Volume 11, 2010

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  Shuangge Ma, Michael R. Kosorok: Detection of gene pathways with predictive power for breast cancer prognosis. 1
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  Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel, Dragi Kocev, Saso Dzeroski: Predicting gene function using hierarchical multi-label decision tree ensembles. 2
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  Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant: State of the art: refinement of multiple sequence alignments. 3
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  Karel Zimmermann, Jean-François Gibrat: Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors. 4
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  Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo: The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. 5
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  Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren: A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. 6
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  Ben C. Stöver, Kai F. Müller: TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. 7
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  Roberto Amato, Michele Pinelli, Daniel D'Andrea, Gennaro Miele, Mario Nicodemi, Giancarlo Raiconi, Sergio Cocozza: A novel approach to simulate gene-environment interactions in complex diseases. 8
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  Benjamin Georgi, Ivan Gesteira Costa, Alexander Schliep: PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. 9
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  Guanqun Shi, Liqing Zhang, Tao Jiang: MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. 10
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  Jingjing Ye, Adam Pavlícek, Elizabeth A. Lunney, Paul A. Rejto, Chi-Hse Teng: Statistical method on nonrandom clustering with application to somatic mutations in cancer. 11
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  Helen A. Arcuri, Geraldo F. D. Zafalon, Evandro A. Marucci, Carlos E. Bonalumi, Nelson J. F. da Silveira, José M. Machado, Walter F. de Azevedo Jr., Mário S. Palma: SKPDB: a structural database of shikimate pathway enzymes. 12
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  Nysia I. George, Joanne R. Lupton, Nancy D. Turner, Robert S. Chapkin, Laurie A. Davidson, Naisyin Wang: Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach. 13
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  Norman E. Davey, Richard J. Edwards, Denis C. Shields: Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. 14
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  Joseph M. Dale, Liviu Popescu, Peter D. Karp: Machine learning methods for metabolic pathway prediction. 15
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  Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, Armita Sheari: A pairwise residue contact area-based mean force potential for discrimination of native protein structure. 16
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  Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, Eric Depiereux: A benchmark for statistical microarray data analysis that preserves actual biological and technical variance. 17
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  David Edwards, Gabriel C. G. de Abreu, Rodrigo Labouriau: Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests. 18
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  Esteban Czwan, Benedikt Brors, David Kipling: Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets. 19
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  Michael Scharfe, Rainer Pielot, Falk Schreiber: Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets. 20
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  Carl Kingsford, Michael C. Schatz, Mihai Pop: Assembly complexity of prokaryotic genomes using short reads. 21
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  Alexander G. Churbanov, Igor Vorechovsky, Chindo Hicks: A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. 22
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  Thomas K. Wolfgruber, Gernot G. Presting: JunctionViewer: customizable annotation software for repeat-rich genomic regions. 23
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  Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón: ETE: a python Environment for Tree Exploration. 24
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  Shuai Cheng Li, Yen Kaow Ng: Calibur: a tool for clustering large numbers of protein decoys. 25
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  Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen: Detecting disease associated modules and prioritizing active genes based on high throughput data. 26
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  Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F. Black, Joachim Selbig, Shreemanta K. Parida, Stefan H. E. Kaufmann, Marc Jacobsen: Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. 27
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  Shi Yu, Léon-Charles Tranchevent, Bart De Moor, Yves Moreau: Gene prioritization and clustering by multi-view text mining. 28
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  Anders Jacobsen, Anders Krogh, Sakari Kauppinen, Morten Lindow: miRMaid: a unified programming interface for microRNA data resources. 29
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  Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C. Schlumberger, Samuel Rout, Péter Horváth, Karol Kozak, Wolf-Dietrich Hardt: Enhanced CellClassifier: a multi-class classification tool for microscopy images. 30
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  Sheng He, Juan Mei, Guiyang Shi, Zhengxiang Wang, Weijiang Li: LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB. 31
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  Seyed Yahya Anvar, Peter A. C. 't Hoen, Allan Tucker: The identification of informative genes from multiple datasets with increasing complexity. 32
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  Lance E. Palmer, Mathäus Dejori, Randall A. Bolanos, Daniel P. Fasulo: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. 33
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  Harald Barsnes, Richard G. Côté, Ingvar Eidhammer, Lennart Martens: OLS Dialog: An open-source front end to the Ontology Lookup Service. 34
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  Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil: Hybridization thermodynamics of NimbleGen Microarrays. 35
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  Junbai Wang, Tianhai Tian: Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. 36
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  Dominik Heider, Jens Verheyen, Daniel Hoffmann: Predicting Bevirimat resistance of HIV-1 from genotype. 37
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  Juan Falgueras, Antonio J. Lara, Noé Fernández-Pozo, Francisco R. Cantón, Guillermo Pérez-Trabado, M. Gonzalo Claros: SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. 38
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  Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, Anna Tramontano: An automatic method for identifying surface proteins in bacteria: SLEP. 39
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  Yaqiang Wang, Zhonghua Yu, Yongguang Jiang, Kaikuo Xu, Xia Chen: Automatic symptom name normalization in clinical records of traditional Chinese medicine. 40
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  Andrew J. Bordner, Hans D. Mittelmann: Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. 41
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  Russell Schwartz, Stanley Shackney: Applying unmixing to gene expression data for tumor phylogeny inference. 42
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  Tamir Tuller, Yifat Felder, Martin Kupiec: Discovering local patterns of co - evolution: computational aspects and biological examples. 43
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  Ulrike Naumann, George Luta, Matthew P. Wand: The curvHDR method for gating flow cytometry samples. 44
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  Satwik Rajaram, Yoshi Oono: NeatMap - non-clustering heat map alternatives in R. 45
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  Svetlana Bulashevska, Alla Bulashevska, Roland Eils: Bayesian statistical modelling of human protein interaction network incorporating protein disorder information. 46
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  Bing Xiong, Jie Wu, David L. Burk, Mengzhu Xue, Hualiang Jiang, Jingkang Shen: BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. 47
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  Wei-Jiun Lin, Huey-miin Hsueh, James J. Chen: Power and sample size estimation in microarray studies. 48
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  Dimitris G. Bariamis, Dimitrios K. Iakovidis, Dimitris Maroulis: M³G: Maximum Margin Microarray Gridding. 49
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  Taeho Hwang, Choong-Hyun Sun, Taegyun Yun, Gwan-Su Yi: FiGS: a filter-based gene selection workbench for microarray data. 50
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  Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin: SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. 51
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  Jeremy D. Selengut, Douglas B. Rusch, Daniel H. Haft: Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. 52
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  Yu-Chao Wang, Chung-Yu Lan, Wen-Ping Hsieh, Luis A. Murillo, Nina Agabian, Bor-Sen Chen: Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. 53
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  Jaebum Kim, Saurabh Sinha: Towards realistic benchmarks for multiple alignments of non-coding sequences. 54
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  Byron C. Wallace, Thomas A. Trikalinos, Joseph Lau, Carla E. Brodley, Christopher H. Schmid: Semi-automated screening of biomedical citations for systematic reviews. 55
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  Javier Garcia-Garcia, Emre Guney, Ramon Aragues, Joan Planas-Iglesias, Baldo Oliva: Biana: a software framework for compiling biological interactions and analyzing networks. 56
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  Pankaj Khurana, Rajesh S. Gokhale, Debasisa Mohanty: Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles. 57
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  Benjamin A. Logsdon, Gabriel E. Hoffman, Jason G. Mezey: A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis. 58
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  Alina Sîrbu, Heather J. Ruskin, Martin Crane: Comparison of evolutionary algorithms in gene regulatory network model inference. 59
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  Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole Yauk: Testing for mean and correlation changes in microarray experiments: an application for pathway analysis. 60
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  Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu, Fuchu He: Computational identification of rare codons of Escherichia coli based on codon pairs preference. 61
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  Yunqi Li, C. Russell Middaugh, Jianwen Fang: A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. 62
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  Corey M. Yanofsky, David R. Bickel: Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing. 63
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  Evgeniy V. Petrotchenko, Christoph H. Borchers: ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. 64
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  Julie Hussin, Philippe Nadeau, Jean-François Lefebvre, Damian Labuda: Haplotype allelic classes for detecting ongoing positive selection. 65
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  Guimei Liu, Yue Wang, Limsoon Wong: FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. 66
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  Ronald van Eijk, Paul H. C. Eilers, Remco Natté, Anne-Marie Cleton-Jansen, Hans Morreau, Tom van Wezel, Jan Oosting: MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification. 67
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  Ritesh Krishna, Chang-Tsun Li, Vicky Buchanan-Wollaston: A temporal precedence based clustering method for gene expression microarray data. 68
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  Bram Slabbinck, Willem Waegeman, Peter Dawyndt, Paul De Vos, Bernard De Baets: From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification. 69
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  Adriano Barbosa-Silva, Theodoros G. Soldatos, Ivan L. F. Magalhães, Georgios A. Pavlopoulos, Jean-Fred Fontaine, Miguel A. Andrade-Navarro, Reinhard Schneider, J. Miguel Ortega: LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. 70
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  Ivaylo Ilinkin, Jieping Ye, Ravi Janardan: Multiple structure alignment and consensus identification for proteins. 71
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  Russell L. Zaretzki, Michael A. Gilchrist, William M. Briggs, Artin Armagan: Bias correction and Bayesian analysis of aggregate counts in SAGE libraries. 72
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  Mark J. Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini: BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets. 73
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  Xiaowu Gai, Juan C. Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M. Xie, Eric F. Rappaport, Tamim H. Shaikh, Peter S. White: CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. 74
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  Leslie Regad, Juliette Martin, Grégory Nuel, Anne-Claude Camproux: Mining protein loops using a structural alphabet and statistical exceptionality. 75
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  Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, Zheng Guo: Extracting consistent knowledge from highly inconsistent cancer gene data sources. 76
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  Ricardo Cao, Mario Francisco-Fernández, Emiliano J. Quinto: A random effect multiplicative heteroscedastic model for bacterial growth. 77
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  Anne-Laure Boulesteix, Torsten Hothorn: Testing the additional predictive value of high-dimensional molecular data. 78
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  Maria Pamela C. David, Gisela P. Concepcion, Eduardo A. Padlan: Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies. 79
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  Martin C. Frith, Michiaki Hamada, Paul Horton: Parameters for accurate genome alignment. 80
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  Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson, Dabing Zhang: An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. 81
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  Hedda Høvik, Tsute Chen: Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. 82
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  Aliah Hazmah Hawari, Zeti-Azura Mohamed-Hussein: Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway. 83
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  Zafer Aydin, John I. Murray, Robert H. Waterston, William Stafford Noble: 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. 84
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  Martin Gerner, Goran Nenadic, Casey M. Bergman: LINNAEUS: A species name identification system for biomedical literature. 85
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  Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst, Berend Snel: Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. 86
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  Alexander Lachmann, Avi Ma'ayan: Lists2Networks: Integrated analysis of gene/protein lists. 87
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  Yi-Ruen Lin, Hsin-Yuan Wei, Tsung-Lin Tsai, Thy-Hou Lin: HDAPD: a web tool for searching the disease-associated protein structures. 88
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  Mindaugas Margelevicius, Ceslovas Venclovas: Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. 89
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  Kirsten Roomp, Iris Antes, Thomas Lengauer: Predicting MHC class I epitopes in large datasets. 90
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  Alexander Martin, Maria Elena Ochagavía, Laya C. Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossío, Ricardo Bringas: BisoGenet: a new tool for gene network building, visualization and analysis. 91
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  Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan: Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. 92
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  Daniel MacLean, Vincent Moulton, David J. Studholme: Finding sRNA generative locales from high-throughput sequencing data with NiBLS. 93
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  James H. Bullard, Elizabeth Purdom, Kasper D. Hansen, Sandrine Dudoit: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. 94
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  Ryan Gill, Somnath Datta, Susmita Datta: A statistical framework for differential network analysis from microarray data. 95
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  Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis Shasha: SING: Subgraph search In Non-homogeneous Graphs. 96
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  Alessandro Pandini, Arianna Fornili, Jens Kleinjung: Structural alphabets derived from attractors in conformational space. 97
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  Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, Ivo Grosse: Unifying generative and discriminative learning principles. 98
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  Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, Véronique Stoven: A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. 99
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  Stacy Duncan, Ruchita Sirkanungo, Leslie Miller, Gregory J. Phillips: DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data. 100
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  Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A. Boucher, Peter M. A. Sloot: Extracting causal relations on HIV drug resistance from literature. 101
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  Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, Chin Lung Lu: Reconstructing genome trees of prokaryotes using overlapping genes. 102
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  J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne: Word add-in for ontology recognition: semantic enrichment of scientific literature. 103
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  Jakub Mieczkowski, Magdalena E. Tyburczy, Michal Dabrowski, Piotr Pokarowski: Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. 104
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  Dan C. Tulpan, Mirela Andronescu, Serge Leger: Free energy estimation of short DNA duplex hybridizations. 105
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  Sandra Ortega-Martorell, Iván Olier, Margarida Julià-Sapé, Carles Arús: SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system. 106
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  Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park: Walk-weighted subsequence kernels for protein-protein interaction extraction. 107
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  Timothy J. Robinson, Michaela A. Dinan, Mark Dewhirst, Mariano A. Garcia-Blanco, James L. Pearson: SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 108
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  Kai-Lin Tang, Tong-Hua Li, Wen-Wei Xiong, Kai Chen: Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data. 109
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  Kristin K. Nicodemus, James D. Malley, Carolin Strobl, Andreas Ziegler: The behaviour of random forest permutation-based variable importance measures under predictor correlation. 110
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  Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, Cathy S. J. Fann: Modeling expression quantitative trait loci in data combining ethnic populations. 111
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  Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler: The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. 112
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  Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, Yutaka Kuroda: Mathematical model for empirically optimizing large scale production of soluble protein domains. 113
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  Weilong Hao: OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. 114
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  Elisa Cilia, Andrea Passerini: Automatic prediction of catalytic residues by modeling residue structural neighborhood. 115
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  Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, Laurent Excoffier: ABCtoolbox: a versatile toolkit for approximate Bayesian computations. 116
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  Aaron M. Newman, James B. Cooper: AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. 117
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  Chongle Pan, Byung-Hoon Park, William H. McDonald, Patricia A. Carey, Jillian F. Banfield, Nathan Verberkmoes, Robert L. Hettich, Nagiza F. Samatova: A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. 118
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  Doug Hyatt, Gwo-Liang Chen, Philip F. LoCascio, Miriam L. Land, Frank W. Larimer, Loren J. Hauser: Prodigal: prokaryotic gene recognition and translation initiation site identification. 119
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  Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro: SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. 120
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  Florian Battke, Stephan Symons, Kay Nieselt: Mayday - integrative analytics for expression data. 121
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  Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg, Anita Brandstätter: eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. 122
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  Jennifer M. Staab, Thomas M. O'Connell, Shawn M. Gomez: Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). 123
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  Tetyana Ivanovska, Andrea Schenk, André Homeyer, Meihong Deng, Uta Dahmen, Olaf Dirsch, Horst K. Hahn, Lars Linsen: A fast and robust hepatocyte quantification algorithm including vein processing. 124
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  Aarti Garg, Rupinder Tewari, Gajendra P. S. Raghava: KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. 125
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  Martin Paluszewski, Thomas Hamelryck: Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks. 126
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  Andrew Williams, Errol M. Thomson: Effects of scanning sensitivity and multiple scan algorithms on microarray data quality. 127
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  Dmitry Rykunov, András Fiser: New statistical potential for quality assessment of protein models and a survey of energy functions. 128
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  Jessica S. Reuter, David H. Mathews: RNAstructure: software for RNA secondary structure prediction and analysis. 129
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  Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes, Stephan C. Schuster, Webb Miller: Calling SNPs without a reference sequence. 130
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  Andrew S. Warren, Jeremy S. Archuleta, Wu-chun Feng, João Carlos Setubal: Missing genes in the annotation of prokaryotic genomes. 131
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  Hsiao Ping Lee, Tzu-Fang Sheu, Chuan Yi Tang: A parallel and incremental algorithm for efficient unique signature discovery on DNA databases. 132
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  José Afonso Guerra-Assunção, Anton J. Enright: MapMi: automated mapping of microRNA loci. 133
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  Yurii S. Aulchenko, Maksim V. Struchalin, Cornelia M. van Duijn: ProbABEL package for genome-wide association analysis of imputed data. 134
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  Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer: miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. 135
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  Luis Quintales, Mar Sánchez, Francisco Antequera: Analysis of DNA strand-specific differential expression with high density tiling microarrays. 136
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  Louis Licamele, Lise Getoor: Indirect two-sided relative ranking: a robust similarity measure for gene expression data. 137
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  Mallika Veeramalai, David Gilbert, Gabriel Valiente: An optimized TOPS+ comparison method for enhanced TOPS models. 138
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  Hunter N. B. Moseley: Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. 139
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  Ioannis A. Maraziotis, Andrei Dragomir, Dimitris Thanos: Gene regulatory networks modelling using a dynamic evolutionary hybrid. 140
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  Brady Olsen, Christopher J. Murakami, Matt Kaeberlein: YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. 141
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  Kirill Kryukov, Naruya Saitou: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. 142
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  Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang: MPprimer: a program for reliable multiplex PCR primer design. 143
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  Martial Hue, Michael Riffle, Jean-Philippe Vert, William Stafford Noble: Large-scale prediction of protein-protein interactions from structures. 144
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  Bobbie-Jo M. Webb-Robertson, Kyle G. Ratuiste, Christopher S. Oehmen: Physicochemical property distributions for accurate and rapid pairwise protein homology detection. 145
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  Michael L. Sierk, Michael E. Smoot, Ellen J. Bass, William R. Pearson: Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. 146
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  Teo Shu Mei, Agus Salim, Stefano Calza, Ku Chee Seng, Kee Seng Chia, Yudi Pawitan: Identification of recurrent regions of copy-number variants across multiple individuals. 147
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  Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, Steffen Neumann: In silico fragmentation for computer assisted identification of metabolite mass spectra. 148
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  Jens Keilwagen, Jan Grau, Stefan Posch, Ivo Grosse: Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. 149
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  Sigrid Rouam, Thierry Moreau, Philippe Broët: Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes. 150
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  Pierre M. Durand, Scott Hazelhurst, Theresa L. Coetzer: Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. 151
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  James Robert White, Saket Navlakha, Niranjan Nagarajan, Mohammadreza Ghodsi, Carl Kingsford, Mihai Pop: Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. 152
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  Feng-Jie Sun, Gustavo Caetano-Anollés: The ancient history of the structure of ribonuclease P and the early origins of Archaea. 153
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  Pietro Zoppoli, Sandro Morganella, Michele Ceccarelli: TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. 154
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  Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek: Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. 155
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  Marc Hulsman, Anouk Mentink, Eugene P. van Someren, Koen J. Dechering, Jan de Boer, Marcel J. T. Reinders: Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization. 156
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  Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano: Moara: a Java library for extracting and normalizing gene and protein mentions. 157
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  Jorn R. de Haan, Ester Piek, René C. van Schaik, Jacob de Vlieg, Susanne Bauerschmidt, Lutgarde M. C. Buydens, Ron Wehrens: Integrating gene expression and GO classification for PCA by preclustering. 158
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  Thomas Kuhn, Egon L. Willighagen, Achim Zielesny, Christoph Steinbeck: CDK-Taverna: an open workflow environment for cheminformatics. 159
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  Hifzur Rahman Ansari, Gajendra P. S. Raghava: Identification of NAD interacting residues in proteins. 160
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  Israel T. da Silva, Ricardo Z. N. Vêncio, Thiago Y. K. Oliveira, Greice A. Molfetta, Wilson A. Silva Jr.: ProbFAST: Probabilistic Functional Analysis System Tool. 161
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  Chen Wang, Jianhua Xuan, Huai Li, Yue Joseph Wang, Ming Zhan, Eric P. Hoffman, Robert Clarke: Knowledge-guided gene ranking by coordinative component analysis. 162
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  Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian, Gad Shaulsky: New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. 163
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  Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew, Hong Yan: Multiconstrained gene clustering based on generalized projections. 164
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  Robert C. McLeay, Timothy L. Bailey: Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. 165
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  Saurin D. Jani, Gary L. Argraves, Jeremy L. Barth, W. Scott Argraves: GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. 166
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  Chi-Yuan Yu, Lih-Ching Chou, Darby Tien-Hao Chang: Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. 167
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  Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang: Using jackknife to assess the quality of gene order phylogenies. 168
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  Johann M. Kraus, Hans A. Kestler: A highly efficient multi-core algorithm for clustering extremely large datasets. 169
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  Ken Tatebe, Ahmet Zeytun, Ruy M. Ribeiro, Robert Hoffmann, Kevin S. Harrod, Christian V. Forst: Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. 170
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  Karl W. Kuschner, Dariya I. Malyarenko, William E. Cooke, Lisa H. Cazares, O. John Semmes, Eugene R. Tracy: A Bayesian network approach to feature selection in mass spectrometry data. 177
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  Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper, David P. Nickerson, Poul M. F. Nielsen: An overview of the CellML API and its implementation. 178
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  Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue, Zhi-Wei Cao, Qiang Yang: Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. 181
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  Bing Wang, Steve Valentine, Manolo Plasencia, Sriram Raghuraman, Xiang Zhang: Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. 182
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  Stephanie Zierke, Jason D. Bakos: FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods. 184
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  Oliver Pelz, Moritz Gilsdorf, Michael Boutros: web cellHTS2: A web-application for the analysis of high-throughput screening data. 185
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  Davide Sisti, Michele Guescini, Marco B. L. Rocchi, Pasquale Tibollo, Mario D'Atri, Vilberto Stocchi: Shape based kinetic outlier detection in real-time PCR. 186
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  Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li: Artificial and natural duplicates in pyrosequencing reads of metagenomic data. 187
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  Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin: Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. 188
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  Felix Sanchez-Garcia, Uri David Akavia, Eyal Mozes, Dana Pe'er: JISTIC: Identification of Significant Targets in Cancer. 189
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  Sanghamitra Bandyopadhyay, Malay Bhattacharyya: PuTmiR: A database for extracting neighboring transcription factors of human microRNAs. 190
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  Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, Magnus Fontes: Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. 191
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  Andrew J. Bordner: Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. 192
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  Tiejun Cheng, Zhihai Liu, Renxiao Wang: A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. 193
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  Benedikt Zacher, Pei Fen Kuan, Achim Tresch: Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. 194
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  Tala Bakheet, Andrew J. Doig: Properties and identification of antibiotic drug targets. 195
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  Hui-Hsien Chou: Shared probe design and existing microarray reanalysis using PICKY. 196
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  Colm Ryan, Derek Greene, Gerard Cagney, Padraig Cunningham: Missing value imputation for epistatic MAPs. 197
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  Antonio Deiana, Andrea Giansanti: Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets. 198
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  Franziska Hoffgaard, Philipp Weil, Kay Hamacher: BioPhysConnectoR: Connecting Sequence Information and Biophysical Models. 199
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  Fuhai Li, Xiaobo Zhou, Wanting Huang, Chung-Che Chang, Stephen T. C. Wong: Conditional random pattern model for copy number aberration detection. 200
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  Olof Görnerup, Martin Nilsson Jacobi: A model-independent approach to infer hierarchical codon substitution dynamics. 201
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  Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck, John M. Burke, Peter K. Sorger, Suzanne Gaudet, Do Hyun Kim: Systematic calibration of a cell signaling network model. 202
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  Pao-Yang Chen, Shawn Cokus, Matteo Pellegrini: BS Seeker: precise mapping for bisulfite sequencing. 203
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  Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert, Michael Schroeder: Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. 204
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  Kevin Horan, Christian R. Shelton, Thomas Girke: Predicting conserved protein motifs with Sub-HMMs. 205
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  Massimiliano Virgilio, Thierry Backeljau, Bruno Nevado, Marc De Meyer: Comparative performances of DNA barcoding across insect orders. 206
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  Mario Fasold, Peter F. Stadler, Hans Binder: G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. 207
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  Mike L. Smith, Mark J. Dunning, Simon Tavaré, Andy G. Lynch: Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. 208
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  Federico Plazzi, Ronald R. Ferrucci, Marco Passamonti: Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. 209
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  Subhadip Basu, Dariusz Plewczynski: AMS 3.0: prediction of post-translational modifications. 210
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  Yi Qu, Fei He, Yuchen Chen: Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. 211
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  Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira: Concept-based query expansion for retrieving gene related publications from MEDLINE. 212
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  Jan Schellenberger, Junyoung O. Park, Tom M. Conrad, Bernhard O. Palsson: BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. 213
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  Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita: Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. 214
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  Jaehee Jung, Gangman Yi, Serenella A. Sukno, Michael R. Thon: PoGO: Prediction of Gene Ontology terms for fungal proteins. 215
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  Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer: TassDB2 - A comprehensive database of subtle alternative splicing events. 216
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  Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya, Yurii S. Aulchenko: ParallABEL: an R library for generalized parallelization of genome-wide association studies. 217
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  Stuart Collins, Michail Stamatakis, Dionisios G. Vlachos: Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. 218
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  Fan Mo, Qun Mo, Yuanyuan Chen, David R. Goodlett, Leroy Hood, Gilbert S. Omenn, Song Li, Biaoyang Lin: WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. 219
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  Andreas Prlic, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose, Philip E. Bourne, J. Lynn Fink: Integration of open access literature into the RCSB Protein Data Bank using BioLit. 220
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  Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas: GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. 221
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  Andreas Bremges, Stefanie Schirmer, Robert Giegerich: Fine-tuning structural RNA alignments in the twilight zone. 222
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  Jérôme Lane, Patrice Duroux, Marie-Paule Lefranc: From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT^® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. 223
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  Ryuichiro Nakato, Osamu Gotoh: Cgaln: fast and space-efficient whole-genome alignment. 224
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  Denitsa Alamanova, Philip Stegmaier, Alexander E. Kel: Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. 225
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  Louis-Philippe Lemieux Perreault, Gregor U. Andelfinger, Géraldine Asselin, Marie-Pierre Dube: Partitioning of copy-number genotypes in pedigrees. 226
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  Hailong Meng, Andrew R. Joyce, Daniel E. Adkins, Priyadarshi Basu, Yankai Jia, Guoya Li, Tapas K. Sengupta, Barbara K. Zedler, Edward Lenn Murrelle, Edwin J. C. G. van den Oord: A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. 227
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  Luigi Cerulo, Charles Elkan, Michele Ceccarelli: Learning gene regulatory networks from only positive and unlabeled data. 228
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  Alain B. Tchagang, Alexander Gawronski, Hugo Bérubé, Sieu Phan, Fazel Famili, Youlian Pan: GOAL: A software tool for assessing biological significance of genes groups. 229
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  Christian Rohde, Yingying Zhang, Richard Reinhardt, Albert Jeltsch: BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. 230
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  Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K. Burke, Jacek Blazewicz, Ryszard W. Adamiak: RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. 231
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  Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita: Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. 232
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  Jan Krumsiek, Sebastian Pölsterl, Dominik M. Wittmann, Fabian J. Theis: Odefy -- From discrete to continuous models. 233
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  Johannes M. Freudenberg, Siva Sivaganesan, Michael Wagner, Mario Medvedovic: A semi-parametric Bayesian model for unsupervised differential co-expression analysis. 234
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  Toshihide Hara, Keiko Sato, Masanori Ohya: MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. 235
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  Nobuyuki Uchikoga, Takatsugu Hirokawa: Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. 236
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  Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. 237
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  Daniel Rios, William M. McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham: A database and API for variation, dense genotyping and resequencing data. 238
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  Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A. Smith, Stephen Trevanion: Using caching and optimization techniques to improve performance of the Ensembl website. 239
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  Jessica Severin, Kathryn Beal, Albert J. Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero: eHive: An Artificial Intelligence workflow system for genomic analysis. 240
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  Chi Kin Chow, Hai Long Zhu, Jessica Lacy, Winston Patrick Kuo: Error margin analysis for feature gene extraction. 241
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  Drew H. Bryant, Mark Moll, Brian Y. Chen, Viacheslav Fofanov, Lydia E. Kavraki: Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. 242
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  Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein: MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. 243
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  Qian Liu, Jinyan Li: Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. 244
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  Henrik Bengtsson, Pierre Neuvial, Terence P. Speed: TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. 245
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  Hong-Xuan Zhang, John Goutsias: A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems. 246
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  Huaien Luo, Juntao Li, Majid Eshaghi, Jianhua Liu, R. Krishna Murthy Karuturi: Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data. 247
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  Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Aimée M. Dudley, Lucas Pelkmans, Olli Yli-Harja: Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. 248
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  Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson: Gene bi-targeting by viral and human miRNAs. 249
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  Qi Liu, Juan Cui, Qiang Yang, Ying Xu: In-silico prediction of blood-secretory human proteins using a ranking algorithm. 250
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  Florian Teichert, Jonas Minning, Ugo Bastolla, Markus Porto: High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH. 251
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  Donald M. Gray, Carla W. Gray, Byong-Hoon Yoo, Tzu-Fang Lou: Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data. 252
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  Inna Chervoneva, Yanyan Li, Stephanie Schulz, Sean Croker, Chantell Wilson, Scott A. Waldman, Terry Hyslop: Selection of optimal reference genes for normalization in quantitative RT-PCR. 253
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  Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M. Teresa Pisabarro, Frank Buchholz: PhenoFam-gene set enrichment analysis through protein structural information. 254
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  Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu, Ying Ding, David J. Wild: Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. 255
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  Edon Sung, Sangsoo Kim, Whanchul Shin: Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. 256
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  Stephen F. Madden, Susan B. Carpenter, Ian B. Jeffery, Harry Björkbacka, Katherine A. Fitzgerald, Luke A. O'Neill, Desmond G. Higgins: Detecting microRNA activity from gene expression data. 257
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  Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, Abhijit Datta: Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. 258
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  Dennis P. Wall, Parul Kudtarkar, Vincent A. Fusaro, Rimma Pivovarov, Prasad Patil, Peter J. Tonellato: Cloud computing for comparative genomics. 259
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  Andrew N. Tolopko, John P. Sullivan, Sean D. Erickson, David Wrobel, Su L. Chiang, Katrina Rudnicki, Stewart Rudnicki, Jennifer Nale, Laura M. Selfors, Dara Greenhouse, Jeremy Muhlich, Caroline E. Shamu: Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. 260
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  Jingming Ma, Carrie Dykes, Tao Wu, Yangxin Huang, Lisa M. Demeter, Hulin Wu: vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. 261
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  Tomás Norambuena, Francisco Melo: The Protein-DNA Interface database. 262
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  Michael Riffle, Trisha N. Davis: The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. 263
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  Arnald Alonso, Antonio Julià, Raül Tortosa, Cristina Canaleta, Juan D. Cañete, Javier Ballina, Alejandro Balsa, Jesús Tornero, Sara Marsal: CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays. 264
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  Troy Hawkins, Meghana Chitale, Daisuke Kihara: Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. 265
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  Jason W. H. Wong, Alexander B. Schwahn, Kevin M. Downard: FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data. 266
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  Guofeng Meng, Axel Mosig, Martin Vingron: A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. 267
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  Miguel Arenas, Mateus Patricio, David Posada, Gabriel Valiente: Characterization of phylogenetic networks with NetTest. 268
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  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, Wim Van Criekinge: Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. 269
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  Marta Blangiardo, Alberto Cassese, Sylvia Richardson: sdef: an R package to synthesize lists of significant features in related experiments. 270
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  Shuangge Ma, Mingyu Shi, Yang Li, Danhui Yi, Ben-Chang Shia: Incorporating gene co-expression network in identification of cancer prognosis markers. 271
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  Xin He, Moushumi Sen Sarma, Xu Ling, Brant W. Chee, Chengxiang Zhai, Bruce R. Schatz: Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. 272
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  Ashis Kumer Biswas, Nasimul Noman, Abdur Rahman Sikder: Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. 273
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  Benjamin Schmid, Johannes E. Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg: A high-level 3D visualization API for Java and ImageJ. 274
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  Erdogan Taskesen, Renee Beekman, Jeroen de Ridder, Bas J. Wouters, Justine K. Peeters, Ivo P. Touw, Marcel J. T. Reinders, Ruud Delwel: HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data. 275
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  Birte Hellwig, Jan G. Hengstler, Marcus Schmidt, Mathias C. Gehrmann, Wiebke Schormann, Jörg Rahnenführer: Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. 276
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  Gad Abraham, Adam Kowalczyk, Sherene Loi, Izhak Haviv, Justin Zobel: Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. 277
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  Hong Cui: Semantic annotation of morphological descriptions: an overall strategy. 278
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  Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis: Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver. 279
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  Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panagiotis Deloukas, Simon Tavaré: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. 280
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  John R. Stevens, Jason L. Bell, Kenneth I. Aston, Kenneth L. White: A comparison of probe-level and probeset models for small-sample gene expression data. 281
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  Jose M. Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe: Optimal contact definition for reconstruction of Contact Maps. 283
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  Steven N. Steinway, Ruth Dannenfelser, Christopher D. Laucius, James E. Hayes, Sudhir Nayak: JCoDA: a tool for detecting evolutionary selection. 284
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  Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon: Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. 285
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  Mainak Guharoy, Pinak Chakrabarti: Conserved residue clusters at protein-protein interfaces and their use in binding site identification. 286
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  Conor Lawless, Darren J. Wilkinson, Alexander Young, Stephen G. Addinall, David A. Lydall: Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. 287
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  Reedik Mägi, Andrew P. Morris: GWAMA: software for genome-wide association meta-analysis. 288
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  Lars Vogt: Spatio-structural granularity of biological material entities. 289
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  Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo: Revealing and avoiding bias in semantic similarity scores for protein pairs. 290
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  Hans Binder, Knut Krohn, Conrad J. Burden: Washing scaling of GeneChip microarray expression. 291
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  Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman: TargetSpy: a supervised machine learning approach for microRNA target prediction. 292
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  Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Hai-Peng Li: Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. 293
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  Javier Tamames, Victor de Lorenzo: EnvMine: A text-mining system for the automatic extraction of contextual information. 294
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  Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arjas: Bayesian integrated modeling of expression data: a case study on RhoG. 295
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  Donghwan Lee, Woojoo Lee, Youngjo Lee, Yudi Pawitan: Super-sparse principal component analyses for high-throughput genomic data. 296
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  Irina Ostrovnaya, Gouri Nanjangud, Adam B. Olshen: A classification model for distinguishing copy number variants from cancer-related alterations. 297
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  Zhong-Ru Xie, Ming-Jing Hwang: An interaction-motif-based scoring function for protein-ligand docking. 298
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  Raghunandan M. Kainkaryam, Angela Bruex, Anna C. Gilbert, John Schiefelbein, Peter J. Woolf: poolMC: Smart pooling of mRNA samples in microarray experiments. 299
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  Assaf Gottlieb, Roy Varshavsky, Michal Linial, David Horn: UFFizi: a generic platform for ranking informative features. 300
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  Jagat Singh Chauhan, Nitish K. Mishra, Gajendra P. S. Raghava: Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. 301
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  Jiye Ai, Barry Smith, Wong T. David: Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base. 302
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  Changhoon Kim, Jodi Basner, Byungkook Lee: Detecting internally symmetric protein structures. 303
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  Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert, Steve Rounsley, David Sankoff: Scaffold filling, contig fusion and comparative gene order inference. 304
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  Leandro A. Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiya, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul T. Spellman, Bahram Parvin: Prediction of epigenetically regulated genes in breast cancer cell lines. 305
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  Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck: Beyond rotamers: a generative, probabilistic model of side chains in proteins. 306
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  Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, Peter Dittrich: Rule-based spatial modeling with diffusing, geometrically constrained molecules. 307
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  Shih Chi Peng, David Shan-Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao, Chien Hua Peng, Yung Jen Chuang, Chuan Yi Tang: Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. 308
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  Shi Yu, Tillmann Falck, Anneleen Daemen, Léon-Charles Tranchevent, Johan A. K. Suykens, Bart De Moor, Yves Moreau: L2-norm multiple kernel learning and its application to biomedical data fusion. 309
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  Kieran Alden, Stella Veretnik, Philip E. Bourne: dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. 310
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  Stephen J. Goodswen, Cedric Gondro, Nathan S. Watson-Haigh, Haja N. Kadarmideen: FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. 311
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  Paul D. Thomas: GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. 312
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  Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey Zakharov, Olga Koborova, Alexander E. Kel, Vladimir Poroikov: Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. 313
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  Osamu Komori, Shinto Eguchi: A boosting method for maximizing the partial area under the ROC curve. 314
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  Pietro Hiram Guzzi, Mario Cannataro: mu-CS: An extension of the TM4 platform to manage Affymetrix binary data. 315
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  Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, Jonathan R. Lane, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Yasushi Okuno, Andreas Bender: A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. 316
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  Amber L. Hartman, Sean Riddle, Timothy M. McPhillips, Bertram Ludäscher, Jonathan A. Eisen: WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. 317
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  Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, H.-Erich Wichmann, Günther Specht, Florian Kronenberg, Anita Kloss-Brandstätter: CONAN: copy number variation analysis software for genome-wide association studies. 318
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  Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards: Accessing the SEED genome databases via Web services API: tools for programmers. 319
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  Mirva Piippo, Niina Lietzén, Olli Nevalainen, Jussi Salmi, Tuula A. Nyman: Pripper: prediction of caspase cleavage sites from whole proteomes. 320
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  Paola M. V. Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee: An integrated Bayesian analysis of LOH and copy number data. 321
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  Emidio Capriotti, Marc A. Martí-Renom: Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. 322
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  Patrick Happel, Kerstin Moller, Ralf Kunz, Irmgard D. Dietzel: A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy. 323
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  Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin: Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. 324
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  Zhanchao Li, Xuan Zhou, Zong Dai, Xiaoyong Zou: Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm. 325
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  Shao-Wu Zhang, Yao-Jun Li, Li Xia, Quan Pan: PPLook: an automated data mining tool for protein-protein interaction. 326
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  Svetlana Kirillova, Silvio C. E. Tosatto, Oliviero Carugo: FRASS: the web-server for RNA structural comparison. 327
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  Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin R. Schiller: MimoSA: a system for minimotif annotation. 328
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  Ivo D. Shterev, Sin-Ho Jung, Stephen L. George, Kouros Owzar: permGPU: Using graphics processing units in RNA microarray association studies. 329
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  Sebastian Bremm, Tobias Schreck, Patrick Boba, Stephanie Held, Kay Hamacher: Computing and visually analyzing mutual information in molecular co-evolution. 330
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  Ilari Scheinin, Jose A. Ferreira, Sakari Knuutila, Gerrit Meijer, Mark A. van de Wiel, Bauke Ylstra: CGHpower: exploring sample size calculations for chromosomal copy number experiments. 331
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  Hiroshi Mori, Fumito Maruyama, Ken Kurokawa: VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. 332
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  Kristoffer Illergård, Simone Callegari, Arne Elofsson: MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. 333
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  Chun-Chi Chou, M. Rajasekaran, Chinpan Chen: An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. 334
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  Kaname Kojima, Masao Nagasaki, Satoru Miyano: An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. 335
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  Marc Bruckskotten, Mario Looso, Franz Cemic, Anne Konzer, Jurgen Hemberger, Markus Kruger, Thomas Braun: PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms. 336
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  Cunlu Zou, Christophe Ladroue, Shuixia Guo, Jianfeng Feng: Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach. 337
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  Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, Kun Zhang: svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification. 338
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  Maris Lapinsh, Jarl E. S. Wikberg: Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. 339
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  Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski, Jaques Reifman: A high-throughput pipeline for the design of real-time PCR signatures. 340
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