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 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, M. R. Southern, N. F. Tsinoremas, P. 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 M. Cesar Jr., 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 Boelle, 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, Josh 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 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).