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Volume 25, Issue 21, November 2009
ORIGINAL PAPERS
GENOME ANALYSIS
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2735–2743, https://doi.org/10.1093/bioinformatics/btp531
SEQUENCE ANALYSIS
Automated inference of molecular mechanisms of disease from amino acid substitutions
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2744–2750, https://doi.org/10.1093/bioinformatics/btp528
STRUCTURAL BIOINFORMATICS
Algorithms for optimal protein structure alignment
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2751–2756, https://doi.org/10.1093/bioinformatics/btp530
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2757–2763, https://doi.org/10.1093/bioinformatics/btp539
GENE EXPRESSION
Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2764–2771, https://doi.org/10.1093/bioinformatics/btp491
The effects of probe binding affinity differences on gene expression measurements and how to deal with them
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2772–2779, https://doi.org/10.1093/bioinformatics/btp492
Statistical methods for gene set co-expression analysis
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2780–2786, https://doi.org/10.1093/bioinformatics/btp502
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2787–2794, https://doi.org/10.1093/bioinformatics/btp510
Bi-correlation clustering algorithm for determining a set of co-regulated genes
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2795–2801, https://doi.org/10.1093/bioinformatics/btp526
GENETICS AND POPULATION ANALYSIS
Multiple testing in genome-wide association studies via hidden Markov models
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2802–2808, https://doi.org/10.1093/bioinformatics/btp476
Quantifying cancer progression with conjunctive Bayesian networks
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2809–2815, https://doi.org/10.1093/bioinformatics/btp505
SYSTEMS BIOLOGY
Accessible methods for the dynamic time-scale decomposition of biochemical systems
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2816–2823, https://doi.org/10.1093/bioinformatics/btp451
Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2824–2830, https://doi.org/10.1093/bioinformatics/btp456
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2831–2838, https://doi.org/10.1093/bioinformatics/btp467
APPLICATIONS NOTE
GENOME ANALYSIS
TagDust—a program to eliminate artifacts from next generation sequencing data
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2839–2840, https://doi.org/10.1093/bioinformatics/btp527
SEQUENCE ANALYSIS
Updates to the RMAP short-read mapping software
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2841–2842, https://doi.org/10.1093/bioinformatics/btp533
STRUCTURAL BIOINFORMATICS
3D-SURFER: software for high-throughput protein surface comparison and analysis
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2843–2844, https://doi.org/10.1093/bioinformatics/btp542
GENETICS AND POPULATION ANALYSIS
COMPASS: a program for generating serial samples under an infinite sites model
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2845–2847, https://doi.org/10.1093/bioinformatics/btp534
SYSTEMS BIOLOGY
iBioSim: a tool for the analysis and design of genetic circuits
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2848–2849, https://doi.org/10.1093/bioinformatics/btp457
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2850–2852, https://doi.org/10.1093/bioinformatics/btp496
ERNEST: a toolbox for chemical reaction network theory
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2853–2854, https://doi.org/10.1093/bioinformatics/btp513
integrOmics: an R package to unravel relationships between two omics datasets
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2855–2856, https://doi.org/10.1093/bioinformatics/btp515
Analyzing biological network parameters with CentiScaPe
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2857–2859, https://doi.org/10.1093/bioinformatics/btp517
DATABASES AND ONTOLOGIES
PathBuilder—open source software for annotating and developing pathway resources
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2860–2862, https://doi.org/10.1093/bioinformatics/btp453
ISMB/ECCB 2009 SPECIAL INTEREST GROUP ON SHORT READ SEQUENCING
REPORT
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2863–2864, https://doi.org/10.1093/bioinformatics/btp525
ORIGINAL PAPERS
GENOME ANALYSIS
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2865–2871, https://doi.org/10.1093/bioinformatics/btp394
SEQUENCE ANALYSIS
De novo transcriptome assembly with ABySS
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2872–2877, https://doi.org/10.1093/bioinformatics/btp367
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2878–2881, https://doi.org/10.1093/bioinformatics/btp377
GENE EXPRESSION
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2882–2889, https://doi.org/10.1093/bioinformatics/btp378
