Ogren, and K Bretonnel Cohen PMCID: PMC2275248 Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes Feng Gao and Chun-Ting Zhang PMCID: PMC2275245 The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology Frédéric Chalmel and Michael Primig PMCID: PMC2375118 High-throughput bioinformatics with the Cyrille2 pipeline system Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot, and Roeland CHJ van Ham PMCID: PMC2268656 Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics Indra Neil Sarkar, Mary G Egan, Gloria Coruzzi, Ernest K Lee, and Rob DeSalle PMCID: PMC2270260 K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space Max Bylesjö, Mattias Rantalainen, Jeremy K Nicholson, Elaine Holmes, and Johan Trygg PMCID: PMC2323673 SPIKE – a database, visualization and analysis tool of cellular signaling pathways Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, and Ron Shamir PMCID: PMC2263022 ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences Hisakazu Iwana, Yukio Hori, Kensuke Matsumoto, Koji Murao, and Toshihiko Ishida PMCID: PMC2267439 CWRML: representing crop wild relative conservation and use data in XML Jonathan D Moore, Shelagh P Kell, Jose M Iriondo, Brian V Ford-Lloyd, and Nigel Maxted PMCID: PMC2375123 SciDBMaker: new software for computer-aided design of specialized biological databases Riadh Hammami, Abdelmajid Zouhir, Karim Naghmouchi, Jeannette Ben Hamida, and Ismail Fliss PMCID: PMC2267701 DOVIS: an implementation for high-throughput virtual screening using AutoDock Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, and Jaques Reifman PMCID: PMC2267697 catmap: Case-control And TDT Meta-Analysis Package Kristin K Nicodemus PMCID: PMC2291045 A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation Mark K Titulaer, Dana AN Mustafa, Ivar Siccama, Marco Konijnenburg, Peter C Burgers, Arno C Andeweg, Peter AE Sillevis Smitt, Johan M Kros, and Theo M Luider PMCID: PMC2323386 Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies Fredrik Pettersson, Andrew P Morris, Michael R Barnes, and Lon R Cardon PMCID: PMC2323971 Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider, and J Miguel Ortega PMCID: PMC2277401 ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts Kwangmin Choi and Sun Kim PMCID: PMC2277404 Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain Christopher Lau, Lydia Ng, Carol Thompson, Sayan Pathak, Leonard Kuan, Allan Jones, and Mike Hawrylycz PMCID: PMC2375125 DNAAlignEditor: DNA alignment editor tool Hector Sanchez-Villeda, Steven Schroeder, Sherry Flint-Garcia, Katherine E Guill, Masanori Yamasaki, and Michael D McMullen PMCID: PMC2322986 BioSAVE: Display of scored annotation within a sequence context Richard F Pollock and Boris Adryan PMCID: PMC2322987 OpenMS – An open-source software framework for mass spectrometry Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher PMCID: PMC2311306 Chromhome: A rich internet application for accessing comparative chromosome homology maps Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, and Malcolm A Ferguson-Smith PMCID: PMC2323974 MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects Holger Maier, Christoph Lengger, Bruno Simic, Helmut Fuchs, Valérie Gailus-Durner, and Martin Hrabé de Angelis PMCID: PMC2292142 PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, and Mitchell J Brittnacher PMCID: PMC2358893 Snagger: A user-friendly program for incorporating additional information for tagSNP selection Christopher K Edlund, Won H Lee, Dalin Li, David J Van Den Berg, and David V Conti PMCID: PMC2375134 A perl package and an alignment tool for phylogenetic networks Gabriel Cardona, Francesc Rosselló, and Gabriel Valiente PMCID: PMC2330044 JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Beth Duhaime, Jörg Peplies, and Frank Oliver Glöckner PMCID: PMC2311307 Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs Michaël Bekaert, Ivaylo P Ivanov, John F Atkins, and Pavel V Baranov PMCID: PMC2375905 annot8r: GO, EC and KEGG annotation of EST datasets Ralf Schmid and Mark L Blaxter PMCID: PMC2324097 Data capture in bioinformatics: requirements and experiences with Pedro Daniel Jameson, Kevin Garwood, Chris Garwood, Tim Booth, Pinar Alper, Stephen G Oliver, and Norman W Paton PMCID: PMC2335277 EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries Robin P Smith, William J Buchser, Marcus B Lemmon, Jose R Pardinas, John L Bixby, and Vance P Lemmon PMCID: PMC2322989 Novel computational methods for increasing PCR primer design effectiveness in directed sequencing Kelvin Li, Anushka Brownley, Timothy B Stockwell, Karen Beeson, Tina C McIntosh, Dana Busam, Steve Ferriera, Sean Murphy, and Samuel Levy PMCID: PMC2396641 uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne PMCID: PMC2375906 Natural Language Processing in aid of FlyBase curators Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale, and Ted Briscoe PMCID: PMC2375127 MPDA: Microarray pooled DNA analyzer Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen, and Cathy SJ Fann PMCID: PMC2387178 anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data Nicola Zamboni, Anne Kümmel, and Matthias Heinemann PMCID: PMC2375130 ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky, and Richard A McIndoe PMCID: PMC2375128 GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique Wei Yu, Melinda Clyne, Siobhan M Dolan, Ajay Yesupriya, Anja Wulf, Tiebin Liu, Muin J Khoury, and Marta Gwinn PMCID: PMC2387176 VariVis: a visualisation toolkit for variation databases Timothy D Smith and Richard GH Cotton PMCID: PMC2375904 Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework Kazutaka Katoh and Hiroyuki Toh PMCID: PMC2387179 An efficient visualization tool for the analysis of protein mutation matrices Maria Pamela C David, Carlo M Lapid, and Vincent Ricardo M Daria PMCID: PMC2390542 GENOMEPOP: A program to simulate genomes in populations Antonio Carvajal-Rodríguez PMCID: PMC2386491 CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies Martin Mann, Sebastian Will, and Rolf Backofen PMCID: PMC2396640 Automating dChip: toward reproducible sharing of microarray data analysis Cheng Li PMCID: PMC2390544 Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes Michael Dekhtyar, Amelie Morin, and Vehary Sakanyan PMCID: PMC2412878 Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm Jeremy D DeBarry, Renyi Liu, and Jeffrey L Bennetzen PMCID: PMC2412881 Compressing DNA sequence databases with coil W Timothy J White and Michael D Hendy PMCID: PMC2426707 MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Raymond T Ng, Calum MacAulay, and Wan L Lam PMCID: PMC2408605 Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp, and Bostjan Kobe PMCID: PMC2412879 TileQC: A system for tile-based quality control of Solexa data Peter C Dolan and Dee R Denver PMCID: PMC2443380 BatchPrimer3: A high throughput web application for PCR and sequencing primer design Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak, and Olin D Anderson PMCID: PMC2438325 SODa: An Mn/Fe superoxide dismutase prediction and design server Jean Marc Kwasigroch, René Wintjens, Dimitri Gilis, and Marianne Rooman PMCID: PMC2442099 StAR: a simple tool for the statistical comparison of ROC curves Ismael A Vergara, Tomás Norambuena, Evandro Ferrada, Alex W Slater, and Francisco Melo PMCID: PMC2435548 Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, and Stephan Waack PMCID: PMC2442105 SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis Jinho Yoo, Youngbok Lee, Yujung Kim, Sun Young Rha, and Yangseok Kim PMCID: PMC2453143 Re-searcher: a system for recurrent detection of homologous protein sequences Valdemaras Repšys, Mindaugas Margelevičius, and Česlovas Venclovas PMCID: PMC2446390 PseudoGeneQuest – Service for identification of different pseudogene types in the human genome Csaba Ortutay and Mauno Vihinen PMCID: PMC2453144 2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments Jens Allmer, Sebastian Kuhlgert, and Michael Hippler PMCID: PMC2475538 GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, and Kai-Tai Yao PMCID: PMC2483997 PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies Brian L Browning PMCID: PMC2483288 Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge Don L Armstrong, Chaim O Jacob, and Raphael Zidovetzki PMCID: PMC2500032 MSDmotif: exploring protein sites and motifs Adel Golovin and Kim Henrick PMCID: PMC2491636 Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies Li Ma, H Birali Runesha, Daniel Dvorkin, John R Garbe, and Yang Da PMCID: PMC2503991 PatternLab for proteomics: a tool for differential shotgun proteomics Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, John R Yates, III, and Valmir C Barbosa PMCID: PMC2488363 Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis Angela P Presson, Eric M Sobel, Paivi Pajukanta, Christopher Plaisier, Daniel E Weeks, Karolina Åberg, and Jeanette C Papp PMCID: PMC2515855 GBParsy: A GenBank flatfile parser library with high speed Tae-Ho Lee, Yeon-Ki Kim, and Baek Hie Nahm PMCID: PMC2516526 PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships Cuong Than, Derek Ruths, and Luay Nakhleh PMCID: PMC2533029 LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, and Gordon Luikart PMCID: PMC2515854 A Java-based tool for the design of classification microarrays Da Meng, Shira L Broschat, and Douglas R Call PMCID: PMC2533577 NullHap – a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles Robert M Nowak and Rafał Płoski PMCID: PMC2526998 HAPSIMU: a genetic simulation platform for population-based association studies Feng Zhang, Jianfeng Liu, Jie Chen, and Hong-Wen Deng PMCID: PMC2518933 The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage Hamilton Ganesan, Anna S Rakitianskaia, Colin F Davenport, Burkhard Tümmler, and Oleg N Reva PMCID: PMC2528017 Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data Peter Li, Juan I Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R Pocock, Carole A Goble, Stephen G Oliver, and Douglas B Kell PMCID: PMC2528018 SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis Martin Kostka, Magdalena Uzlikova, Ivan Cepicka, and Jaroslav Flegr PMCID: PMC2529323 SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool Zhike Zi, Yanan Zheng, Ann E Rundell, and Edda Klipp PMCID: PMC2529325 VisualRepbase: an interface for the study of occurrences of transposable element families Sébastien Tempel, Matthew Jurka, and Jerzy Jurka PMCID: PMC2527617 AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images János Roszik, János Szöllősi, and György Vereb PMCID: PMC2571114 FERN – a Java framework for stochastic simulation and evaluation of reaction networks Florian Erhard, Caroline C Friedel, and Ralf Zimmer PMCID: PMC2553347 Fregene: Simulation of realistic sequence-level data in populations and ascertained samples Marc Chadeau-Hyam, Clive J Hoggart, Paul F O'Reilly, John C Whittaker, Maria De Iorio, and David J Balding PMCID: PMC2542380 LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens Wah Heng Lee, Christopher W Wong, Wan Yee Leong, Lance D Miller, and Wing Kin Sung PMCID: PMC2553803 Kismeth: Analyzer of plant methylation states through bisulfite sequencing Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen, and Ravi Sachidanandam PMCID: PMC2553349 GenomeMatcher: A graphical user interface for DNA sequence comparison Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, and Masataka Tsuda PMCID: PMC2553346 CBESW: Sequence Alignment on the Playstation 3 Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, and Bertil Schmidt PMCID: PMC2571991 MetWAMer: eukaryotic translation initiation site prediction Michael E Sparks and Volker Brendel PMCID: PMC2603428 The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, and RA Edwards PMCID: PMC2563014 R/parallel – speeding up bioinformatics analysis with R Gonzalo Vera, Ritsert C Jansen, and Remo L Suppi PMCID: PMC2557021 FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects David Lagorce, Olivier Sperandio, Hervé Galons, Maria A Miteva, and Bruno O Villoutreix PMCID: PMC2561050 Presenting and exploring biological pathways with PathVisio Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, and Chris Evelo PMCID: PMC2569944 MetaMQAP: A meta-server for the quality assessment of protein models Marcin Pawlowski, Michal J Gajda, Ryszard Matlak, and Janusz M Bujnicki PMCID: PMC2573893 BibGlimpse: The case for a light-weight reprint manager in distributed literature research Thomas Tüchler, Golda Velez, Alexandra Graf, and David P Kreil PMCID: PMC2571996 BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, and Marianna Pensky PMCID: PMC2579305 XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data Daniel N Frank PMCID: PMC2577119 SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes Raj Chari, Bradley P Coe, Craig Wedseltoft, Marie Benetti, Ian M Wilson, Emily A Vucic, Calum MacAulay, Raymond T Ng, and Wan L Lam PMCID: PMC2571113 LC-MSsim – a simulation software for liquid chromatography mass spectrometry data Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert PMCID: PMC2577660 SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access Jorge Amigo, Antonio Salas, Christopher Phillips, and Ángel Carracedo PMCID: PMC2576268 easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu, and Hsei-Wei Wang PMCID: PMC2579307 Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission Benjamin Roche, Jean-François Guégan, and François Bousquet PMCID: PMC2600827 OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology Kieran O'Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson, and Henning Hermjakob PMCID: PMC2579441 Envelope: interactive software for modeling and fitting complex isotope distributions Michael T Sykes and James R Williamson PMCID: PMC2605472 Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking Jung Soh, Paul MK Gordon, Morgan L Taschuk, Anguo Dong, Andrew C Ah-Seng, Andrei L Turinsky, and Christoph W Sensen PMCID: PMC2590619 CompMoby: Comparative MobyDick for detection of cis-regulatory motifs Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, and Hao Li PMCID: PMC2605473 MetaMine – A tool to detect and analyse gene patterns in their environmental context Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, and Frank O Glöckner PMCID: PMC2615450 QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, and Bernd Mueller-Roeber PMCID: PMC2612009 A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, and Livia Torterolo PMCID: PMC2596147 CellProfiler Analyst: data exploration and analysis software for complex image-based screens Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland, and Anne E Carpenter PMCID: PMC2614436 mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences Hwan Young Lee, Injee Song, Eunho Ha, Sung-Bae Cho, Woo Ick Yang, and Kyoung-Jin Shin PMCID: PMC2621369 CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments Paolo Uva and Emanuele de Rinaldis PMCID: PMC2596149 EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman, J Darlington, L Game, MJE Sternberg, and SA Butcher PMCID: PMC2615452 ExonMiner: Web service for analysis of GeneChip Exon array data Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, and Satoru Miyano PMCID: PMC2621370 CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes Matthew S Hestand, Michiel van Galen, Michel P Villerius, Gert-Jan B van Ommen, Johan T den Dunnen, and Peter AC 't Hoen PMCID: PMC2613159 Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features Derek Huntley, Y Amy Tang, Tatyana B Nesterova, Sarah Butcher, and Neil Brockdorff PMCID: PMC2614995 ElliPro: a new structure-based tool for the prediction of antibody epitopes Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, and Bjoern Peters PMCID: PMC2607291 Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases Wei Yu, Anja Wulf, Tiebin Liu, Muin J Khoury, and Marta Gwinn PMCID: PMC2613935 Research Articles Evaluation of time profile reconstruction from complex two-color microarray designs Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, and Nicolas Pollet PMCID: PMC2265676 Supervised inference of gene-regulatory networks Cuong C To and Jiri Vohradsky PMCID: PMC2266705 Extending pathways based on gene lists using InterPro domain signatures Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, and Tim Beissbarth PMCID: PMC2245903 An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis Romesh Stanislaus, John M Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, and Jonas S Almeida PMCID: PMC2231339 Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? Jean-François Taly, Antoine Marin, and Jean-François Gibrat PMCID: PMC2245900 A novel method for high accuracy sumoylation site prediction from protein sequences Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng, and Xian-Ming Pan PMCID: PMC2245905 Corpus annotation for mining biomedical events from literature Jin-Dong Kim, Tomoko Ohta, and Jun'ichi Tsujii PMCID: PMC2267702 Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes Guy N Brock, John R Shaffer, Richard E Blakesley, Meredith J Lotz, and George C Tseng PMCID: PMC2253514 Prediction of enzyme function based on 3D templates of evolutionarily important amino acids David M Kristensen, R Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki, and Olivier Lichtarge PMCID: PMC2219985 Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations Jonathan G Lees and Robert W Janes PMCID: PMC2253515 Prioritization of gene regulatory interactions from large-scale modules in yeast Ho-Joon Lee, Thomas Manke, Ricardo Bringas, and Martin Vingron PMCID: PMC2244593 A statistical toolbox for metagenomics: assessing functional diversity in microbial communities Patrick D Schloss and Jo Handelsman PMCID: PMC2238731 Enhancing the prediction of protein pairings between interacting families using orthology information Jose MG Izarzugaza, David Juan, Carles Pons, Florencio Pazos, and Alfonso Valencia PMCID: PMC2263026 Universal seeds for cDNA-to-genome comparison Leming Zhou, Jonathan Stanton, and Liliana Florea PMCID: PMC2375135 Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution Rekin's Janky and Jacques van Helden PMCID: PMC2248561 A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles Samiran Ghosh, David F Grant, Dipak K Dey, and Dennis W Hill PMCID: PMC2253516 Predicting biological system objectives de novo from internal state measurements Erwin P Gianchandani, Matthew A Oberhardt, Anthony P Burgard, Costas D Maranas, and Jason A Papin PMCID: PMC2258290 A genetic approach for building different alphabets for peptide and protein classification Loris Nanni and Alessandra Lumini PMCID: PMC2246158 Discrimination of outer membrane proteins with improved performance Changhui Yan, Jing Hu, and Yingfeng Wang PMCID: PMC2254589 The Average Mutual Information Profile as a Genomic Signature Mark Bauer, Sheldon M Schuster, and Khalid Sayood PMCID: PMC2335307 A dynamic Bayesian network approach to protein secondary structure prediction Xin-Qiu Yao, Huaiqiu Zhu, and Zhen-Su She PMCID: PMC2266706 The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction Jonathan R Manning, Emily R Jefferson, and Geoffrey J Barton PMCID: PMC2267696 Designing multiple degenerate primers via consecutive pairwise alignments Hamed Shateri Najafabadi, Noorossadat Torabi, and Mahmood Chamankhah PMCID: PMC2253518 A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data Chang Sik Kim, Cheol Soo Bae, and Hong Joon Tcha PMCID: PMC2335309 Gene function prediction using labeled and unlabeled data Xing-Ming Zhao, Yong Wang, Luonan Chen, and Kazuyuki Aihara PMCID: PMC2275242 Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification Irene Kouskoumvekaki, Zhiyong Yang, Svava Ó Jónsdóttir, Lisbeth Olsson, and Gianni Panagiotou PMCID: PMC2248563 Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities Usman Roshan, Satish Chikkagoudar, and Dennis R Livesay PMCID: PMC2248559 Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation David D Smith, Pål Sætrom, Ola Snøve, Jr, Cathryn Lundberg, Guillermo E Rivas, Carlotta Glackin, and Garrett P Larson PMCID: PMC2275244 CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions Woochang Hwang, Young-Rae Cho, Aidong Zhang, and Murali Ramanathan PMCID: PMC2253513 Validation of protein models by a neural network approach Paolo Mereghetti, Maria Luisa Ganadu, Elena Papaleo, Piercarlo Fantucci, and Luca De Gioia PMCID: PMC2276493 Evaluation of two methods for computational HLA haplotypes inference using a real dataset Bruno F Bettencourt, Margarida R Santos, Raquel N Fialho, Ana R Couto, Maria J Peixoto, João P Pinheiro, Hélder Spínola, Marian G Mora, Cristina Santos, António Brehm, and Jácome Bruges-Armas PMCID: PMC2268655 PEPOP: Computational design of immunogenic peptides Violaine Moreau, Cécile Fleury, Dominique Piquer, Christophe Nguyen, Nicolas Novali, Sylvie Villard, Daniel Laune, Claude Granier, and Franck Molina PMCID: PMC2262870 Subfamily specific conservation profiles for proteins based on n-gram patterns John K Vries and Xiong Liu PMCID: PMC2267698 Towards an automatic classification of protein structural domains based on structural similarity Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-Francois Gibrat, Byungkook Lee, and Peter J Munson PMCID: PMC2267780 Rank-based edge reconstruction for scale-free genetic regulatory networks Guanrao Chen, Peter Larsen, Eyad Almasri, and Yang Dai PMCID: PMC2275249 Statistical issues in the analysis of Illumina data Mark J Dunning, Nuno L Barbosa-Morais, Andy G Lynch, Simon Tavaré, and Matthew E Ritchie PMCID: PMC2291044 Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Jos H Beijnen, Marcel JT Reinders, and Lodewyk FA Wessels PMCID: PMC2258289 An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance Ana C Casimiro, Susana Vinga, Ana T Freitas, and Arlindo L Oliveira PMCID: PMC2375121 Modularization of biochemical networks based on classification of Petri net t-invariants Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, and Ina Koch PMCID: PMC2277402 Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons Sacha AFT van Hijum, Richard JS Baerends, Aldert L Zomer, Harma A Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok, and Oscar P Kuipers PMCID: PMC2275246 Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction Ching-Wai Tan and David T Jones PMCID: PMC2267779 Using a logical model to predict the growth of yeast KE Whelan and RD King PMCID: PMC2335308 A perspective for biomedical data integration: Design of databases for flow cytometry John Drakos, Marina Karakantza, Nicholas C Zoumbos, John Lakoumentas, George C Nikiforidis, and George C Sakellaropoulos PMCID: PMC2267440 Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian Theis, Elmar W Lang, and Gerd Schmitz PMCID: PMC2277398 Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng, and Ziding Zhang PMCID: PMC2335299 Fuzzy association rules for biological data analysis: A case study on yeast Francisco J Lopez, Armando Blanco, Fernando Garcia, Carlos Cano, and Antonio Marin PMCID: PMC2277399 MScanner: a classifier for retrieving Medline citations Graham L Poulter, Daniel L Rubin, Russ B Altman, and Cathal Seoighe PMCID: PMC2263023 Evolutionary Pareto-optimization of stably folding peptides Wolfram Gronwald, Tim Hohm, and Daniel Hoffmann PMCID: PMC2263021 Effects of dependence in high-dimensional multiple testing problems Kyung In Kim and Mark A van de Wiel PMCID: PMC2375137 High-precision high-coverage functional inference from integrated data sources Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, and Charles DeLisi PMCID: PMC2292694 Strategies for measuring evolutionary conservation of RNA secondary structures Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker, and Stefan Washietl PMCID: PMC2335298 Assessment of composite motif discovery methods Kjetil Klepper, Geir K Sandve, Osman Abul, Jostein Johansen, and Finn Drablos PMCID: PMC2311304 A gene pattern mining algorithm using interchangeable gene sets for prokaryotes Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, and Jiong Yang PMCID: PMC2279103 Merging microarray data from separate breast cancer studies provides a robust prognostic test Lei Xu, Aik Choon Tan, Raimond L Winslow, and Donald Geman PMCID: PMC2409450 Using quality scores and longer reads improves accuracy of Solexa read mapping Andrew D Smith, Zhenyu Xuan, and Michael Q Zhang PMCID: PMC2335322 Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster Wensheng Zhang, Sige Zou, and Jiuzhou Song PMCID: PMC2322984 Shape based indexing for faster search of RNA family databases Stefan Janssen, Jens Reeder, and Robert Giegerich PMCID: PMC2277397 Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling Grace S Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang, and Yi-Chen Lo PMCID: PMC2323972 Functional discrimination of membrane proteins using machine learning techniques M Michael Gromiha and Yukimitsu Yabuki PMCID: PMC2375119 Mining phenotypes for gene function prediction Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz, and Ulf Leser PMCID: PMC2311305 Information transfer in signaling pathways: A study using coupled simulated and experimental data Jürgen Pahle, Anne K Green, C Jane Dixon, and Ursula Kummer PMCID: PMC2323387 Normalization of oligonucleotide arrays based on the least-variant set of genes Stefano Calza, Davide Valentini, and Yudi Pawitan PMCID: PMC2324100 Discovering gene annotations in biomedical text databases Ali Cakmak and Gultekin Ozsoyoglu PMCID: PMC2335285 Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt, and Thomas Simonson PMCID: PMC2292695 Optimizations for the EcoPod field identification tool Aswath Manoharan, Jeannie Stamberger, YuanYuan Yu, and Andreas Paepcke PMCID: PMC2322985 13C labeling experiments at metabolic nonstationary conditions: An exploratory study Sebastian Aljoscha Wahl, Katharina Nöh, and Wolfgang Wiechert PMCID: PMC2373788 Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania Martin Smith, Mathieu Blanchette, and Barbara Papadopoulou PMCID: PMC2335281 Synonym set extraction from the biomedical literature by lexical pattern discovery John McCrae and Nigel Collier PMCID: PMC2335115 Adaptive diffusion kernel learning from biological networks for protein function prediction Liang Sun, Shuiwang Ji, and Jieping Ye PMCID: PMC2409449 A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods Richard D Pearson PMCID: PMC2324099 Stability analysis of mixtures of mutagenetic trees Jasmina Bogojeska, Thomas Lengauer, and Jörg Rahnenführer PMCID: PMC2335279 Fast NJ-like algorithms to deal with incomplete distance matrices Alexis Criscuolo and Olivier Gascuel PMCID: PMC2335114 Interrogating domain-domain interactions with parsimony based approaches Katia S Guimarães and Teresa M Przytycka PMCID: PMC2358894 Predicting cancer involvement of genes from heterogeneous data Ramon Aragues, Chris Sander, and Baldo Oliva PMCID: PMC2330045 Proteochemometric modeling of HIV protease susceptibility Maris Lapins, Martin Eklund, Ola Spjuth, Peteris Prusis, and Jarl ES Wikberg PMCID: PMC2375133 Local conservation scores without a priori assumptions on neutral substitution rates Janis Dingel, Pavol Hanus, Niccolò Leonardi, Joachim Hagenauer, Jürgen Zech, and Jakob C Mueller PMCID: PMC2375903 Improving protein function prediction methods with integrated literature data Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, and Debra S Goldberg PMCID: PMC2375131 Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish C Varshney, and Gajendra PS Raghava PMCID: PMC2358896 Missing value imputation improves clustering and interpretation of gene expression microarray data Johannes Tuikkala, Laura L Elo, Olli S Nevalainen, and Tero Aittokallio PMCID: PMC2386492 Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke, and Habtom W Ressom PMCID: PMC2386822 Major copy proportion analysis of tumor samples using SNP arrays Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers, and Matthew Meyerson PMCID: PMC2375907 Extraction of semantic biomedical relations from text using conditional random fields Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp, and Hans-Peter Kriegel PMCID: PMC2386138 A new protein linear motif benchmark for multiple sequence alignment software Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, and Julie D Thompson PMCID: PMC2374782 M-BISON: Microarray-based integration of data sources using networks Bernie J Daigle, Jr and Russ B Altman PMCID: PMC2396182 Normalization for triple-target microarray experiments Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou, and Jean-Jacques Daudin PMCID: PMC2412880 Studying the functional conservation of cis-regulatory modules and their transcriptional output Denis C Bauer and Timothy L Bailey PMCID: PMC2386823 Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites Jill L Wegrzyn, Thomas M Drudge, Faramarz Valafar, and Vivian Hook PMCID: PMC2396638 Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces Andrew J Bordner and Andrey A Gorin PMCID: PMC2413245 A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins Kevin Brick and Elisabetta Pizzi PMCID: PMC2408606 Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction William S Bush, Todd L Edwards, Scott M Dudek, Brett A McKinney, and Marylyn D Ritchie PMCID: PMC2412877 Aspects of coverage in medical DNA sequencing Michael C Wendl and Richard K Wilson PMCID: PMC2430974 A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model Richard Judson, Fathi Elloumi, R Woodrow Setzer, Zhen Li, and Imran Shah PMCID: PMC2409339 Missing value imputation for microarray gene expression data using histone acetylation information Qian Xiang, Xianhua Dai, Yangyang Deng, Caisheng He, Jiang Wang, Jihua Feng, and Zhiming Dai PMCID: PMC2432074 New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background Silvana Penco, Massimo Buscema, Maria Cristina Patrosso, Alessandro Marocchi, and Enzo Grossi PMCID: PMC2443147 Protein contact order prediction from primary sequences Yi Shi, Jianjun Zhou, David Arndt, David S Wishart, and Guohui Lin PMCID: PMC2440764 poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening Raghunandan M Kainkaryam and Peter J Woolf PMCID: PMC2438324 Word correlation matrices for protein sequence analysis and remote homology detection Thomas Lingner and Peter Meinicke PMCID: PMC2438326 Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, and John L Spouge PMCID: PMC2432075 GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors Chiara Parravicini, Graziella Ranghino, Maria P Abbracchio, and Piercarlo Fantucci PMCID: PMC2443813 Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data Sudhakar Jonnalagadda and Rajagopalan Srinivasan PMCID: PMC2435549 PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval Jimmy Lin PMCID: PMC2442104 SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles Paul D Yoo, Yung Shwen Ho, Bing Bing Zhou, and Albert Y Zomaya PMCID: PMC2442102 A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins Armita Sheari, Mehdi Kargar, Ali Katanforoush, Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, and Sayed-Amir Marashi PMCID: PMC2474621 Discovering functional interaction patterns in protein-protein interaction networks Mehmet E Turanalp and Tolga Can PMCID: PMC2442100 Semantic role labeling for protein transport predicates Steven Bethard, Zhiyong Lu, James H Martin, and Lawrence Hunter PMCID: PMC2474622 Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping Guohui Lin, Zhipeng Cai, Junfeng Wu, Xiu-Feng Wan, Lizhe Xu, and Randy Goebel PMCID: PMC2438327 PURE: A webserver for the prediction of domains in unassigned regions in proteins Chilamakuri CS Reddy, Khader Shameer, Bernard O Offmann, and Ramanathan Sowdhamini PMCID: PMC2474620 The combination approach of SVM and ECOC for powerful identification and classification of transcription factor Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, and Yixue Li PMCID: PMC2440765 Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions Ki-Yeol Kim, Dong Hyuk Ki, Hei-Cheul Jeung, Hyun Cheol Chung, and Sun Young Rha PMCID: PMC2442106 Methods for evaluating gene expression from Affymetrix microarray datasets Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J Kearsey, and Zewei W Luo PMCID: PMC2442103 Precise detection of rearrangement breakpoints in mammalian chromosomes Claire Lemaitre, Eric Tannier, Christian Gautier, and Marie-France Sagot PMCID: PMC2443379 Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient Jianchao Yao, Chunqi Chang, Mari L Salmi, Yeung Sam Hung, Ann Loraine, and Stanley J Roux PMCID: PMC2459189 Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models Dawei Liu, Debashis Ghosh, and Xihong Lin PMCID: PMC2483287 Relating gene expression data on two-component systems to functional annotations in Escherichia coli Anne M Denton, Jianfei Wu, Megan K Townsend, Preeti Sule, and Birgit M Prüß PMCID: PMC2478693 Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information Jing Hu and Changhui Yan PMCID: PMC2446391 Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection Inkyung Jung, Jaehyung Lee, Soo-Young Lee, and Dongsup Kim PMCID: PMC2459191 A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data Liping Huang, Wenying Zhu, Christopher P Saunders, James N MacLeod, Mai Zhou, Arnold J Stromberg, and Arne C Bathke PMCID: PMC2474617 Deducing topology of protein-protein interaction networks from experimentally measured sub-networks Ling Yang, Thomas M Vondriska, Zhangang Han, W Robb MacLellan, James N Weiss, and Zhilin Qu PMCID: PMC2474618 Investigating selection on viruses: a statistical alignment approach Saskia de Groot, Thomas Mailund, Gerton Lunter, and Jotun Hein PMCID: PMC2478691 Grammar-based distance in progressive multiple sequence alignment David J Russell, Hasan H Otu, and Khalid Sayood PMCID: PMC2478692 Computational identification of ubiquitylation sites from protein sequences Chun-Wei Tung and Shinn-Ying Ho PMCID: PMC2488362 Assessing probe-specific dye and slide biases in two-color microarray data Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H Rice, Zelanna Goldberg, Patrick S Schnable, Pamela Ronald, and David M Rocke PMCID: PMC2496918 A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification Alexander Statnikov, Lily Wang, and Constantin F Aliferis PMCID: PMC2492881 Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements Qingwu Yang and Sing-Hoi Sze PMCID: PMC2527578 A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data Cong Zhou, Lucas D Bowler, and Jianfeng Feng PMCID: PMC2529326 Gene Ontology term overlap as a measure of gene functional similarity Meeta Mistry and Paul Pavlidis PMCID: PMC2518162 Evaluation of genomic island predictors using a comparative genomics approach Morgan GI Langille, William WL Hsiao, and Fiona SL Brinkman PMCID: PMC2518932 Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores Olivier Bastien and Eric Maréchal PMCID: PMC2529321 Determining significance of pairwise co-occurrences of events in bursty sequences Niina Haiminen, Heikki Mannila, and Evimaria Terzi PMCID: PMC2547115 A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics Arnab Bhattacharya, Sasha Levy, Adria LeBoeuf, Michelle Gaylord, Leslie Wilson, Ambuj K Singh, and Stuart C Feinstein PMCID: PMC2533028 A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time Hua Xu, Lanhao Yang, and Michael A Freitas PMCID: PMC2553802 Identification and correction of abnormal, incomplete and mispredicted proteins in public databases Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, and László Patthy PMCID: PMC2542381 Impact of residue accessible surface area on the prediction of protein secondary structures Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, and Sayed-Amir Marashi PMCID: PMC2553345 TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model Mallika Veeramalai, Yuzhen Ye, and Adam Godzik PMCID: PMC2553092 Methodology capture: discriminating between the "best" and the rest of community practice James M Eales, John W Pinney, Robert D Stevens, and David L Robertson PMCID: PMC2553348 Virtual screening of GPCRs: An in silico chemogenomics approach Laurent Jacob, Brice Hoffmann, Véronique Stoven, and Jean-Philippe Vert PMCID: PMC2553090 IgTM: An algorithm to predict transmembrane domains and topology in proteins Piedachu Peris, Damián López, and Marcelino Campos PMCID: PMC2566583 Automatic detection of exonic splicing enhancers (ESEs) using SVMs Britta Mersch, Alexander Gepperth, Sándor Suhai, and Agnes Hotz-Wagenblatt PMCID: PMC2567995 Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, and Bik K Tye PMCID: PMC2566582 Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy Marco AJ Iafolla, Guang Qiang Dong, and David R McMillen PMCID: PMC2543029 Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements Eva Lange, Ralf Tautenhahn, Steffen Neumann, and Clemens Gröpl PMCID: PMC2570366 Improving peptide-MHC class I binding prediction for unbalanced datasets Ana Paula Sales, Georgia D Tomaras, and Thomas B Kepler PMCID: PMC2586639 "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter, and Paul D Gershon PMCID: PMC2561049 Combining classifiers for improved classification of proteins from sequence or structure Iain Melvin, Jason Weston, Christina S Leslie, and William S Noble PMCID: PMC2561051 SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase Fabrice PA David and Yum L Yip PMCID: PMC2567350 PredGPI: a GPI-anchor predictor Andrea Pierleoni, Pier Luigi Martelli, and Rita Casadio PMCID: PMC2571997 Predicting protein linkages in bacteria: Which method is best depends on task Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, and Lawrence E Hunter PMCID: PMC2570368 Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem Lianyi Han, Yanli Wang, and Stephen H Bryant PMCID: PMC2572623 Abbreviation definition identification based on automatic precision estimates Sunghwan Sohn, Donald C Comeau, Won Kim, and W John Wilbur PMCID: PMC2576267 Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells Atsushi Niida, Andrew D Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q Zhang, and Tetsu Akiyama PMCID: PMC2572072 iRefIndex: A consolidated protein interaction database with provenance Sabry Razick, George Magklaras, and Ian M Donaldson PMCID: PMC2573892 Towards a lightweight generic computational grid framework for biological research Mark D Halling-Brown, David S Moss, and Adrian J Shepherd PMCID: PMC2566987 Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools Kevin Bleakley, Marie-Paule Lefranc, and Gérard Biau PMCID: PMC2576266 Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method Pelin Armutlu, Muhittin E Ozdemir, Fadime Uney-Yuksektepe, I Halil Kavakli, and Metin Turkay PMCID: PMC2572625 PhySIC_IST: cleaning source trees to infer more informative supertrees Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel JP Douzery, and Vincent Ranwez PMCID: PMC2576265 Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md Mehedi Hasan, Mohammad Shoyaib, Haseena Khan, and Ray Walshe PMCID: PMC2575220 Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks Iaroslav Ispolatov and Sergei Maslov PMCID: PMC2603427 Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems Yu-Shuen Tsai, Chin-Teng Lin, George C Tseng, I-Fang Chung, and Nikhil Ranjan Pal PMCID: PMC2620271 Mining protein networks for synthetic genetic interactions Sri R Paladugu, Shan Zhao, Animesh Ray, and Alpan Raval PMCID: PMC2577120 Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations Guillaume Launay and Thomas Simonson PMCID: PMC2586029 Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure Christopher Bystroff and Bobbie-Jo Webb-Robertson PMCID: PMC2579440 Comparative optimism in models involving both classical clinical and gene expression information Caroline Truntzer, Delphine Maucort-Boulch, and Pascal Roy PMCID: PMC2588601 Prediction of TF target sites based on atomistic models of protein-DNA complexes Vladimir Espinosa Angarica, Abel González Pérez, Ana T Vasconcelos, Julio Collado-Vides, and Bruno Contreras-Moreira PMCID: PMC2585596 PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data Laurent Bréhélin, Jean-François Dufayard, and Olivier Gascuel PMCID: PMC2605471 Structural assembly of two-domain proteins by rigid-body docking Tammy MK Cheng, Tom L Blundell, and Juan Fernandez-Recio PMCID: PMC2579442 An incremental approach to automated protein localisation Marko Tscherepanow, Nickels Jensen, and Franz Kummert PMCID: PMC2603336 Identification of hot-spot residues in protein-protein interactions by computational docking Solène Grosdidier and Juan Fernández-Recio PMCID: PMC2579439 Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces Salim Bougouffa and Jim Warwicker PMCID: PMC2596146 A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification Ning Wei, Erwin Flaschel, Karl Friehs, and Tim Wilhelm Nattkemper PMCID: PMC2582244 Probe signal correction for differential methylation hybridization experiments Dustin P Potter, Pearlly Yan, Tim HM Huang, and Shili Lin PMCID: PMC2603337 In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites Mohd Zeeshan Ansari, Jyoti Sharma, Rajesh S Gokhale, and Debasisa Mohanty PMCID: PMC2613160 Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles Hailong Meng, Edward L Murrelle, and Guoya Li PMCID: PMC2613930 Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies Peter A DiMaggio, Jr, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, and Herschel A Rabitz PMCID: PMC2605474 Information-based methods for predicting gene function from systematic gene knock-downs Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne, and Joshua M Stuart PMCID: PMC2596148 Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information Weijun Luo, Kurt D Hankenson, and Peter J Woolf PMCID: PMC2613931 Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham Hury, Ran Hoffer, Yaara Ziporen, Shulamit Michaeli, and Ron Unger PMCID: PMC2613932 Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data Tao Xu, LinFang Du, and Yan Zhou PMCID: PMC2612010 Improved identification of conserved cassette exons using Bayesian networks Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, and Rolf Backofen PMCID: PMC2621368 Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification Michael Gormley and Aydin Tozeren PMCID: PMC2620272 Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes Josephine F Reyes, Andrew R Francis, and Mark M Tanaka PMCID: PMC2620273 Natural computation meta-heuristics for the in silico optimization of microbial strains Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil, and Isabel Rocha PMCID: PMC2612012 ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins Aarti Garg and Gajendra PS Raghava PMCID: PMC2612013 MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids Jianguo Xia, Trent C Bjorndahl, Peter Tang, and David S Wishart PMCID: PMC2612014 A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, and Xuan Wang PMCID: PMC2613933 Improved machine learning method for analysis of gas phase chemistry of peptides Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar, and Krzysztof Cios PMCID: PMC2612015 Barcodes for genomes and applications Fengfeng Zhou, Victor Olman, and Ying Xu PMCID: PMC2621371 Methodology Articles Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models Harald Binder and Martin Schumacher PMCID: PMC2245904 Multiple organism algorithm for finding ultraconserved elements Scott Christley, Neil F Lobo, and Greg Madey PMCID: PMC2244594 A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, and Bernard Klein PMCID: PMC2248160 NestedMICA as an ab initio protein motif discovery tool Mutlu Doğruel, Thomas A Down, and Tim JP Hubbard PMCID: PMC2267705 A simplified approach to disulfide connectivity prediction from protein sequences Marc Vincent, Andrea Passerini, Matthieu Labbé, and Paolo Frasconi PMCID: PMC2375136 Function approximation approach to the inference of reduced NGnet models of genetic networks Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, and Mariko Hatakeyama PMCID: PMC2258286 Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau, and Xuhua Xia PMCID: PMC2275243 t2prhd: a tool to study the patterns of repeat evolution Botond Sipos, Kálmán Somogyi, István Andó, and Zsolt Pénzes PMCID: PMC2267704 A nonparametric model for quality control of database search results in shotgun proteomics Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, and Fuchu He PMCID: PMC2267700 The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem Andrey M Leontovich, Konstantin Y Tokmachev, and Hans C van Houwelingen PMCID: PMC2267706 A fast structural multiple alignment method for long RNA sequences Yasuo Tabei, Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai PMCID: PMC2375124 New resampling method for evaluating stability of clusters Irina M Gana Dresen, Tanja Boes, Johannes Huesing, Markus Neuhaeuser, and Karl-Heinz Joeckel PMCID: PMC2265265 Defining functional distances over Gene Ontology Angela del Pozo, Florencio Pazos, and Alfonso Valencia PMCID: PMC2375122 The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J Stevens, and Jaques Reifman PMCID: PMC2259298 Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes Cornelia Frömke, Ludwig A Hothorn, and Siegfried Kropf PMCID: PMC2268654 Inferring gene expression dynamics via functional regression analysis Hans-Georg Müller, Jeng-Min Chiou, and Xiaoyan Leng PMCID: PMC2335302 VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens Aarti Garg and Dinesh Gupta PMCID: PMC2254373 VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz, Thomas M Gress, Hongfang Liu, David W Kane, Barry R Zeeberg, and John N Weinstein PMCID: PMC2335321 The strength of co-authorship in gene name disambiguation Richárd Farkas PMCID: PMC2262057 SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, and Pierre Leblond PMCID: PMC2375139 Response projected clustering for direct association with physiological and clinical response data Sung-Gon Yi, Taesung Park, and Jae K Lee PMCID: PMC2275250 ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization Wen-Lin Huang, Chun-Wei Tung, Shih-Wen Ho, Shiow-Fen Hwang, and Shinn-Ying Ho PMCID: PMC2262056 Visualizing and clustering high throughput sub-cellular localization imaging Nicholas A Hamilton and Rohan D Teasdale PMCID: PMC2248560 A comparison of common programming languages used in bioinformatics Mathieu Fourment and Michael R Gillings PMCID: PMC2267699 OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature Laura I Furlong, Holger Dach, Martin Hofmann-Apitius, and Ferran Sanz PMCID: PMC2277400 Building pathway clusters from Random Forests classification using class votes Herbert Pang and Hongyu Zhao PMCID: PMC2335306 Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset Cédric Auliac, Vincent Frouin, Xavier Gidrol, and Florence d'Alché-Buc PMCID: PMC2335304 Microarray data mining using landmark gene-guided clustering Pankaj Chopra, Jaewoo Kang, Jiong Yang, HyungJun Cho, Heenam Stanley Kim, and Min-Goo Lee PMCID: PMC2262871 Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig, and Dirk Gründemann PMCID: PMC2276494 Statistical methodology for the analysis of dye-switch microarray experiments Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra, and Jean-Jacques Daudin PMCID: PMC2277403 Clustering exact matches of pairwise sequence alignments by weighted linear regression Alvaro J González and Li Liao PMCID: PMC2263025 Piecewise multivariate modelling of sequential metabolic profiling data Mattias Rantalainen, Olivier Cloarec, Timothy MD Ebbels, Torbjörn Lundstedt, Jeremy K Nicholson, Elaine Holmes, and Johan Trygg PMCID: PMC2373572 Simple integrative preprocessing preserves what is shared in data sources Abhishek Tripathi, Arto Klami, and Samuel Kaski PMCID: PMC2278131 Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, and Li-Qian Zhou PMCID: PMC2292139 Novel methodology for construction and pruning of quasi-median networks Sarah C Ayling and Terence A Brown PMCID: PMC2267707 A mixture model approach to sample size estimation in two-sample comparative microarray experiments Tommy S Jørstad, Herman Midelfart, and Atle M Bones PMCID: PMC2335282 Exon level integration of proteomics and microarray data Danny A Bitton, Michał J Okoniewski, Yvonne Connolly, and Crispin J Miller PMCID: PMC2267708 A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards Mano Sivaganesan, Shawn Seifring, Manju Varma, Richard A Haugland, and Orin C Shanks PMCID: PMC2292693 Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols Fabien Campagne PMCID: PMC2292696 How reliably can we predict the reliability of protein structure predictions? István Miklós, Ádám Novák ', Balázs Dombai, and Jotun Hein PMCID: PMC2324098 Ranking analysis of F-statistics for microarray data Yuan-De Tan, Myriam Fornage, and Hongyan Xu PMCID: PMC2323973 Empirical Bayes analysis of single nucleotide polymorphisms Holger Schwender and Katja Ickstadt PMCID: PMC2335278 Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions Leah E Mechanic, Brian T Luke, Julie E Goodman, Stephen J Chanock, and Curtis C Harris PMCID: PMC2335300 Conditional clustering of temporal expression profiles Ling Wang, Monty Montano, Matt Rarick, and Paola Sebastiani PMCID: PMC2335301 Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses René Natowicz, Roberto Incitti, Euler Guimarães Horta, Benoît Charles, Philippe Guinot, Kai Yan, Charles Coutant, Fabrice Andre, Lajos Pusztai, and Roman Rouzier PMCID: PMC2292140 H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments Rainer Merkl and Matthias Zwick PMCID: PMC2323388 Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu, and Chun-Houh Chen PMCID: PMC2322988 Empirical Bayes models for multiple probe type microarrays at the probe level Magnus Åstrand, Petter Mostad, and Mats Rudemo PMCID: PMC2358895 Computational evaluation of TIS annotation for prokaryotic genomes Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, and Zhen-Su She PMCID: PMC2362131 A simple and fast heuristic for protein structure comparison David A Pelta, Juan R González, and Marcos Moreno Vega PMCID: PMC2335283 Efficient computation of absent words in genomic sequences Julia Herold, Stefan Kurtz, and Robert Giegerich PMCID: PMC2375138 LocateP: Genome-scale subcellular-location predictor for bacterial proteins Miaomiao Zhou, Jos Boekhorst, Christof Francke, and Roland J Siezen PMCID: PMC2375117 RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, and Xiuzi Ye PMCID: PMC2335284 Multidimensional scaling for large genomic data sets Jengnan Tzeng, Henry Horng-Shing Lu, and Wen-Hsiung Li PMCID: PMC2375126 Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering Shibu Yooseph, Weizhong Li, and Granger Sutton PMCID: PMC2362130 MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening Nicolas Sauton, David Lagorce, Bruno O Villoutreix, and Maria A Miteva PMCID: PMC2373571 A high-throughput pipeline for designing microarray-based pathogen diagnostic assays Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, and Jaques Reifman PMCID: PMC2375140 Significance analysis of microarray for relative quantitation of LC/MS data in proteomics Bryan AP Roxas and Qingbo Li PMCID: PMC2335280 A novel representation of RNA secondary structure based on element-contact graphs Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, and Shengqi Wang PMCID: PMC2373570 Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci Sang Hong Lee, Julius HJ Van der Werf, and Brian P Kinghorn PMCID: PMC2375132 A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays Huanying Ge, Chao Cheng, and Lei M Li PMCID: PMC2375129 A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations Harri T Kiiveri PMCID: PMC2390543 Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research Yoginder S Dandass, Shane C Burgess, Mark Lawrence, and Susan M Bridges PMCID: PMC2374783 Conserved co-expression for candidate disease gene prioritization Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen, and Han G Brunner PMCID: PMC2383918 Discovering biclusters in gene expression data based on high-dimensional linear geometries Xiangchao Gan, Alan Wee-Chung Liew, and Hong Yan PMCID: PMC2386490 Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu, and Alan Wee-Chung Liew PMCID: PMC2396181 Binning sequences using very sparse labels within a metagenome Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge, and Sen-Lin Tang PMCID: PMC2383919 Gene prediction in metagenomic fragments: A large scale machine learning approach Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, and Peter Meinicke PMCID: PMC2409338 ConStruct: Improved construction of RNA consensus structures Andreas Wilm, Kornelia Linnenbrink, and Gerhard Steger PMCID: PMC2408607 Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry Andrej-Nikolai Spiess, Caroline Feig, and Christian Ritz PMCID: PMC2386824 An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions Alexander Churkin and Danny Barash PMCID: PMC2386494 Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory Alexander Churbanov and Stephen Winters-Hilt PMCID: PMC2430973 A copula method for modeling directional dependence of genes Jong-Min Kim, Yoon-Sung Jung, Engin A Sungur, Kap-Hoon Han, Changyi Park, and Insuk Sohn PMCID: PMC2386493 SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences Lukasz Kurgan, Krzysztof Cios, and Ke Chen PMCID: PMC2391167 The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks Anatolij P Potapov, Björn Goemann, and Edgar Wingender PMCID: PMC2396639 Inferring the role of transcription factors in regulatory networks Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, and Anne Siegel PMCID: PMC2422845 A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo López, and Toby J Gibson PMCID: PMC2396637 Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation Leonid Zaslavsky, Yiming Bao, and Tatiana A Tatusova PMCID: PMC2416652 Estimating the size of the solution space of metabolic networks Alfredo Braunstein, Roberto Mulet, and Andrea Pagnani PMCID: PMC2483728 Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis Shameek Biswas, John D Storey, and Joshua M Akey PMCID: PMC2424053 Using the longest significance run to estimate region-specific p-values in genetic association mapping studies Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang, and Cathy SJ Fann PMCID: PMC2430975 A visual analytics approach for understanding biclustering results from microarray data Rodrigo Santamaría, Roberto Therón, and Luis Quintales PMCID: PMC2416653 Dinucleotide controlled null models for comparative RNA gene prediction Tanja Gesell and Stefan Washietl PMCID: PMC2453142 Prediction of enzyme function by combining sequence similarity and protein interactions Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom, and Baldomero Oliva PMCID: PMC2430716 Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases Min Zhang, Dabao Zhang, and Martin T Wells PMCID: PMC2435550 A simple and robust method for connecting small-molecule drugs using gene-expression signatures Shu-Dong Zhang and Timothy W Gant PMCID: PMC2464610 Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA) Juan R González, Josep L Carrasco, Lluís Armengol, Sergi Villatoro, Lluís Jover, Yutaka Yasui, and Xavier Estivill PMCID: PMC2492880 Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon, and Stephen TC Wong PMCID: PMC2443381 An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, and Esko Ukkonen PMCID: PMC2430715 Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures Meng P Tan, Erin N Smith, James R Broach, and Christodoulos A Floudas PMCID: PMC2442101 Flexible boosting of accelerated failure time models Matthias Schmid and Torsten Hothorn PMCID: PMC2453145 Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles Guangtao Ge and G William Wong PMCID: PMC2440392 Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification Manli Zhu and Aleix M Martinez PMCID: PMC2443146 Inferring modules of functionally interacting proteins using the Bond Energy Algorithm Ryosuke LA Watanabe, Enrique Morett, and Edgar E Vallejo PMCID: PMC2474619 Partial mixture model for tight clustering of gene expression time-course Yinyin Yuan, Chang-Tsun Li, and Roland Wilson PMCID: PMC2492882 Stability of gene contributions and identification of outliers in multivariate analysis of microarray data Florent Baty, Daniel Jaeger, Frank Preiswerk, Martin M Schumacher, and Martin H Brutsche PMCID: PMC2441634 Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease Rob Jelier, Peter AC 't Hoen, Ellen Sterrenburg, Johan T den Dunnen, Gert-Jan B van Ommen, Jan A Kors, and Barend Mons PMCID: PMC2459190 Systems biology driven software design for the research enterprise John Boyle, Christopher Cavnor, Sarah Killcoyne, and Ilya Shmulevich PMCID: PMC2478690 A unified approach to false discovery rate estimation Korbinian Strimmer PMCID: PMC2475539 MAID : An effect size based model for microarray data integration across laboratories and platforms Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E Heathcote, Aled M Edwards, Michael Katze, Zhaolei Zhang, and Ian D McGilvray PMCID: PMC2483727 Conditional variable importance for random forests Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, and Achim Zeileis PMCID: PMC2491635 Directed acyclic graph kernels for structural RNA analysis Kengo Sato, Toutai Mituyama, Kiyoshi Asai, and Yasubumi Sakakibara PMCID: PMC2515856 Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis Yuanxin Xi and David M Rocke PMCID: PMC2516527 A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi, and Vilberto Stocchi PMCID: PMC2533027 Combining transcriptional datasets using the generalized singular value decomposition Andreas W Schreiber, Neil J Shirley, Rachel A Burton, and Geoffrey B Fincher PMCID: PMC2562393 Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands Wei Dai, Jens M Teodoridis, Janet Graham, Constanze Zeller, Tim HM Huang, Pearlly Yan, J Keith Vass, Robert Brown, and Jim Paul PMCID: PMC2529322 New time-scale criteria for model simplification of bio-reaction systems Junwon Choi, Kyung-won Yang, Tai-yong Lee, and Sang Yup Lee PMCID: PMC2553091 Parameter estimation for robust HMM analysis of ChIP-chip data Peter Humburg, David Bulger, and Glenn Stone PMCID: PMC2536674 An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, and Yusu Wang PMCID: PMC2571979 Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments Stephen W Tanner and Pankaj Agarwal PMCID: PMC2543031 Protein structure search and local structure characterization Shih-Yen Ku and Yuh-Jyh Hu PMCID: PMC2529324 Integration of relational and hierarchical network information for protein function prediction Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, and Eric D Kolaczyk PMCID: PMC2535605 SynBlast: Assisting the analysis of conserved synteny information Jörg Lehmann, Peter F Stadler, and Sonja J Prohaska PMCID: PMC2543028 Alignment of protein structures in the presence of domain motions Roberto Mosca, Barbara Brannetti, and Thomas R Schneider PMCID: PMC2535786 Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration Yulan Liang and Arpad Kelemen PMCID: PMC2579308 The C1C2: A framework for simultaneous model selection and assessment Martin Eklund, Ola Spjuth, and Jarl ES Wikberg PMCID: PMC2556350 Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution Stefano Moretti, Danitsja van Leeuwen, Hans Gmuender, Stefano Bonassi, Joost van Delft, Jos Kleinjans, Fioravante Patrone, and Domenico Franco Merlo PMCID: PMC2556684 Testing gene set enrichment for subset of genes: Sub-GSE Xiting Yan and Fengzhu Sun PMCID: PMC2543030 Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions E Andres Houseman, Brock C Christensen, Ru-Fang Yeh, Carmen J Marsit, Margaret R Karagas, Margaret Wrensch, Heather H Nelson, Joseph Wiemels, Shichun Zheng, John K Wiencke, and Karl T Kelsey PMCID: PMC2553421 ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS) Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda, and Wim M Degrave PMCID: PMC2559850 Mixture models for analysis of melting temperature data Christoffer Nellåker, Fredrik Uhrzander, Joanna Tyrcha, and Håkan Karlsson PMCID: PMC2567994 Large-scale identification of polymorphic microsatellites using an in silico approach Jifeng Tang, Samantha J Baldwin, Jeanne ME Jacobs, C Gerard van der Linden, Roeland E Voorrips, Jack AM Leunissen, Herman van Eck, and Ben Vosman PMCID: PMC2562394 A Population Proportion approach for ranking differentially expressed genes Mugdha Gadgil PMCID: PMC2566584 A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge Young-Rae Cho, Lei Shi, Murali Ramanathan, and Aidong Zhang PMCID: PMC2570367 caBIG™ VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data Yitan Zhu, Huai Li, David J Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P Hoffman, and Yue Wang PMCID: PMC2566986 Sequence based residue depth prediction using evolutionary information and predicted secondary structure Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, and Lukasz Kurgan PMCID: PMC2567998 HECTAR: A method to predict subcellular targeting in heterokonts Bernhard Gschloessl, Yann Guermeur, and J Mark Cock PMCID: PMC2567999 Comparison study on k-word statistical measures for protein: From sequence to 'sequence space' Qi Dai and Tianming Wang PMCID: PMC2571980 GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach Li Shen, Jie Liu, and Wei Wang PMCID: PMC2571992 Modifying the DPClus algorithm for identifying protein complexes based on new topological structures Min Li, Jian-er Chen, Jian-xin Wang, Bin Hu, and Gang Chen PMCID: PMC2570695 Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction Stefan Kuhn, Björn Egert, Steffen Neumann, and Christoph Steinbeck PMCID: PMC2605476 Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios Johan Staaf, Johan Vallon-Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, and Markus Ringnér PMCID: PMC2572624 Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments Stefano Parodi, Vito Pistoia, and Marco Muselli PMCID: PMC2576270 Gene and pathway identification with Lp penalized Bayesian logistic regression Zhenqiu Liu, Ronald B Gartenhaus, Ming Tan, Feng Jiang, and Xiaoli Jiao PMCID: PMC2567351 Knowledge-guided multi-scale independent component analysis for biomarker identification Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Wang, Zhen Zhang, Eric Hoffman, and Robert Clarke PMCID: PMC2576264 A method for analyzing censored survival phenotype with gene expression data Tongtong Wu, Wei Sun, Shinsheng Yuan, Chun-Houh Chen, and Ker-Chau Li PMCID: PMC2579309 Bayesian modeling of recombination events in bacterial populations Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam, and Jukka Corander PMCID: PMC2579306 Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments Ce Zheng and Lukasz Kurgan PMCID: PMC2613158 Probabilistic base calling of Solexa sequencing data Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, and Felix Naef PMCID: PMC2575221 Reranking candidate gene models with cross-species comparison for improved gene prediction Qian Liu, Koby Crammer, Fernando CN Pereira, and David S Roos PMCID: PMC2587481 AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O Villoutreix, and Maria A Miteva PMCID: PMC2588602 Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data Michael J Gilchrist, Mikkel B Christensen, Richard Harland, Nicolas Pollet, James C Smith, Naoto Ueno, and Nancy Papalopulu PMCID: PMC2587480 Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, and Tim W Nattkemper PMCID: PMC2600826 Assessment of protein set coherence using functional annotations Monica Chagoyen, Jose M Carazo, and Alberto Pascual-Montano PMCID: PMC2588600 Background correction using dinucleotide affinities improves the performance of GCRMA Raad Z Gharaibeh, Anthony A Fodor, and Cynthia J Gibas PMCID: PMC2579310 Gene set analyses for interpreting microarray experiments on prokaryotic organisms Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, and Ronald C Taylor PMCID: PMC2587482 Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi, and Niels Grabe PMCID: PMC2615451 RNAalifold: improved consensus structure prediction for RNA alignments Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, and Peter F Stadler PMCID: PMC2621365 RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences James K Hane and Richard P Oliver PMCID: PMC2621366 Identifying differential correlation in gene/pathway combinations Rosemary Braun, Leslie Cope, and Giovanni Parmigiani PMCID: PMC2613418 Determining gene expression on a single pair of microarrays Robert W Reid and Anthony A Fodor PMCID: PMC2605475 Microarray-based gene set analysis: a comparison of current methods Sarah Song and Michael A Black PMCID: PMC2607289 Use of normalization methods for analysis of microarrays containing a high degree of gene effects Terri T Ni, William J Lemon, Yu Shyr, and Tao P Zhong PMCID: PMC2612699 Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method Joseph W Foley and Fumiaki Katagiri PMCID: PMC2607290 Systematic identification of yeast cell cycle transcription factors using multiple data sources Wei-Sheng Wu and Wen-Hsiung Li PMCID: PMC2613934 Compo: composite motif discovery using discrete models Geir Kjetil Sandve, Osman Abul, and Finn Drabløs PMCID: PMC2614996 Correction Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations Hyunsoo Kim, Haesun Park, and Barry L Drake PMCID: PMC2387177 Corrects: Joshua S Yuan, et al. Statistical tools for transgene copy number estimation based on real-time PCR. BMC Bioinformatics. 2007; 8(Suppl 7): S6. |
