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 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.
  
• K. E. Whelan, R. 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 J. Lopez, Armando Blanco, Fernando Garcia, 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 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 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 C. S. 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 W. 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 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.