BMC Bioinformatics, Volume 8

Volume 8, 2007

• Gilles Didier, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, Claudine Devauchelle, Ivan Laprevotte:
  Comparing sequences without using alignments: application to HIV/SIV subtyping.
  
• Manjunatha R. Karpenahalli, Andrei N. Lupas, Johannes Söding:
  TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.
  
• Limin Fu, Enzo Medico:
  FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data.
  
• Irini A. Doytchinova, Darren R. Flower:
  VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines.
  
• Nikhil R. Pal, Kripamoy Aguan, Animesh Sharma, Shun-ichi Amari:
  Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering.
  
• Roger A. Craig, Li Liao:
  Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices.
  
• Wei Zou, David L. Aylor, Zhao-Bang Zeng:
  eQTL Viewer: visualizing how sequence variation affects genome-wide transcription.
  
• Jongrae Kim, Declan G. Bates, Ian Postlethwaite, Pat Heslop-Harrison, Kwang-Hyun Cho:
  Least-squares methods for identifying biochemical regulatory networks from noisy measurements.
  
• Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte:
  IDconverter and IDClight: Conversion and annotation of gene and protein IDs.
  
• Eric Yang, Timothy Maguire, Martin L. Yarmush, Francois Berthiaume, Ioannis P. Androulakis:
  Bioinformatics analysis of the early inflammatory response in a rat thermal injury model.
  
• Yukiko Yagi, Kotaro Terada, Takahisa Noma, Kazunori Ikebukuro, Koji Sode:
  In silico panning for a non-competitive peptide inhibitor.
  
• Lars Kuepfer, Uwe Sauer, Pablo A. Parrilo:
  Efficient classification of complete parameter regions based on semidefinite programming.
  
• Maria A. Stalteri, Andrew P. Harrison:
  Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.
  
• Rob Jelier, Guido Jenster, Lambert C. J. Dorssers, Bas J. Wouters, Peter J. M. Hendriksen, Barend Mons, Ruud Delwel, Jan A. Kors:
  Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation.
  
• Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano:
  AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.
  
• Mark C. Emerick, Giovanni Parmigiani, William S. Agnew:
  Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes.
  
• Michael R. Seringhaus, Mark B. Gerstein:
  Publishing perishing? Towards tomorrow's information architecture.
  
• Robert C. Edgar:
  PILER-CR: Fast and accurate identification of CRISPR repeats.
  
• Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang:
  Statistical significance of cis-regulatory modules.
  
• Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Ortoleva:
  Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory.
  
• Jamie M. Thomas, Daniel Horspool, Gordon Brown, Vasily Tcherepanov, Chris Upton:
  GraphDNA: a Java program for graphical display of DNA composition analyses.
  
• Andy M. Yip, Steve Horvath:
  Gene network interconnectedness and the generalized topological overlap measure.
  
• Tony Håndstad, Arne J. H. Hestnes, Pål Sætrom:
  Motif kernel generated by genetic programming improves remote homology and fold detection.
  
• Andrew B. Clegg, Adrian J. Shepherd:
  Benchmarking natural-language parsers for biological applications using dependency graphs.
  
• Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis, Torsten Hothorn:
  Bias in random forest variable importance measures: Illustrations, sources and a solution.
  
• Andy G. Lynch, David E. Neal, John D. Kelly, Glyn J. Burtt, Natalie P. Thorne:
  Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data.
  
• Chrysi Konstantinou-Kirtay, John B. O. Mitchell, James A. Lumley:
  Scoring functions and enrichment: a case study on Hsp90.
  
• Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan:
  Detecting differential expression in microarray data: comparison of optimal procedures.
  
• Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J. Feldman, Haiyan Huang:
  Measuring similarities between gene expression profiles through new data transformations.
  
• Ana P. Teixeira, Carlos Alves, Paula M. Alves, Manuel J. T. Carrondo, Rui Oliveira:
  Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control.
  
• Kacy K. Verdi, Heidi J. C. Ellis, Michael R. Gryk:
  Conceptual-level workflow modeling of scientific experiments using NMR as a case study.
  
• Meng Wang, Xiaobo Zhou, Randy W. King, Stephen T. C. Wong:
  Context based mixture model for cell phase identification in automated fluorescence microscopy.
  
• Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes:
  Considerations in the identification of functional RNA structural elements in genomic alignments.
  
• Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon:
  Computational RNA secondary structure design: empirical complexity and improved methods.
  
• Franck Rapaport, Andrei Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert:
  Classification of microarray data using gene networks.
  
• Ofir Davidovich, Gad Kimmel, Ron Shamir:
  GEVALT: An integrated software tool for genotype analysis.
  
• Haseong Kim, Jae K. Lee, Taesung Park:
  Boolean networks using the chi-square test for inferring large-scale gene regulatory networks.
  
• Zailong Wang, Pearlly Yan, Dustin P. Potter, Charis Eng, Tim Hui-Ming Huang, Shili Lin:
  Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data.
  
• Andrea Passerini, Claudia Andreini, Sauro Menchetti, Antonio Rosato, Paolo Frasconi:
  Predicting zinc binding at the proteome level.
  
• Carl Gustafson, William J. Bug, Jonathan Nissanov:
  NeuroTerrain - a client-server system for browsing 3D biomedical image data sets.
  
• Kay Prüfer, Bjoern Muetzel, Hong Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann, Wolfgang Enard:
  FUNC: a package for detecting significant associations between gene sets and ontological annotations.
  
• Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer, Bernd Mueller-Roeber:
  PlnTFDB: an integrative plant transcription factor database.
  
• Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese, Qingshun Quinn Li:
  Predictive modeling of plant messenger RNA polyadenylation sites.
  
• Francisco R. Pinto, João A. Carriço, Mário Ramirez, Jonas S. Almeida:
  Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement.
  
• Jenny Gu, Philip E. Bourne:
  Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2.
  
• Giulio Pavesi, Federico Zambelli, Graziano Pesole:
  WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
  
• Yuko Makita, Michiel J. L. de Hoon, Antoine Danchin:
  Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes.
  
• Rickard Sandberg, Ola Larsson:
  Improved precision and accuracy for microarrays using updated probe set definitions.
  
• Jean-Baptiste Veyrieras, Bruno Goffinet, Alain Charcosset:
  MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments.
  
• Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
  BioInfer: a corpus for information extraction in the biomedical domain.
  
• Jason W. H. Wong, Matthew J. Sullivan, Hugh M. Cartwright, Gerard Cagney:
  msmsEval: tandem mass spectral quality assignment for high-throughput proteomics.
  
• Juris Viksna, Edgars Celms, Martins Opmanis, Karlis Podnieks, Peteris Rucevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brazma, Ugis Sarkans:
  PASSIM - an open source software system for managing information in biomedical studies.
  
• Ji He, Xinbin Dai, Xuechun Zhao:
  PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.
  
• Brian Fristensky:
  BIRCH: A user-oriented, locally-customizable, bioinformatics system.
  
• Najib Naamane, Jacques van Helden, Decio L. Eizirik:
  In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells.
  
• Elena A. Ananko, Yury V. Kondrakhin, Tatyana I. Merkulova, Nikolay A. Kolchanov:
  Recognition of interferon-inducible sites, promoters, and enhancers.
  
• Mikel Egaña Aranguren, Sean Bechhofer, Phillip W. Lord, Ulrike Sattler, Robert D. Stevens:
  Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL.
  
• Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Cinzia Di Pietro, Michele Purrello, Marco Ragusa:
  Sequence similarity is more relevant than species specificity in probabilistic backtranslation.
  
• Ola Spjuth, Tobias Helmus, Egon L. Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E. S. Wikberg:
  Bioclipse: an open source workbench for chemo- and bioinformatics.
  
• Shuangge Ma, Xiao Song, Jian Huang:
  Supervised group Lasso with applications to microarray data analysis.
  
• Iosifina Pournara, Lorenz Wernisch:
  Factor analysis for gene regulatory networks and transcription factor activity profiles.
  
• Anne Friedrich, Raymond Ripp, Nicolas Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch, Luc Moulinier:
  Blast sampling for structural and functional analyses.
  
• Arthur Chun-Chieh Shih, D. T. Lee, Chin-Lin Peng, Yu-Wei Wu:
  Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences.
  
• Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop:
  Minimus: a fast, lightweight genome assembler.
  
• Oscar Conchillo-Solé, Natalia S. de Groot, Francesc X. Avilés, Josep Vendrell, Xavier Daura, Salvador Ventura:
  AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides.
  
• Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, D. T. Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao, Chi-Ying F. Huang:
  Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).
  
• Xin Zhao, Leo Wang-Kit Cheung:
  Kernel-imbedded Gaussian processes for disease classification using microarray gene expression data.
  
• Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich:
  False occurrences of functional motifs in protein sequences highlight evolutionary constraints.
  
• Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan:
  Inference of miRNA targets using evolutionary conservation and pathway analysis.
  
• John Moriarty, Julian R. Marchesi, Anthony Metcalfe:
  Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects.
  
• Kenneth Evans, Sascha Ott, Annika Hansen, Georgy Koentges, Lorenz Wernisch:
  A comparative study of S/MAR prediction tools.
  
• Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita:
  Visualization of three-way comparisons of omics data.
  
• Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki:
  Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
  
• James J. Chen, Chen-An Tsai, ShengLi Tzeng, Chun-Houh Chen:
  Gene selection with multiple ordering criteria.
  
• Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein:
  SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.
  
• Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano:
  An efficient grid layout algorithm for biological networks utilizing various biological attributes.
  
• Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra:
  Comparison of protein structures by growing neighborhood alignments.
  
• Kana Shimizu, Yoichi Muraoka, Shuichi Hirose, Kentaro Tomii, Tamotsu Noguchi:
  Predicting mostly disordered proteins by using structure-unknown protein data.
  
• Nicolas Rodriguez, Marco Donizelli, Nicolas Le Novère:
  SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML).
  
• Erin M. Conlon, Joon J. Song, Anna Liu:
  Bayesian meta-analysis models for microarray data: a comparative study.
  
• Gerhard G. Thallinger, Kerstin Baumgartner, Martin Pirklbauer, Martina Uray, Elke Pauritsch, Gabor Mehes, Charles R. Buck, Kurt Zatloukal, Zlatko Trajanoski:
  TAMEE: data management and analysis for tissue microarrays.
  
• Amit U. Sinha, Jaroslaw Meller:
  Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
  
• René T. J. M. van der Heijden, Berend Snel, Vera van Noort, Martijn A. Huynen:
  Orthology prediction at scalable resolution by phylogenetic tree analysis.
  
• Stéphane Robin, Sophie Schbath, Vincent Vandewalle:
  Statistical tests to compare motif count exceptionalities.
  
• Mariano J. Alvarez, Guillermo J. Vila-Ortiz, Mariano C. Salibe, Osvaldo L. Podhajcer, Fernando J. Pitossi:
  Model based analysis of real-time PCR data from DNA binding dye protocols.
  
• Russell L. Marsden, Tony A. Lewis, Christine A. Orengo:
  Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
  
• Nicolas Goffard, Georg Weiller:
  GeneBins: a database for classifying gene expression data, with application to plant genome arrays.
  
• Alex Gutteridge, Minoru Kanehisa, Susumu Goto:
  Regulation of metabolic networks by small molecule metabolites.
  
• Isaac Elias, Jens Lagergren:
  Fast computation of distance estimators.
  
• Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier, Pascal Roy:
  Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data.
  
• Jung-Hsien Chiang, Shih-Yi Chao:
  Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms.
  
• Jeppe Emmersen, Anna M. Heidenblut, Annabeth Laursen Høgh, Stephan A. Hahn, Karen G. Welinder, Kåre L. Nielsen:
  Discarding duplicate ditags in LongSAGE analysis may introduce significant error.
  
• Marko Sysi-Aho, Mikko Katajamaa, Laxman Yetukuri, Matej Oresic:
  Normalization method for metabolomics data using optimal selection of multiple internal standards.
  
• Sung Tae Doh, Yunyu Zhang, Matthew H. Temple, Li Cai:
  Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements.
  
• Robert P. Hanzlik, Yakov M. Koen, Bhargav Theertham, Yinghua Dong, Jianwen Fang:
  The reactive metabolite target protein database (TPDB) - a web-accessible resource.
  
• César L. Avila, Viviana A. Rapisarda, Ricardo N. Farías, Javier De Las Rivas, Rosana Chehín:
  Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases.
  
• Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She:
  MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.
  
• Xuejun Liu, Kevin K. Lin, Bogi Andersen, Magnus Rattray:
  Including probe-level uncertainty in model-based gene expression clustering.
  
• Aurélia Boissin-Quillon, Didier Piau, Caroline Leroux:
  In silico segmentations of lentivirus envelope sequences.
  
• Mamoru Kato, Tatsuhiko Tsunoda:
  MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs.
  
• Dante Mantini, Francesca Petrucci, Damiana Pieragostino, Piero Del Boccio, Marta Di Nicola, Carmine Di Ilio, Giorgio Federici, Paolo Sacchetta, Silvia Comani, Andrea Urbani:
  LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.
  
• Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker:
  SAMPI: Protein Identification with Mass Spectra Alignments.
  
• Johannes J. Mandel, Hendrik Fuß, Niall M. Palfreyman, Werner Dubitzky:
  Modeling biochemical transformation processes and information processing with Narrator.
  
• Prashant K. Srivastava, Dhwani K. Desai, Soumyadeep Nandi, Andrew M. Lynn:
  HMM-ModE - Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences.
  
• Tobias Kind, Oliver Fiehn:
  Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry.
  
• Minko Dudev, Carmay Lim:
  Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites.
  
• John P. Rasmussen, Christopher P. Saint, Paul T. Monis:
  Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes.
  
• Jun Lu, Joseph C. Lee, Marc L. Salit, Margaret C. Cam:
  Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays.
  
• Rebecka Jörnsten, Ming Ouyang, Hui-Yu Wang:
  A meta-data based method for DNA microarray imputation.
  
• Nicholas A. Hamilton, Radosav S. Pantelic, Kelly Hanson, Rohan D. Teasdale:
  Fast automated cell phenotype image classification.
  
• Ido Priness, Oded Maimon, Irad E. Ben-Gal:
  Evaluation of gene-expression clustering via mutual information distance measure.
  
• Michael C. Riley, Amanda Clare, Ross D. King:
  Locational distribution of gene functional classes in Arabidopsis thaliana.
  
• Jianlin Cheng, Pierre Baldi:
  Improved residue contact prediction using support vector machines and a large feature set.
  
• Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquín Dopazo:
  From genes to functional classes in the study of biological systems.
  
• Thomas L. York, Richard Durrett, Rasmus Nielsen:
  Dependence of paracentric inversion rate on tract length.
  
• Daron M. Standley, Hiroyuki Toh, Haruki Nakamura:
  ASH structure alignment package: Sensitivity and selectivity in domain classification.
  
• Negar Memarian, Matthew Jessulat, Javad Alirezaie, Nadereh Mir-Rashed, Jianhua Xu, Mehri Zareie, Myron Smith, Ashkan Golshani:
  Colony size measurement of the yeast gene deletion strains for functional genomics.
  
• Xinan Yang, Xiao Sun:
  Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers.
  
• Ying Wei, Jaeju Ko, Leonel F. Murga, Mary Jo Ondrechen:
  Selective prediction of interaction sites in protein structures with THEMATICS.
  
• Maria S. Poptsova, J. Peter Gogarten:
  BranchClust: a phylogenetic algorithm for selecting gene families.
  
• Wei-chung Liu, Wen-hsien Lin, Andrew J. Davis, Ferenc Jordán, Hsih-te Yang, Ming-jing Hwang:
  A network perspective on the topological importance of enzymes and their phylogenetic conservation.
  
• Daniel P. Depledge, Ryan P. J. Lower, Deborah F. Smith:
  RepSeq - A database of amino acid repeats present in lower eukaryotic pathogens.
  
• Nathan C. Rockwell, J. Clark Lagarias:
  Flexible mapping of homology onto structure with Homolmapper.
  
• Samuel O. M. Manda, Rebecca E. Walls, Mark S. Gilthorpe:
  A full Bayesian hierarchical mixture model for the variance of gene differential expression.
  
• Sébastien Leclercq, Eric Rivals, Philippe Jarne:
  Detecting microsatellites within genomes: significant variation among algorithms.
  
• Alexander L. Chernorudskiy, Alejandro Garcia, Eugene V. Eremin, Anastasia S. Shorina, Ekaterina V. Kondratieva, Murat R. Gainullin:
  UbiProt: a database of ubiquitylated proteins.
  
• Michael C. Wendl:
  Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping.
  
• Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han, Sheng Zhong:
  TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays.
  
• Xianfeng Chen, Thomas W. Laudeman, Paul J. Rushton, Thomas A. Spraggins, Michael P. Timko:
  CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.
  
• Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
  Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.
  
• Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza, Nicolas Mermod:
  Statistical significance of quantitative PCR.
  
• Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V. Bystrykh, Gerald de Haan, Rainer Breitling, Jan Peter Nap, Ritsert C. Jansen:
  A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat.
  
• Hua Xu, Michael A. Freitas:
  A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data.
  
• Stefan Schulz, Kornél G. Markó, Udo Hahn:
  Spatial location and its relevance for terminological inferences in bio-ontologies.
  
• Iain M. Wallace, Desmond G. Higgins:
  Supervised multivariate analysis of sequence groups to identify specificity determining residues.
  
• Alena Shmygelska, Holger H. Hoos:
  An adaptive bin framework search method for a beta-sheet protein homopolymer model.
  
• Alan Wee-Chung Liew, Jun Xian, Shuanhu Wu, David Keith Smith, Hong Yan:
  Spectral estimation in unevenly sampled space of periodically expressed microarray time series data.
  
• Enrique Blanco, Roderic Guigó, Xavier Messeguer:
  Multiple non-collinear TF-map alignments of promoter regions.
  
• Matthew DeJongh, Kevin Formsma, Paul Boillot, John Gould, Matthew Rycenga, Aaron A. Best:
  Toward the automated generation of genome-scale metabolic networks in the SEED.
  
• Charles J. Colbourn, Sudhir Kumar:
  Lower bounds on multiple sequence alignment using exact 3-way alignment.
  
• Benoit H. Dessailly, Marc F. Lensink, Shoshana J. Wodak:
  Relating destabilizing regions to known functional sites in proteins.
  
• Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B. Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope:
  Pre-processing Agilent microarray data.
  
• Lucio Marcello, Suraj Menon, Pauline Ward, Jonathan M. Wilkes, Nicola G. Jones, Mark Carrington, J. David Barry:
  VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins.
  
• Malik Yousef, Segun Jung, Louise C. Showe, Michael K. Showe:
  Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data.
  
• Tianwei Yu, Hui Ye, Wei Sun, Ker-Chau Li, Zugen Chen, Sharoni Jacobs, Dione K. Bailey, David T. Wong, Xiaofeng Zhou:
  A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.
  
• Alexander C. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson:
  Analysis of probe level patterns in Affymetrix microarray data.
  
• Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan:
  Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins.
  
• Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad:
  primetv: a viewer for reconciled trees.
  
• Gunnar Schramm, Marc Zapatka, Roland Eils, Rainer König:
  Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli.
  
• Roland Nilsson, José M. Peña, Johan Björkegren, Jesper Tegnér:
  Detecting multivariate differentially expressed genes.
  
• Qunfeng Dong, Matthew D. Wilkerson, Volker Brendel:
  Tracembler - software for in-silico chromosome walking in unassembled genomes.
  
• Tao-Wei Huang, Chung-Yen Lin, Cheng-Yan Kao:
  Reconstruction of human protein interolog network using evolutionary conserved network.
  
• Eric Chea, Dennis R. Livesay:
  How accurate and statistically robust are catalytic site predictions based on closeness centrality?
  
• Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon:
  Unexpected observations after mapping LongSAGE tags to the human genome.
  
• Silvio C. E. Tosatto, Roberto Battistutta:
  TAP score: torsion angle propensity normalization applied to local protein structure evaluation.
  
• B. D. Pascal, M. J. Chalmers, S. A. Busby, C. C. Mader, Mark R. Southern, N. F. Tsinoremas, Patrick R. Griffin:
  The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data.
  
• Xin Lu, David L. Perkins:
  Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures.
  
• Roderic D. M. Page:
  TBMap: a taxonomic perspective on the phylogenetic database TreeBASE.
  
• Mihaela Pertea, Stephen M. Mount, Steven L. Salzberg:
  A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.
  
• Renato Vicentini, Marcelo Menossi:
  TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets.
  
• Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C. Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki:
  Large-scale clustering of CAGE tag expression data.
  
• Frank Kose, Jan Budczies, Matthias Holschneider, Oliver Fiehn:
  Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors.
  
• David S. H. Chew, Ming-Ying Leung, Kwok Pui Choi:
  AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions.
  
• Chun-Chi Liu, Chin-Chung Lin, Ker-Chau Li, Wen-Shyen E. Chen, Jiun-Ching Chen, Ming-Te Yang, Pan-Chyr Yang, Pei-Chun Chang, Jeremy J. W. Chen:
  Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.
  
• Marc Strickert, Nese Sreenivasulu, Björn Usadel, Udo Seiffert:
  Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue.
  
• Holger Fröhlich, Nora Speer, Annemarie Poustka, Tim Beißbarth:
  GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products.
  
• Samuel Flores, Long J. Lu, Julie Yang, Nicholas Carriero, Mark Gerstein:
  Hinge Atlas: relating protein sequence to sites of structural flexibility.
  
• Ganesh A. Viswanathan, German Nudelman, Sonali Patil, Stuart C. Sealfon:
  BioPP: a tool for web-publication of biological networks.
  
• Junior Barrera, Roberto Marcondes Cesar Junior, Carlos Humes Jr., David Correa Martins Jr., Diogo F. C. Patrão, Paulo J. S. Silva, Helena Brentani:
  A feature selection approach for identification of signature genes from SAGE data.
  
• Craig E. Jones, Alfred L. Brown, Ute Baumann:
  Estimating the annotation error rate of curated GO database sequence annotations.
  
• Niina Haiminen, Heikki Mannila, Evimaria Terzi:
  Comparing segmentations by applying randomization techniques.
  
• Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel:
  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.
  
• Raja Jothi, Teresa M. Przytycka, L. Aravind:
  Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.
  
• Davide Corà, Ferdinando Di Cunto, Michele Caselle, Paolo Provero:
  Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.
  
• Asawari Samant, Babatunde A. Ogunnaike, Dionisios G. Vlachos:
  A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks.
  
• Dominik Heider, Angelika Barnekow:
  DNA-based watermarks using the DNA-Crypt algorithm.
  
• Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R. George, Martin J. Lohse, Graeme Milligan, Richard R. Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A. Javitch, Fabien Campagne, Marta Filizola:
  Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base.
  
• Jyoti K. Shah, Harold R. Garner, Michael A. White, David S. Shames, John D. Minna:
  sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database.
  
• Markus Weniger, Julia C. Engelmann, Jörg Schultz:
  Genome Expression Pathway Analysis Tool - Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context.
  
• Pierre de la Grange, Martin Dutertre, Margot Correa, Didier Auboeuf:
  A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants.
  
• Katrijn Van Deun, Kathleen Marchal, Willem J. Heiser, Kristof Engelen, Iven Van Mechelen:
  Joint mapping of genes and conditions via multidimensional unfolding analysis.
  
• Andrew S. Peek:
  Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features.
  
• R. Brent Calder, Rudolf B. Beems, Harry van Steeg, I. Saira Mian, Paul H. M. Lohman, Jan Vijg:
  MPHASYS: a mouse phenotype analysis system.
  
• Kyle A. McQuisten, Andrew S. Peek:
  Identification of sequence motifs significantly associated with antisense activity.
  
• Isaac T. S. Li, Warren Shum, Kevin Truong:
  160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA).
  
• Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein:
  An efficient pseudomedian filter for tiling microrrays.
  
• Sujay Chattopadhyay, Daniel E. Dykhuizen, Evgeni V. Sokurenko:
  ZPS: visualization of recent adaptive evolution of proteins.
  
• Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen:
  Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.
  
• Matti Kankainen, Ari Löytynoja:
  MATLIGN: a motif clustering, comparison and matching tool.
  
• Amelia B. Bellamy-Royds, Marcel Turcotte:
  Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?
  
• Thomas Hladish, Vivek Gopalan, Chengzhi Liang, Wei-Gang Qiu, Peter Yang, Arlin Stoltzfus:
  Bio: : NEXUS: a Perl API for the NEXUS format for comparative biological data.
  
• Shuangge Ma, Jian Huang:
  Additive risk survival model with microarray data.
  
• Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs:
  Improved benchmarks for computational motif discovery.
  
• Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li:
  Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data.
  
• Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo:
  Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips.
  
• Andrew Yates, Cliburn Chan, Jessica Strid, Simon Moon, Robin Callard, Andrew J. T. George, Jaroslav Stark:
  Reconstruction of cell population dynamics using CFSE.
  
• Jürgen Hartler, Gerhard G. Thallinger, Gernot Stocker, Alexander Sturn, Thomas R. Burkard, Erik Körner, Robert Rader, Andreas Schmidt, Karl Mechtler, Zlatko Trajanoski:
  MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.
  
• Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E. Mohr, Janice Williamson, Joshua LaBaer:
  A novel approach to sequence validating protein expression clones with automated decision making.
  
• Mudita Singhal, Haluk Resat:
  A domain-based approach to predict protein-protein interactions.
  
• Dai Osabe, Toshihito Tanahashi, Kyoko Nomura, Shuichi Shinohara, Naoto Nakamura, Toshikazu Yoshikawa, Hiroshi Shiota, Parvaneh Keshavarz, Yuka Yamaguchi, Kiyoshi Kunika, Maki Moritani, Hiroshi Inoue, Mitsuo Itakura:
  Evaluation of sample size effect on the identification of haplotype blocks.
  
• Gianluca Pollastri, Alberto J. M. Martin, Catherine Mooney, Alessandro Vullo:
  Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information.
  
• Zheng Li, Shireesh Srivastava, Sheenu Mittal, Xuerui Yang, Lufang Sheng, Christina Chan:
  A Three Stage Integrative Pathway Search (TIPS^(c)) framework to identify toxicity relevant genes and pathways.
  
• Dmitriy Skvortsov, Diana Abdueva, Michael E. Stitzer, Steven E. Finkel, Simon Tavaré:
  Using expression arrays for copy number detection: an example from E. coli.
  
• Jason D. Gans, Murray Wolinsky:
  Genomorama: genome visualization and analysis.
  
• Olivier Delaneau, Cédric Coulonges, Pierre-Yves Boëlle, George Nelson, Jean-Louis Spadoni, Jean-François Zagury:
  ISHAPE: new rapid and accurate software for haplotyping.
  
• Zhipeng Cai, Randy Goebel, Mohammad R. Salavatipour, Guohui Lin:
  Selecting dissimilar genes for multi-class classification, an application in cancer subtyping.
  
• Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Stefan Jansson, Thomas Moritz, Johan Trygg:
  Orthogonal projections to latent structures as a strategy for microarray data normalization.
  
• Paul M. K. Gordon, Christoph W. Sensen:
  Seahawk: moving beyond HTML in Web-based bioinformatics analysis.
  
• Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz:
  CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
  
• Amina Chebira, Yann Barbotin, Charles Jackson, Thomas E. Merryman, Gowri Srinivasa, Robert F. Murphy, Jelena Kovacevic:
  A multiresolution approach to automated classification of protein subcellular location images.
  
• Vladimir Vacic, Vladimir N. Uversky, A. Keith Dunker, Stefano Lonardi:
  Composition Profiler: a tool for discovery and visualization of amino acid composition differences.
  
• Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas:
  Optimization based automated curation of metabolic reconstructions.
  
• Namshin Kim, Christopher Lee:
  Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization.
  
• Andreas M. Boehm, Stephanie Pütz, Daniela Altenhöfer, Albert Sickmann, Michael Falk:
  Precise protein quantification based on peptide quantification using iTRAQ^TM.
  
• Samuel Flores, Mark Gerstein:
  FlexOracle: predicting flexible hinges by identification of stable domains.
  
• Jan Hummel, Michaela Niemann, Stefanie Wienkoop, Waltraud X. Schulze, Dirk Steinhauser, Joachim Selbig, Dirk Walther, Wolfram Weckwerth:
  ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.
  
• Nathan Salomonis, Kristina Hanspers, Alexander C. Zambon, Karen Vranizan, Steven C. Lawlor, Kam D. Dahlquist, Scott Doniger, Joshua M. Stuart, Bruce R. Conklin, Alexander R. Pico:
  GenMAPP 2: new features and resources for pathway analysis.
  
• Ki-Yeol Kim, Dong Hyuk Ki, Ha Jin Jeong, Hei-Cheul Jeung, Hyun Cheol Chung, Sun Young Rha:
  Novel and simple transformation algorithm for combining microarray data sets.
  
• Shouyong Peng, Artyom A. Alekseyenko, Erica Larschan, Mitzi I. Kuroda, Peter J. Park:
  Normalization and experimental design for ChIP-chip data.
  
• Johanna S. Hardin, Aya Mitani, Leanne Hicks, Brian VanKoten:
  A robust measure of correlation between two genes on a microarray.
  
• Joern Toedling, Oleg Sklyar, Wolfgang Huber:
  Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts.
  
• Eric A. Stone, Arend Sidow:
  Constructing a meaningful evolutionary average at the phylogenetic center of mass.
  
• Jo-Lan Chung, Wei Wang, Philip E. Bourne:
  High-throughput identification of interacting protein-protein binding sites.
  
• Alexander Platzer, Paul Perco, Arno Lukas, Bernd Mayer:
  Characterization of protein-interaction networks in tumors.
  
• Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa:
  Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.
  
• Dror Tobi, Ivet Bahar:
  Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?
  
• Simon K. Chan, Michael Hsing, Fereydoun Hormozdiari, Artem Cherkasov:
  Relationship between insertion/deletion (indel) frequency of proteins and essentiality.
  
• Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis:
  A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data.
  
• Cyril Dalmasso, Avner Bar-Hen, Philippe Broët:
  A constrained polynomial regression procedure for estimating the local False Discovery Rate.
  
• Shunpu Zhang:
  A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance.
  
• Nian Liu, Chiquito J. Crasto, Minghong Ma:
  Integrated olfactory receptor and microarray gene expression databases.
  
• Lars Skjaerven, Inge Jonassen, Nathalie Reuter:
  TMM@: a web application for the analysis of transmembrane helix mobility.
  
• Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja:
  Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.
  
• Helen M. Parsons, Christian Ludwig, Ulrich L. Günther, Mark R. Viant:
  Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation.
  
• Julie Chabalier, Jean Mosser, Anita Burgun:
  A transversal approach to predict gene product networks from ontology-based similarity.
  
• G. Traver Hart, Insuk Lee, Edward M. Marcotte:
  A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.
  
• Frank Emmert-Streib, Arcady R. Mushegian:
  A topological algorithm for identification of structural domains of proteins.
  
• Morten Nielsen, Claus Lundegaard, Ole Lund:
  Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
  
• Michelle S. Scott, Geoffrey J. Barton:
  Probabilistic prediction and ranking of human protein-protein interactions.
  
• Randall Hulshizer, Eric M. Blalock:
  Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data.
  
• A. K. M. A. Baten, Bill C. H. Chang, Saman K. Halgamuge, Jason Li:
  Correction: Splice site identification using probabilistic parameters and SVM classification.
  
• Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui:
  Improving gene set analysis of microarray data by SAM-GS.
  
• Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo, Iaroslav Ispolatov:
  Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.
  
• Yannick Pouliot, Peter D. Karp:
  A survey of orphan enzyme activities.
  
• Eunkyoung Jung, Junhyoung Kim, Minkyoung Kim, Dong Hyun Jung, Hokyoung Rhee, Jae-Min Shin, Kihang Choi, Sang-Kee Kang, Min-Kook Kim, Cheol-Heui Yun, Yun-Jaie Choi, Seung-Hoon Choi:
  Artificial neural network models for prediction of intestinal permeability of oligopeptides.
  
• Ricardo Z. N. Vêncio, Leonardo Varuzza, Carlos A. de B. Pereira, Helena Brentani, Ilya Shmulevich:
  Simcluster: clustering enumeration gene expression data on the simplex space.
  
• Morgane Thomas-Chollier, Luc Leyns, Valérie Ledent:
  HoxPred: automated classification of Hox proteins using combinations of generalised profiles.
  
• Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan:
  Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis.
  
• Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Robert H. Gross:
  A novel ensemble learning method for de novo computational identification of DNA binding sites.
  
• Curtis Huttenhower, Avi I. Flamholz, Jessica N. Landis, Sauhard Sahi, Chad L. Myers, Kellen L. Olszewski, Matthew A. Hibbs, Nathan O. Siemers, Olga G. Troyanskaya, Hilary A. Coller:
  Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.
  
• Chang Sik Kim:
  Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks.
  
• Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini, Gabriel Valiente:
  Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
  
• Jihoon Kim, Ju Han Kim:
  Difference-based clustering of short time-course microarray data with replicates.
  
• Matthias Kruspe, Peter F. Stadler:
  Progressive multiple sequence alignments from triplets.
  
• Mario Cannataro, Giovanni Cuda, Marco Gaspari, Sergio Greco, Giuseppe Tradigo, Pierangelo Veltri:
  The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments.
  
• Hongya Zhao, Hong Yan:
  HoughFeature, a novel method for assessing drug effects in three-color cDNA microarray experiments.
  
• Kanti V. Mardia, Vysaul B. Nyirongo, Peter J. Green, Nicola D. Gold, David R. Westhead:
  Bayesian refinement of protein functional site matching.
  
• Suman Datta, Bahrad A. Sokhansanj:
  Accelerated search for biomolecular network models to interpret high-throughput experimental data.
  
• Benjamin Schuster-Böckler, Alex Bateman:
  Reuse of structural domain-domain interactions in protein networks.
  
• David Talavera, Adam Hospital, Modesto Orozco, Xavier de la Cruz:
  A procedure for identifying homologous alternative splicing events.
  
• Irena I. Artamonova, Goar Frishman, Dmitrij Frishman:
  Applying negative rule mining to improve genome annotation.
  
• Mahmood A. Mahdavi, Yen-Han Lin:
  False positive reduction in protein-protein interaction predictions using gene ontology annotations.
  
• Sneh Lata, B. K. Sharma, G. P. S. Raghava:
  Analysis and prediction of antibacterial peptides.
  
• Jung-Wei Fan, Hua Xu, Carol Friedman:
  Using contextual and lexical features to restructure and validate the classification of biomedical concepts.
  
• Young-Rae Cho, Woochang Hwang, Murali Ramanathan, Aidong Zhang:
  Semantic integration to identify overlapping functional modules in protein interaction networks.
  
• Yingqin Luo, Cong Fu, Da-Yong Zhang, Kui Lin:
  BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
  
• Wataru Fujibuchi, Tsuyoshi Kato:
  Classification of heterogeneous microarray data by maximum entropy kernel.
  
• Michael J. Hickerson, Eli Stahl, Naoki Takebayashi:
  msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation.
  
• Peng Wang, Alexander A. Morgan, Qing Zhang, Alessandro Sette, Björn Peters:
  Automating document classification for the Immune Epitope Database.
  
• Guillaume Launay, Raul Mendez, Shoshana J. Wodak, Thomas Simonson:
  Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.
  
• Markus Bauer, Gunnar W. Klau, Knut Reinert:
  Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
  
• Robert D. Zeigler, Jason Gertz, Barak A. Cohen:
  A cis-regulatory logic simulator.
  
• Stuart D. Pepper, Emma K. Saunders, Laura E. Edwards, Claire L. Wilson, Crispin J. Miller:
  The utility of MAS5 expression summary and detection call algorithms.
  
• Benjamin B. Andken, In Lim, Gary Benson, John J. Vincent, Matthew T. Ferenc, Bianca Heinrich, Larissa A. Jarzylo, Heng-Ye Man, James O. Deshler:
  3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions.
  
• Lei Xu, Donald Geman, Raimond L. Winslow:
  Large-scale integration of cancer microarray data identifies a robust common cancer signature.
  
• Sunita Kumari, Lalit K. Verma, Jennifer W. Weller:
  AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip^TM expression arrays with respect to SNPs.
  
• Chung Mo Nam, Dae Ryong Kang, Jinheum Kim:
  Haplotype-based score test for linkage in nuclear families.
  
• Erin P. Price, John Inman-Bamber, Venugopal Thiruvenkataswamy, Flavia Huygens, Philip M. Giffard:
  Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.
  
• Philipp Heuser, Dietmar Schomburg:
  Combination of scoring schemes for protein docking.
  
• Timur Shtatland, Daniel Guettler, Misha Kossodo, Misha Pivovarov, Ralph Weissleder:
  PepBank - a database of peptides based on sequence text mining and public peptide data sources.
  
• Naoto Tanaka, Masataka Uchino, Satoru Miyazaki, Hideaki Sugawara:
  Identification of discriminative characteristics for clusters from biologic data with InforBIO software.
  
• Scott D. Zuyderduyn:
  Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model.
  
• Xiangdong Liu, Walter J. Jessen, Siva Sivaganesan, Bruce J. Aronow, Mario Medvedovic:
  Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.
  
• Carson M. Andorf, Drena Dobbs, Vasant Honavar:
  Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach.
  
• Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yongjing Xia, Yiqing Wu, Xiangjun Liu:
  miRAS: a data processing system for miRNA expression profiling study.
  
• Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski, Alain Fleury:
  CLUSS: Clustering of protein sequences based on a new similarity measure.
  
• Yasunori Yamamoto, Toshihisa Takagi:
  OReFiL: an online resource finder for life sciences.
  
• Cédric Messaoudi, Thomas Boudier, Carlos Oscar Sánchez Sorzano, Sergio Marco:
  TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy.
  
• Brian J. Holden, John W. Pinney, Simon C. Lovell, Grigoris Amoutzias, David L. Robertson:
  An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network.
  
• Andreas Keller, Christina Backes, Hans-Peter Lenhof:
  Computation of significance scores of unweighted Gene Set Enrichment Analyses.
  
• Gul S. Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P. Mesirov, Shridar Ganesan, Charles DeLisi, Gyan Bhanot:
  Portraits of breast cancer progression.
  
• Eric C. Rouchka, C. Timothy Hardin:
  rMotifGen: random motif generator for DNA and protein sequences.
  
• Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides:
  Automatic reconstruction of a bacterial regulatory network using Natural Language Processing.
  
• Vineet Sangar, Daniel J. Blankenberg, Naomi Altman, Arthur M. Lesk:
  Quantitative sequence-function relationships in proteins based on gene ontology.
  
• Marija Cvijovic, Daniel Dalevi, Elizabeth Bilsland, Graham J. L. Kemp, Per Sunnerhagen:
  Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.
  
• Nigam H. Shah, Daniel L. Rubin, Inigo Espinosa, Kelli Montgomery, Mark A. Musen:
  Annotation and query of tissue microarray data using the NCI Thesaurus.
  
• Caroline C. Friedel, Ralf Zimmer:
  Influence of degree correlations on network structure and stability in protein-protein interaction networks.
  
• Jaina Mistry, Alex Bateman, Robert D. Finn:
  Predicting active site residue annotations in the Pfam database.
  
• Feng Luo, Yunfeng Yang, Jianxin Zhong, Haichun Gao, Latifur Khan, Dorothea K. Thompson, Jizhong Zhou:
  Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory.
  
• Serene A. K. Ong, Hong Huang Lin, Yu Zong Chen, Ze-Rong Li, Zhi Wei Cao:
  Efficacy of different protein descriptors in predicting protein functional families.
  
• David F. Burke, Catherine L. Worth, Eva-Maria Priego, Tammy M. K. Cheng, Luc J. Smink, John A. Todd, Tom L. Blundell:
  Genome bioinformatic analysis of nonsynonymous SNPs.
  
• Yungki Park, Sikander Hayat, Volkhard Helms:
  Prediction of the burial status of transmembrane residues of helical membrane proteins.
  
• Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu:
  Correlation between structure and temperature in prokaryotic metabolic networks.
  
• László Kaján, Leszek Rychlewski:
  Evaluation of 3D-Jury on CASP7 models.
  
• Marco Vilela, Carlos Cristiano H. Borges, Susana Vinga, Ana Tereza R. Vasconcelos, Helena Santos, Eberhard O. Voit, Jonas S. Almeida:
  Automated smoother for the numerical decoupling of dynamics models.
  
• Leandro Martínez, Roberto Andreani, José Mario Martínez:
  Convergent algorithms for protein structural alignment.
  
• Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang, Ping-Chiang Lyu:
  Protein structural similarity search by Ramachandran codes.
  
• Zhan Yu, David Morais, Mahine Ivanga, Paul M. Harrison:
  Analysis of the role of retrotransposition in gene evolution in vertebrates.
  
• Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein:
  PARE: A tool for comparing protein abundance and mRNA expression data.
  
• Luis A. Diago, Persy Morell, Longendri Aguilera, Ernesto Moreno:
  Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms.
  
• Jing Zhao, Guohui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li:
  Modular co-evolution of metabolic networks.
  
• Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Anders Gorm Pedersen:
  MaxAlign: maximizing usable data in an alignment.
  
• Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar:
  Integrated network reconstruction, visualization and analysis using YANAsquare.
  
• Yuan Qi, Ruslan Sadreyev, Yong Wang, Bong-Hyun Kim, Nick V. Grishin:
  A comprehensive system for evaluation of remote sequence similarity detection.
  
• Michael Weitzel, Wolfgang Wiechert, Katharina Nöh:
  The topology of metabolic isotope labeling networks.
  
• Aleksey A. Porollo, Jaroslaw Meller:
  Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.
  
• Peter E. Larsen, Eyad Almasri, Guanrao Chen, Yang Dai:
  A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments.
  
• Alexey V. Kochetov, Andrey Palyanov, Igor I. Titov, Dmitry A. Grigorovich, Akinori Sarai, Nikolay A. Kolchanov:
  AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
  
• Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao:
  antiCODE: a natural sense-antisense transcripts database.
  
• Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus F. X. Mayer:
  Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.
  
• Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert:
  Automatic generation of 3D motifs for classification of protein binding sites.
  
• Daniel J. Vis, Johan A. Westerhuis, Age K. Smilde, Jan van der Greef:
  Statistical validation of megavariate effects in ASCA.
  
• Xinning Jiang, Xiaogang Jiang, Guanghui Han, Mingliang Ye, Hanfa Zou:
  Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics.
  
• Xiaohua Hu, Fang-Xiang Wu:
  Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks.
  
• Richard Tzong-Han Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung, Wen-Lian Hsu:
  BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features.
  
• Brian J. Parker, Simon Günter, Justin Bedo:
  Stratification bias in low signal microarray studies.
  
• Hongseok Tae, Eun-Bae Kong, Kiejung Park:
  ASMPKS: an analysis system for modular polyketide synthases.
  
• Ramón Díaz-Uriarte:
  GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.
  
• Angelica Tulipano, Giacinto Donvito, Flavio Licciulli, Giorgio Pietro Maggi, Andreas Gisel:
  Gene analogue finder: a GRID solution for finding functionally analogous gene products.
  
• Emily Chia-Yu Su, Hua-Sheng Chiu, Allan Lo, Jenn-Kang Hwang, Ting-Yi Sung, Wen-Lian Hsu:
  Protein subcellular localization prediction based on compartment-specific features and structure conservation.
  
• Jianhua Wu, Keith M. Kendrick, Jianfeng Feng:
  A novel approach to detect hot-spots in large-scale multivariate data.
  
• Roland Barriot, David J. Sherman, Isabelle Dutour:
  How to decide which are the most pertinent overly-represented features during gene set enrichment analysis.
  
• Andreas Prlic, Thomas A. Down, Eugene Kulesha, Robert D. Finn, Andreas Kähäri, Tim J. P. Hubbard:
  Integrating sequence and structural biology with DAS.
  
• Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell:
  EDISA: extracting biclusters from multiple time-series of gene expression profiles.
  
• Gürkan Bebek, Jiong Yang:
  PathFinder: mining signal transduction pathway segments from protein-protein interaction networks.
  
• Markus Koschorreck, Holger Conzelmann, Sybille Ebert, Michael Ederer, Ernst Dieter Gilles:
  Reduced modeling of signal transduction - a modular approach.
  
• Mamoon Rashid, Sudipto Saha, Gajendra P. S. Raghava:
  Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs.
  
• Catherine Beauheim, Farrell Wymore, Michael Nitzberg, Zachariah K. Zachariah, Heng Jin, J. H. Pate Skene, Catherine A. Ball, Gavin Sherlock:
  OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.
  
• Antonio Lijoi, Ramsés H. Mena, Igor Prünster:
  A Bayesian nonparametric method for prediction in EST analysis.
  
• Andrew A. Hill, Peter LaPan, Yizheng Li, Steve Haney:
  Impact of image segmentation on high-content screening data quality for SK-BR-3 cells.
  
• Ting-Hua Huang, Bin Fan, Max F. Rothschild, Zhi-Liang Hu, Kui Li, Shu-Hong Zhao:
  MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
  
• Chris Thachuk, Alena Shmygelska, Holger H. Hoos:
  A replica exchange Monte Carlo algorithm for protein folding in the HP model.
  
• Ryoko Morioka, Shigehiko Kanaya, Masami Y. Hirai, Mitsuru Yano, Naotake Ogasawara, Kazuki Saito:
  Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model.
  
• Jeremiah J. Faith, Andrew J. Olson, Timothy S. Gardner, Ravi Sachidanandam:
  Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.
  
• Liam J. McGuffin:
  Benchmarking consensus model quality assessment for protein fold recognition.
  
• Lars Halvor Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjørn K. Alsberg:
  A framework for significance analysis of gene expression data using dimension reduction methods.
  
• Jahangheer S. Shaik, Mohammed Yeasin:
  A unified framework for finding differentially expressed genes from microarray experiments.
  
• Hwanseok Rhee, Jin-Sung Lee:
  PADB : Published Association Database.
  
• Heng Li, Liang Guan, Tao Liu, Yiran Guo, Wei-Mou Zheng, Gane Ka-Shu Wong, Jun Wang:
  A cross-species alignment tool (CAT).
  
• Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser, Zbynek Bozdech:
  Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy.
  
• Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Govindaraju Archunan, Ramanathan Sowdhamini:
  A machine learning approach for the identification of odorant binding proteins from sequence-derived properties.
  
• Keng Wah Choo, Wai Mun Tham:
  Tandem mass spectrometry data quality assessment by self-convolution.
  
• Qingliang Li, Luhua Lai:
  Prediction of potential drug targets based on simple sequence properties.
  
• Fathi Elloumi, Martha Nason:
  SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences.
  
• Changhoon Kim, Byungkook Lee:
  Accuracy of structure-based sequence alignment of automatic methods.
  
• Jos Boekhorst, Berend Snel:
  Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.
  
• Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel-Bennett, Anders Krogh:
  An evolutionary method for learning HMM structure: prediction of protein secondary structure.
  
• Hui Lan, Rachel Carson, Nicholas J. Provart, Anthony J. Bonner:
  Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements.
  
• Srinka Ghosh, Heather A. Hirsch, Edward A. Sekinger, Philipp Kapranov, Kevin Struhl, Thomas R. Gingeras:
  Differential analysis for high density tiling microarray data.
  
• Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. A. Evelo:
  Linking microarray reporters with protein functions.
  
• Huynh-Hoa Bui, John Sidney, Wei Li, Nicholas Fusseder, Alessandro Sette:
  Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines.
  
• Michael C. Wendl, Scott Smith, Craig S. Pohl, David J. Dooling, Asif T. Chinwalla, Kevin Crouse, Todd Hepler, Shin Leong, Lynn K. Carmichael, Mike Nhan, Benjamin J. Oberkfell, Elaine R. Mardis, LaDeana W. Hillier, Richard K. Wilson:
  Design and implementation of a generalized laboratory data model.
  
• Matthew Yeung, Ines Thiele, Bernhard O. Palsson:
  Estimation of the number of extreme pathways for metabolic networks.
  
• Hyungwon Choi, Ronglai Shen, Arul M. Chinnaiyan, Debashis Ghosh:
  A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments.
  
• Israel Mark Martínez-Pérez, Gong Zhang, Zoya Ignatova, Karl-Heinz Zimmermann:
  Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype.
  
• Yair Horesh, Tirza Doniger, Shulamit Michaeli, Ron Unger:
  RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules.
  
• Jan Küntzer, Christina Backes, Torsten Blum, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof:
  BNDB - The Biochemical Network Database.
  
• Ágnes Baross, Allen D. Delaney, H. Irene Li, Tarun Nayar, Stephane Flibotte, Hong Qian, Susanna Y. Chan, Jennifer Asano, Adrian Ally, Manqiu Cao, Patricia Birch, Mabel Brown-John, Nicole Fernandes, Anne Go, Giulia C. Kennedy, Sylvie Langlois, Patrice Eydoux, J. M. Friedman, Marco A. Marra:
  Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.
  
• Jakob Fredslund, Mette Lange:
  Primique: automatic design of specific PCR primers for each sequence in a family.
  
• Ji-Gang Zhang, Hong-Wen Deng:
  Gene selection for classification of microarray data based on the Bayes error.
  
• Kathleen F. Kerr:
  Extended analysis of benchmark datasets for Agilent two-color microarrays.
  
• Seth I. Berger, Jeremy M. Posner, Avi Ma'ayan:
  Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
  
• Razif R. Gabdoulline, Matthias Stein, Rebecca C. Wade:
  qPIPSA: Relating enzymatic kinetic parameters and interaction fields.
  
• Xiaodan Fan, Jun Zhu, Eric E. Schadt, Jun S. Liu:
  Statistical power of phylo-HMM for evolutionarily conserved element detection.
  
• Bingjun Jiang, Hong Qu, Yuanlei Hu, Ting Ni, Zhongping Lin:
  Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid.
  
• Tomasz Lipniacki, Krzysztof Puszynski, Pawel Paszek, Allan R. Brasier, Marek Kimmel:
  Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling.
  
• Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre:
  Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies.
  
• William O. Ward, Carol D. Swartz, Steffen Porwollik, Sarah H. Warren, Nancy M. Hanley, Geremy W. Knapp, Michael McClelland, David M. DeMarini:
  Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella.
  
• Dianhui Zhu, George E. Fox, Sugoto Chakravarty:
  RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses.
  
• Oliviero Carugo:
  Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots.
  
• Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Marco Ocano, Eun-Jong Hong, Yaoyu E. Wang, Shyamal Somaroo, Brian E. Caffrey, Shobha Potluri, Enoch S. Huang:
  PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments.
  
• Aaron M. Newman, James B. Cooper:
  XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
  
• Ricardo Z. N. Vêncio, Ilya Shmulevich:
  ProbCD: enrichment analysis accounting for categorization uncertainty.
  
• Yung-Keun Kwon, Sun Shim Choi, Kwang-Hyun Cho:
  Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling.
  
• Emma Redhead, Timothy L. Bailey:
  Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.
  
• Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth:
  Large scale statistical inference of signaling pathways from RNAi and microarray data.
  
• Anders Sjögren, Erik Kristiansson, Mats Rudemo, Olle Nerman:
  Weighted analysis of general microarray experiments.
  
• Joe Dundas, T. Andrew Binkowski, Bhaskar DasGupta, Jie Liang:
  Topology independent protein structural alignment.
  
• Eider B. Moore, Andrew V. Poliakov, Peter Lincoln, James F. Brinkley:
  MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.
  
• William A. McLaughlin, Ken Chen, Tingjun Hou, Wei Wang:
  On the detection of functionally coherent groups of protein domains with an extension to protein annotation.
  
• Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen:
  Analysis on multi-domain cooperation for predicting protein-protein interactions.
  
• Jing Chen, Huan Xu, Bruce J. Aronow, Anil G. Jegga:
  Improved human disease candidate gene prioritization using mouse phenotype.
  
• Susana Vinga, Jonas S. Almeida:
  Local Renyi entropic profiles of DNA sequences.
  
• Oscar M. Rueda, Ramón Díaz-Uriarte:
  A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.
  
• Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble:
  Permutation test for periodicity in short time series data.
  
• Tobias Wittkop, Jan Baumbach, Francisco P. Lobo, Sven Rahmann:
  Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
  
• Dennis R. Livesay, Patrick D. Kidd, Sepehr Eskandari, Usman Roshan:
  Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na⁺ symporter family.
  
• John M. Eppley, Gene W. Tyson, Wayne M. Getz, Jillian F. Banfield:
  Strainer: software for analysis of population variation in community genomic datasets.
  
• Randy Z. Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang:
  fREDUCE: Detection of degenerate regulatory elements using correlation with expression.
  
• Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin T. R. Kuiper, Pierre Hilson:
  CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.
  
• Richard G. Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob:
  The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
  
• Daniel Dalevi, Todd Z. DeSantis, Jakob Fredslund, Gary L. Andersen, Victor M. Markowitz, Philip Hugenholtz:
  Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
  
• Michael A. Gilchrist, Hong Qin, Russell L. Zaretzki:
  Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework.
  
• Y.-h. Taguchi, M. Michael Gromiha:
  Application of amino acid occurrence for discriminating different folding types of globular proteins.
  
• Alexandros Stamatakis, Alexander F. Auch, Jan P. Meier-Kolthoff, Markus Göker:
  AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
  
• Thierry Lombardot, Renzo Kottmann, Gregory Giuliani, Andrea de Bono, Nans Addor, Frank Oliver Glöckner:
  MetaLook: a 3D visualisation software for marine ecological genomics.
  
• Charles G. Danko, Vera A. McIlvain, Maochun Qin, Barry E. Knox, Arkady M. Pertsov:
  Bioinformatic identification of novel putative photoreceptor specific cis-elements.
  
• Ioannis A. Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos:
  Growing functional modules from a seed protein via integration of protein interaction and gene expression data.
  
• Marjo V. Smith, Chris R. Miller, Michael Kohn, Nigel J. Walker, Chris J. Portier:
  Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process.
  
• Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
  Features generated for computational splice-site prediction correspond to functional elements.
  
• Dario Gasbarra, Matti Pirinen, Mikko J. Sillanpää, Elja Arjas:
  Estimating genealogies from linked marker data: a Bayesian approach.
  
• James J. Chen, Huey-miin Hsueh, Robert R. Delongchamp, Chien-Ju Lin, Chen-An Tsai:
  Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data.
  
• David J. Irons, Nicholas A. M. Monk:
  Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network.
  
• Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao:
  InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
  
• Michael Gormley, William Dampier, Adam Ertel, Bilge Karaçali, Aydin Tozeren:
  Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets.
  
• Daniel Barthel, Jonathan D. Hirst, Jacek Blazewicz, Edmund K. Burke, Natalio Krasnogor:
  ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information.
  
• Adrienne X. Wang, Walter L. Ruzzo, Martin Tompa:
  How accurately is ncRNA aligned within whole-genome multiple alignments?
  
• Erik Larsson, Per Lindahl, Petter Mostad:
  HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing.
  
• Mark D. Robinson, David P. De Souza, Woon Wai Keen, Eleanor C. Saunders, Malcolm J. McConville, Terence P. Speed, Vladimir A. Likic:
  A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.
  
• Yao Qing Shen, Gertraud Burger:
  'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools.
  
• Francisco Llaneras, Jesús Picó:
  A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient.
  
• Carmen Lai, Hugo M. Horlings, Marc J. van de Vijver, Eric H. van Beers, Petra M. Nederlof, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets.
  
• Jimmy J. Lin, W. John Wilbur:
  PubMed related articles: a probabilistic topic-based model for content similarity.
  
• Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen:
  Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
  
• Florian Teichert, Ugo Bastolla, Markus Porto:
  SABERTOOTH: protein structural alignment based on a vectorial structure representation.
  
• Brad T. Sherman, Da Wei Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert M. Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki:
  DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.
  
• Jeff W. Chou, Tong Zhou, William K. Kaufmann, Richard S. Paules, Pierre R. Bushel:
  Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes.
  
• Tom R. Gaunt, Santiago Rodríguez, Ian N. M. Day:
  Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.
  
• Jan Baumbach:
  CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
  
• Yung-Keun Kwon, Kwang-Hyun Cho:
  Analysis of feedback loops and robustness in network evolution based on Boolean models.
  
• Qi Liu, Irina Dinu, Adeniyi J. Adewale, John D. Potter, Yutaka Yasui:
  Comparative evaluation of gene-set analysis methods.
  
• Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li:
  Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila.
  
• Anastasia Yartseva, Hanna Klaudel, Raymond R. Devillers, François Képès:
  Incremental and unifying modelling formalism for biological interaction networks.
  
• Philippe Lamy, Claus L. Andersen, Lars Dyrskjot, Niels Torring, Carsten Wiuf:
  A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.
  
• Juliana S. Bernardes, Alberto M. R. Dávila, Vítor Santos Costa, Gerson Zaverucha:
  Improving model construction of profile HMMs for remote homology detection through structural alignment.
  
• Wei Yu, Ajay Yesupriya, Anja Wulf, Junfeng Qu, Muin J. Khoury, Marta Gwinn:
  An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.
  
• Xueping Yu, Jimmy J. Lin, Donald J. Zack, Jiang Qian:
  Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.
  
• Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant Honavar:
  Glycosylation site prediction using ensembles of Support Vector Machine classifiers.
  
• Ernest Turro, Natalia Bochkina, Anne-Mette K. Hein, Sylvia Richardson:
  BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
  
• Francois Besnier, Örjan Carlborg:
  A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL.
  
• Konstantin Yu Popadin, Leila A. Mamirova, Fyodor A. Kondrashov:
  A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
  
• Antonio Marco, Ignacio Marín:
  A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification.
  
• Joern Toedling, Oleg Sklyar, Tammo Krueger, Jenny J. Fischer, Silke Sperling, Wolfgang Huber:
  Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts.
  
• Haiyan Jiang, Christian Blouin:
  Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions.
  
• Xochitl C. Morgan, Shulin Ni, Daniel P. Miranker, Vishwanath R. Iyer:
  Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining.
  
• Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato:
  Novel definition files for human GeneChips based on GeneAnnot.
  
• Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T. Garrett:
  Application of a correlation correction factor in a microarray cross-platform reproducibility study.
  
• Karen Curtin, Jathine Wong, Kristina Allen-Brady, Nicola J. Camp:
  PedGenie: meta genetic association testing in mixed family and case-control designs.
  
• Mark D. Robinson, Terence P. Speed:
  A comparison of Affymetrix gene expression arrays.
  
• Jian Tian, Ningfeng Wu, Xuexia Guo, Jun Guo, Juhua Zhang, Yunliu Fan:
  Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.
  
• Koichi Abe, Natsuki Kobayashi, Koji Sode, Kazunori Ikebukuro:
  Peptide ligand screening of alpha-synuclein aggregation modulators by in silico panning.
  
• Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M. Li:
  Inferring activity changes of transcription factors by binding association with sorted expression profiles.
  
• Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong Ho Jung:
  Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.
  
• Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A. Hannah:
  Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana.
  
• Carmen Pin, Mark Reuter:
  Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach.
  
• J. Christopher Bare, Paul T. Shannon, Amy K. Schmid, Nitin S. Baliga:
  The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
  
• André Fujita, João Ricardo Sato, Carlos Eduardo Ferreira, Mari Cleide Sogayar:
  GEDI: a user-friendly toolbox for analysis of large-scale gene expression data.
  
• Miguel Arenas, David Posada:
  Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography.
  
• Menaka Rajapakse, Bertil Schmidt, Lin Feng, Vladimir Brusic:
  Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms.
  
• Daniel H. Huson, Daniel C. Richter, Christian Rausch, Tobias Dezulian, Markus Franz, Regula Rupp:
  Dendroscope: An interactive viewer for large phylogenetic trees.
  
• Tineke Casneuf, Yves Van de Peer, Wolfgang Huber:
  In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.
  
• Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza:
  Dynamic simulation of regulatory networks using SQUAD.
  
• Manish Kumar, M. Michael Gromiha, Gajendra P. S. Raghava:
  Identification of DNA-binding proteins using support vector machines and evolutionary profiles.
  
• Stefan Engelen, Fariza Tahi:
  Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences.
  
• Alexis Dereeper, Xavier Argout, Claire Billot, Jean-François Rami, Manuel Ruiz:
  SAT, a flexible and optimized Web application for SSR marker development.
  
• Takeyuki Tamura, Tatsuya Akutsu:
  Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
  
• Thomas Thorne, Michael P. H. Stumpf:
  Generating confidence intervals on biological networks.
  
• Nico Pfeifer, Andreas Leinenbach, Christian G. Huber, Oliver Kohlbacher:
  Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.
  
• Yu Shao, Susan Wu, Chi Yu Chan, Jessie R. Klapper, Erasmus Schneider, Ye Ding:
  A structural analysis of in vitro catalytic activities of hammerhead ribozymes.
  
• Dengming Ming, Michael E. Wall, Kevin Y. Sanbonmatsu:
  Domain motions of Argonaute, the catalytic engine of RNA interference.
  
• Minho Lee, Chan-seok Jeong, Dongsup Kim:
  Predicting and improving the protein sequence alignment quality by support vector regression.
  
• Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz:
  Direct maximum parsimony phylogeny reconstruction from genotype data.
  
• Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen:
  A systematic approach to detecting transcription factors in response to environmental stresses.
  
• Michael C. Schatz, Cole Trapnell, Arthur L. Delcher, Amitabh Varshney:
  High-throughput sequence alignment using Graphics Processing Units.
  
• Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang:
  Predicting gene ontology functions from protein's regional surface structures.
  
• Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, Peter Bühlmann:
  Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries.
  
• Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B. Lebrilla, David M. Rocke:
  On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.
  
• Markus Brameier, Carsten Wiuf:
  Ab initio identification of human microRNAs based on structure motifs.
  
• Scott A. Givan, Christopher M. Sullivan, James C. Carrington:
  The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases.
  
• Sriram Kosuri, Jason R. Kelly, Drew Endy:
  TABASCO: A single molecule, base-pair resolved gene expression simulator.
  
• Victor G. Levitsky, Elena V. Ignatieva, Elena A. Ananko, Igor I. Turnaev, Tatyana I. Merkulova, Nikolay A. Kolchanov, T. Charles Hodgman:
  Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.
  
• Wasinee Rungsarityotin, Roland Krause, Arno Schödl, Alexander Schliep:
  Identifying protein complexes directly from high-throughput TAP data with Markov random fields.
  
• Arnaud Droit, Joanna M. Hunter, Michèle Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais, Guy G. Poirier:
  PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system.
  
• Nina Zhou, Lipo Wang:
  Effective selection of informative SNPs and classification on the HapMap genotype data.
  
• Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong-Sung Lee, Young Seek Lee, Jin Hyuk Kim:
  Characterization and simulation of cDNA microarray spots using a novel mathematical model.
  
• Yvonne E. Pittelkow, Susan R. Wilson:
  h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data.
  
• Egon L. Willighagen, Noel M. O'Boyle, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck, David J. Wild:
  Userscripts for the Life Sciences.
  
• I. Mihalek, I. Res, Olivier Lichtarge:
  Background frequencies for residue variability estimates: BLOSUM revisited.