Volume 27, Issue 7, April 2011

DISCOVERY NOTE

GENOME ANALYSIS

Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome

K. J. Siddle and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 895–898, https://doi.org/10.1093/bioinformatics/btr067

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SEQUENCE ANALYSIS

Phage display can select over-hydrophobic sequences that may impair prediction of natural domain–peptide interactions

Katja Luck and Gilles Travé

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 899–902, https://doi.org/10.1093/bioinformatics/btr060

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ORIGINAL PAPERS

GENOME ANALYSIS

Conveyor: a workflow engine for bioinformatic analyses

Burkhard Linke and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 903–911, https://doi.org/10.1093/bioinformatics/btr040

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Modeling and comparing the organization of circular genomes

Grace S. Shieh and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 912–918, https://doi.org/10.1093/bioinformatics/btr049

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B2G-FAR, a species-centered GO annotation repository

Stefan Götz and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 919–924, https://doi.org/10.1093/bioinformatics/btr059

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STRUCTURAL BIOINFORMATICS

GOSSIP: a method for fast and accurate global alignment of protein structures

I. Kifer and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 925–932, https://doi.org/10.1093/bioinformatics/btr044

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FISH Finder: a high-throughput tool for analyzing FISH images

James W. Shirley and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 933–938, https://doi.org/10.1093/bioinformatics/btr053

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Entropy-accelerated exact clustering of protein decoys

Francois Berenger and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 939–945, https://doi.org/10.1093/bioinformatics/btr072

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GENE EXPRESSION

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions

Christoph Hafemeister and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 946–952, https://doi.org/10.1093/bioinformatics/btr037

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Cross-platform comparison of microarray data using order restricted inference

Florian Klinglmueller and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 953–960, https://doi.org/10.1093/bioinformatics/btr066

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Automated analysis of biological oscillator models using mode decomposition

Tomasz Konopka

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 961–967, https://doi.org/10.1093/bioinformatics/btr069

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GENETICS AND POPULATION ANALYSIS

HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes

Alexander T. Dilthey and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 968–972, https://doi.org/10.1093/bioinformatics/btr061

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SYSTEMS BIOLOGY

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

Goksel Misirli and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 973–979, https://doi.org/10.1093/bioinformatics/btr048

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DATA AND TEXT MINING

Annotating genes and genomes with DNA sequences extracted from biomedical articles

Maximilian Haeussler and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 980–986, https://doi.org/10.1093/bioinformatics/btr043

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SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists

Björn Voss and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 987–993, https://doi.org/10.1093/bioinformatics/btr051

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Network clustering: probing biological heterogeneity by sparse graphical models

Sach Mukherjee and Steven M. Hill

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 994–1000, https://doi.org/10.1093/bioinformatics/btr070

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DATABASES AND ONTOLOGIES

A common layer of interoperability for biomedical ontologies based on OWL EL

Robert Hoehndorf and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1001–1008, https://doi.org/10.1093/bioinformatics/btr058

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APPLICATIONS NOTE

GENOME ANALYSIS

Easyfig: a genome comparison visualizer

Mitchell J. Sullivan and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1009–1010, https://doi.org/10.1093/bioinformatics/btr039

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SHRiMP2: Sensitive yet Practical Short Read Mapping

Matei David and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1011–1012, https://doi.org/10.1093/bioinformatics/btr046

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A Ruby API to query the Ensembl database for genomic features

Francesco Strozzi and Jan Aerts

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1013–1014, https://doi.org/10.1093/bioinformatics/btr050

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Gobe: an interactive, web-based tool for comparative genomic visualization

Brent S. Pedersen and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1015–1016, https://doi.org/10.1093/bioinformatics/btr056

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SEQUENCE ANALYSIS

FIMO: scanning for occurrences of a given motif

Charles E. Grant and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1017–1018, https://doi.org/10.1093/bioinformatics/btr064

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uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

Zachary Dwight and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1019–1020, https://doi.org/10.1093/bioinformatics/btr065

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STRUCTURAL BIOINFORMATICS

fconv: format conversion, manipulation and feature computation of molecular data

Gerd Neudert and Gerhard Klebe

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1021–1022, https://doi.org/10.1093/bioinformatics/btr055

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GENE EXPRESSION

LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data

Rendong Yang and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1023–1025, https://doi.org/10.1093/bioinformatics/btr041

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tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor

Antti Honkela and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1026–1027, https://doi.org/10.1093/bioinformatics/btr057

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SYSTEMS BIOLOGY

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models

Zhike Zi

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1028–1029, https://doi.org/10.1093/bioinformatics/btr038

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PiNGO: a Cytoscape plugin to find candidate genes in biological networks

Michael Smoot and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1030–1031, https://doi.org/10.1093/bioinformatics/btr045

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DATA AND TEXT MINING

GeneTUKit: a software for document-level gene normalization

Minlie Huang and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1032–1033, https://doi.org/10.1093/bioinformatics/btr042

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GeneReporter—sequence-based document retrieval and annotation

Annekathrin Bartsch and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1034–1035, https://doi.org/10.1093/bioinformatics/btr047

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DDN: a caBIG^® analytical tool for differential network analysis

Bai Zhang and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1036–1038, https://doi.org/10.1093/bioinformatics/btr052

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ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins

Kamil Tamiola and Frans A. A. Mulder

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1039–1040, https://doi.org/10.1093/bioinformatics/btr054

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Flower: extracting information from pyrosequencing data

Ketil Malde

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1041–1042, https://doi.org/10.1093/bioinformatics/btr063

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DATABASES AND ONTOLOGIES

BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID

Andrew G. Winter and others

Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1043–1044, https://doi.org/10.1093/bioinformatics/btr062

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