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Correspondence Scanner calibration revisited Alexander E Pozhitkov PMCID: PMC2908103 Database SKPDB: a structural database of shikimate pathway enzymes Helen A Arcuri, Geraldo FD Zafalon, Evandro A Marucci, Carlos E Bonalumi, Nelson JF da Silveira, José M Machado, Walter F de Azevedo, Jr, and Mário S Palma PMCID: PMC2824673 HDAPD: a web tool for searching the disease-associated protein structures Yi-Ruen Lin, Hsin-Yuan Wei, Tsung-Lin Tsai, and Thy-Hou Lin PMCID: PMC2833151 eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg, and Anita Brandstätter PMCID: PMC2841209 PuTmiR: A database for extracting neighboring transcription factors of human microRNAs Sanghamitra Bandyopadhyay and Malay Bhattacharyya PMCID: PMC2873535 BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Jan Schellenberger, Junyoung O Park, Tom M Conrad, and Bernhard Ø Palsson PMCID: PMC2874806 TassDB2 - A comprehensive database of subtle alternative splicing events Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, and Matthias Platzer PMCID: PMC2878309 GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs Alberto Risueño, Celia Fontanillo, Marcel E Dinger, and Javier De Las Rivas PMCID: PMC2875241 RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K Burke, Jacek Blazewicz, and Ryszard W Adamiak PMCID: PMC2873543 The Protein-DNA Interface database Tomás Norambuena and Francisco Melo PMCID: PMC2885377 The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images Michael Riffle and Trisha N Davis PMCID: PMC2882934 FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh, and Haja N Kadarmideen PMCID: PMC2901372 KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes Stephanie Heinen, Bernhard Thielen, and Dietmar Schomburg PMCID: PMC2912889 The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets Adam J Carroll, Murray R Badger, and A Harvey Millar PMCID: PMC2912306 CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies Yoji Nakamura, Tomoyoshi Komiyama, Motoki Furue, Takashi Gojobori, and Yasuto Akiyama PMCID: PMC2919518 Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database Wei-Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun-Yi Shu, Yun-Shien Lee, Tzu-Hao Wang, Ji-Hong Hong, Chia-Yang Li, and Ian C Hsu PMCID: PMC2928207 Research articles Predicting gene function using hierarchical multi-label decision tree ensembles Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel, Dragi Kocev, and Sašo Džeroski PMCID: PMC2824675 A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S Furey, Marie Öhman, and Jens Lagergren PMCID: PMC2831006 Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins Norman E Davey, Richard J Edwards, and Denis C Shields PMCID: PMC2819990 A pairwise residue contact area-based mean force potential for discrimination of native protein structure Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, and Armita Sheari PMCID: PMC2821318 Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets Michael Scharfe, Rainer Pielot, and Falk Schreiber PMCID: PMC2821319 Assembly complexity of prokaryotic genomes using short reads Carl Kingsford, Michael C Schatz, and Mihai Pop PMCID: PMC2821320 Detecting disease associated modules and prioritizing active genes based on high throughput data Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen PMCID: PMC2825224 The identification of informative genes from multiple datasets with increasing complexity S Yahya Anvar, Peter AC 't Hoen, and Allan Tucker PMCID: PMC2822754 Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction Lance E Palmer, Mathaeus Dejori, Randall Bolanos, and Daniel Fasulo PMCID: PMC2824677 Hybridization thermodynamics of NimbleGen Microarrays Ulrike Mueckstein, Germán G Leparc, Alexandra Posekany, Ivo Hofacker, and David P Kreil PMCID: PMC2823707 Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53 Junbai Wang and Tianhai Tian PMCID: PMC2832896 Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model Andrew J Bordner and Hans D Mittelmann PMCID: PMC2828437 Bayesian statistical modelling of human protein interaction network incorporating protein disorder information Svetlana Bulashevska, Alla Bulashevska, and Roland Eils PMCID: PMC2831004 M3G: Maximum Margin Microarray Gridding Dimitris Bariamis, Dimitris K Iakovidis, and Dimitris Maroulis PMCID: PMC2823709 Global screening of potential Candida albicans biofilm-related transcription factors via network comparison Yu-Chao Wang, Chung-Yu Lan, Wen-Ping Hsieh, Luis A Murillo, Nina Agabian, and Bor-Sen Chen PMCID: PMC2842261 Towards realistic benchmarks for multiple alignments of non-coding sequences Jaebum Kim and Saurabh Sinha PMCID: PMC2823711 Semi-automated screening of biomedical citations for systematic reviews Byron C Wallace, Thomas A Trikalinos, Joseph Lau, Carla Brodley, and Christopher H Schmid PMCID: PMC2824679 Comparison of evolutionary algorithms in gene regulatory network model inference Alina Sîrbu, Heather J Ruskin, and Martin Crane PMCID: PMC2831005 Computational identification of rare codons of Escherichia coli based on codon pairs preference Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu, and Fuchu He PMCID: PMC2828438 A temporal precedence based clustering method for gene expression microarray data Ritesh Krishna, Chang-Tsun Li, and Vicky Buchanan-Wollaston PMCID: PMC2841598 From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification Bram Slabbinck, Willem Waegeman, Peter Dawyndt, Paul De Vos, and Bernard De Baets PMCID: PMC2828439 Mining protein loops using a structural alphabet and statistical exceptionality Leslie Regad, Juliette Martin, Gregory Nuel, and Anne-Claude Camproux PMCID: PMC2833150 Extracting consistent knowledge from highly inconsistent cancer gene data sources Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, and Zheng Guo PMCID: PMC2832783 Parameters for accurate genome alignment Martin C Frith, Michiaki Hamada, and Paul Horton PMCID: PMC2829014 An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, and Dabing Zhang PMCID: PMC2831849 Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway Aliah Hazmah Hawari and Zeti-Azura Mohamed-Hussein PMCID: PMC2838867 Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo Zafer Aydin, John I Murray, Robert H Waterston, and William S Noble PMCID: PMC2838868 LINNAEUS: A species name identification system for biomedical literature Martin Gerner, Goran Nenadic, and Casey M Bergman PMCID: PMC2836304 Enrichment of homologs in insignificant BLAST hits by co-complex network alignment Like Fokkens, Sandra MC Botelho, Jos Boekhorst, and Berend Snel PMCID: PMC2836305 Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison Mindaugas Margelevičius and Česlovas Venclovas PMCID: PMC2837030 Predicting MHC class I epitopes in large datasets Kirsten Roomp, Iris Antes, and Thomas Lengauer PMCID: PMC2836306 Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments James H Bullard, Elizabeth Purdom, Kasper D Hansen, and Sandrine Dudoit PMCID: PMC2838869 Structural alphabets derived from attractors in conformational space Alessandro Pandini, Arianna Fornili, and Jens Kleinjung PMCID: PMC2838871 A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, and Véronique Stoven PMCID: PMC2838872 Extracting causal relations on HIV drug resistance from literature Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A Boucher, and Peter MA Sloot PMCID: PMC2841207 Reconstructing genome trees of prokaryotes using overlapping genes Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, and Chin Lung Lu PMCID: PMC2845580 Free energy estimation of short DNA duplex hybridizations Dan Tulpan, Mirela Andronescu, and Serge Leger PMCID: PMC2837027 Walk-weighted subsequence kernels for protein-protein interaction extraction Seonho Kim, Juntae Yoon, Jihoon Yang, and Seog Park PMCID: PMC2844389 Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data Kai-Lin Tang, Tong-Hua Li, Wen-Wei Xiong, and Kai Chen PMCID: PMC2846906 The behaviour of random forest permutation-based variable importance measures under predictor correlation Kristin K Nicodemus, James D Malley, Carolin Strobl, and Andreas Ziegler PMCID: PMC2848005 Modeling expression quantitative trait loci in data combining ethnic populations Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, and Cathy SJ Fann PMCID: PMC2844390 Mathematical model for empirically optimizing large scale production of soluble protein domains Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, and Yutaka Kuroda PMCID: PMC2843616 Automatic prediction of catalytic residues by modeling residue structural neighborhood Elisa Cilia and Andrea Passerini PMCID: PMC2844391 A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry Chongle Pan, Byung H Park, William H McDonald, Patricia A Carey, Jillian F Banfield, Nathan C VerBerkmoes, Robert L Hettich, and Nagiza F Samatova PMCID: PMC2838866 Effects of scanning sensitivity and multiple scan algorithms on microarray data quality Andrew Williams and Errol M Thomson PMCID: PMC2846908 New statistical potential for quality assessment of protein models and a survey of energy functions Dmitry Rykunov and Andras Fiser PMCID: PMC2853469 Analysis of DNA strand-specific differential expression with high density tiling microarrays Luis Quintales, Mar Sánchez, and Francisco Antequera PMCID: PMC2858035 Gene regulatory networks modelling using a dynamic evolutionary hybrid Ioannis A Maraziotis, Andrei Dragomir, and Dimitris Thanos PMCID: PMC2848237 Large-scale prediction of protein-protein interactions from structures Martial Hue, Michael Riffle, Jean-Philippe Vert, and William S Noble PMCID: PMC2845582 Identification of recurrent regions of copy-number variants across multiple individuals Teo Shu Mei, Agus Salim, Stefano Calza, Ku Chee Seng, Chia Kee Seng, and Yudi Pawitan PMCID: PMC2851607 Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis Jens Keilwagen, Jan Grau, Stefan Posch, and Ivo Grosse PMCID: PMC2859755 Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes Sigrid Rouam, Thierry Moreau, and Philippe Broët PMCID: PMC2863163 Alignment and clustering of phylogenetic markers - implications for microbial diversity studies James R White, Saket Navlakha, Niranjan Nagarajan, Mohammad-Reza Ghodsi, Carl Kingsford, and Mihai Pop PMCID: PMC2859756 The ancient history of the structure of ribonuclease P and the early origins of Archaea Feng-Jie Sun and Gustavo Caetano-Anollés PMCID: PMC2858038 Integrating gene expression and GO classification for PCA by preclustering Jorn R De Haan, Ester Piek, Rene C van Schaik, Jacob de Vlieg, Susanne Bauerschmidt, Lutgarde MC Buydens, and Ron Wehrens PMCID: PMC2860362 Identification of NAD interacting residues in proteins Hifzur R Ansari and Gajendra PS Raghava PMCID: PMC2853471 New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian, and Gad Shaulsky PMCID: PMC2873529 Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data Robert C McLeay and Timothy L Bailey PMCID: PMC2868005 Predicting protein-protein interactions in unbalanced data using the primary structure of proteins Chi-Yuan Yu, Lih-Ching Chou, and Darby Tien-Hao Chang PMCID: PMC2868006 Using jackknife to assess the quality of gene order phylogenies Jian Shi, Yiwei Zhang, Haiwei Luo, and Jijun Tang PMCID: PMC2858039 Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections Ken Tatebe, Ahmet Zeytun, Ruy M Ribeiro, Robert Hoffmann, Kevin S Harrod, and Christian V Forst PMCID: PMC2868837 Directionality in protein fold prediction Jonathan J Ellis, Fabien PE Huard, Charlotte M Deane, Sheenal Srivastava, and Graham R Wood PMCID: PMC2871273 APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility Jun-Feng Xia, Xing-Ming Zhao, Jiangning Song, and De-Shuang Huang PMCID: PMC2874803 Protein sequences classification by means of feature extraction with substitution matrices Rabie Saidi, Mondher Maddouri, and Engelbert Mephu Nguifo PMCID: PMC2868007 The value of position-specific priors in motif discovery using MEME Timothy L Bailey, Mikael Bodén, Tom Whitington, and Philip Machanick PMCID: PMC2868008 Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study Qi Liu, Qian Xu, Vincent W Zheng, Hong Xue, Zhiwei Cao, and Qiang Yang PMCID: PMC2873531 Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry Bing Wang, Steve Valentine, Manolo Plasencia, Sriram Raghuraman, and Xiang Zhang PMCID: PMC2874804 A robust method for estimating gene expression states using Affymetrix microarray probe level data Megu Ohtaki, Keiko Otani, Keiko Hiyama, Naomi Kamei, Kenichi Satoh, and Eiso Hiyama PMCID: PMC2873532 FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods Stephanie Zierke and Jason D Bakos PMCID: PMC2868009 Artificial and natural duplicates in pyrosequencing reads of metagenomic data Beifang Niu, Limin Fu, Shulei Sun, and Weizhong Li PMCID: PMC2874554 Integrative analysis of gene expression and copy number alterations using canonical correlation analysis Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, and Magnus Fontes PMCID: PMC2873536 Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design Andrew J Bordner PMCID: PMC2874805 Properties and identification of antibiotic drug targets Tala M Bakheet and Andrew J Doig PMCID: PMC2873537 Missing value imputation for epistatic MAPs Colm Ryan, Derek Greene, Gerard Cagney, and Pádraig Cunningham PMCID: PMC2873538 Conditional random pattern model for copy number aberration detection Fuhai Li, Xiaobo Zhou, Wanting Huang, Chung-Che Chang, and Stephen TC Wong PMCID: PMC2876128 A model-independent approach to infer hierarchical codon substitution dynamics Olof Görnerup and Martin Nilsson Jacobi PMCID: PMC2868013 Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert, and Michael Schroeder PMCID: PMC2876129 Predicting conserved protein motifs with Sub-HMMs Kevin Horan, Christian R Shelton, and Thomas Girke PMCID: PMC2879284 Comparative performances of DNA barcoding across insect orders Massimiliano Virgilio, Thierry Backeljau, Bruno Nevado, and Marc De Meyer PMCID: PMC2885370 G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration Mario Fasold, Peter F Stadler, and Hans Binder PMCID: PMC2884167 Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data Mike L Smith, Mark J Dunning, Simon Tavaré, and Andy G Lynch PMCID: PMC2880029 AMS 3.0: prediction of post-translational modifications Subhadip Basu and Dariusz Plewczynski PMCID: PMC2874555 Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays Yi Qu, Fei He, and Yuchen Chen PMCID: PMC2873539 From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences Jérôme Lane, Patrice Duroux, and Marie-Paule Lefranc PMCID: PMC2880031 Cgaln: fast and space-efficient whole-genome alignment Ryuichiro Nakato and Osamu Gotoh PMCID: PMC2873541 Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies Denitsa Alamanova, Philip Stegmaier, and Alexander Kel PMCID: PMC2879287 Learning gene regulatory networks from only positive and unlabeled data Luigi Cerulo, Charles Elkan, and Michele Ceccarelli PMCID: PMC2887423 Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, and Masaru Tomita PMCID: PMC2875242 A semi-parametric Bayesian model for unsupervised differential co-expression analysis Johannes M Freudenberg, Siva Sivaganesan, Michael Wagner, and Mario Medvedovic PMCID: PMC2876132 Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes Nobuyuki Uchikoga and Takatsugu Hirokawa PMCID: PMC2873953 Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction Drew H Bryant, Mark Moll, Brian Y Chen, Viacheslav Y Fofanov, and Lydia E Kavraki PMCID: PMC2885373 Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective Qian Liu and Jinyan Li PMCID: PMC2882391 A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems Hong-Xuan Zhang and John Goutsias PMCID: PMC2894038 Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data Huaien Luo, Juntao Li, Majid Eshaghi, Jianhua Liu, and R Krishna Murthy Karuturi PMCID: PMC2885374 In-silico prediction of blood-secretory human proteins using a ranking algorithm Qi Liu, Juan Cui, Qiang Yang, and Ying Xu PMCID: PMC2877692 High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH Florian Teichert, Jonas Minning, Ugo Bastolla, and Markus Porto PMCID: PMC2885375 Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data Donald M Gray, Carla W Gray, Byong-Hoon Yoo, and Tzu-Fang Lou PMCID: PMC2877693 Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu, Ying Ding, and David J Wild PMCID: PMC2881087 Detecting microRNA activity from gene expression data Stephen F Madden, Susan B Carpenter, Ian B Jeffery, Harry Björkbacka, Katherine A Fitzgerald, Luke A O'Neill, and Desmond G Higgins PMCID: PMC2885376 Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP Troy Hawkins, Meghana Chitale, and Daisuke Kihara PMCID: PMC2882935 Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model Xin He, Moushumi Sen Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, and Bruce Schatz PMCID: PMC2885378 Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information Ashis Kumer Biswas, Nasimul Noman, and Abdur Rahman Sikder PMCID: PMC2887807 Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes Birte Hellwig, Jan G Hengstler, Marcus Schmidt, Mathias C Gehrmann, Wiebke Schormann, and Jörg Rahnenführer PMCID: PMC2892466 Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context Gad Abraham, Adam Kowalczyk, Sherene Loi, Izhak Haviv, and Justin Zobel PMCID: PMC2895626 Semantic annotation of morphological descriptions: an overall strategy Hong Cui PMCID: PMC2887808 Conserved residue clusters at protein-protein interfaces and their use in binding site identification Mainak Guharoy and Pinak Chakrabarti PMCID: PMC2894039 Revealing and avoiding bias in semantic similarity scores for protein pairs Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, and Zheng Guo PMCID: PMC2903568 Washing scaling of GeneChip microarray expression Hans Binder, Knut Krohn, and Conrad J Burden PMCID: PMC2901370 TargetSpy: a supervised machine learning approach for microRNA target prediction Martin Sturm, Michael Hackenberg, David Langenberger, and Dmitrij Frishman PMCID: PMC2889937 Bayesian integrated modeling of expression data: a case study on RhoG Rashi Gupta, Dario Greco, Petri Auvinen, and Elja Arjas PMCID: PMC2894040 Super-sparse principal component analyses for high-throughput genomic data Donghwan Lee, Woojoo Lee, Youngjo Lee, and Yudi Pawitan PMCID: PMC2902448 A classification model for distinguishing copy number variants from cancer-related alterations Irina Ostrovnaya, Gouri Nanjangud, and Adam B Olshen PMCID: PMC2897829 poolMC: Smart pooling of mRNA samples in microarray experiments Raghunandan M Kainkaryam, Angela Bruex, Anna C Gilbert, John Schiefelbein, and Peter J Woolf PMCID: PMC2900278 UFFizi: a generic platform for ranking informative features Assaf Gottlieb, Roy Varshavsky, Michal Linial, and David Horn PMCID: PMC2893168 Detecting internally symmetric protein structures Changhoon Kim, Jodi Basner, and Byungkook Lee PMCID: PMC2894822 Scaffold filling, contig fusion and comparative gene order inference Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A Albert, Steve Rounsley, and David Sankoff PMCID: PMC2902449 Beyond rotamers: a generative, probabilistic model of side chains in proteins Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E Johansson, and Thomas Hamelryck PMCID: PMC2902450 A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization Eelke van der Horst, Julio E Peironcely, Adriaan P IJzerman, Margot W Beukers, Jonathan R Lane, Herman WT van Vlijmen, Michael TM Emmerich, Yasushi Okuno, and Andreas Bender PMCID: PMC2897831 Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach Cunlu Zou, Christophe Ladroue, Shuixia Guo, and Jianfeng Feng PMCID: PMC2897832 Software The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services Martijn P van Iersel, Alexander R Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R Conklin, and Chris T Evelo PMCID: PMC2824678 TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses Ben C Stöver and Kai F Müller PMCID: PMC2806359 PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data Benjamin Georgi, Ivan Gesteira Costa, and Alexander Schliep PMCID: PMC2823712 JunctionViewer: customizable annotation software for repeat-rich genomic regions Thomas K Wolfgruber and Gernot G Presting PMCID: PMC2824676 ETE: a python Environment for Tree Exploration Jaime Huerta-Cepas, Joaquín Dopazo, and Toni Gabaldón PMCID: PMC2820433 Calibur: a tool for clustering large numbers of protein decoys Shuai Cheng Li and Yen Kaow Ng PMCID: PMC2881085 miRMaid: a unified programming interface for microRNA data resources Anders Jacobsen, Anders Krogh, Sakari Kauppinen, and Morten Lindow PMCID: PMC2831003 Enhanced CellClassifier: a multi-class classification tool for microscopy images Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C Schlumberger, Samuel Rout, Peter Horvath, Karol Kozak, and Wolf-Dietrich Hardt PMCID: PMC2821321 LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB Sheng He, Juan Mei, Guiyang Shi, Zhengxiang Wang, and Weijiang Li PMCID: PMC2825225 OLS Dialog: An open-source front end to the Ontology Lookup Service Harald Barsnes, Richard G Côté, Ingvar Eidhammer, and Lennart Martens PMCID: PMC2823706 SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read Juan Falgueras, Antonio J Lara, Noé Fernández-Pozo, Francisco R Cantón, Guillermo Pérez-Trabado, and M Gonzalo Claros PMCID: PMC2832897 An automatic method for identifying surface proteins in bacteria: SLEP Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, and Anna Tramontano PMCID: PMC2832898 SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes Mickaël Krzeminski, Karine Loth, Rolf Boelens, and Alexandre MJJ Bonvin PMCID: PMC2823710 ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite Evgeniy V Petrotchenko and Christoph H Borchers PMCID: PMC2827373 Multiple structure alignment and consensus identification for proteins Ivaylo Ilinkin, Jieping Ye, and Ravi Janardan PMCID: PMC2829528 BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets Mark J Alston, John Seers, Jay CD Hinton, and Sacha Lucchini PMCID: PMC2829013 CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics Xiaowu Gai, Juan C Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M Xie, Eric F Rappaport, Tamim H Shaikh, and Peter S White PMCID: PMC2827374 Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays Hedda Høvik and Tsute Chen PMCID: PMC2836303 Lists2Networks: Integrated analysis of gene/protein lists Alexander Lachmann and Avi Ma'ayan PMCID: PMC2843617 Word add-in for ontology recognition: semantic enrichment of scientific literature J Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Gregory B Quinn, and Philip E Bourne PMCID: PMC2837026 SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system Sandra Ortega-Martorell, Iván Olier, Margarida Julià-Sapé, and Carles Arús PMCID: PMC2846905 The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W Hentze, Thomas Dandekar, and Martina U Muckenthaler PMCID: PMC2838865 OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs Weilong Hao PMCID: PMC2842260 ABCtoolbox: a versatile toolkit for approximate Bayesian computations Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, and Laurent Excoffier PMCID: PMC2848233 Prodigal: prokaryotic gene recognition and translation initiation site identification Doug Hyatt, Gwo-Liang Chen, Philip F LoCascio, Miriam L Land, Frank W Larimer, and Loren J Hauser PMCID: PMC2848648 SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale Tamás Nepusz, Rajkumar Sasidharan, and Alberto Paccanaro PMCID: PMC2841596 Mayday - integrative analytics for expression data Florian Battke, Stephan Symons, and Kay Nieselt PMCID: PMC2848234 Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks Martin Paluszewski and Thomas Hamelryck PMCID: PMC2848649 Calling SNPs without a reference sequence Aakrosh Ratan, Yu Zhang, Vanessa M Hayes, Stephan C Schuster, and Webb Miller PMCID: PMC2851604 MapMi: automated mapping of microRNA loci José Afonso Guerra-Assunção and Anton J Enright PMCID: PMC2858034 ProbABEL package for genome-wide association analysis of imputed data Yurii S Aulchenko, Maksim V Struchalin, and Cornelia M van Duijn PMCID: PMC2846909 miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature Haroon Naeem, Robert Küffner, Gergely Csaba, and Ralf Zimmer PMCID: PMC2845581 YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast Brady Olsen, Christopher J Murakami, and Matt Kaeberlein PMCID: PMC2850362 MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data Kirill Kryukov and Naruya Saitou PMCID: PMC2848238 MPprimer: a program for reliable multiplex PCR primer design Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, and Chenggang Zhang PMCID: PMC2858037 Moara: a Java library for extracting and normalizing gene and protein mentions Mariana L Neves, José-María Carazo, and Alberto Pascual-Montano PMCID: PMC2851609 CDK-Taverna: an open workflow environment for cheminformatics Thomas Kuhn, Egon L Willighagen, Achim Zielesny, and Christoph Steinbeck PMCID: PMC2862046 ProbFAST: Probabilistic Functional Analysis System Tool Israel T Silva, Ricardo ZN Vêncio, Thiago YK Oliveira, Greice A Molfetta, and Wilson A Silva, Jr PMCID: PMC2868004 A highly efficient multi-core algorithm for clustering extremely large datasets Johann M Kraus and Hans A Kestler PMCID: PMC2865495 SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping Hsueh-Wei Chang, Yu-Huei Cheng, Li-Yeh Chuang, and Cheng-Hong Yang PMCID: PMC2858040 An overview of the CellML API and its implementation Andrew K Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt Halstead, Jonathan Cooper, David P Nickerson, and Poul F Nielsen PMCID: PMC2858041 JISTIC: Identification of Significant Targets in Cancer Felix Sanchez-Garcia, Uri David Akavia, Eyal Mozes, and Dana Pe'er PMCID: PMC2873534 Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data Benedikt Zacher, Pei Fen Kuan, and Achim Tresch PMCID: PMC2868012 Shared probe design and existing microarray reanalysis using PICKY Hui-Hsien Chou PMCID: PMC2875240 BioPhysConnectoR: Connecting Sequence Information and Biophysical Models Franziska Hoffgaard, Philipp Weil, and Kay Hamacher PMCID: PMC2868838 BS Seeker: precise mapping for bisulfite sequencing Pao-Yang Chen, Shawn J Cokus, and Matteo Pellegrini PMCID: PMC2871274 Concept-based query expansion for retrieving gene related publications from MEDLINE Sérgio Matos, Joel P Arrais, João Maia-Rodrigues, and José Luis Oliveira PMCID: PMC2873540 Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, and Masanori Arita PMCID: PMC2879285 PoGO: Prediction of Gene Ontology terms for fungal proteins Jaehee Jung, Gangman Yi, Serenella A Sukno, and Michael R Thon PMCID: PMC2882390 ParallABEL: an R library for generalized parallelization of genome-wide association studies Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya, and Yurii S Aulchenko PMCID: PMC2879286 WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis Fan Mo, Qun Mo, Yuanyuan Chen, David R Goodlett, Leroy Hood, Gilbert S Omenn, Song Li, and Biaoyang Lin PMCID: PMC2878310 Integration of open access literature into the RCSB Protein Data Bank using BioLit Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne, and J Lynn Fink PMCID: PMC2880030 Partitioning of copy-number genotypes in pedigrees Louis-Philippe Lemieux Perreault, Gregor U Andelfinger, Géraldine Asselin, and Marie-Pierre Dubé PMCID: PMC2874807 GOAL: A software tool for assessing biological significance of genes groups Alain B Tchagang, Alexander Gawronski, Hugo Bérubé, Sieu Phan, Fazel Famili, and Youlian Pan PMCID: PMC2873542 BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences Christian Rohde, Yingying Zhang, Richard Reinhardt, and Albert Jeltsch PMCID: PMC2877691 Odefy -- From discrete to continuous models Jan Krumsiek, Sebastian Pölsterl, Dominik M Wittmann, and Fabian J Theis PMCID: PMC2873544 MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues Toshihide Hara, Keiko Sato, and Masanori Ohya PMCID: PMC2875243 A database and API for variation, dense genotyping and resequencing data Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, and Fiona Cunningham PMCID: PMC2882931 PhenoFam-gene set enrichment analysis through protein structural information Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M Teresa Pisabarro, and Frank Buchholz PMCID: PMC2881086 vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments Jingming Ma, Carrie Dykes, Tao Wu, Yangxin Huang, Lisa Demeter, and Hulin Wu PMCID: PMC2882933 Characterization of phylogenetic networks with NetTest Miguel Arenas, Mateus Patricio, David Posada, and Gabriel Valiente PMCID: PMC2880032 Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline Joachim M De Schrijver, Kim De Leeneer, Steve Lefever, Nick Sabbe, Filip Pattyn, Filip Van Nieuwerburgh, Paul Coucke, Dieter Deforce, Jo Vandesompele, Sofie Bekaert, Jan Hellemans, and Wim Van Criekinge PMCID: PMC2880033 A high-level 3D visualization API for Java and ImageJ Benjamin Schmid, Johannes Schindelin, Albert Cardona, Mark Longair, and Martin Heisenberg PMCID: PMC2896381 JCoDA: a tool for detecting evolutionary selection Steven N Steinway, Ruth Dannenfelser, Christopher D Laucius, James E Hayes, and Sudhir Nayak PMCID: PMC2887424 Colonyzer: automated quantification of micro-organism growth characteristics on solid agar Conor Lawless, Darren J Wilkinson, Alexander Young, Stephen G Addinall, and David A Lydall PMCID: PMC2901369 GWAMA: software for genome-wide association meta-analysis Reedik Mägi and Andrew P Morris PMCID: PMC2893603 dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment Kieran Alden, Stella Veretnik, and Philip E Bourne PMCID: PMC2897830 μ-CS: An extension of the TM4 platform to manage Affymetrix binary data Pietro H Guzzi and Mario Cannataro PMCID: PMC2907348 Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences Amber L Hartman, Sean Riddle, Timothy McPhillips, Bertram Ludäscher, and Jonathan A Eisen PMCID: PMC2898799 CONAN: copy number variation analysis software for genome-wide association studies Lukas Forer, Sebastian Schönherr, Hansi Weissensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg, and Anita Kloss-Brandstätter PMCID: PMC2894823 Accessing the SEED Genome Databases via Web Services API: Tools for Programmers Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens, and Robert A Edwards PMCID: PMC2900279 Pripper: prediction of caspase cleavage sites from whole proteomes Mirva Piippo, Niina Lietzén, Olli S Nevalainen, Jussi Salmi, and Tuula A Nyman PMCID: PMC2893604 PPLook: an automated data mining tool for protein-protein interaction Shao-Wu Zhang, Yao-Jun Li, Li Xia, and Quan Pan PMCID: PMC2906489 FRASS: the web-server for RNA structural comparison Svetlana Kirillova, Silvio CE Tosatto, and Oliviero Carugo PMCID: PMC2902451 MimoSA: a system for minimotif annotation Jay Vyas, Ronald J Nowling, Thomas Meusburger, David Sargeant, Krishna Kadaveru, Michael R Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, and Martin R Schiller PMCID: PMC2905367 permGPU: Using graphics processing units in RNA microarray association studies Ivo D Shterev, Sin-Ho Jung, Stephen L George, and Kouros Owzar PMCID: PMC2910023 Computing and visually analyzing mutual information in molecular co-evolution Sebastian Bremm, Tobias Schreck, Patrick Boba, Stephanie Held, and Kay Hamacher PMCID: PMC2906490 CGHpower: exploring sample size calculations for chromosomal copy number experiments Ilari Scheinin, José A Ferreira, Sakari Knuutila, Gerrit A Meijer, Mark A van de Wiel, and Bauke Ylstra PMCID: PMC2911457 VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences Hiroshi Mori, Fumito Maruyama, and Ken Kurokawa PMCID: PMC2894824 A high-throughput pipeline for the design of real-time PCR signatures Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski, and Jaques Reifman PMCID: PMC2905370 TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets Robert Schmieder, Yan Wei Lim, Forest Rohwer, and Robert Edwards PMCID: PMC2910026 TabSQL: a MySQL tool to facilitate mapping user data to public databases Xiao-Qin Xia, Michael McClelland, and Yipeng Wang PMCID: PMC2909216 ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data John C Dittmar, Robert JD Reid, and Rodney Rothstein PMCID: PMC2909220 MetaBar - a tool for consistent contextual data acquisition and standards compliant submission Wolfgang Hankeln, Pier Luigi Buttigieg, Dennis Fink, Renzo Kottmann, Pelin Yilmaz, and Frank Oliver Glöckner PMCID: PMC2912304 Flexible network reconstruction from relational databases with Cytoscape and CytoSQL Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, and Koenraad Van Leemput PMCID: PMC2910028 A flexible R package for nonnegative matrix factorization Renaud Gaujoux and Cathal Seoighe PMCID: PMC2912887 Predicting changes in protein thermostability brought about by single- or multi-site mutations Jian Tian, Ningfeng Wu, Xiaoyu Chu, and Yunliu Fan PMCID: PMC2906492 Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing David-Olivier D Azulay, Hendrik Neubert, and Mireia Fernández Ocaña PMCID: PMC2908104 SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments David B Burdick, Chris C Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, and John Boyle PMCID: PMC2916924 MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics Raphaël Helaers and Michel C Milinkovitch PMCID: PMC2912891 R-Gada: a fast and flexible pipeline for copy number analysis in association studies Roger Pique-Regi, Alejandro Cáceres, and Juan R González PMCID: PMC2915992 Integration and visualization of systems biology data in context of the genome J Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, and Nitin S Baliga PMCID: PMC2912892 GeneBrowser 2: an application to explore and identify common biological traits in a set of genes Joel P Arrais, João Fernandes, João Pereira, and José Luís Oliveira PMCID: PMC2919517 MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data Tomáš Pluskal, Sandra Castillo, Alejandro Villar-Briones, and Matej Orešič PMCID: PMC2918584 RuleMonkey: software for stochastic simulation of rule-based models Joshua Colvin, Michael I Monine, Ryan N Gutenkunst, William S Hlavacek, Daniel D Von Hoff, and Richard G Posner PMCID: PMC2921409 OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data Philip Wenig and Juergen Odermatt PMCID: PMC2920884 PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci Mali Salmon-Divon, Heidi Dvinge, Kairi Tammoja, and Paul Bertone PMCID: PMC2923140 eGIFT: Mining Gene Information from the Literature Catalina O Tudor, Carl J Schmidt, and K Vijay-Shanker PMCID: PMC2929241 Research Articles Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base Jiye Ai, Barry Smith, and David T Wong PMCID: PMC2898059 Rule-based spatial modeling with diffusing, geometrically constrained molecules Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, and Peter Dittrich PMCID: PMC2911456 An integrated Bayesian analysis of LOH and copy number data Paola MV Rancoita, Marcus Hutter, Francesco Bertoni, and Ivo Kwee PMCID: PMC2912301 Quantifying the relationship between sequence and three-dimensional structure conservation in RNA Emidio Capriotti and Marc A Marti-Renom PMCID: PMC2904352 Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm Zhanchao Li, Xuan Zhou, Zong Dai, and Xiaoyong Zou PMCID: PMC2905366 MPRAP: An accessibility predictor for a-helical transmem-brane proteins that performs well inside and outside the membrane Kristoffer Illergård, Simone Callegari, and Arne Elofsson PMCID: PMC2904353 An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking Chun-Chi Chou, M Rajasekaran, and Chinpan Chen PMCID: PMC2905368 An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information Kaname Kojima, Masao Nagasaki, and Satoru Miyano PMCID: PMC2904761 Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques Maris Lapins and Jarl ES Wikberg PMCID: PMC2910025 A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network Zhu-Hong You, Zheng Yin, Kyungsook Han, De-Shuang Huang, and Xiaobo Zhou PMCID: PMC2909217 Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays Benjamin Chain, Helen Bowen, John Hammond, Wilfried Posch, Jane Rasaiyaah, Jhen Tsang, and Mahdad Noursadeghi PMCID: PMC2909218 SOPRA: Scaffolding algorithm for paired reads via statistical optimization Adel Dayarian, Todd P Michael, and Anirvan M Sengupta PMCID: PMC2909219 Local alignment of generalized k-base encoded DNA sequence Nils Homer, Stanley F Nelson, and Barry Merriman PMCID: PMC2911458 Modular composition predicts kinase/substrate interactions Yichuan Liu and Aydin Tozeren PMCID: PMC2912303 Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation Albert Solernou and Juan Fernandez-Recio PMCID: PMC2911459 Interaction prediction and classification of PDZ domains Sibel Kalyoncu, Ozlem Keskin, and Attila Gursoy PMCID: PMC2909223 Robust probabilistic superposition and comparison of protein structures Martin Mechelke and Michael Habeck PMCID: PMC2912885 Automatic structure classification of small proteins using random forest Pooja Jain and Jonathan D Hirst PMCID: PMC2916923 Knowledge-based annotation of small molecule binding sites in proteins Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, and Thomas Madej PMCID: PMC2909224 Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster Denis C Bauer, Fabian A Buske, and Timothy L Bailey PMCID: PMC2912886 Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images Jo A Helmuth, Grégory Paul, and Ivo F Sbalzarini PMCID: PMC2919515 The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand Giovanni Capone, Giuseppe Novello, Candida Fasano, Brett Trost, Mik Bickis, Anthony Kusalik, and Darja Kanduc PMCID: PMC2919516 VIPR: A probabilistic algorithm for analysis of microbial detection microarrays Adam F Allred, Guang Wu, Tuya Wulan, Kael F Fischer, Michael R Holbrook, Robert B Tesh, and David Wang PMCID: PMC2921407 Applications of a formal approach to decipher discrete genetic networks Fabien Corblin, Eric Fanchon, and Laurent Trilling PMCID: PMC2918581 S3DB core: a framework for RDF generation and management in bioinformatics infrastructures Jonas S Almeida, Helena F Deus, and Wolfgang Maass PMCID: PMC2918582 A comparative study of conservation and variation scores Fredrik Johansson and Hiroyuki Toh PMCID: PMC2920274 Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks Lina Chen, Hong Wang, Liangcai Zhang, Wan Li, Qian Wang, Yukui Shang, Yuehan He, Weiming He, Xu Li, Jingxie Tai, and Xia Li PMCID: PMC2914056 Compartmentalization of the Edinburgh Human Metabolic Network Tong Hao, Hong-Wu Ma, Xue-Ming Zhao, and Igor Goryanin PMCID: PMC2918583 A comparison of internal validation techniques for multifactor dimensionality reduction Stacey J Winham, Andrew J Slater, and Alison A Motsinger-Reif PMCID: PMC2920275 Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression Xiaojiang Xu, Stephen Hoang, Marty W Mayo, and Stefan Bekiranov PMCID: PMC2928206 Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes Amit Zeisel, Amnon Amir, Wolfgang J Köstler, and Eytan Domany PMCID: PMC2920277 Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0) Jean-Marie Cornuet, Virgine Ravigné, and Arnaud Estoup PMCID: PMC2919520 Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information Peng Chen and Jinyan Li PMCID: PMC2921408 MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences Eduardo Corel, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, Gilles Didier, and Claudine Devauchelle PMCID: PMC2923138 Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures Petros Kountouris and Jonathan D Hirst PMCID: PMC2920885 Comparison study of microarray meta-analysis methods Anna Campain and Yee Hwa Yang PMCID: PMC2922198 Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau, Kristel van Laethem, Philippe Lemey, Ricardo J Camacho, Soo-Yon Rhee, Robert W Shafer, Eric Van Wijngaerden, and Anne-Mieke Vandamme PMCID: PMC2921410 Extracting the abstraction pyramid from complex networks Chia-Ying Cheng and Yuh-Jyh Hu PMCID: PMC2921411 The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data Junbai Wang PMCID: PMC2921412 Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data Lorenzo Beretta, Alessandro Santaniello, Piet LCM van Riel, Marieke JH Coenen, and Raffaella Scorza PMCID: PMC2928804 baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data Thomas J Hardcastle and Krystyna A Kelly PMCID: PMC2928208 Hidden Markov model speed heuristic and iterative HMM search procedure L Steven Johnson, Sean R Eddy, and Elon Portugaly PMCID: PMC2931519 Methodology Articles Detection of gene pathways with predictive power for breast cancer prognosis Shuangge Ma and Michael R Kosorok PMCID: PMC2837025 A novel approach to simulate gene-environment interactions in complex diseases Roberto Amato, Michele Pinelli, Daniel D'Andrea, Gennaro Miele, Mario Nicodemi, Giancarlo Raiconi, and Sergio Cocozza PMCID: PMC2824681 MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement Guanqun Shi, Liqing Zhang, and Tao Jiang PMCID: PMC2821317 Statistical method on nonrandom clustering with application to somatic mutations in cancer Jingjing Ye, Adam Pavlicek, Elizabeth A Lunney, Paul A Rejto, and Chi-Hse Teng PMCID: PMC2822753 Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach Nysia I George, Joanne R Lupton, Nancy D Turner, Robert S Chapkin, Laurie A Davidson, and Naisyin Wang PMCID: PMC2827371 A benchmark for statistical microarray data analysis that preserves actual biological and technical variance Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, and Eric Depiereux PMCID: PMC2831002 Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests David Edwards, Gabriel CG de Abreu, and Rodrigo Labouriau PMCID: PMC2823705 Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets Esteban Czwan, Benedikt Brors, and David Kipling PMCID: PMC2824674 Applying unmixing to gene expression data for tumor phylogeny inference Russell Schwartz and Stanley E Shackney PMCID: PMC2823708 The curvHDR method for gating flow cytometry samples Ulrike Naumann, George Luta, and Matthew P Wand PMCID: PMC2832899 Power and sample size estimation in microarray studies Wei-Jiun Lin, Huey-Miin Hsueh, and James J Chen PMCID: PMC2837028 A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis Benjamin A Logsdon, Gabriel E Hoffman, and Jason G Mezey PMCID: PMC2824680 Haplotype allelic classes for detecting ongoing positive selection Julie Hussin, Philippe Nadeau, Jean-François Lefebvre, and Damian Labuda PMCID: PMC2831848 Bias correction and Bayesian analysis of aggregate counts in SAGE libraries Russell L Zaretzki, Michael A Gilchrist, William M Briggs, and Artin Armagan PMCID: PMC2829012 A random effect multiplicative heteroscedastic model for bacterial growth Ricardo Cao, Mario Francisco-Fernández, and Emiliano J Quinto PMCID: PMC2829529 Testing the additional predictive value of high-dimensional molecular data Anne-Laure Boulesteix and Torsten Hothorn PMCID: PMC2837029 Finding sRNA generative locales from high-throughput sequencing data with NiBLS Daniel MacLean, Vincent Moulton, and David J Studholme PMCID: PMC2837031 A statistical framework for differential network analysis from microarray data Ryan Gill, Somnath Datta, and Susmita Datta PMCID: PMC2838870 SING: Subgraph search In Non-homogeneous Graphs Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, and Dennis Shasha PMCID: PMC2850364 Unifying generative and discriminative learning principles Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, and Ivo Grosse PMCID: PMC2848239 Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski, and Piotr Pokarowski PMCID: PMC2841208 SplicerAV: a tool for mining microarray expression data for changes in RNA processing Timothy J Robinson, Michaela A Dinan, Mark Dewhirst, Mariano A Garcia-Blanco, and James L Pearson PMCID: PMC2838864 AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number Aaron M Newman and James B Cooper PMCID: PMC2846907 Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS) Jennifer M Staab, Thomas M O'Connell, and Shawn M Gomez PMCID: PMC2851603 A fast and robust hepatocyte quantification algorithm including vein processing Tetyana Ivanovska, Andrea Schenk, André Homeyer, Meihong Deng, Uta Dahmen, Olaf Dirsch, Horst K Hahn, and Lars Linsen PMCID: PMC2848235 KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials Aarti Garg, Rupinder Tewari, and Gajendra PS Raghava PMCID: PMC2841597 A parallel and incremental algorithm for efficient unique signature discovery on DNA databases Hsiao Ping Lee, Tzu-Fang Sheu, and Chuan Yi Tang PMCID: PMC2848650 Indirect two-sided relative ranking: a robust similarity measure for gene expression data Louis Licamele and Lise Getoor PMCID: PMC2851605 An optimized TOPS+ comparison method for enhanced TOPS models Mallika Veeramalai, David Gilbert, and Gabriel Valiente PMCID: PMC2858036 Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry Hunter NB Moseley PMCID: PMC2848236 Physicochemical property distributions for accurate and rapid pairwise protein homology detection Bobbie-Jo M Webb-Robertson, Kyle G Ratuiste, and Christopher S Oehmen PMCID: PMC2851606 Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments Michael L Sierk, Michael E Smoot, Ellen J Bass, and William R Pearson PMCID: PMC2850363 In silico fragmentation for computer assisted identification of metabolite mass spectra Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, and Steffen Neumann PMCID: PMC2853470 Evolutionary rates at codon sites may be used to align sequences and infer protein domain function Pierre M Durand, Scott Hazelhurst, and Theresa L Coetzer PMCID: PMC2851608 TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach Pietro Zoppoli, Sandro Morganella, and Michele Ceccarelli PMCID: PMC2862045 Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization Marc Hulsman, Anouk Mentink, Eugene P van Someren, Koen J Dechering, Jan de Boer, and Marcel JT Reinders PMCID: PMC2857856 Knowledge-guided gene ranking by coordinative component analysis Chen Wang, Jianhua Xuan, Huai Li, Yue Wang, Ming Zhan, Eric P Hoffman, and Robert Clarke PMCID: PMC2865494 Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates Mehar S Khatkar, Matthew Hobbs, Markus Neuditschko, Johann Sölkner, Frank W Nicholas, and Herman W Raadsma PMCID: PMC2859757 Optimization algorithms for functional deimmunization of therapeutic proteins Andrew S Parker, Wei Zheng, Karl E Griswold, and Chris Bailey-Kellogg PMCID: PMC2873530 Shape based kinetic outlier detection in real-time PCR Davide Sisti, Michele Guescini, Marco BL Rocchi, Pasquale Tibollo, Mario D'Atri, and Vilberto Stocchi PMCID: PMC2873533 Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity Márton Münz, Rune Lyngsø, Jotun Hein, and Philip C Biggin PMCID: PMC2868010 A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction Tiejun Cheng, Zhihai Liu, and Renxiao Wang PMCID: PMC2868011 Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets Antonio Deiana and Andrea Giansanti PMCID: PMC2877690 Systematic calibration of a cell signaling network model Kyoung Ae Kim, Sabrina L Spencer, John G Albeck, John M Burke, Peter K Sorger, Suzanne Gaudet, and Do Hyun Kim PMCID: PMC2880028 Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies Federico Plazzi, Ronald R Ferrucci, and Marco Passamonti PMCID: PMC2871275 Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes Stuart Collins, Michail Stamatakis, and Dionisios G Vlachos PMCID: PMC2868014 Fine-tuning structural RNA alignments in the twilight zone Andreas Bremges, Stefanie Schirmer, and Robert Giegerich PMCID: PMC2876130 A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling Hailong Meng, Andrew R Joyce, Daniel E Adkins, Priyadarshi Basu, Yankai Jia, Guoya Li, Tapas K Sengupta, Barbara K Zedler, E Lenn Murrelle, and Edwin JCG van den Oord PMCID: PMC2876131 eHive: An Artificial Intelligence workflow system for genomic analysis Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, and Javier Herrero PMCID: PMC2885371 Error margin analysis for feature gene extraction Chi Kin Chow, Hai Long Zhu, Jessica Lacy, and Winston P Kuo PMCID: PMC2885372 MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains Hugo YK Lam, Philip M Kim, Janine Mok, Raffi Tonikian, Sachdev S Sidhu, Benjamin E Turk, Michael Snyder, and Mark B Gerstein PMCID: PMC2882932 TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays Henrik Bengtsson, Pierre Neuvial, and Terence P Speed PMCID: PMC2894037 Selection of optimal reference genes for normalization in quantitative RT-PCR Inna Chervoneva, Yanyan Li, Stephanie Schulz, Sean Croker, Chantell Wilson, Scott A Waldman, and Terry Hyslop PMCID: PMC2889935 Incorporating gene co-expression network in identification of cancer prognosis markers Shuangge Ma, Mingyu Shi, Yang Li, Danhui Yi, and Ben-Chang Shia PMCID: PMC2881088 HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data Erdogan Taskesen, Renee Beekman, Jeroen de Ridder, Bas J Wouters, Justine K Peeters, Ivo P Touw, Marcel JT Reinders, and Ruud Delwel PMCID: PMC2892465 Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver Tung T Nguyen, Richard R Almon, Debra C DuBois, William J Jusko, and Ioannis P Androulakis PMCID: PMC2889936 Data analysis issues for allele-specific expression using Illumina's GoldenGate assay Matthew E Ritchie, Matthew S Forrest, Antigone S Dimas, Caroline Daelemans, Emmanouil T Dermitzakis, Panagiotis Deloukas, and Simon Tavaré PMCID: PMC2887809 A comparison of probe-level and probeset models for small-sample gene expression data John R Stevens, Jason L Bell, Kenneth I Aston, and Kenneth L White PMCID: PMC2901368 An eScience-Bayes strategy for analyzing omics data Martin Eklund, Ola Spjuth, and Jarl ES Wikberg PMCID: PMC2887810 Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset Qianqian Zhu, Jeffrey C Miecznikowski, and Marc S Halfon PMCID: PMC2897828 EnvMine: A text-mining system for the automatic extraction of contextual information Javier Tamames and Victor de Lorenzo PMCID: PMC2901371 Prediction of epigenetically regulated genes in breast cancer cell lines Leandro A Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiyal, Diane Flaucher, Victoria EH Carlton, Martin Moorhead, Yontao Lu, Joe W Gray, Malek Faham, Paul Spellman, and Bahram Parvin PMCID: PMC2903569 Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-κB signaling-induced gene expression responses in inflammation Shih Chi Peng, David Shan Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao, Chien Hua Peng, Yung Jen Chuang, and Chuan Yi Tang PMCID: PMC2889938 L2-norm multiple kernel learning and its application to biomedical data fusion Shi Yu, Tillmann Falck, Anneleen Daemen, Leon-Charles Tranchevent, Johan AK Suykens, Bart De Moor, and Yves Moreau PMCID: PMC2906488 GIGA: a simple, efficient algorithm for gene tree inference in the genomic age Paul D Thomas PMCID: PMC2905364 A boosting method for maximizing the partial area under the ROC curve Osamu Komori and Shinto Eguchi PMCID: PMC2898798 A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy Patrick Happel, Kerstin Möller, Ralf Kunz, and Irmgard D Dietzel PMCID: PMC2912302 Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests Sophie S Abby, Eric Tannier, Manolo Gouy, and Vincent Daubin PMCID: PMC2905365 PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms Marc Bruckskotten, Mario Looso, Franz Cemiĉ, Anne Konzer, Jürgen Hemberger, Marcus Krüger, and Thomas Braun PMCID: PMC2910024 svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, and Kun Zhang PMCID: PMC2905369 Predicting nucleosome positioning using a duration Hidden Markov Model Liqun Xi, Yvonne Fondufe-Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom, and Ji-Ping Wang PMCID: PMC2900280 Metamotifs - a generative model for building families of nucleotide position weight matrices Matias Piipari, Thomas A Down, and Tim JP Hubbard PMCID: PMC2906491 Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, and Masaru Tomita PMCID: PMC2905371 Identifying differentially regulated subnetworks from phosphoproteomic data Martin Klammer, Klaus Godl, Andreas Tebbe, and Christoph Schaab PMCID: PMC2914729 Nonparametric methods for the analysis of single-color pathogen microarrays Omar J Jabado, Sean Conlan, Phenix-Lan Quan, Jeffrey Hui, Gustavo Palacios, Mady Hornig, Thomas Briese, and W Ian Lipkin PMCID: PMC2909221 Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach Marc Bailly-Bechet, Alfredo Braunstein, Andrea Pagnani, Martin Weigt, and Riccardo Zecchina PMCID: PMC2909222 Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays High Seng Chai, Terry M Therneau, Kent R Bailey, and Jean-Pierre A Kocher PMCID: PMC2910027 On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence David S Huen and Steven Russell PMCID: PMC2910723 Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse Lars Carlsson, Ola Spjuth, Samuel Adams, Robert C Glen, and Scott Boyer PMCID: PMC2912884 A factor model to analyze heterogeneity in gene expression Yuna Blum, Guillaume Le Mignon, Sandrine Lagarrigue, and David Causeur PMCID: PMC2911460 HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data Zhaohui S Qin, Jianjun Yu, Jincheng Shen, Christopher A Maher, Ming Hu, Shanker Kalyana-Sundaram, Jindan Yu, and Arul M Chinnaiyan PMCID: PMC2912305 Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images Yoshitaka Kimori, Norio Baba, and Nobuhiro Morone PMCID: PMC2914730 Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions Vladimir Potapov, Mati Cohen, Yuval Inbar, and Gideon Schreiber PMCID: PMC2912888 Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data Petr Novák, Pavel Neumann, and Jiří Macas PMCID: PMC2912890 EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias, and Chi Zhang PMCID: PMC2910724 Efficiency clustering for low-density microarrays and its application to QPCR Eric F Lock, Ryan Ziemiecke, JS Marron, and Dirk P Dittmer PMCID: PMC2912893 Deriving enzymatic and taxonomic signatures of metagenomes from short read data Uri Weingart, Erez Persi, Uri Gophna, and David Horn PMCID: PMC2922197 Robust test method for time-course microarray experiments Insuk Sohn, Kouros Owzar, Stephen L George, Sujong Kim, and Sin-Ho Jung PMCID: PMC2914731 Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes Shaoqiang Zhang, Shan Li, Phuc T Pham, and Zhengchang Su PMCID: PMC2920276 Quantized correlation coefficient for measuring reproducibility of ChIP-chip data Shouyong Peng, Mitzi I Kuroda, and Peter J Park PMCID: PMC2919519 Data reduction for spectral clustering to analyze high throughput flow cytometry data Habil Zare, Parisa Shooshtari, Arvind Gupta, and Ryan R Brinkman PMCID: PMC2923634 A method for automatically extracting infectious disease-related primers and probes from the literature Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez, and Víctor Maojo PMCID: PMC2923139 Global parameter estimation methods for stochastic biochemical systems Suresh Kumar Poovathingal and Rudiyanto Gunawan PMCID: PMC2928803 TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs Ming Lu, Bing Shi, Juan Wang, Qun Cao, and Qinghua Cui PMCID: PMC2924873 Correction State of the art: refinement of multiple sequence alignments Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen, and Stephen H Bryant PMCID: PMC2827372 Corrects: Saikat Chakrabarti, et al. State of the art: refinement of multiple sequence alignments. BMC Bioinformatics. 2006; 7: 499. Retraction Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, and Abhijit Datta PMCID: PMC2873545 Retracts: Sayak Ganguli, et al. In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. BMC Bioinformatics. 2010; 11(Suppl 1): S13. Other Issues: Journal List
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