Bioinformatics

ORIGINAL PAPER

Abstract ORIGINAL PAPER

Daniel L. Mace, Nicole Varnado, Weiping Zhang, Erwin Frise, and Uwe Ohler
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images
Bioinformatics Advance Access published on November 26, 2009.
doi:10.1093/bioinformatics/btp658
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Abstract ORIGINAL PAPER

Danzhi Huang, Ting Zhou, Karine Lafleur, Cristina Nevado, and Amedeo Caflisch
Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis
Bioinformatics Advance Access published on November 26, 2009.
doi:10.1093/bioinformatics/btp650
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Abstract ORIGINAL PAPER

Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, and Yvan Saeys
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods
Bioinformatics Advance Access published on November 25, 2009.
doi:10.1093/bioinformatics/btp630
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Abstract ORIGINAL PAPER

Bin Wang, Xiao-Feng Wang, Paul Howell, Xuemin Qian, Kun Huang, Adam I. Riker, Jingfang Ju, and Yaguang Xi
A personalized microRNA microarray normalization method using a logistic regression model
Bioinformatics Advance Access published on November 23, 2009.
doi:10.1093/bioinformatics/btp655
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Abstract ORIGINAL PAPER

Raj K. Gaire, James Bailey, Jennifer Bearfoot, Ian G. Campbell, Peter J. Stuckey, and Izhak Haviv
MIRAGAA - A methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer
Bioinformatics Advance Access published on November 23, 2009.
doi:10.1093/bioinformatics/btp654
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Abstract ORIGINAL PAPER

Nancy R. Zhang, Yasin Senbabaoglu, and Jun Z. Li
Joint Estimation of DNA Copy Number from Multiple Platforms
Bioinformatics Advance Access published on November 20, 2009.
doi:10.1093/bioinformatics/btp653
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Abstract ORIGINAL PAPER

Herbert Pang, Debayan Datta, and Hongyu Zhao
Pathway analysis using random forests with bivariate node-split for survival outcomes
Bioinformatics Advance Access published on November 18, 2009.
doi:10.1093/bioinformatics/btp640
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Abstract ORIGINAL PAPER

William Ritchie, Stephane Flamant, and John E J Rasko
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp649
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Abstract ORIGINAL PAPER

Eric R. Gamazon, Wei Zhang, Anuar Konkashbaev, Shiwei Duan, Emily O. Kistner, Dan L. Nicolae, M. Eileen Dolan, and Nancy J. Cox
SCAN: SNP and Copy number Annotation
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp644
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Abstract ORIGINAL PAPER

Yang Aijun and Song Xinyuan
Bayesian variable selection for disease classification using gene expression data
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp638
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Abstract ORIGINAL PAPER

Fenix W.D. Huang, Jing Qin, Christian M. Reidys, and Peter F. Stadler
Target prediction and a statistical sampling algorithm for RNA-RNA interaction
Bioinformatics Advance Access published on November 12, 2009.
doi:10.1093/bioinformatics/btp635
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Abstract ORIGINAL PAPER

Narendra Kumar and Debasisa Mohanty
Identification of substrates for Ser/Thr kinases using residue based statistical pair potentials
Bioinformatics Advance Access published on November 12, 2009.
doi:10.1093/bioinformatics/btp633
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Abstract ORIGINAL PAPER

Ramon Xulvi-Brunet and Hongzhe Li
Co-expression Networks: Graph Properties and Topological Comparisons
Bioinformatics Advance Access published on November 12, 2009.
doi:10.1093/bioinformatics/btp632
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Abstract ORIGINAL PAPER

Guillaume Bouvier, Nathalie Evrard-Todeschi, Jean-Pierre Girault, and Gildas Bertho
Automatic clustering of docking poses in virtual screening process using self-organising map
Bioinformatics Advance Access published on November 12, 2009.
doi:10.1093/bioinformatics/btp623
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Abstract ORIGINAL PAPER

Benilton Carvalho, Thomas A. Louis, and Rafael A. Irizarry
Quantifying Uncertainty in Genotype Calls
Bioinformatics Advance Access published on November 11, 2009.
doi:10.1093/bioinformatics/btp624
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Abstract ORIGINAL PAPER

Liam J. McGuffin and Daniel B. Roche
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
Bioinformatics Advance Access published on November 6, 2009.
doi:10.1093/bioinformatics/btp629
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Abstract ORIGINAL PAPER Stefano Volinia, Rosa Visone, Marco Galasso, Elda Rossi, and Carlo M Croce Identification of microRNA activity by Targets' Reverse EXpression Bioinformatics Advance Access published on November 6, 2009. doi:10.1093/bioinformatics/btp598 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Brian Carrillo, Corey Yanofsky, Sylvie Laboissiere, Robert Nadon, and Robert E. Kearney
Methods for combining peptide intensities to estimate relative protein abundance
Bioinformatics Advance Access published on November 5, 2009.
doi:10.1093/bioinformatics/btp610
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Abstract ORIGINAL PAPER

Robert A. Forties and Ralf Bundschuh
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
Bioinformatics Advance Access published on November 4, 2009.
doi:10.1093/bioinformatics/btp627
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Abstract ORIGINAL PAPER

Axel Rasche and Ralf Herwig
ARH: Predicting Splice Variants from Genome-wide Data with Modified Entropy
Bioinformatics Advance Access published on November 4, 2009.
doi:10.1093/bioinformatics/btp626
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L.S. Tang, and Weichuan Yu
Predictive rule inference for epistatic interaction detection in genome-wide association studies
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp622
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Runqing Yang, Xin Wang, Zeyuan Wu, Daniel R. Prows, and Min Lin
Bayesian Model Selection for Characterizing Genomic Imprinting Effects and Patterns
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp620
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER Tina Toni and Michael P. H. Stumpf Simulation-based model selection for dynamical systems in systems and population biology Bioinformatics Advance Access published on October 29, 2009. doi:10.1093/bioinformatics/btp619 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Ranjit Randhawa, Clifford A. Shaffer, and John J. Tyson
Model Aggregation: a building-block approach to creating large macromolecular regulatory networks
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp581
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Abstract ORIGINAL PAPER

Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, and W. Evan Johnson
The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp614
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Abstract ORIGINAL PAPER

Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, and Judith A. J. Steen
Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp607
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Matti Pirinen
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp584
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER

Youngik Yang, Donald Gilbert, and Sun Kim
Annotation Confidence Score for Genome Annotation: A Genome Comparison Approach
Bioinformatics Advance Access published on October 24, 2009.
doi:10.1093/bioinformatics/btp613
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Abstract ORIGINAL PAPER

Shuangge Ma, Yawei Zhang, Jian Huang, Xuesong Han, Theodore Holford, Qing Lan, Nathaniel Rothman, Peter Boyle, and Tongzhang Zheng
Identification of Non-Hodgkin's Lymphoma Prognosis Signatures Using the CTGDR Method
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp604
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER Yun Niu, David Otasek, and Igor Jurisica Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D Bioinformatics Advance Access published on October 22, 2009. doi:10.1093/bioinformatics/btp602 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Mohammadmahdi R. Yousefi, Jianping Hua, Chao Sima, and Edward R. Dougherty
Reporting bias when using real data sets to analyze classification performance
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp605
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Abstract ORIGINAL PAPER

Bart P.P. van Houte and Jaap Heringa
Accurate confidence aware clustering of array CGH tumor profiles
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp603
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Jian Yu, Yong Zhou, Isao Tanaka, and Min Yao
Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp599
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Christine Herold, Michael Steffens, Felix F. Brockschmidt, Max P. Baur, and Tim Becker
INTERSNP: Genome-wide Interaction Analysis Guided by A Priori Information
Bioinformatics Advance Access published on October 16, 2009.
doi:10.1093/bioinformatics/btp596
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER Michael Beckstette, Robert Homann, Robert Giegerich, and Stefan Kurtz Significant speedup of database searches with HMMs by search space reduction with PSSM family models Bioinformatics Advance Access published on October 14, 2009. doi:10.1093/bioinformatics/btp593 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Martin Schäfer, Holger Schwender, Sylvia Merk, Claudia Haferlach, Katja Ickstadt, and Martin Dugas
Integrated Analysis of Copy Number Alterations and Gene Expression: A Bivariate Assessment of Equally Directed Abnormalities
Bioinformatics Advance Access published on October 14, 2009.
doi:10.1093/bioinformatics/btp592
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Mirjana Domazet-Loso and Bernhard Haubold
Efficient Estimation of Pairwise Distances between Genomes
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp590
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER Qingliang Li, Yanli Wang, and Stephen H. Bryant A novel method for mining highly imbalanced high-throughput screening data in PubChem Bioinformatics Advance Access published on October 13, 2009. doi:10.1093/bioinformatics/btp589 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Curtis Huttenhower, K. Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J. Forman, Olga G. Troyanskaya, and Hilary A. Coller
Detailing regulatory networks through large scale data integration
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp588
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Alfonso Ibáñez, Pedro Larrañaga, and Concha Bielza
Predicting citation count of Bioinformatics papers within four years of publication
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp585
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER

I. M. Carr, J. I. Robinson, R. Dimitriou, A. F. Markham, A. W. Morgan, and D. T. Bonthron
Inferring relative proportions of DNA variants from sequencing electropherograms
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp583
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

Xiaoxiao Kong and Cavan Reilly
A Bayesian approach to the alignment of mass spectra
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp582
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER Magdalena A. Jonikas, Randall J. Radmer, and Russ B. Altman Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models Bioinformatics Advance Access published on October 7, 2009. doi:10.1093/bioinformatics/btp576 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, and Kiyoshi Asai
CentroidAlign: Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-pairs Score
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp580
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER Jacob F. Degner, John C. Marioni, Athma A. Pai, Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, and Jonathan K. Pritchard Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics Advance Access published on October 6, 2009. doi:10.1093/bioinformatics/btp579 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

P. Gerlee, L. Lizana, and K. Sneppen
Pathway identification by network pruning in the metabolic network of Escherichia coli
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp575
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

LETTER TO THE EDITOR

LETTER TO THE EDITOR

Anne-Laure Boulesteix
Over-optimism in bioinformatics research
Bioinformatics Advance Access published on November 26, 2009.
doi:10.1093/bioinformatics/btp648
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LETTER TO THE EDITOR Pawel Smialowski, Dmitrij Frishman, and Stefan Kramer Pitfalls of supervised feature selection Bioinformatics Advance Access published on October 29, 2009. doi:10.1093/bioinformatics/btp621 [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

LETTER TO THE EDITOR

Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, and David A. Fell
Response to comment on ’Can sugars be produced from fatty acids? A test case for pathway analysis tools’
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp591
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APPLICATIONS NOTE

Abstract APPLICATIONS NOTE

Chris Duran, Zoran Boskovic, Michael Imelfort, Jacqueline Batley, Nicholas A. Hamilton, and David Edwards
CMap3D: A 3D visualisation tool for comparative genetic maps
Bioinformatics Advance Access published on November 25, 2009.
doi:10.1093/bioinformatics/btp646
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Tomás Levitner, Stepán Timr, and Dalibor Stys
Expertomica Cells: Analysis of cell monolayer development
Bioinformatics Advance Access published on November 24, 2009.
doi:10.1093/bioinformatics/btp637
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Jesse Paquette and Taku Tokuyasu
EGAN: Exploratory Gene Association Networks
Bioinformatics Advance Access published on November 23, 2009.
doi:10.1093/bioinformatics/btp656
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Jean Muller, Christopher J. Creevey, Julie D. Thompson, Detlev Arendt, and Peer Bork
AQUA: Automated quality improvement for multiple sequence alignments
Bioinformatics Advance Access published on November 19, 2009.
doi:10.1093/bioinformatics/btp651
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, and Lam-Son Phan Tran
LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp645
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Shihao Shen, Claude Warzecha, Russ Carstens, and Yi Xing
MADS+: discovery of differential splicing events from Affymetrix exon junction array data
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp643
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Falko Krause, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp, and Wolfram Liebermeister
Annotation and merging of SBML models with semanticSBML
Bioinformatics Advance Access published on November 17, 2009.
doi:10.1093/bioinformatics/btp642
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Kanchana Narayanan and Jing Li MAVEN: a Tool for Visualization and Functional Analysis of Genome-Wide Association Results Bioinformatics Advance Access published on November 17, 2009. doi:10.1093/bioinformatics/btp641 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE Nathaniel Beagley, Kelly G. Stratton, and Bobbie-Jo M. Webb-Robertson VIBE 2.0: Visual Integration for Bayesian Evaluation Bioinformatics Advance Access published on November 17, 2009. doi:10.1093/bioinformatics/btp639 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics Advance Access published on November 13, 2009. doi:10.1093/bioinformatics/btp636 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Fei Li, Peng Li, Wenjian Xu, Yuxing Peng, Xiaochen Bo, and Shengqi Wang
PerturbationAnalyzer: A tool for investigating the effects of concentration perturbation on protein interaction networks
Bioinformatics Advance Access published on November 13, 2009.
doi:10.1093/bioinformatics/btp634
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Mark D. Robinson, Davis J. McCarthy, and Gordon K. Smyth edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics Advance Access published on November 11, 2009. doi:10.1093/bioinformatics/btp616 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Zhi Xie, Shaohui Hu, Seth Blackshaw, Heng Zhu, and Jiang Qian
hPDI: a database of experimental human protein-DNA interactions
Bioinformatics Advance Access published on November 9, 2009.
doi:10.1093/bioinformatics/btp631
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Ben D. MacArthur, Alexander Lachmann, Ihor R. Lemischka, and Avi Ma'ayan
GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data
Bioinformatics Advance Access published on November 5, 2009.
doi:10.1093/bioinformatics/btp628
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, and Teresa M. Przytycka SimBoolNet - A Cytoscape Plugin for Dynamic Simulation of Signaling Networks Bioinformatics Advance Access published on November 3, 2009. doi:10.1093/bioinformatics/btp617 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE W. Yu, M. Clyne, M.J. Khoury, and M. Gwinn Phenopedia and Genopedia: Disease-centered and Gene-centered Views of the Evolving Knowledge of Human Genetic Associations Bioinformatics Advance Access published on October 30, 2009. doi:10.1093/bioinformatics/btp618 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Andrew L. Hipp and Marcial Escudero
MATICCE: mapping transitions in continuous character evolution
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp625
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Ji Qi, Fangqing Zhao, Anne Buboltz, and Stephan C. Schuster inGAP: an integrated next-generation genome analysis pipeline Bioinformatics Advance Access published on October 30, 2009. doi:10.1093/bioinformatics/btp615 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, and Silke R. Sperling
MicroRazerS: Rapid alignment of small RNA reads
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp601
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, and Xuegong Zhang
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Bioinformatics Advance Access published on October 24, 2009.
doi:10.1093/bioinformatics/btp612
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE Erik Arner, Yoshihide Hayashizaki, and Carsten O. Daub NGSView: an extensible open source editor for next-generation sequencing data Bioinformatics Advance Access published on October 24, 2009. doi:10.1093/bioinformatics/btp611 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Joshua Buckner, Justin Wilson, Mark Seligman, Brian Athey, Stanley Watson, and Fan Meng
The gputools package enables GPU computing in R
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp608
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Abdoulaye Banire Diallo, Vladimir Makarenkov, and Mathieu Blanchette
Ancestors 1.0: A Web Server For Ancestral Sequence Reconstruction
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp600
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Christine Rousseau, Jacques Nicolas, and Mathieu Gonnet CRISPI: a CRISPR Interactive database Bioinformatics Advance Access published on October 21, 2009. doi:10.1093/bioinformatics/btp586 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE Troy Zerr, Gregory M. Cooper, Evan E. Eichler, and Deborah A. Nickerson Targeted Interrogation of Copy Number Variation using SCIMMkit Bioinformatics Advance Access published on October 21, 2009. doi:10.1093/bioinformatics/btp606 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE Yoshihiro Kawahara, Ryuichi Sakate, Akihiro Matsuya, Katsuhiko Murakami, Yoshiharu Sato, Hao Zhang, Takashi Gojobori, Takeshi Itoh, and Tadashi Imanishi G-compass: A web-based comparative genome browser between human and other vertebrate genomes Bioinformatics Advance Access published on October 21, 2009. doi:10.1093/bioinformatics/btp594 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Martijn J. Schuemie, Ning Kang, Maarten L. Hekkelman, and Jan A. Kors
GeneE: Gene and protein query expansion with disambiguation
Bioinformatics Advance Access published on October 16, 2009.
doi:10.1093/bioinformatics/btp597
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Kevin R. Brown, David Otasek, Muhammad Ali, Michael McGuffin, Wing Xie, Baiju Devani, Ian Lawson van Toch, and Igor Jurisica NAViGaTOR: Network Analysis, Visualization & Graphing Toronto Bioinformatics Advance Access published on October 16, 2009. doi:10.1093/bioinformatics/btp595 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Sarbashis Das, Anchal Vishnoi, and Alok Bhattacharya
ABWGAT: Anchor Based Whole Genome Analysis Tool.
Bioinformatics Advance Access published on October 14, 2009.
doi:10.1093/bioinformatics/btp587
[Abstract] [Accepted Manuscript] [Supplementary Data 1] [Request Permissions]  

Abstract APPLICATIONS NOTE

Pascal Gellert, Shizuka Uchida, and Thomas Braun
Exon Array Analyzer: a web interface for Affymetrix exon array analysis
Bioinformatics Advance Access published on October 12, 2009.
doi:10.1093/bioinformatics/btp577
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE Heidi Dvinge and Paul Bertone HTqPCR: High-throughput analysis and visualization of quantitative real-time PCR data in R Bioinformatics Advance Access published on October 6, 2009. doi:10.1093/bioinformatics/btp578 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

DISCOVERY NOTE

Abstract DISCOVERY NOTE Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1 Bioinformatics Advance Access published on October 22, 2009. doi:10.1093/bioinformatics/btp609 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

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