BMC Bioinformatics, Volume 9

Volume 9, 2008

• Ana C. Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet:
  Evaluation of time profile reconstruction from complex two-color microarray designs.
  
• Cuong To, Jiri Vohradsky:
  Supervised inference of gene-regulatory networks.
  
• Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth:
  Extending pathways based on gene lists using InterPro domain signatures.
  
• Romesh Stanislaus, John M. Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S. Almeida:
  An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.
  
• Javier Forment, Francisco Gilabert Villamón, Antonio Robles, Vicente Conejero, Fernando Nuez, Jose M. Blanca:
  EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.
  
• Jean-François Taly, Antoine Marin, Jean-François Gibrat:
  Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
  
• Michelle N. Knowlton, Tongbin Li, Yongliang Ren, Brent R. Bill, Lynda B. M. Ellis, Stephen C. Ekker:
  A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.
  
• Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng, Xian-Ming Pan:
  A novel method for high accuracy sumoylation site prediction from protein sequences.
  
• Joan Teyra, Maciej Paszkowski-Rogacz, Gerd Anders, M. Teresa Pisabarro:
  SCOWLP classification: Structural comparison and analysis of protein binding regions.
  
• Jin-Dong Kim, Tomoko Ohta, Jun-ichi Tsujii:
  Corpus annotation for mining biomedical events from literature.
  
• Andreas Döring, David Weese, Tobias Rausch, Knut Reinert:
  SeqAn An efficient, generic C++ library for sequence analysis.
  
• Guy N. Brock, John R. Shaffer, Richard E. Blakesley, Meredith J. Lotz, George C. Tseng:
  Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes.
  
• Paolo Verderio, Sara Pizzamiglio, Fabio Gallo, Simon C. Ramsden:
  FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification.
  
• Harald Binder, Martin Schumacher:
  Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models.
  
• Scott Christley, Neil F. Lobo, Gregory R. Madey:
  Multiple organism algorithm for finding ultraconserved elements.
  
• Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, Bernard Klein:
  A new method for class prediction based on signed-rank algorithms applied to Affymetrix^® microarray experiments.
  
• David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge:
  Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.
  
• David Ellinghaus, Stefan Kurtz, Ute Willhoeft:
  LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
  
• Mutlu Dogruel, Thomas A. Down, Tim J. P. Hubbard:
  NestedMICA as an ab initio protein motif discovery tool.
  
• Marc Vincent, Andrea Passerini, Matthieu Labbé, Paolo Frasconi:
  A simplified approach to disulfide connectivity prediction from protein sequences.
  
• Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy:
  LeARN: a platform for detecting, clustering and annotating non-coding RNAs.
  
• Yu-Ching Fang, Hsuan-Cheng Huang, Hsueh-Fen Juan:
  MeInfoText: associated gene methylation and cancer information from text mining.
  
• Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama:
  Function approximation approach to the inference of reduced NGnet models of genetic networks.
  
• Jonathan G. Lees, Robert W. Janes:
  Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations.
  
• Huiling Xiong, Dapeng Zhang, Christopher J. Martyniuk, Vance L. Trudeau, Xuhua Xia:
  Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data.
  
• Alexandre Kuhn, Ruth Luthi-Carter, Mauro Delorenzi:
  Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.
  
• Botond Sipos, Kálmán Somogyi, István Andó, Zsolt Pénzes:
  t2prhd: a tool to study the patterns of repeat evolution.
  
• Donald Maier, Farrell Wymore, Gavin Sherlock, Catherine A. Ball:
  The XBabelPhish MAGE-ML and XML Translator.
  
• Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He:
  A nonparametric model for quality control of database search results in shotgun proteomics.
  
• Ramón Díaz-Uriarte:
  SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.
  
• Andrey M. Leontovich, Konstantin Y. Tokmachev, Hans C. van Houwelingen:
  The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem.
  
• Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron:
  Prioritization of gene regulatory interactions from large-scale modules in yeast.
  
• Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
  A fast structural multiple alignment method for long RNA sequences.
  
• Patrick D. Schloss, Jo Handelsman:
  A statistical toolbox for metagenomics: assessing functional diversity in microbial communities.
  
• José M. G. Izarzugaza, David de Juan, Carles Pons, Florencio Pazos, Alfonso Valencia:
  Enhancing the prediction of protein pairings between interacting families using orthology information.
  
• Leming Zhou, Jonathan Stanton, Liliana Florea:
  Universal seeds for cDNA-to-genome comparison.
  
• Rekin's Janky, Jacques van Helden:
  Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution.
  
• Samiran Ghosh, David F. Grant, Dipak K. Dey, Dennis W. Hill:
  A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles.
  
• Shay Artzi, Adam Kiezun, Noam Shomron:
  miRNAminer: A tool for homologous microRNA gene search.
  
• Yang Zhang:
  I-TASSER server for protein 3D structure prediction.
  
• Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee, Jong Bhak:
  Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.
  
• Irina Gana Dresen, Tanja Boes, Johannes Hüsing, Markus Neuhäuser, Karl-Heinz Jöckel:
  New resampling method for evaluating stability of clusters.
  
• Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin:
  Predicting biological system objectives de novo from internal state measurements.
  
• Jing Li, Yixuan Chen:
  Generating samples for association studies based on HapMap data.
  
• Loris Nanni, Alessandra Lumini:
  A genetic approach for building different alphabets for peptide and protein classification.
  
• Yuerong Zhu, Yuelin Zhu, Wei Xu:
  EzArray: A web-based highly automated Affymetrix expression array data management and analysis system.
  
• Changhui Yan, Jing Hu, Yingfeng Wang:
  Discrimination of outer membrane proteins with improved performance.
  
• Mark Bauer, Sheldon M. Schuster, Khalid Sayood:
  The Average Mutual Information Profile as a Genomic Signature.
  
• Xin-Qiu Yao, Huaiqiu Zhu, Zhen-Su She:
  A dynamic Bayesian network approach to protein secondary structure prediction.
  
• Angela del Pozo, Florencio Pazos, Alfonso Valencia:
  Defining functional distances over Gene Ontology.
  
• Jonathan R. Manning, Emily R. Jefferson, Geoffrey J. Barton:
  The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction.
  
• Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J. Stevens, Jaques Reifman:
  The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.
  
• Paul J. Rushton, Marta T. Bokowiec, Thomas W. Laudeman, Jennifer F. Brannock, Xianfeng Chen, Michael P. Timko:
  TOBFAC: the database of tobacco transcription factors.
  
• Cornelia Frömke, Ludwig A. Hothorn, Siegfried Kropf:
  Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes.
  
• Hamed Shateri Najafabadi, Noorossadat Torabi, Mahmood Chamankhah:
  Designing multiple degenerate primers via consecutive pairwise alignments.
  
• Chang Sik Kim, Cheol Soo Bae, Hong Joon Tcha:
  A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data.
  
• Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara:
  Gene function prediction using labeled and unlabeled data.
  
• Chih-Hung Jen, Tsun-Po Yang, Chien-Yi Tung, Shu-Han Su, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang:
  Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures.
  
• Irene Kouskoumvekaki, Zhiyong Yang, Svava Óisk Jónsdóttir, Lisbeth Olsson, Gianni Panagiotou:
  Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification.
  
• Hans-Georg Müller, Jeng-Min Chiou, Xiaoyan Leng:
  Inferring gene expression dynamics via functional regression analysis.
  
• Usman Roshan, Satish Chikkagoudar, Dennis R. Livesay:
  Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.
  
• Aarti Garg, Dinesh Gupta:
  VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens.
  
• David D. Smith, Pål Sætrom, Ola R. Snøve Jr., Cathryn Lundberg, Guillermo E. Rivas, Carlotta Glackin, Garrett P. Larson:
  Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation.
  
• Woochang Hwang, Young-Rae Cho, Aidong Zhang, Murali Ramanathan:
  CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions.
  
• Pere Puigbò, Ignacio G. Bravo, Santiago Garcia-Vallvé:
  E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).
  
• Paolo Mereghetti, Maria Luisa Ganadu, Elena Papaleo, Piercarlo Fantucci, Luca De Gioia:
  Validation of protein models by a neural network approach.
  
• Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein:
  VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays.
  
• Bruno F. Bettencourt, Margarida R. Santos, Raquel N. Fialho, Ana R. Couto, Maria J. Peixoto, João P. Pinheiro, Hélder Spínola, Marian G. Mora, Cristina Santos, António Brehm, Jácome Bruges-Armas:
  Evaluation of two methods for computational HLA haplotypes inference using a real dataset.
  
• Richárd Farkas:
  The strength of co-authorship in gene name disambiguation.
  
• Tijana Milenkovic, Jason Lai, Natasa Przulj:
  GraphCrunch: A tool for large network analyses.
  
• Violaine Moreau, Cécile Fleury, Dominique Piquer, Christophe Nguyen, Nicolas Novali, Sylvie Villard, Daniel Laune, Claude Granier, Franck Molina:
  PEPOP: Computational design of immunogenic peptides.
  
• John K. Vries, Xiong Liu:
  Subfamily specific conservation profiles for proteins based on n-gram patterns.
  
• Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond:
  SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.
  
• Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-François Gibrat, Byungkook Lee, Peter J. Munson:
  Towards an automatic classification of protein structural domains based on structural similarity.
  
• Guanrao Chen, Peter E. Larsen, Eyad Almasri, Yang Dai:
  Rank-based edge reconstruction for scale-free genetic regulatory networks.
  
• Sung-Gon Yi, Taesung Park, Jae K. Lee:
  Response projected clustering for direct association with physiological and clinical response data.
  
• Xiaoyi Gao, Joshua D. Starmer:
  AWclust: point-and-click software for non-parametric population structure analysis.
  
• Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen:
  OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.
  
• Feng Gao, Chun-Ting Zhang:
  Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes.
  
• Wen-Lin Huang, Chun-Wei Tung, Shih-Wen Ho, Shiow-Fen Hwang, Shinn-Ying Ho:
  ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization.
  
• Nicholas A. Hamilton, Rohan D. Teasdale:
  Visualizing and clustering high throughput sub-cellular localization imaging.
  
• Mathieu Fourment, Michael R. Gillings:
  A comparison of common programming languages used in bioinformatics.
  
• Mathieu Fourment, Mark J. Gibbs:
  The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.
  
• Laura Inés Furlong, Holger Dach, Martin Hofmann-Apitius, Ferran Sanz:
  OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature.
  
• Mark J. Dunning, Nuno L. Barbosa-Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie:
  Statistical issues in the analysis of Illumina data.
  
• Frédéric Chalmel, Michael Primig:
  The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology.
  
• Herbert Pang, Hongyu Zhao:
  Building pathway clusters from Random Forests classification using class votes.
  
• Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels:
  Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data.
  
• Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira:
  An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.
  
• Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch:
  Modularization of biochemical networks based on classification of Petri net t-invariants.
  
• Cédric Auliac, Vincent Frouin, Xavier Gidrol, Florence d'Alché-Buc:
  Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset.
  
• Pankaj Chopra, Jaewoo Kang, Jiong Yang, HyungJun Cho, Heenam Stanley Kim, Min-Goo Lee:
  Microarray data mining using landmark gene-guided clustering.
  
• Sacha A. F. T. van Hijum, Richard J. S. Baerends, Aldert L. Zomer, Harma A. Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok, Oscar P. Kuipers:
  Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons.
  
• Ching-Wai Tan, David T. Jones:
  Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction.
  
• Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig, Dirk Gründemann:
  Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence.
  
• Mark W. E. J. Fiers, Ate van der Burgt, Erwin Datema, Joost C. W. de Groot, Roeland C. H. J. van Ham:
  High-throughput bioinformatics with the Cyrille2 pipeline system.
  
• Ken E. Whelan, Ross D. King:
  Using a logical model to predict the growth of yeast.
  
• Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra, Jean-Jacques Daudin:
  Statistical methodology for the analysis of dye-switch microarray experiments.
  
• John Drakos, Marina Karakantza, Nicholas C. Zoumbos, John Lakoumentas, George Nikiforidis, George Sakellaropoulos:
  A perspective for biomedical data integration: Design of databases for flow cytometry.
  
• Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian J. Theis, Elmar Wolfgang Lang, Gerd Schmitz:
  Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis.
  
• Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng, Ziding Zhang:
  Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs.
  
• Alvaro J. González, Li Liao:
  Clustering exact matches of pairwise sequence alignments by weighted linear regression.
  
• Indra Neil Sarkar, Mary G. Egan, Gloria M. Coruzzi, Ernest K. Lee, Robert DeSalle:
  Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics.
  
• Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang:
  PDTD: a web-accessible protein database for drug target identification.
  
• Mattias Rantalainen, Olivier Cloarec, Timothy M. D. Ebbels, Torbjörn Lundstedt, Jeremy K. Nicholson, Elaine Holmes, Johan Trygg:
  Piecewise multivariate modelling of sequential metabolic profiling data.
  
• Max Bylesjö, Mattias Rantalainen, Jeremy K. Nicholson, Elaine Holmes, Johan Trygg:
  K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space.
  
• Francisco-Javier Lopez, Armando Blanco, Fernando Garcia-Alcalde, Carlos Cano, Antonio Marin:
  Fuzzy association rules for biological data analysis: A case study on yeast.
  
• Graham L. Poulter, Daniel L. Rubin, Russ B. Altman, Cathal Seoighe:
  MScanner: a classifier for retrieving Medline citations.
  
• Wolfram Gronwald, Tim Hohm, Daniel Hoffmann:
  Evolutionary Pareto-optimization of stably folding peptides.
  
• Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir:
  SPIKE - a database, visualization and analysis tool of cellular signaling pathways.
  
• Abhishek Tripathi, Arto Klami, Samuel Kaski:
  Simple integrative preprocessing preserves what is shared in data sources.
  
• Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida:
  ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.
  
• Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian Zhou:
  Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides.
  
• Kyung In Kim, Mark A. van de Wiel:
  Effects of dependence in high-dimensional multiple testing problems.
  
• Sarah C. Ayling, Terence A. Brown:
  Novel methodology for construction and pruning of quasi-median networks.
  
• Jonathan D. Moore, Shelagh P. Kell, Jose M. Iriondo, Brian V. Ford-Lloyd, Nigel Maxted:
  CWRML: representing crop wild relative conservation and use data in XML.
  
• Tommy S. Jørstad, Herman Midelfart, Atle M. Bones:
  A mixture model approach to sample size estimation in two-sample comparative microarray experiments.
  
• Danny A. Bitton, Michal J. Okoniewski, Yvonne Connolly, Crispin J. Miller:
  Exon level integration of proteomics and microarray data.
  
• Bolan Linghu, Evan S. Snitkin, Dustin T. Holloway, Adam M. Gustafson, Yu Xia, Charles DeLisi:
  High-precision high-coverage functional inference from integrated data sources.
  
• Mano Sivaganesan, Shawn Seifring, Manju Varma, Richard A. Haugland, Orin C. Shanks:
  A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards.
  
• Riadh Hammami, Abdelmajid Zouhir, Karim Naghmouchi, Jeannette Ben Hamida, Ismail Fliss:
  SciDBMaker: new software for computer-aided design of specialized biological databases.
  
• Andreas R. Gruber, Stephan H. F. Bernhart, Ivo L. Hofacker, Stefan Washietl:
  Strategies for measuring evolutionary conservation of RNA secondary structures.
  
• Kjetil Klepper, Geir Kjetil Sandve, Osman Abul, Jostein Johansen, Finn Drabløs:
  Assessment of composite motif discovery methods.
  
• Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, Jiong Yang:
  A gene pattern mining algorithm using interchangeable gene sets for prokaryotes.
  
• Lei Xu, Aik Choon Tan, Raimond L. Winslow, Donald Geman:
  Merging microarray data from separate breast cancer studies provides a robust prognostic test.
  
• Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman:
  DOVIS: an implementation for high-throughput virtual screening using AutoDock.
  
• Song Zhang, Xuefeng Xia, Jincheng Shen, Yun Zhou, Zhirong Sun:
  DBMLoc: a Database of proteins with multiple subcellular localizations.
  
• Andrew D. Smith, Zhenyu Xuan, Michael Q. Zhang:
  Using quality scores and longer reads improves accuracy of Solexa read mapping.
  
• Wensheng Zhang, Sige Zou, Jiuzhou Song:
  Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster.
  
• Kristin K. Nicodemus:
  catmap: Case-control And TDT Meta-Analysis Package.
  
• Stefan Janssen, Jens Reeder, Robert Giegerich:
  Shape based indexing for faster search of RNA family databases.
  
• Fabien Campagne:
  Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols.
  
• Mark K. Titulaer, Dana A. N. Mustafa, Ivar Siccama, Marco Konijnenburg, Peter C. Burgers, Arno C. Andeweg, Peter A. E. Sillevis Smitt, Johan M. Kros, Theo M. Luider:
  A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation.
  
• Grace S. Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang, Yi-Chen Lo:
  Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling.
  
• M. Michael Gromiha, Yukimitsu Yabuki:
  Functional discrimination of membrane proteins using machine learning techniques.
  
• Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz, Ulf Leser:
  Mining phenotypes for gene function prediction.
  
• István Miklós, Ádám Novák, Balázs Dombai, Jotun Hein:
  How reliably can we predict the reliability of protein structure predictions?
  
• Fredrik Pettersson, Andrew P. Morris, Michael R. Barnes, Lon R. Cardon:
  Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies.
  
• Jürgen Pahle, Anne K. Green, C. Jane Dixon, Ursula Kummer:
  Information transfer in signaling pathways: A study using coupled simulated and experimental data.
  
• Stefano Calza, Davide Valentini, Yudi Pawitan:
  Normalization of oligonucleotide arrays based on the least-variant set of genes.
  
• Adriano Barbosa-Silva, Venkata P. Satagopam, Reinhard Schneider, J. Miguel Ortega:
  Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.
  
• Yuan-De Tan, Myriam Fornage, Hongyan Xu:
  Ranking analysis of F-statistics for microarray data.
  
• Ali Cakmak, Gultekin Özsoyoglu:
  Discovering gene annotations in biomedical text databases.
  
• Holger Schwender, Katja Ickstadt:
  Empirical Bayes analysis of single nucleotide polymorphisms.
  
• Kwangmin Choi, Sun Kim:
  ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts.
  
• Leah E. Mechanic, Brian T. Luke, Julie E. Goodman, Stephen J. Chanock, Curtis C. Harris:
  Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions.
  
• Ling Wang, Monty Montano, Matt Rarick, Paola Sebastiani:
  Conditional clustering of temporal expression profiles.
  
• Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson:
  Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.
  
• René Natowicz, Roberto Incitti, Euler Guimarães Horta, Benoît Charles, Philippe Guinot, Kai Yan, Charles Coutant, Fabrice Andre, Lajos Pusztai, Roman Rouzier:
  Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses.
  
• Aswath Manoharan, Jeannie A. Stamberger, YuanYuan Yu, Andreas Paepcke:
  Optimizations for the EcoPod field identification tool.
  
• Rainer Merkl, Matthias Zwick:
  H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
  
• Sebastian Aljoscha Wahl, Katharina Nöh, Wolfgang Wiechert:
  ¹³C labeling experiments at metabolic nonstationary conditions: An exploratory study.
  
• Christopher Lau, Lydia Ng, Carol Thompson, Sayan D. Pathak, Leonard Kuan, Allan Jones, Michael Hawrylycz:
  Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain.
  
• Hector Sanchez-Villeda, Steven G. Schroeder, Sherry Flint-Garcia, Katherine E. Guill, Masanori Yamasaki, Michael D. McMullen:
  DNAAlignEditor: DNA alignment editor tool.
  
• Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu, Chun-Houh Chen:
  Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles.
  
• Magnus Åstrand, Petter Mostad, Mats Rudemo:
  Empirical Bayes models for multiple probe type microarrays at the probe level.
  
• Richard F. Pollock, Boris Adryan:
  BioSAVE: Display of scored annotation within a sequence context.
  
• Martin Smith, Mathieu Blanchette, Barbara Papadopoulou:
  Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.
  
• John McCrae, Nigel Collier:
  Synonym set extraction from the biomedical literature by lexical pattern discovery.
  
• Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, Zhen-Su She:
  Computational evaluation of TIS annotation for prokaryotic genomes.
  
• David A. Pelta, Juan Ramón González, Marcos Moreno Vega:
  A simple and fast heuristic for protein structure comparison.
  
• Liang Sun, Shuiwang Ji, Jieping Ye:
  Adaptive diffusion kernel learning from biological networks for protein function prediction.
  
• Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher:
  OpenMS - An open-source software framework for mass spectrometry.
  
• Richard D. Pearson:
  A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods.
  
• Jasmina Bogojeska, Thomas Lengauer, Jörg Rahnenführer:
  Stability analysis of mixtures of mutagenetic trees.
  
• Alexis Criscuolo, Olivier Gascuel:
  Fast NJ-like algorithms to deal with incomplete distance matrices.
  
• Julia Herold, Stefan Kurtz, Robert Giegerich:
  Efficient computation of absent words in genomic sequences.
  
• Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, Malcolm A. Ferguson-Smith:
  Chromhome: A rich internet application for accessing comparative chromosome homology maps.
  
• Holger Maier, Christoph Lengger, Bruno Simic, Helmut Fuchs, Valérie Gailus-Durner, Martin Hrabé de Angelis:
  MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects.
  
• Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, Mitchell J. Brittnacher:
  PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes.
  
• Katia S. Guimarães, Teresa M. Przytycka:
  Interrogating domain-domain interactions with parsimony based approaches.
  
• Ramon Aragues, Chris Sander, Baldo Oliva:
  Predicting cancer involvement of genes from heterogeneous data.
  
• Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland J. Siezen:
  LocateP: Genome-scale subcellular-location predictor for bacterial proteins.
  
• Christopher K. Edlund, Won H. Lee, Dalin Li, David J. Van Den Berg, David V. Conti:
  Snagger: A user-friendly program for incorporating additional information for tagSNP selection.
  
• Gabriel Cardona, Francesc Rosselló, Gabriel Valiente:
  A perl package and an alignment tool for phylogenetic networks.
  
• Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, Xiuzi Ye:
  RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.
  
• Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Beth Duhaime, Jörg Peplies, Frank Oliver Glöckner:
  JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes.
  
• Michaël Bekaert, Ivaylo P. Ivanov, John F. Atkins, Pavel V. Baranov:
  Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs.
  
• Jengnan Tzeng, Henry Horng-Shing Lu, Wen-Hsiung Li:
  Multidimensional scaling for large genomic data sets.
  
• Ralf Schmid, Mark L. Blaxter:
  annot8r: GO, EC and KEGG annotation of EST datasets.
  
• Maris Lapinsh, Martin Eklund, Ola Spjuth, Peteris Prusis, Jarl E. S. Wikberg:
  Proteochemometric modeling of HIV protease susceptibility.
  
• Shibu Yooseph, Weizhong Li, Granger G. Sutton:
  Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering.
  
• Daniel Jameson, Kevin L. Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton:
  Data capture in bioinformatics: requirements and experiences with Pedro.
  
• Nicolas Sauton, David Lagorce, Bruno O. Villoutreix, Maria A. Miteva:
  MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.
  
• Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Jaques Reifman:
  A high-throughput pipeline for designing microarray-based pathogen diagnostic assays.
  
• Robin P. Smith, William J. Buchser, Marcus B. Lemmon, Jose R. Pardinas, John L. Bixby, Vance P. Lemmon:
  EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.
  
• Bryan A. P. Roxas, Qingbo Li:
  Significance analysis of microarray for relative quantitation of LC/MS data in proteomics.
  
• Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
  A novel representation of RNA secondary structure based on element-contact graphs.
  
• Sang Hong Lee, Julius H. J. Van der Werf, Brian P. Kinghorn:
  Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci.
  
• Janis Dingel, Pavol Hanus, Niccolò Leonardi, Joachim Hagenauer, Jürgen Zech, Jakob C. Mueller:
  Local conservation scores without a priori assumptions on neutral substitution rates.
  
• Kelvin Li, Anushka Brownley, Timothy B. Stockwell, Karen Beeson, Tina C. McIntosh, Dana Busam, Steve Ferriera, Sean Murphy, Samuel Levy:
  Novel computational methods for increasing PCR primer design effectiveness in directed sequencing.
  
• Minghui Jiang, James Anderson, Joel Gillespie, Martin Mayne:
  uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts.
  
• Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel A. Drysdale, Ted Briscoe:
  Natural Language Processing in aid of FlyBase curators.
  
• Huanying Ge, Chao Cheng, Lei M. Li:
  A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays.
  
• Harri T. Kiiveri:
  A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations.
  
• Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L. T. Yu, Mitchell B. Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy S. J. Fann:
  MPDA: Microarray pooled DNA analyzer.
  
• Yoginder S. Dandass, Shane C. Burgess, Mark L. Lawrence, Susan M. Bridges:
  Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research.
  
• Aaron Gabow, Sonia M. Leach, William A. Baumgartner Jr., Lawrence Hunter, Debra Goldberg:
  Improving protein function prediction methods with integrated literature data.
  
• Nicola Zamboni, Anne Kümmel, Matthias Heinemann:
  anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data.
  
• Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky, Richard A. McIndoe:
  ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use.
  
• Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish C. Varshney, Gajendra P. S. Raghava:
  Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles.
  
• Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio:
  Missing value imputation improves clustering and interpretation of gene expression microarray data.
  
• Yuji Zhang, Jianhua Xuan, Benildo de los Reyes, Robert Clarke, Habtom W. Ressom:
  Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.
  
• Cheng Li, Rameen Beroukhim, Barbara A. Weir, Wendy Winckler, Levi A. Garraway, William R. Sellers, Matthew Meyerson:
  Major copy proportion analysis of tumor samples using SNP arrays.
  
• Wei Yu, Melinda Clyne, Siobhan M. Dolan, Ajay Yesupriya, Anja Wulf, Tiebin Liu, Muin J. Khoury, Marta Gwinn:
  GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.
  
• Timothy D. Smith, Richard G. H. Cotton:
  VariVis: a visualisation toolkit for variation databases.
  
• Markus Bundschus, Mathäus Dejori, Martin Stetter, Volker Tresp, Hans-Peter Kriegel:
  Extraction of semantic biomedical relations from text using conditional random fields.
  
• Martin Oti, Jeroen van Reeuwijk, Martijn A. Huynen, Han G. Brunner:
  Conserved co-expression for candidate disease gene prioritization.
  
• Xiangchao Gan, Alan Wee-Chung Liew, Hong Yan:
  Discovering biclusters in gene expression data based on high-dimensional linear geometries.
  
• Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu, Alan Wee-Chung Liew:
  Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization.
  
• Hyunsoo Kim, Haesun Park, Barry L. Drake:
  Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations.
  
• Kazutaka Katoh, Hiroyuki Toh:
  Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
  
• Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J. Gibson, Julie Dawn Thompson:
  A new protein linear motif benchmark for multiple sequence alignment software.
  
• Bernie J. Daigle Jr., Russ B. Altman:
  M-BISON: Microarray-based integration of data sources using networks.
  
• Chon-Kit Kenneth Chan, Arthur L. Hsu, Saman K. Halgamuge, Sen-Lin Tang:
  Binning sequences using very sparse labels within a metagenome.
  
• Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou, Jean-Jacques Daudin:
  Normalization for triple-target microarray experiments.
  
• Katharina J. Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke:
  Gene prediction in metagenomic fragments: A large scale machine learning approach.
  
• Maria Pamela C. David, Carlo M. Lapid, Vincent Ricardo M. Daria:
  An efficient visualization tool for the analysis of protein mutation matrices.
  
• Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger:
  ConStruct: Improved construction of RNA consensus structures.
  
• Denis C. Bauer, Timothy L. Bailey:
  Studying the functional conservation of cis-regulatory modules and their transcriptional output.
  
• Andrej-Nikolai Spiess, Caroline Feig, Christian Ritz:
  Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry.
  
• Alexander Churkin, Danny Barash:
  An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.
  
• Antonio Carvajal-Rodríguez:
  GENOMEPOP: A program to simulate genomes in populations.
  
• Alexander G. Churbanov, Stephen Winters-Hilt:
  Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory.
  
• Jong-Min Kim, Yoon-Sung Jung, Engin A. Sungur, Kap-Hoon Han, Changyi Park, Insuk Sohn:
  A copula method for modeling directional dependence of genes.
  
• Lukasz A. Kurgan, Krzysztof J. Cios, Ke Chen:
  SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.
  
• Anatolij Potapov, Björn Goemann, Edgar Wingender:
  The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks.
  
• Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel:
  Inferring the role of transcription factors in regulatory networks.
  
• Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson:
  A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
  
• Martin Mann, Sebastian Will, Rolf Backofen:
  CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies.
  
• Cheng Li:
  Automating dChip: toward reproducible sharing of microarray data analysis.
  
• Jill L. Wegrzyn, Thomas M. Drudge, Faramarz Valafar, Vivian Hook:
  Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites.
  
• Michael I. Dekhtyar, Amelie Morin, Vehary Sakanyan:
  Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes.
  
• Andrew J. Bordner, Andrey A. Gorin:
  Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.
  
• Jeremy D. DeBarry, Renyi Liu, Jeffrey Bennetzen:
  Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm.
  
• Kevin Brick, Elisabetta Pizzi:
  A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins.
  
• Leonid Zaslavsky, Yiming Bao, Tatiana A. Tatusova:
  Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation.
  
• William S. Bush, Todd L. Edwards, Scott M. Dudek, Brett A. McKinney, Marylyn D. Ritchie:
  Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction.
  
• Michael C. Wendl, Richard K. Wilson:
  Aspects of coverage in medical DNA sequencing.
  
• Alfredo Braunstein, Roberto Mulet, Andrea Pagnani:
  Estimating the size of the solution space of metabolic networks.
  
• Richard Judson, Fathi Elloumi, R. Woodrow Setzer, Zhen Li, Imran Shah:
  A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model.
  
• W. Timothy J. White, Michael D. Hendy:
  Compressing DNA sequence databases with coil.
  
• Bryan Chi, Ronald J. deLeeuw, Bradley P. Coe, Raymond T. Ng, Calum MacAulay, Wan L. Lam:
  MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data.
  
• Shameek Biswas, John D. Storey, Joshua M. Akey:
  Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis.
  
• Neil F. W. Saunders, Ross I. Brinkworth, Thomas Huber, Bruce E. Kemp, Bostjan Kobe:
  Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites.
  
• Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang, Cathy S. J. Fann:
  Using the longest significance run to estimate region-specific p-values in genetic association mapping studies.
  
• Rodrigo Santamaría, Roberto Therón, Luis Quintales:
  A visual analytics approach for understanding biclustering results from microarray data.
  
• Tanja Gesell, Stefan Washietl:
  Dinucleotide controlled null models for comparative RNA gene prediction.
  
• Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X. Avilés, Andrej Sali, Marc A. Martí-Renom, Baldomero Oliva:
  Prediction of enzyme function by combining sequence similarity and protein interactions.
  
• Peter C. Dolan, Dee R. Denver:
  TileQC: A system for tile-based quality control of Solexa data.
  
• Min Zhang, Dabao Zhang, Martin T. Wells:
  Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases.
  
• Qian Xiang, Xianhua Dai, Yangyang Deng, Caisheng He, Jiang Wang, Jihua Feng, Zhiming Dai:
  Missing value imputation for microarray gene expression data using histone acetylation information.
  
• Frank M. You, Naxin Huo, Yong Qiang Gu, Ming-Cheng Luo, Yaqin Ma, Dave Hane, Gerard R. Lazo, Jan Dvorak, Olin D. Anderson:
  BatchPrimer3: A high throughput web application for PCR and sequencing primer design.
  
• Silvana Penco, Massimo Buscema, Maria Cristina Patrosso, Alessandro Marocchi, Enzo Grossi:
  New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background.
  
• Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart, Guohui Lin:
  Protein contact order prediction from primary sequences.
  
• Raghunandan M. Kainkaryam, Peter J. Woolf:
  poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening.
  
• Jean Marc Kwasigroch, René Wintjens, Dimitri Gilis, Marianne Rooman:
  SODa: An Mn/Fe superoxide dismutase prediction and design server.
  
• Shu-Dong Zhang, Timothy W. Gant:
  A simple and robust method for connecting small-molecule drugs using gene-expression signatures.
  
• Thomas Lingner, Peter Meinicke:
  Word correlation matrices for protein sequence analysis and remote homology detection.
  
• Wei Dong, Litao Yang, Kailin Shen, Banghyun Kim, Gijs A. Kleter, Hans J. P. Marvin, Rong Guo, Wanqi Liang, Dabing Zhang:
  GMDD: a database of GMO detection methods.
  
• Juan R. González, Josep L. Carrasco, Lluís Armengol, Sergi Villatoro, Lluís Jover, Yutaka Yasui, Xavier Estivill:
  Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA).
  
• Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, John L. Spouge:
  Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites.
  
• Chiara Parravicini, Graziella Ranghino, Maria P. Abbracchio, Piercarlo Fantucci:
  GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors.
  
• Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon, Stephen T. C. Wong:
  Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens.
  
• Ismael A. Vergara, Tomás Norambuena, Evandro Ferrada, Alex W. Slater, Francisco Melo:
  StAR: a simple tool for the statistical comparison of ROC curves.
  
• Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen:
  An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments.
  
• Sudhakar Jonnalagadda, Rajagopalan Srinivasan:
  Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data.
  
• Meng Piao Tan, Erin N. Smith, James R. Broach, Christodoulos A. Floudas:
  Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures.
  
• Matthias Schmid, Torsten Hothorn:
  Flexible boosting of accelerated failure time models.
  
• Jimmy J. Lin:
  PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval.
  
• Xiong Liu, Xueping Yu, Donald J. Zack, Heng Zhu, Jiang Qian:
  TiGER: A database for tissue-specific gene expression and regulation.
  
• Paul D. Yoo, Yung Shwen Ho, Bing Bing Zhou, Albert Y. Zomaya:
  SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles.
  
• Sandrine Pawlicki, Antony Le Béchec, Christian Delamarche:
  AMYPdb: A database dedicated to amyloid precursor proteins.
  
• Armita Sheari, Mehdi Kargar, Ali Katanforoush, Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sayed-Amir Marashi:
  A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins.
  
• Guangtao Ge, G. William Wong:
  Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles.
  
• Mehmet E. Turanalp, Tolga Can:
  Discovering functional interaction patterns in protein-protein interaction networks.
  
• Steven Bethard, Zhiyong Lu, James H. Martin, Lawrence Hunter:
  Semantic role labeling for protein transport predicates.
  
• Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack:
  Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.
  
• Guohui Lin, Zhipeng Cai, Junfeng Wu, Xiu-Feng Wan, Lizhe Xu, Randy Goebel:
  Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping.
  
• Manli Zhu, Aleix M. Martínez:
  Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification.
  
• Chilamakuri Chandra Sekhar Reddy, Khader Shameer, Bernard O. Offmann, Ramanathan Sowdhamini:
  PURE: A webserver for the prediction of domains in unassigned regions in proteins.
  
• Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li:
  The combination approach of SVM and ECOC for powerful identification and classification of transcription factor.
  
• Ki-Yeol Kim, Dong Hyuk Ki, Hei-Cheul Jeung, Hyun Cheol Chung, Sun Young Rha:
  Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions.
  
• Ning Jiang, Lindsey J. Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei Luo:
  Methods for evaluating gene expression from Affymetrix microarray datasets.
  
• Ryosuke Watanabe, Enrique Morett, Edgar E. Vallejo:
  Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.
  
• Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot:
  Precise detection of rearrangement breakpoints in mammalian chromosomes.
  
• Yinyin Yuan, Chang-Tsun Li, Roland Wilson:
  Partial mixture model for tight clustering of gene expression time-course.
  
• Jianchao Yao, Chunqi Chang, Mari L. Salmi, Yeung Sam Hung, Ann E. Loraine, Stanley J. Roux:
  Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.
  
• Florent Baty, Daniel Jaeger, Frank Preiswerk, Martin M. Schumacher, Martin H. Brutsche:
  Stability of gene contributions and identification of outliers in multivariate analysis of microarray data.
  
• Jinho Yoo, Youngbok Lee, Yujung Kim, Sun Young Rha, Yangseok Kim:
  SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis.
  
• Rob Jelier, Peter A. C. 't Hoen, Ellen Sterrenburg, Johan T. den Dunnen, Gert-Jan B. van Ommen, Jan A. Kors, Barend Mons:
  Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease.
  
• Dawei Liu, Debashis Ghosh, Xihong Lin:
  Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models.
  
• Michael Hsing, Artem Cherkasov:
  Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins.
  
• Anne M. Denton, Jianfei Wu, Megan K. Townsend, Preeti Sule, Birgit M. Prüß:
  Relating gene expression data on two-component systems to functional annotations in Escherichia coli.
  
• John Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich:
  Systems biology driven software design for the research enterprise.
  
• Valdemaras Repsys, Mindaugas Margelevicius, Ceslovas Venclovas:
  Re-searcher: a system for recurrent detection of homologous protein sequences.
  
• Jing Hu, Changhui Yan:
  Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.
  
• Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup Kim:
  Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection.
  
• Csaba P. Ortutay, Mauno Vihinen:
  PseudoGeneQuest - Service for identification of different pseudogene types in the human genome.
  
• Liping Huang, Wenying Zhu, Christopher P. Saunders, James N. MacLeod, Mai Zhou, Arnold J. Stromberg, Arne C. Bathke:
  A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data.
  
• Ling Yang, Thomas M. Vondriska, Zhangang Han, W. Robb MacLellan, James N. Weiss, Zhilin Qu:
  Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.
  
• Jens Allmer, Sebastian Kuhlgert, Michael Hippler:
  2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.
  
• Korbinian Strimmer:
  A unified approach to false discovery rate estimation.
  
• Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein:
  Investigating selection on viruses: a statistical alignment approach.
  
• Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E. Heathcote, Aled M. Edwards, Michael Katze, Zhaolei Zhang, Ian D. McGilvray:
  MAID : An effect size based model for microarray data integration across laboratories and platforms.
  
• David J. Russell, Hasan H. Otu, Khalid Sayood:
  Grammar-based distance in progressive multiple sequence alignment.
  
• Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis:
  Conditional variable importance for random forests.
  
• Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, Kai-Tai Yao:
  GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
  
• Brian L. Browning:
  PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.
  
• Chun-Wei Tung, Shinn-Ying Ho:
  Computational identification of ubiquitylation sites from protein sequences.
  
• Don L. Armstrong, Chaim O. Jacob, Raphael Zidovetzki:
  Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.
  
• Adel Golovin, Kim Henrick:
  MSDmotif: exploring protein sites and motifs.
  
• Michael C. Ryan, Barry Zeeberg, Natasha J. Caplen, James A. Cleland, Ari B. Kahn, Hongfang Liu, John N. Weinstein:
  SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.
  
• Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H. Rice, Zelanna Goldberg, Patrick S. Schnable, Pamela C. Ronald, David M. Rocke:
  Assessing probe-specific dye and slide biases in two-color microarray data.
  
• Li Ma, H. Birali Runesha, Daniel Dvorkin, John R. Garbe, Yang Da:
  Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies.
  
• Paulo C. Carvalho, Juliana S. G. Fischer, Emily I. Chen, John R. Yates III, Valmir C. Barbosa:
  PatternLab for proteomics: a tool for differential shotgun proteomics.
  
• Angela P. Presson, Eric M. Sobel, Paivi Pajukanta, Christopher Plaisier, Daniel E. Weeks, Karolina Åberg, Jeanette C. Papp:
  Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis.
  
• Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
  Directed acyclic graph kernels for structural RNA analysis.
  
• Alexander R. Statnikov, Lily Wang, Constantin F. Aliferis:
  A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification.
  
• Qingwu Yang, Sing-Hoi Sze:
  Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.
  
• Tae-Ho Lee, Yeon-Ki Kim, Baek Hie Nahm:
  GBParsy: A GenBank flatfile parser library with high speed.
  
• Cuong Than, Derek A. Ruths, Luay Nakhleh:
  PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.
  
• Tiago Antao, Ana Lopes, Ricardo J. Lopes, Albano Beja-Pereira, Gordon Luikart:
  LOSITAN: A workbench to detect molecular adaptation based on a F_st-outlier method.
  
• Yuanxin Xi, David M. Rocke:
  Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis.
  
• Cong Zhou, Lucas D. Bowler, Jianfeng Feng:
  A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data.
  
• Michele Guescini, Davide Sisti, Marco B. L. Rocchi, Laura Stocchi, Vilberto Stocchi:
  A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition.
  
• Meeta Mistry, Paul Pavlidis:
  Gene Ontology term overlap as a measure of gene functional similarity.
  
• Da Meng, Shira L. Broschat, Douglas R. Call:
  A Java-based tool for the design of classification microarrays.
  
• Morgan G. I. Langille, William W. L. Hsiao, Fiona S. L. Brinkman:
  Evaluation of genomic island predictors using a comparative genomics approach.
  
• Robert M. Nowak, Rafal Ploski:
  NullHap - a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles.
  
• Feng Zhang, Jianfeng Liu, Jie Chen, Hong-Wen Deng:
  HAPSIMU: a genetic simulation platform for population-based association studies.
  
• Olivier Bastien, Eric Maréchal:
  Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.
  
• Hamilton Ganesan, Anna S. Rakitianskaia, Colin F. Davenport, Burkhard Tümmler, Oleg N. Reva:
  The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage.
  
• Peter Li, Juan I. Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R. Pocock, Carole A. Goble, Stephen G. Oliver, Douglas B. Kell:
  Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data.
  
• Andreas W. Schreiber, Neil J. Shirley, Rachel A. Burton, Geoffrey B. Fincher:
  Combining transcriptional datasets using the generalized singular value decomposition.
  
• Niina Haiminen, Heikki Mannila, Evimaria Terzi:
  Determining significance of pairwise co-occurrences of events in bursty sequences.
  
• Wei Dai, Jens M. Teodoridis, Janet Graham, Constanze Zeller, Tim Hui-Ming Huang, Pearlly Yan, J. Keith Vass, Robert Brown, Jim Paul:
  Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands.
  
• Junwon Choi, Kyung-won Yang, Tai-yong Lee, Sang Yup Lee:
  New time-scale criteria for model simplification of bio-reaction systems.
  
• Arnab Bhattacharya, Sasha Levy, Adria LeBoeuf, Michelle Gaylord, Leslie Wilson, Ambuj K. Singh, Stuart C. Feinstein:
  A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics.
  
• Mirela Andronescu, Vera Bereg, Holger H. Hoos, Anne Condon:
  RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database.
  
• Martin Kostka, Magdalena Uzlikova, Ivan Cepicka, Jaroslav Flegr:
  SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis.
  
• Zhike Zi, Yanan Zheng, Ann E. Rundell, Edda Klipp:
  SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
  
• Peter Humburg, David Bulger, Glenn Stone:
  Parameter estimation for robust HMM analysis of ChIP-chip data.
  
• Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang:
  An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories.
  
• Sébastien Tempel, Matthew Jurka, Jerzy Jurka:
  VisualRepbase: an interface for the study of occurrences of transposable element families.
  
• János Roszik, János Szöllösi, György Vereb:
  AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images.
  
• Hua Xu, Lanhao Yang, Michael A. Freitas:
  A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time.
  
• Stephen W. Tanner, Pankaj Agarwal:
  Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments.
  
• Shih-Yen Ku, Yuh-Jyh Hu:
  Protein structure search and local structure characterization.
  
• Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, Eric D. Kolaczyk:
  Integration of relational and hierarchical network information for protein function prediction.
  
• Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska:
  SynBlast: Assisting the analysis of conserved synteny information.
  
• Roberto Mosca, Barbara Brannetti, Thomas R. Schneider:
  Alignment of protein structures in the presence of domain motions.
  
• Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy:
  Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.
  
• Yulan Liang, Arpad Kelemen:
  Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration.
  
• Bernhard Y. Renard, Marc Kirchner, Hanno Steen, Judith A. J. Steen, Fred A. Hamprecht:
  NITPICK: peak identification for mass spectrometry data.
  
• Florian Erhard, Caroline C. Friedel, Ralf Zimmer:
  FERN - a Java framework for stochastic simulation and evaluation of reaction networks.
  
• Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi:
  Impact of residue accessible surface area on the prediction of protein secondary structures.
  
• Mallika Veeramalai, Yuzhen Ye, Adam Godzik:
  TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model.
  
• James M. Eales, John W. Pinney, Robert D. Stevens, David L. Robertson:
  Methodology capture: discriminating between the "best" and the rest of community practice.
  
• Martin Eklund, Ola Spjuth, Jarl E. S. Wikberg:
  The C¹C²: A framework for simultaneous model selection and assessment.
  
• Stefano Moretti, Danitsja van Leeuwen, Hans Gmuender, Stefano Bonassi, Joost van Delft, Jos Kleinjans, Fioravante Patrone, Domenico Franco Merlo:
  Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution.
  
• Xiting Yan, Fengzhu Sun:
  Testing gene set enrichment for subset of genes: Sub-GSE.
  
• Laurent Jacob, Brice Hoffmann, Véronique Stoven, Jean-Philippe Vert:
  Virtual screening of GPCRs: An in silico chemogenomics approach.
  
• Marc Chadeau-Hyam, Clive J. Hoggart, Paul F. O'Reilly, John C. Whittaker, Maria De Iorio, David J. Balding:
  Fregene: Simulation of realistic sequence-level data in populations and ascertained samples.
  
• E. Andres Houseman, Brock C. Christensen, Ru-Fang Yeh, Carmen J. Marsit, Margaret R. Karagas, Margaret R. Wrensch, Heather H. Nelson, Joseph Wiemels, Shichun Zheng, John Wiencke, Karl Kelsey:
  Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions.
  
• Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alves-Ferreira, Antonio Basílio de Miranda, Wim M. Degrave:
  ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS).
  
• Piedachu Peris, Damián López, Marcelino Campos:
  IgTM: An algorithm to predict transmembrane domains and topology in proteins.
  
• Wah-Heng Lee, Christopher W. Wong, Wan Yee Leong, Lance D. Miller, Wing-Kin Sung:
  LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens.
  
• Britta Mersch, Alexander Gepperth, Sándor Suhai, Agnes Hotz-Wagenblatt:
  Automatic detection of exonic splicing enhancers (ESEs) using SVMs.
  
• Christoffer Nellåker, Fredrik Uhrzander, Joanna Tyrcha, Håkan Karlsson:
  Mixture models for analysis of melting temperature data.
  
• Eyal Gruntman, Yijun Qi, R. Keith Slotkin, Ted Roeder, Robert A. Martienssen, Ravi Sachidanandam:
  Kismeth: Analyzer of plant methylation states through bisulfite sequencing.
  
• Uri Keich, Hong Gao, Jeffrey S. Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, Bik K. Tye:
  Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.
  
• Marco A. J. Iafolla, Guang Qiang Dong, David R. McMillen:
  Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy.
  
• Jifeng Tang, Samantha J. Baldwin, Jeanne M. E. Jacobs, C. Gerard van der Linden, Roeland E. Voorrips, Jack A. M. Leunissen, Herman van Eck, Ben Vosman:
  Large-scale identification of polymorphic microsatellites using an in silico approach.
  
• Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Gröpl:
  Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements.
  
• Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda:
  GenomeMatcher: A graphical user interface for DNA sequence comparison.
  
• Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt:
  CBESW: Sequence Alignment on the Playstation 3.
  
• Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, Jean-François Boulicaut, Jérémy Besson, Ruggero G. Pensa, Olivier Gandrillon:
  SQUAT: A web tool to mine human, murine and avian SAGE data.
  
• Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L. Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Timothy J. Aitman, Laurence Game:
  MiMiR - an integrated platform for microarray data sharing, mining and analysis.
  
• Mugdha Gadgil:
  A Population Proportion approach for ranking differentially expressed genes.
  
• Michael E. Sparks, Volker Brendel:
  MetWAMer: eukaryotic translation initiation site prediction.
  
• Young-Rae Cho, Lei Shi, Murali Ramanathan, Aidong Zhang:
  A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge.
  
• Yitan Zhu, Huai Li, David J. Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P. Hoffman, Yue Joseph Wang:
  caBIG^TM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data.
  
• René Ranzinger, Stephan Herget, Thomas Wetter, Claus-Wilhelm von der Lieth:
  GlycomeDB - integration of open-access carbohydrate structure databases.
  
• Ana Paula Sales, Georgia D. Tomaras, Thomas B. Kepler:
  Improving peptide-MHC class I binding prediction for unbalanced datasets.
  
• Folker Meyer, Daniel Paarmann, Mark D'Souza, Robert Olson, Elizabeth M. Glass, Michael Kubal, Tobias Paczian, Alexis A. Rodriguez, Rick Stevens, Andreas Wilke, Jared Wilkening, Robert A. Edwards:
  The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
  
• Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D. Koter, Paul D. Gershon:
  "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis.
  
• Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz A. Kurgan:
  Sequence based residue depth prediction using evolutionary information and predicted secondary structure.
  
• Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble:
  Combining classifiers for improved classification of proteins from sequence or structure.
  
• Gonzalo Vera, Ritsert C. Jansen, Remo Suppi:
  R/parallel - speeding up bioinformatics analysis with R.
  
• Fabrice P. A. David, Yum Lina Yip:
  SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase.
  
• Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio:
  PredGPI: a GPI-anchor predictor.
  
• Bernhard Gschloessl, Yann Guermeur, J. Mark Cock:
  HECTAR: A method to predict subcellular targeting in heterokonts.
  
• Qi Dai, Tian-Ming Wang:
  Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'.
  
• Li Shen, Jie Liu, Wei Wang:
  GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach.
  
• David Lagorce, Olivier Sperandio, Hervé Galons, Maria A. Miteva, Bruno O. Villoutreix:
  FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects.
  
• Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill, Lawrence Hunter:
  Predicting protein linkages in bacteria: Which method is best depends on task.
  
• Min Li, Jianer Chen, Jianxin Wang, Bin Hu, Gang Chen:
  Modifying the DPClus algorithm for identifying protein complexes based on new topological structures.
  
• Martijn P. van Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Susan Coort, Bruce R. Conklin, Chris T. A. Evelo:
  Presenting and exploring biological pathways with PathVisio.
  
• Stefan Kuhn, Björn Egert, Steffen Neumann, Christoph Steinbeck:
  Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction.
  
• Lianyi Han, Yanli Wang, Stephen H. Bryant:
  Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem.
  
• Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur:
  Abbreviation definition identification based on automatic precision estimates.
  
• Marcin Pawlowski, Michal J. Gajda, Ryszard Matlak, Janusz M. Bujnicki:
  MetaMQAP: A meta-server for the quality assessment of protein models.
  
• Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
  Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
  
• Sabry Razick, George Magklaras, Ian M. Donaldson:
  iRefIndex: A consolidated protein interaction database with provenance.
  
• Thomas Tüchler, Golda Velez, Alexandra Graf, David P. Kreil:
  BibGlimpse: The case for a light-weight reprint manager in distributed literature research.
  
• Mark D. Halling-Brown, David S. Moss, Adrian J. Shepherd:
  Towards a lightweight generic computational grid framework for biological research.
  
• Kevin Bleakley, Marie-Paule Lefranc, Gérard Biau:
  Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools.
  
• Johan Staaf, Johan Vallon-Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér:
  Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.
  
• Stefano Parodi, Vito Pistoia, Marco Muselli:
  Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments.
  
• Pelin Armutlu, Muhittin Emre Ozdemir, Fadime Üney Yüksektepe, I. Halil Kavakli, Metin Türkay:
  Classification of drug molecules considering their IC₅₀ values using mixed-integer linear programming based hyper-boxes method.
  
• Zhenqiu Liu, Ronald B. Gartenhaus, Ming Tan, Feng Jiang, Xiaoli Jiao:
  Gene and pathway identification with L_p penalized Bayesian logistic regression.
  
• Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel J. P. Douzery, Vincent Ranwez:
  PhySIC_IST: cleaning source trees to infer more informative supertrees.
  
• Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md. Mehedi Hasan, Mohammad Shoyaib, Haseena Khan, Ray Walshe:
  Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.
  
• Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky:
  BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments.
  
• Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Joseph Wang, Zhen Zhang, Eric P. Hoffman, Robert Clarke:
  Knowledge-guided multi-scale independent component analysis for biomarker identification.
  
• Tongtong Wu, Wei Sun, Shinsheng Yuan, Chun-Houh Chen, Ker-Chau Li:
  A method for analyzing censored survival phenotype with gene expression data.
  
• Lisa E. M. McMillan, Andrew C. R. Martin:
  Automatically extracting functionally equivalent proteins from SwissProt.
  
• Sheila Podell, Terry Gaasterland, Eric E. Allen:
  A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.
  
• Daniel N. Frank:
  XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data.
  
• Pekka Marttinen, Adam Baldwin, William P. Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander:
  Bayesian modeling of recombination events in bacterial populations.
  
• Raj Chari, Bradley P. Coe, Craig Wedseltoft, Marie Benetti, Ian M. Wilson, Emily A. Vucic, Calum MacAulay, Raymond T. Ng, Wan L. Lam:
  SIGMA²: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.
  
• Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert:
  LC-MSsim - a simulation software for liquid chromatography mass spectrometry data.
  
• Iaroslav Ispolatov, Sergei Maslov:
  Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.
  
• Yu-Shuen Tsai, Chin-Teng Lin, George C. Tseng, I-Fang Chung, Nikhil R. Pal:
  Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems.
  
• Sri R. Paladugu, Shan Zhao, Animesh Ray, Alpan Raval:
  Mining protein networks for synthetic genetic interactions.
  
• Guillaume Launay, Thomas Simonson:
  Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.
  
• Jorge Amigo, Antonio Salas, Christopher Phillips, Ángel Carracedo:
  SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.
  
• Christopher Bystroff, Bobbie-Jo M. Webb-Robertson:
  Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure.
  
• Ce Zheng, Lukasz A. Kurgan:
  Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments.
  
• Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef:
  Probabilistic base calling of Solexa sequencing data.
  
• Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang:
  easyExon - A Java-based GUI tool for processing and visualization of Affymetrix exon array data.
  
• Qian Liu, Koby Crammer, Fernando C. N. Pereira, David S. Roos:
  Reranking candidate gene models with cross-species comparison for improved gene prediction.
  
• Caroline Truntzer, Delphine Maucort-Boulch, Pascal Roy:
  Comparative optimism in models involving both classical clinical and gene expression information.
  
• Benjamin Roche, Jean-François Guégan, François Bousquet:
  Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission.
  
• Vladimir Espinosa Angarica, Abel González Pérez, Ana Tereza R. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira:
  Prediction of TF target sites based on atomistic models of protein-DNA complexes.
  
• Kieran O'Neill, Alexander García Castro, Anita Schwegmann, Rafael C. Jimenez, Dan Jacobson, Henning Hermjakob:
  OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
  
• Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, Maria A. Miteva:
  AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
  
• Martin Slawski, Martin Daumer, Anne-Laure Boulesteix:
  CMA - a comprehensive Bioconductor package for supervised classification with high dimensional data.
  
• Laurent Bréhélin, Jean-François Dufayard, Olivier Gascuel:
  PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.
  
• Tammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio:
  Structural assembly of two-domain proteins by rigid-body docking.
  
• Michael J. Gilchrist, Mikkel B. Christensen, Richard Harland, Nicolas Pollet, James C. Smith, Naoto Ueno, Nancy Papalopulu:
  Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.
  
• Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W. Nattkemper:
  Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics.
  
• Monica Chagoyen, José María Carazo, Alberto D. Pascual-Montano:
  Assessment of protein set coherence using functional annotations.
  
• Marko Tscherepanow, Nickels Jensen, Franz Kummert:
  An incremental approach to automated protein localisation.
  
• Michael T. Sykes, James R. Williamson:
  Envelope: interactive software for modeling and fitting complex isotope distributions.
  
• Solène Grosdidier, Juan Fernández-Recio:
  Identification of hot-spot residues in protein-protein interactions by computational docking.
  
• Salim Bougouffa, Jim Warwicker:
  Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces.
  
• Ning Wei, Erwin Flaschel, Karl Friehs, Tim W. Nattkemper:
  A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification.
  
• Jung Soh, Paul M. K. Gordon, Morgan L. Taschuk, Anguo Dong, Andrew C. Ah-Seng, Andrei L. Turinsky, Christoph W. Sensen:
  Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking.
  
• Fabrício Martins Lopes, David Correa Martins Jr., Roberto Marcondes Cesar Junior:
  Feature selection environment for genomic applications.
  
• Raad Z. Gharaibeh, Anthony Fodor, Cynthia Gibas:
  Background correction using dinucleotide affinities improves the performance of GCRMA.
  
• Dustin P. Potter, Pearlly Yan, Tim Hui-Ming Huang, Shili Lin:
  Probe signal correction for differential methylation hybridization experiments.
  
• Mohd. Zeeshan Ansari, Jyoti Sharma, Rajesh S. Gokhale, Debasisa Mohanty:
  In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites.
  
• Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li:
  CompMoby: Comparative MobyDick for detection of cis-regulatory motifs.
  
• Sylvain Marthey, Gabriela Aguileta, François Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angélique Gautier, Marc-Henri Lebrun, Hélène Chiapello:
  FUNYBASE: a FUNgal phYlogenomic dataBASE.
  
• Hailong Meng, Edward Lenn Murrelle, Guoya Li:
  Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles.
  
• Peter A. DiMaggio Jr., Scott R. McAllister, Christodoulos A. Floudas, Xiao-Jiang Feng, Joshua D. Rabinowitz, Herschel Rabitz:
  Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.
  
• Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank Oliver Glöckner:
  MetaMine - A tool to detect and analyse gene patterns in their environmental context.
  
• Sabine Pérès, Laurence Molina, Nicolas Salvetat, Claude Granier, Franck Molina:
  A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics.
  
• Patrick Emmanuel Meyer, Frédéric Lafitte, Gianluca Bontempi:
  minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information.
  
• Raffaele Giancarlo, Davide Scaturro, Filippo Utro:
  Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer.
  
• Matthew T. Weirauch, Christopher K. Wong, Alexandra B. Byrne, Joshua M. Stuart:
  Information-based methods for predicting gene function from systematic gene knock-downs.
  
• Thomas Jörg, Olivier C. Martin, Andreas Wagner:
  Neutral network sizes of biological RNA molecules can be computed and are not atypically small.
  
• Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber:
  QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR.
  
• Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandic, Matko Gluncic, Nils Paar:
  Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
  
• Weijun Luo, Kurt D. Hankenson, Peter J. Woolf:
  Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.
  
• Brendan Sheehan, Aaron J. Quigley, Benoit Gaudin, Simon Dobson:
  A relation based measure of semantic similarity for Gene Ontology annotations.
  
• Nathan L. Tintle, Aaron A. Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C. Taylor:
  Gene set analyses for interpreting microarray experiments on prokaryotic organisms.
  
• Kenneth Bryan, Lorraine Brennan, Padraig Cunningham:
  MetaFIND: A feature analysis tool for metabolomics data.
  
• Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham Hury, Ran Hoffer, Yaara Ziporen, Shulamit Michaeli, Ron Unger:
  Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes.
  
• Tao Xu, LinFang Du, Yan Zhou:
  Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data.
  
• Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi, Niels Grabe:
  Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling.
  
• Stephan H. F. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler:
  RNAalifold: improved consensus structure prediction for RNA alignments.
  
• Peter Frommolt, Roman K. Thomas:
  Standardized high-throughput evaluation of cell-based compound screens.
  
• Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch:
  CoCoNUT: an efficient system for the comparison and analysis of genomes.
  
• Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen:
  Improved identification of conserved cassette exons using Bayesian networks.
  
• James K. Hane, Richard P. Oliver:
  RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
  
• Florian Meereis, Michael Kaufmann:
  Extension of the COG and arCOG databases by amino acid and nucleotide sequences.
  
• Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, Livia Torterolo:
  A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data.
  
• Rongheng Lin, Shuangshuang Dai, Richard D. Irwin, Alexandra N. Heinloth, Gary A. Boorman, Leping Li:
  Gene set enrichment analysis for non-monotone association and multiple experimental categories.
  
• Thouis R. Jones, In Han Kang, Douglas B. Wheeler, Robert A. Lindquist, Adam Papallo, David M. Sabatini, Polina Golland, Anne E. Carpenter:
  CellProfiler Analyst: data exploration and analysis software for complex image-based screens.
  
• Hwan Young Lee, Injee Song, Eunho Ha, Sung-Bae Cho, Woo Ick Yang, Kyoung-Jin Shin:
  mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences.
  
• Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Henryk Jan Komorowski:
  Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
  
• Paolo Uva, Emanuele de Rinaldis:
  CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments.
  
• Michael Gormley, Aydin Tozeren:
  Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification.
  
• Myron Peto, Andrzej Kloczkowski, Vasant Honavar, Robert L. Jernigan:
  Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable.
  
• Rosemary Braun, Leslie Cope, Giovanni Parmigiani:
  Identifying differential correlation in gene/pathway combinations.
  
• Robert W. Reid, Anthony A. Fodor:
  Determining gene expression on a single pair of microarrays.
  
• Alexander L. Richards, Peter Holmans, Michael C. O'Donovan, Michael J. Owen, Lesley Jones:
  A comparison of four clustering methods for brain expression microarray data.
  
• Daniel R. Caffrey, Elizabeth A. Lunney, Deborah J. Moshinsky:
  Prediction of specificity-determining residues for small-molecule kinase inhibitors.
  
• Juliana S. Bernardes, Jorge H. Fernandez, Ana Tereza R. Vasconcelos:
  Structural descriptor database: a new tool for sequence-based functional site prediction.
  
• Geraint Barton, J. C. Abbott, Norie Chiba, D. W. Huang, Y. Huang, Marko Krznaric, J. Mack-Smith, A. Saleem, B. T. Sherman, B. Tiwari, Chris Tomlinson, Timothy J. Aitman, John Darlington, Laurence Game, Michael J. E. Sternberg, S. A. Butcher:
  EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management.
  
• Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano:
  ExonMiner: Web service for analysis of GeneChip Exon array data.
  
• Matthew S. Hestand, Michiel van Galen, Michel P. Villerius, Gert-Jan B. van Ommen, Johan T. den Dunnen, Peter A. C. 't Hoen:
  CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.
  
• Josephine F. Reyes, Andrew R. Francis, Mark M. Tanaka:
  Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes.
  
• Marcílio Carlos Pereira de Souto, Ivan G. Costa, Daniel S. A. de Araujo, Teresa Bernarda Ludermir, Alexander Schliep:
  Clustering cancer gene expression data: a comparative study.
  
• Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit, Meriem El Karoui:
  MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.
  
• Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha:
  Natural computation meta-heuristics for the in silico optimization of microbial strains.
  
• Stephen E. Hamby, Jonathan D. Hirst:
  Prediction of glycosylation sites using random forests.
  
• Derek Huntley, Y. Amy Tang, Tatyana B. Nesterova, Sarah Butcher, Neil Brockdorff:
  Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features.
  
• Sarah Song, Michael A. Black:
  Microarray-based gene set analysis: a comparison of current methods.
  
• Aarti Garg, Gajendra P. S. Raghava:
  ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins.
  
• Ralf Tautenhahn, Christoph Böttcher, Steffen Neumann:
  Highly sensitive feature detection for high resolution LC/MS.
  
• Terri T. Ni, William J. Lemon, Yu Shyr, Tao P. Zhong:
  Use of normalization methods for analysis of microarrays containing a high degree of gene effects.
  
• Katerina Kechris, Hao Li:
  c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression.
  
• Jianguo Xia, Trent C. Bjorndahl, Peter Tang, David S. Wishart:
  MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.
  
• Joseph W. Foley, Fumiaki Katagiri:
  Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method.
  
• Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel, Albrecht Ott:
  Position dependent mismatch discrimination on DNA microarrays - experiments and model.
  
• Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan Wang:
  A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.
  
• Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A. Huttley, Manuel E. Lladser, Rob Knight:
  Comparison of methods for estimating the nucleotide substitution matrix.
  
• Marta Blangiardo, Sylvia Richardson:
  A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips.
  
• Shu-Yi Su, Jonathan White, David J. Balding, Lachlan J. M. Coin:
  Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions.
  
• Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters:
  ElliPro: a new structure-based tool for the prediction of antibody epitopes.
  
• Allison Gehrke, Shaojun Sun, Lukasz A. Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar, Krzysztof J. Cios:
  Improved machine learning method for analysis of gas phase chemistry of peptides.
  
• Martin Bader, Mohamed Ibrahim Abouelhoda, Enno Ohlebusch:
  A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions.
  
• Patrick Slama, Ioannis Filippis, Michael Lappe:
  Detection of protein catalytic residues at high precision using local network properties.
  
• Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz:
  Algorithm of OMA for large-scale orthology inference.
  
• David A. Cairns, David N. Perkins, Anthea J. Stanley, Douglas Thompson, Jennifer H. Barrett, Peter J. Selby, Rosamonde E. Banks:
  Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.
  
• Carl R. Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C. Sears:
  Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data.
  
• Akito Taneda:
  An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast.
  
• Wei-Sheng Wu, Wen-Hsiung Li:
  Systematic identification of yeast cell cycle transcription factors using multiple data sources.
  
• David A. Nix, Samir J. Courdy, Kenneth M. Boucher:
  Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.
  
• Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H. Badger, Jane M. Carlton, Joana C. Silva:
  IDEA: Interactive Display for Evolutionary Analyses.
  
• Bo Jin, Brian Muller, Chengxiang Zhai, Xinghua Lu:
  Multi-label literature classification based on the Gene Ontology graph.
  
• Jesper Nielsen, Thomas Mailund:
  SNPFile - A software library and file format for large scale association mapping and population genetics studies.
  
• Geir Kjetil Sandve, Osman Abul, Finn Drabløs:
  Compo: composite motif discovery using discrete models.
  
• Wei Yu, Anja Wulf, Tiebin Liu, Muin J. Khoury, Marta Gwinn:
  Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.
  
• John C. Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M. Marcotte, Alan R. Rodrigues, Rong Wang, Shih-Ting Huang, Erik S. Ferlanti, Alexander I. Saeed, Robert D. Fleischmann, Scott N. Peterson, Rembert Pieper:
  The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results.
  
• Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi, David M. Gilbert:
  ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data.
  
• Shashi Bhushan Pandit, Jeffrey Skolnick:
  Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.
  
• Gabriel Cardona, Francesc Rosselló, Gabriel Valiente:
  Extended Newick: it is time for a standard representation of phylogenetic networks.
  
• Arnaud Krebs, Mattia Frontini, Làszlò Tora:
  GPAT: Retrieval of genomic annotation from large genomic position datasets.
  
• Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud:
  Optimal neighborhood indexing for protein similarity search.
  
• Evert-Jan Blom, Sacha A. F. T. van Hijum, Klaas J. Hofstede, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
  DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites.
  
• Frédéric Lemoine, Bernard Labedan, Olivier Lespinet:
  SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.
  
• Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin:
  A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.
  
• Yanxin Huang, Yongli Bao, Shu Yan Guo, Yan Wang, Chunguang Zhou, Yuxin Li:
  Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.
  
• Jukka Corander, Pekka Marttinen, Jukka Sirén, Jing Tang:
  Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.
  
• Olivier Delaneau, Cédric Coulonges, Jean-François Zagury:
  Shape-IT: new rapid and accurate algorithm for haplotype inference.
  
• Anton Kratz, Masaru Tomita, Arun Krishnan:
  GeNESiS: gene network evolution simulation software.
  
• Mi-Youn K. Brusniak, Bernd Bodenmiller, David Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N. Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold, Julian D. Watts:
  Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.
  
• Kalidas Yeturu, Nagasuma Chandra:
  PocketMatch: A new algorithm to compare binding sites in protein structures.
  
• Thomas D. Otto, Ana Carolina R. Guimarães, Wim M. Degrave, Antonio Basílio de Miranda:
  AnEnPi: identification and annotation of analogous enzymes.
  
• Brian T. Luke, Jack R. Collins:
  Examining the significance of fingerprint-based classifiers.
  
• Fengfeng Zhou, Victor Olman, Ying Xu:
  Barcodes for genomes and applications.
  
• Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang:
  Prediction of regulatory elements in mammalian genomes using chromatin signatures.
  
• Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte:
  GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed.
  
• Avril Coghlan, Tristan J. Fiedler, Sheldon J. McKay, Paul Flicek, Todd W. Harris, Darin Blasiar, Lincoln D. Stein:
  nGASP - the nematode genome annotation assessment project.
  
• Harold W. Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A. Huttley:
  Pathological rate matrices: from primates to pathogens.
  
• Matteo Brilli, Alessio Mengoni, Marco Fondi, Marco Bazzicalupo, Pietro Liò, Renato Fani:
  Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network.
  
• Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof:
  GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
  
• Nan Li, Zhonghua Sun, Fan Jiang:
  Prediction of protein-protein binding site by using core interface residue and support vector machine.
  
• Alberto I. Roca, Albert E. Almada, Aaron C. Abajian:
  ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
  
• Romesh Stanislaus, Mark Carey, Helena F. Deus, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills, Jonas S. Almeida:
  RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays.
  
• Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
  The meaning of alignment: lessons from structural diversity.
  
• Kim W. Carter, Pamela A. McCaskie, Lyle J. Palmer:
  SimHap GUI: An intuitive graphical user interface for genetic association analysis.
  
• Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M. Sloan, Florian Scharinger, Arthur S. Trew, Peter Ghazal:
  SPRINT: A new parallel framework for R.
  
• Peter Langfelder, Steve Horvath:
  WGCNA: an R package for weighted correlation network analysis.