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Volume 25, Issue 20, October 2009
ORIGINAL PAPERS
GENOME ANALYSIS
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2625–2631, https://doi.org/10.1093/bioinformatics/btp503
SEQUENCE ANALYSIS
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2632–2638, https://doi.org/10.1093/bioinformatics/btp482
STRUCTURAL BIOINFORMATICS
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2639–2645, https://doi.org/10.1093/bioinformatics/btp449
Partition function and base pairing probabilities for RNA–RNA interaction prediction
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2646–2654, https://doi.org/10.1093/bioinformatics/btp481
A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2655–2662, https://doi.org/10.1093/bioinformatics/btp500
MISTRAL: a tool for energy-based multiple structural alignment of proteins
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2663–2669, https://doi.org/10.1093/bioinformatics/btp506
GENE EXPRESSION
Statistical lower bounds on protein copy number from fluorescence expression images
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2670–2676, https://doi.org/10.1093/bioinformatics/btp415
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2677–2684, https://doi.org/10.1093/bioinformatics/btp442
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2685–2691, https://doi.org/10.1093/bioinformatics/btp443
Moderated effect size and P-value combinations for microarray meta-analyses
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2692–2699, https://doi.org/10.1093/bioinformatics/btp444
Gene ranking and biomarker discovery under correlation
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2700–2707, https://doi.org/10.1093/bioinformatics/btp460
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2708–2714, https://doi.org/10.1093/bioinformatics/btp478
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2715–2722, https://doi.org/10.1093/bioinformatics/btp490
SYSTEMS BIOLOGY
An optimization model for metabolic pathways
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2723–2729, https://doi.org/10.1093/bioinformatics/btp441
APPLICATIONS NOTE
GENOME ANALYSIS
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2730–2731, https://doi.org/10.1093/bioinformatics/btp472
SnoopCGH: software for visualizing comparative genomic hybridization data
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2732–2733, https://doi.org/10.1093/bioinformatics/btp488
SEQUENCE ANALYSIS
YADA: a tool for taking the most out of high-resolution spectra
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2734–2736, https://doi.org/10.1093/bioinformatics/btp489
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2737–2738, https://doi.org/10.1093/bioinformatics/btp508
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2739–2740, https://doi.org/10.1093/bioinformatics/btp519
STRUCTURAL BIOINFORMATICS
massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2741–2742, https://doi.org/10.1093/bioinformatics/btp504
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2743–2744, https://doi.org/10.1093/bioinformatics/btp512
ANCHOR: web server for predicting protein binding regions in disordered proteins
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2745–2746, https://doi.org/10.1093/bioinformatics/btp518
GENETICS AND POPULATION ANALYSIS
PopABC: a program to infer historical demographic parameters
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2747–2749, https://doi.org/10.1093/bioinformatics/btp487
GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2750–2752, https://doi.org/10.1093/bioinformatics/btp497
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2753–2754, https://doi.org/10.1093/bioinformatics/btp499
SYSTEMS BIOLOGY
FBA-SimVis: interactive visualization of constraint-based metabolic models
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2755–2757, https://doi.org/10.1093/bioinformatics/btp408
FRED—a framework for T-cell epitope detection
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2758–2759, https://doi.org/10.1093/bioinformatics/btp409
Caleydo: connecting pathways and gene expression
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2760–2761, https://doi.org/10.1093/bioinformatics/btp432
The SNP ratio test: pathway analysis of genome-wide association datasets
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2762–2763, https://doi.org/10.1093/bioinformatics/btp448
DATA AND TEXT MINING
Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2764–2767, https://doi.org/10.1093/bioinformatics/btp427
DATABASES AND ONTOLOGIES
A System for Information Management in BioMedical Studies—SIMBioMS
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2768–2769, https://doi.org/10.1093/bioinformatics/btp420
LETTERS TO THE EDITOR
DATA AND TEXT MINING
Comment on ‘MeSH-up: effective MeSH text classification for improved document retrieval’
Bioinformatics, Volume 25, Issue 20, October 2009, Pages 2770–2771, https://doi.org/10.1093/bioinformatics/btp483
Response to comment on ‘MeSH-up: effective MeSH text classification for improved document retrieval’
Bioinformatics, Volume 25, Issue 20, October 2009, Page 2772, https://doi.org/10.1093/bioinformatics/btp484
DATABASES AND ONTOLOGIES
Corrigendum for Elliott,B. et al., ‘PathCase pathways database system’, Bioinformatics, Nov. 2008, 24(21), pp.
Bioinformatics, Volume 25, Issue 20, October 2009, Page 2773, https://doi.org/10.1093/bioinformatics/btp520
