BMC Bioinformatics, Volume 10

Volume 10, 2009

• Shuangge Ma, Jian Huang:
  Regularized gene selection in cancer microarray meta-analysis.
  
• Steffen Durinck, James Bullard, Paul T. Spellman, Sandrine Dudoit:
  GenomeGraphs: integrated genomic data visualization with R.
  
• Alessandro Ferrantini, Joke Allemeersch, Paul van Hummelen, Enrico Carlon:
  Thermodynamic scaling behavior in genechips.
  
• Chao Yang, Zengyou He, Weichuan Yu:
  Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.
  
• Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, Michael A. White:
  Bayesian optimal discovery procedure for simultaneous significance testing.
  
• Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor:
  Automated Alphabet Reduction for Protein Datasets.
  
• Michael Hackenberg, Gorka Lasso, Rune Matthiesen:
  ContDist: a tool for the analysis of quantitative gene and promoter properties.
  
• Pengfei Han, Xiuzhen Zhang, Raymond S. Norton, Zhi-Ping Feng:
  Large-scale prediction of long disordered regions in proteins using random forests.
  
• Takashi Yoneya, Reina Nishida:
  TCP: a tool for designing chimera proteins based on the tertiary structure information.
  
• Paola M. V. Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee:
  Bayesian DNA copy number analysis.
  
• Amber J. Hackstadt, Ann M. Hess:
  Filtering for increased power for microarray data analysis.
  
• Kai Wang, Jian Li, Shengting Li, Lars Bolund, Carsten Wiuf:
  Estimation of tumor heterogeneity using CGH array data.
  
• Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L. S. Tang, Weichuan Yu:
  MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study.
  
• Yun Xu, ZhiHao Wang, YiMing Lei, YuZhong Zhao, Yu Xue:
  MBA: a literature mining system for extracting biomedical abbreviations.
  
• Kuo-ching Liang, Xiaodong Wang, Ta-Hsin Li:
  Robust discovery of periodically expressed genes using the laplace periodogram.
  
• Victoria Martin-Requena, Antonio Muñoz-Merida, M. Gonzalo Claros, Oswaldo Trelles:
  PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.
  
• Kyle C. Chipman, Ambuj K. Singh:
  Predicting genetic interactions with random walks on biological networks.
  
• Harald Binder, Martin Schumacher:
  Incorporating pathway information into boosting estimation of high-dimensional risk prediction models.
  
• Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano:
  BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
  
• Rui Hu, Xing Qiu, Galina V. Glazko, Lev Klebanov, Andrei Yakovlev:
  Detecting intergene correlation changes in microarray analysis: a new approach to gene selection.
  
• Christian Frech, Michael Kommenda, Viktoria Dorfer, Thomas Kern, Helmut Hintner, Johann W. Bauer, Kamil Önder:
  Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis.
  
• Manish Kumar, Gajendra P. S. Raghava:
  Prediction of nuclear proteins using SVM and HMM models.
  
• Debayan Datta, Hongyu Zhao:
  Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data.
  
• Tsong Yueh Chen, Joshua W. K. Ho, Huai Liu, Xiaoyuan Xie:
  An innovative approach for testing bioinformatics programs using metamorphic testing.
  
• J. B. Brown, Tatsuya Akutsu:
  Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
  
• Sonia H. Shah, Jacqueline A. Pallas:
  Identifying differential exon splicing using linear models and correlation coefficients.
  
• Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay:
  Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes.
  
• Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien L. Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter:
  Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.
  
• Yu-Shen Liu, Yi Fang, Karthik Ramani:
  Using least median of squares for structural superposition of flexible proteins.
  
• Bart H. J. van den Berg, Jay H. Konieczka, Fiona M. McCarthy, Shane C. Burgess:
  ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.
  
• Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita:
  Genome Projector: zoomable genome map with multiple views.
  
• Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber:
  VASCo: computation and visualization of annotated protein surface contacts.
  
• Nils Arrigo, Jarek W. Tuszynski, Dorothee Ehrich, Tommy Gerdes, Nadir Alvarez:
  Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring.
  
• Kim-Anh Lê Cao, Pascal G. P. Martin, Christèle Robert-Granié, Philippe Besse:
  Sparse canonical methods for biological data integration: application to a cross-platform study.
  
• Andrew S. Warren, João Carlos Setubal:
  The Genome Reverse Compiler: an explorative annotation tool.
  
• Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim:
  Prediction of protein-protein interaction types using association rule based classification.
  
• Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz, Florentino Fdez-Riverola:
  DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data.
  
• Roland Nilsson, Johan Björkegren, Jesper Tegnér:
  On reliable discovery of molecular signatures.
  
• Sarah K. Kummerfeld, Sarah A. Teichmann:
  Protein domain organisation: adding order.
  
• Sudhakar Jonnalagadda, Rajagopalan Srinivasan:
  NIFTI: An evolutionary approach for finding number of clusters in microarray data.
  
• Lars Kraemer, Bánk Beszteri, Steffi Gäbler-Schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan Frickenhaus:
  STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
  
• Vlad Popovici, Darlene R. Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi, Pratyaksha Wirapati:
  Selecting control genes for RT-QPCR using public microarray data.
  
• Qingbo Li, Bryan A. P. Roxas:
  An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters.
  
• Pei-Chun Chen, Su-Yun Huang, Wei J. Chen, Chuhsing Kate Hsiao:
  A new regularized least squares support vector regression for gene selection.
  
• Carl Murie, Owen Z. Woody, Anna Y. Lee, Robert Nadon:
  Comparison of small n statistical tests of differential expression applied to microarrays.
  
• Jimmy Lin:
  Is searching full text more effective than searching abstracts?
  
• Marit Ackermann, Korbinian Strimmer:
  A general modular framework for gene set enrichment analysis.
  
• Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini:
  GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
  
• Sergio Barlati, Sergio Chiesa, Chiara Magri:
  "GenotypeColour^TM": colour visualisation of SNPs and CNVs.
  
• Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K. Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann:
  EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data.
  
• José Carlos Clemente, Kazuho Ikeo, Gabriel Valiente, Takashi Gojobori:
  Optimized ancestral state reconstruction using Sankoff parsimony.
  
• Uwe Thissen, Suzan Wopereis, Sjoerd A. A. van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen, Age K. Smilde:
  Improving the analysis of designed studies by combining statistical modelling with study design information.
  
• Michalis E. Zervakis, Michalis E. Blazadonakis, Georgia Tsiliki, Vasiliki Danilatou, Manolis Tsiknakis, Dimitris Kafetzopoulos:
  Outcome prediction based on microarray analysis: a critical perspective on methods.
  
• André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner, Rainer Merkl:
  TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis.
  
• Eric Yang, Ioannis P. Androulakis:
  Assessing and selecting gene expression signals based upon the quality of the measured dynamics.
  
• Naryttza N. Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus, Tim W. Nattkemper:
  TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
  
• Ivan Erill, Michael C. O'Neill:
  A reexamination of information theory-based methods for DNA-binding site identification.
  
• Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang:
  An effective docking strategy for virtual screening based on multi-objective optimization algorithm.
  
• Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen:
  The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
  
• David P. Leader, E. James Milner-White:
  Motivated Proteins: A web application for studying small three-dimensional protein motifs.
  
• Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi:
  A comparison on effects of normalisations in the detection of differentially expressed genes.
  
• Vasyl Pihur, Susmita Datta, Somnath Datta:
  RankAggreg, an R package for weighted rank aggregation.
  
• Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver, Daniel J. Schaid:
  Genotype determination for polymorphisms in linkage disequilibrium.
  
• Geert C. W. M. Mulders, Gerard T. Barkema, Enrico Carlon:
  Inverse Langmuir method for oligonucleotide microarray analysis.
  
• Leng Han, Zhongming Zhao:
  CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
  
• Shaleen K. Botting, Jerome P. Trzeciakowski, Michelle F. Benoit, Salama A. Salama, Concepcion R. Diaz-Arrastia:
  Sample entropy analysis of cervical neoplasia gene-expression signatures.
  
• Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell:
  Quantitative measures for the management and comparison of annotated genomes.
  
• Joshua N. Sampson, Hongyu Zhao:
  Genotyping and inflated type I error rate in genome-wide association case/control studies.
  
• Douglas W. Bryant Jr., Weng-Keen Wong, Todd C. Mockler:
  QSRA - a quality-value guided de novo short read assembler.
  
• Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, Lindsay G. Cowell:
  An improved ontological representation of dendritic cells as a paradigm for all cell types.
  
• Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
  Gene set-based module discovery in the breast cancer transcriptome.
  
• Amalia Annest, Roger Eugene Bumgarner, Adrian E. Raftery, Ka Yee Yeung:
  Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.
  
• Jing Chen, Bruce J. Aronow, Anil G. Jegga:
  Disease candidate gene identification and prioritization using protein interaction networks.
  
• Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhaeusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner:
  RGG: A general GUI Framework for R scripts.
  
• Tobias Gebäck, Petros Koumoutsakos:
  Edge detection in microscopy images using curvelets.
  
• Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger:
  RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.
  
• Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia:
  Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.
  
• Yan A. Meng, Yi Yu, L. Adrienne Cupples, Lindsay A. Farrer, Kathryn L. Lunetta:
  Performance of random forest when SNPs are in linkage disequilibrium.
  
• John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich:
  Adaptable data management for systems biology investigations.
  
• Chao Xie, Martti T. Tammi:
  CNV-seq, a new method to detect copy number variation using high-throughput sequencing.
  
• Markus Teuber, Michael H. Wenz, Stefan Schreiber, Andre Franke:
  GMFilter and SXTestPlate: software tools for improving the SNPlex^TM genotyping system.
  
• Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn:
  Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.
  
• Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin, Bin Xia:
  Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.
  
• Mickaël Guedj, Stéphane Robin, Alain Celisse, Grégory Nuel:
  Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation.
  
• Li-Yu D. Liu, Chien-Yu Chen, Mei-Ju M. Chen, Ming-Shian Tsai, Cho-Han S. Lee, Tzu L. Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang, Fon-Jou Hsieh:
  Statistical identification of gene association by CID in application of constructing ER regulatory network.
  
• Frank P. Y. Lin, Enrico W. Coiera, Ruiting Lan, Vitali Sintchenko:
  In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.
  
• Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith:
  Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.
  
• Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu:
  Analyses of domains and domain fusions in human proto-oncogenes.
  
• Michael Knoll, Thomas M. Hamm, Florian Wagner, Virginia Martinez, Jürgen Pleiss:
  The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases.
  
• Pekka Marttinen, Samuel Myllykangas, Jukka Corander:
  Bayesian clustering and feature selection for cancer tissue samples.
  
• Lars Snipen, Otto L. Nyquist, Margrete Solheim, Ågot Aakra, Ingolf F. Nes:
  Improved analysis of bacterial CGH data beyond the log-ratio paradigm.
  
• Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Peter Meinicke:
  MarVis: a tool for clustering and visualization of metabolic biomarkers.
  
• Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdei Sadeghi, Abbas Nowzari-Dalini, Bahram Goliaei:
  New scoring schema for finding motifs in DNA Sequences.
  
• Nicholas A. Hamilton, Jack T. H. Wang, Markus C. Kerr, Rohan D. Teasdale:
  Statistical and visual differentiation of subcellular imaging.
  
• Jamie I. MacPherson, John W. Pinney, David L. Robertson:
  JNets: Exploring networks by integrating annotation.
  
• Stephen C. Billups, Margaret C. Neville, Michael Rudolph, Weston Porter, Pepper Schedin:
  Identifying significant temporal variation in time course microarray data without replicates.
  
• Norbert Busch, Gero Wedemann:
  Modeling genomic data with type attributes, balancing stability and maintainability.
  
• Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck, Marie-Hélène Mucchielli-Giorgi:
  Characterisation and correction of signal fluctuations in successive acquisitions of microarray images.
  
• James Vlasblom, Shoshana J. Wodak:
  Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.
  
• Jonas S. Almeida, Susana Vinga:
  Biological sequences as pictures - a generic two dimensional solution for iterated maps.
  
• Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, Hualiang Jiang:
  Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.
  
• High-Seng Chai, Hugues Sicotte, Kent R. Bailey, Stephen T. Turner, Yan W. Asmann, Jean-Pierre Kocher:
  GLOSSI: a method to assess the association of genetic loci-sets with complex diseases.
  
• Arumay Pal, Ranjit Prasad Bahadur, Partha Sarathi Ray, Pinak Chakrabarti:
  Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display.
  
• Jorge Estrada, Pau Bernadó, Martin Blackledge, Javier Sancho:
  ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble.
  
• Firoz Ahmed, Hifzur Rahman Ansari, Gajendra P. S. Raghava:
  Prediction of guide strand of microRNAs from its sequence and secondary structure.
  
• Florian Hahne, Nolwenn LeMeur, Ryan R. Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman:
  flowCore: a Bioconductor package for high throughput flow cytometry.
  
• Adrian K. Arakaki, Ying Huang, Jeffrey Skolnick:
  EFICAz²: enzyme function inference by a combined approach enhanced by machine learning.
  
• Manoj Hariharan, Vinod Scaria, Samir K. Brahmachari:
  dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation.
  
• Sung-Bum Cho, Jihun Kim, Ju Han Kim:
  Identifying set-wise differential co-expression in gene expression microarray data.
  
• Jessica C. Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush:
  Data-driven normalization strategies for high-throughput quantitative RT-PCR.
  
• Todd Riley, Xin Yu, Eduardo Sontag, Arnold Levine:
  The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes.
  
• Aleksandar Poleksic:
  Island method for estimating the statistical significance of profile-profile alignment scores.
  
• Costas P. Exarchos, Themis P. Exarchos, Costas Papaloukas, Anastassios N. Troganis, Dimitrios I. Fotiadis:
  Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation.
  
• Sheng-An Lee, Chen-hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
  POINeT: protein interactome with sub-network analysis and hub prioritization.
  
• Zhipeng Cai, Hadi Sabaa, Yining Wang, Randy Goebel, Zhiquan Wang, Jiaofen Xu, Paul Stothard, Guohui Lin:
  Most parsimonious haplotype allele sharing determination.
  
• Christopher Previti, Oscar Harari, Igor Zwir, Coral del Val:
  Profile analysis and prediction of tissue-specific CpG island methylation classes.
  
• Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig, Dirk Walther:
  Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
  
• Michael J. Joss, Jeremy E. Koenig, Maurizio Labbate, Martin F. Polz, Michael R. Gillings, Harold W. Stokes, W. Ford Doolittle, Yan Boucher:
  ACID: annotation of cassette and integron data.
  
• Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye:
  A bag-of-words approach for Drosophila gene expression pattern annotation.
  
• Eric Tannier, Chunfang Zheng, David Sankoff:
  Multichromosomal median and halving problems under different genomic distances.
  
• Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji:
  SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
  
• Cunlu Zou, Jianfeng Feng:
  Granger causality vs. dynamic Bayesian network inference: a comparative study.
  
• Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao, Xiaokun Li:
  FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.
  
• Carlos Oscar Sánchez Sorzano, Cédric Messaoudi, Matthias Eibauer, Jose-Roman Bilbao-Castro, Reiner Hegerl, S. Nickell, Sergio Marco, José María Carazo:
  Marker-free image registration of electron tomography tilt-series.
  
• Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone:
  Survey-based naming conventions for use in OBO Foundry ontology development.
  
• Philippe Lemey, Martin Lott, Darren P. Martin, Vincent Moulton:
  Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.
  
• Simone Scalabrin, Michele Morgante, Alberto Policriti:
  Automated FingerPrint Background removal: FPB.
  
• Taeyoung Hwang, Taesung Park:
  Identification of differentially expressed subnetworks based on multivariate ANOVA.
  
• Antonis Koussounadis, Oliver Redfern, David T. Jones:
  Improving classification in protein structure databases using text mining.
  
• Heping Zhang, Minghui Wang, Xiang Chen:
  Willows: a memory efficient tree and forest construction package.
  
• Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi, Nori Kurata:
  SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.
  
• James Anderson, Antonis Papachristodoulou:
  On validation and invalidation of biological models.
  
• Hideya Kawaji, Yoshihide Hayashizaki, Carsten O. Daub:
  SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes.
  
• Daniel Restrepo-Montoya, Carolina Vizcaíno, Luis F. Niño, Marisol Ocampo, Manuel E. Patarroyo, Manuel A. Patarroyo:
  Validating subcellular localization prediction tools with mycobacterial proteins.
  
• Pufeng Du, Liyan Jia, Yanda Li:
  CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants.
  
• Eric Jain, Amos Bairoch, Severine Duvaud, Isabelle Phan, Nicole Redaschi, Baris E. Suzek, Maria Jesus Martin, Peter B. McGarvey, Elisabeth Gasteiger:
  Infrastructure for the life sciences: design and implementation of the UniProt website.
  
• Armando J. Pinho, Paulo Jorge S. G. Ferreira, Sara P. Garcia, João M. O. S. Rodrigues:
  On finding minimal absent words.
  
• Mario Huerta, Juan Cedano, Dario Peña, Antonio Rodriguez, Enrique Querol:
  PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships.
  
• Sebastian Schönherr, Hansi Weißensteiner, Stefan Coassin, Günther Specht, Florian Kronenberg, Anita Brandstätter:
  eCOMPAGT - efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology.
  
• Chih-Lung Ko, Eberhard O. Voit, Feng-Sheng Wang:
  Estimating parameters for generalized mass action models with connectivity information.
  
• Claus A. Andersen, Stefano Gotta, Letizia Magnoni, Roberto Raggiaschi, Andreas Kremer, Georg C. Terstappen:
  Robust MS quantification method for phospho-peptides using ¹⁸O/¹⁶O labeling.
  
• Gaurav Pandey, Chad L. Myers, Vipin Kumar:
  Incorporating functional inter-relationships into protein function prediction algorithms.
  
• Robert Kofler, Tatiana Teixeira Torres, Tamas Lelley, Christian Schlötterer:
  PanGEA: Identification of allele specific gene expression using the 454 technology.
  
• Niclas Chiang Tan, Wayne G. Fisher, Kevin P. Rosenblatt, Harold R. Garner:
  Application of multiple statistical tests to enhance mass spectrometry-based biomarker discovery.
  
• Kenneth Lo, Florian Hahne, Ryan R. Brinkman, Raphael Gottardo:
  flowClust: a Bioconductor package for automated gating of flow cytometry data.
  
• Tianqing Liu, Nan Lin, Ningzhong Shi, Baoxue Zhang:
  Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.
  
• Seon-Young Kim:
  Effects of sample size on robustness and prediction accuracy of a prognostic gene signature.
  
• Szymon Kaczanowski, Pawel Siedlecki, Piotr Zielenkiewicz:
  The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words.
  
• Thorsteinn S. Rögnvaldsson, Terence A. Etchells, Liwen You, Daniel Garwicz, Ian H. Jarman, Paulo J. G. Lisboa:
  How to find simple and accurate rules for viral protease cleavage specificities.
  
• Nazar Zaki, Sanja Lazarova-Molnar, Wassim El-Hajj, Piers Campbell:
  Protein-protein interaction based on pairwise similarity.
  
• Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig:
  MIMAS 3.0 is a Multiomics Information Management and Annotation System.
  
• Alexandre P. Francisco, Miguel Bugalho, Mário Ramirez, João A. Carriço:
  Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach.
  
• Alex Stivala, Anthony Wirth, Peter J. Stuckey:
  Tableau-based protein substructure search using quadratic programming.
  
• Jochen Blom, Stefan P. Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, Alexander Goesmann:
  EDGAR: A software framework for the comparative analysis of prokaryotic genomes.
  
• Iftach Nachman, Aviv Regev:
  BRNI: Modular analysis of transcriptional regulatory programs.
  
• Mark D. Robinson, Terence P. Speed:
  Differential splicing using whole-transcript microarrays.
  
• Yu-Shen Liu, Yi Fang, Karthik Ramani:
  IDSS: deformation invariant signatures for molecular shape comparison.
  
• Jaume Mercadé, Antonio Espinosa, José-Enrique Adsuara, Rosa Adrados, Jordi Segura, Tamara Maes:
  Orymold: ontology based gene expression data integration and analysis tool applied to rice.
  
• Timothy Nugent, David T. Jones:
  Transmembrane protein topology prediction using support vector machines.
  
• Tzong-Yuan Wu, Chi-Chun Hsieh, Jun-Jie Hong, Chung-Yung Chen, Yuh-Show Tsai:
  IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.
  
• Weijun Luo, Michael S. Friedman, Kerby Shedden, Kurt D. Hankenson, Peter J. Woolf:
  GAGE: generally applicable gene set enrichment for pathway analysis.
  
• Gordon W. Slysz, Charles A. H. Baker, Benjamin M. Bozsa, Anthony Dang, Andrew J. Percy, Melissa Bennett, David C. Schriemer:
  Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses.
  
• Sanghamitra Bandyopadhyay, Malay Bhattacharyya:
  Analyzing miRNA co-expression networks to explore TF-miRNA regulation.
  
• Sin-Ho Jung, Insuk Sohn, Stephen L. George, Liping Feng, Phyllis C. Leppert:
  Sample size calculation for microarray experiments with blocked one-way design.
  
• Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja, Harri Lähdesmäki:
  A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data.
  
• Kosuke M. Teshima, Hideki Innan:
  mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection.
  
• Haruo Suzuki, Rintaro Saito, Masaru Tomita:
  Measure of synonymous codon usage diversity among genes in bacteria.
  
• Vincent Le Guilloux, Peter Schmidtke, Pierre Tufféry:
  Fpocket: An open source platform for ligand pocket detection.
  
• Min Wu, Xiaoli Li, Chee-Keong Kwoh, See-Kiong Ng:
  A core-attachment based method to detect protein complexes in PPI networks.
  
• Daniel G. Pinheiro, Pedro A. F. Galante, Sandro J. de Souza, Marco A. Zago, Wilson A. Silva Jr.:
  A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.
  
• Steven W. Culman, Robert Bukowski, Hugh G. Gauch, Hinsby Cadillo-Quiroz, Daniel H. Buckley:
  T-REX: software for the processing and analysis of T-RFLP data.
  
• Juan R. González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier Estivill, Lluís Armengol:
  Accounting for uncertainty when assessing association between copy number and disease: a latent class model.
  
• Wei Sun, Michael J. Buck, Mukund Patel, Ian J. Davis:
  Improved ChIP-chip analysis by a mixture model approach.
  
• Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell:
  Combining specificity determining and conserved residues improves functional site prediction.
  
• Nils Homer, Barry Merriman, Stanley F. Nelson:
  Local alignment of two-base encoded DNA sequence.
  
• Ursula K. Frei, Bernd Wollenweber, Thomas Lübberstedt:
  "PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation.
  
• Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M. Greene, Nicole T. Perna, Jeremy D. Glasner, Guy Plunkett III, Matthew Shaker, David Pot:
  Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.
  
• Jose-Jesus Fernandez:
  TOMOBFLOW: feature-preserving noise filtering for electron tomography.
  
• Lau Sennels, Jimi-Carlo Bukowski-Wills, Juri Rappsilber:
  Improved results in proteomics by use of local and peptide-class specific false discovery rates.
  
• Helen I. Field, Serena A. Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M. Dunning, Douglas F. Easton, Paul D. P. Pharoah:
  Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design.
  
• Steffen Klamt, Axel von Kamp:
  Computing paths and cycles in biological interaction graphs.
  
• Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich:
  Structural motifs recurring in different folds recognize the same ligand fragments.
  
• Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter:
  The textual characteristics of traditional and Open Access scientific journals are similar.
  
• Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R. Jones, Frank J. Manion, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan R. Brinkman:
  FuGEFlow: data model and markup language for flow cytometry.
  
• Michael H. T. Li, Peter M. U. Ung, James Zajkowski, Sylvie Garneau-Tsodikova, David H. Sherman:
  Automated genome mining for natural products.
  
• Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, Joachim L. Schultze:
  The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays.
  
• Daniel Glez-Peña, Fernando Díaz, Jesús M. Hernández, Juan M. Corchado, Florentino Fdez-Riverola:
  geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research.
  
• Yang Li, Morris A. Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C. Jansen:
  designGG: an R-package and web tool for the optimal design of genetical genomics experiments.
  
• Rose Du, Kelan Tantisira, Vincent J. Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T. Kho, Barbara J. Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J. Mariani, J. Steven Leeder, Scott T. Weiss:
  Platform dependence of inference on gene-wise and gene-set involvement in human lung development.
  
• Tingzhe Sun, Chun Chen, Yuanyuan Wu, Shuai Zhang, Jun Cui, Pingping Shen:
  Modeling the role of p53 pulses in DNA damage- induced cell death decision.
  
• Brian E. Howard, Beate Sick, Steffen Heber:
  Unsupervised assessment of microarray data quality using a Gaussian mixture model.
  
• Man-Ping Ng, Ismael A. Vergara, Christian Frech, Qingkang Chen, Xinghuo Zeng, Jian Pei, Nansheng Chen:
  OrthoClusterDB: an online platform for synteny blocks.
  
• David Tritchler, Elena Parkhomenko, Joseph Beyene:
  Filtering Genes for Cluster and Network Analysis.
  
• Otávio J. B. Brustolini, Luciano G. Fietto, Cosme D. Cruz, Flávia M. L. Passos:
  Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis.
  
• Ian Walsh, Alberto J. M. Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri:
  Ab initio and homology based prediction of protein domains by recursive neural networks.
  
• Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder:
  Triangle network motifs predict complexes by complementing high-error interactomes with structural information.
  
• Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander:
  ResBoost: characterizing and predicting catalytic residues in enzymes.
  
• Shane T. Jensen, Sameer Soi, Li-San Wang:
  A Bayesian approach to efficient differential allocation for resampling-based significance testing.
  
• Tomás Hirmajer, Eva Balsa-Canto, Julio R. Banga:
  DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
  
• Ming Yi, Uma Mudunuri, Anney Che, Robert M. Stephens:
  Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.
  
• Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi:
  A-MADMAN: Annotation-based microarray data meta-analysis tool.
  
• Alex N. Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, Alan M. Moses:
  NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
  
• Renée X. de Menezes, Marten Boetzer, Melle Sieswerda, Gert-Jan B. van Ommen, Judith M. Boer:
  Integrated analysis of DNA copy number and gene expression microarray data using gene sets.
  
• Ho-Ryun Chung, Martin Vingron:
  Comparison of sequence-dependent tiling array normalization approaches.
  
• Tsutomu Matsunaga, Chikara Yonemori, Etsuji Tomita, Masaaki Muramatsu:
  Clique-based data mining for related genes in a biomedical database.
  
• Jia Zeng, Reda Alhajj, Douglas J. Demetrick:
  Representative transcript sets for evaluating a translational initiation sites predictor.
  
• Saikat Chakrabarti, Anna R. Panchenko:
  Ensemble approach to predict specificity determinants: benchmarking and validation.
  
• Amar Drawid, Nupur Gupta, Vijayalakshmi H. Nagaraj, Céline Gélinas, Anirvan M. Sengupta:
  OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.
  
• Antonio Carvajal-Rodríguez, Jacobo de Uña-Álvarez, Emilio Rolán-Alvarez:
  A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests.
  
• Changhoon Kim, Chin-Hsien Tai, Byungkook Lee:
  Iterative refinement of structure-based sequence alignments by Seed Extension.
  
• Richard D. Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D. Lawrence, Magnus Rattray:
  puma: a Bioconductor package for propagating uncertainty in microarray analysis.
  
• Lee Aaron Newberg:
  Error statistics of hidden Markov model and hidden Boltzmann model results.
  
• Bjoern H. Menze, B. Michael Kelm, Ralf Masuch, Uwe Himmelreich, Peter Bachert, Wolfgang Petrich, Fred A. Hamprecht:
  A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data.
  
• Jérôme Hennetin, Petri Pehkonen, Michel Bellis:
  Construction and use of gene expression covariation matrix.
  
• Sivakumar Gowrisankar, Anil G. Jegga:
  Regression based predictor for p53 transactivation.
  
• Lusheng Wang, Zhanyong Wang, Wanling Yang:
  Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference.
  
• Serdar Bozdag, Timothy J. Close, Stefano Lonardi:
  A compartmentalized approach to the assembly of physical maps.
  
• John E. Reid, Sascha Ott, Lorenz Wernisch:
  Transcriptional programs: Modelling higher order structure in transcriptional control.
  
• Fabian Schreiber, Kerstin Pick, Dirk Erpenbeck, Gert Wörheide, Burkhard Morgenstern:
  OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.
  
• Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz:
  Algorithm of OMA for large-scale orthology inference.
  
• Jan Aerts, Andy Law:
  An introduction to scripting in Ruby for biologists.
  
• James R. Green, Michael J. Korenberg, Mohammed O. Aboul-Magd:
  PCI-SS: MISO dynamic nonlinear protein secondary structure prediction.
  
• Yanpeng Li, Hongfei Lin, Zhihao Yang:
  Incorporating rich background knowledge for gene named entity classification and recognition.
  
• Fernando Garcia, Francisco J. Lopez, Carlos Cano, Armando Blanco:
  FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral.
  
• Wei Zhao, Kirk E. Hevener, Stephen W. White, Richard E. Lee, James M. Boyett:
  A statistical framework to evaluate virtual screening.
  
• Daniel Jameson, David A. Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G. Spiller, Stephen G. Oliver, Michael R. H. White, Douglas B. Kell, Norman W. Paton:
  Information management for high content live cell imaging.
  
• John Draper, David P. Enot, David Parker, Manfred Beckmann, Stuart Snowdon, Wanchang Lin, Hassan Zubair:
  Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'.
  
• Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael Müller, Paul W. Sternberg:
  Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation.
  
• Bernhard Thielen, Stephanie Heinen, Dietmar Schomburg:
  mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics.
  
• Francisco Fernandes, Luísa Pereira, Ana T. Freitas:
  CSA: An efficient algorithm to improve circular DNA multiple alignment.
  
• Daniel Faria, António E. N. Ferreira, André O. Falcão:
  Enzyme classification with peptide programs: a comparative study.
  
• Yuanxin Xi, Wei Li:
  BSMAP: whole genome bisulfite sequence MAPping program.
  
• Renata Kabiljo, Andrew B. Clegg, Adrian J. Shepherd:
  A realistic assessment of methods for extracting gene/protein interactions from free text.
  
• Johannes M. Freudenberg, Vinnet K. Joshi, Zhen Hu, Mario Medvedovic:
  CLEAN: CLustering Enrichment ANalysis.
  
• Christian Schwager, Amir Abdollahi, Ute Wirkner, Peter Huber:
  TableButler - A tool for combining, handling and processing of huge data tables.
  
• Shu-Dong Zhang, Timothy W. Gant:
  sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures.
  
• Yiyuan She, Earl Hubbell, Hui Wang:
  Resolving deconvolution ambiguity in gene alternative splicing.
  
• Feng Qi, Ranjan K. Dash, Yu Han, Daniel A. Beard:
  Generating rate equations for complex enzyme systems by a computer-assisted systematic method.
  
• Roberto T. Arrial, Roberto C. Togawa, Marcelo M. Brigido:
  Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis.
  
• Tao Xu, Jianlei Gu, Yan Zhou, LinFang Du:
  Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology.
  
• Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein:
  Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
  
• Richard S. Savage, Katherine A. Heller, Yang Xu, Zoubin Ghahramani, William M. Truman, Murray Grant, Katherine J. Denby, David L. Wild:
  R/BHC: fast Bayesian hierarchical clustering for microarray data.
  
• Chris Thachuk, Jose Crossa, Jorge Franco, Susanne Dreisigacker, Marilyn Warburton, Guy F. Davenport:
  Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures.
  
• Jason W. H. Wong, Alexander B. Schwahn, Kevin M. Downard:
  ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics.
  
• Flavien Quintus, Olivier Sperandio, Julien Grynberg, Michel Petitjean, Pierre Tufféry:
  Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
  
• Katrijn Van Deun, Age K. Smilde, Mariet J. van der Werf, Henk A. L. Kiers, Iven Van Mechelen:
  A structured overview of simultaneous component based data integration.
  
• Bjarne Knudsen, Michael M. Miyamoto:
  Accurate and fast methods to estimate the population mutation rate from error prone sequences.
  
• David J. Jeffries, Neil Abernethy, Bouke C. de Jong:
  Supervised learning for the automated transcription of spacer classification from spoligotype films.
  
• Wenjie Shu, Ming Ni, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
  EvoRSR: an integrated system for exploring evolution of RNA structural robustness.
  
• Michael Hartung, Toralf Kirsten, Anika Gross, Erhard Rahm:
  OnEX: Exploring changes in life science ontologies.
  
• Igor A. Sidorov, Denis A. Reshetov, Alexander E. Gorbalenya:
  SNAD: Sequence Name Annotation-based Designer.
  
• Trevor Paterson, Andy Law:
  An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.
  
• Dejan Stokic, Rudolf Hanel, Stefan Thurner:
  A fast and efficient gene-network reconstruction method from multiple over-expression experiments.
  
• Christopher W. Maier, Jeffrey G. Long, Bradley M. Hemminger, Morgan C. Giddings:
  Ultra-Structure database design methodology for managing systems biology data and analyses.
  
• Alain B. Tchagang, Kevin V. Bui, Thomas McGinnis, Panayiotis V. Benos:
  Extracting biologically significant patterns from short time series gene expression data.
  
• Xue Lin, Bahman Asfari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Q. Naiman, Donald Geman:
  The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.
  
• Tao Xu, Lujia Zhang, Xuedong Wang, Dongzhi Wei, Tianbi Li:
  Structure-based substrate screening for an enzyme.