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Volume 31, Issue 19, October 2015
DISCOVERY NOTE
GENOME ANALYSIS
GC3-biased gene domains in mammalian genomes
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3081–3084, https://doi.org/10.1093/bioinformatics/btv329
ORIGINAL PAPERS
GENOME ANALYSIS
FourCSeq: analysis of 4C sequencing data
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3085–3091, https://doi.org/10.1093/bioinformatics/btv335
Mango: a bias-correcting ChIA-PET analysis pipeline
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3092–3098, https://doi.org/10.1093/bioinformatics/btv336
DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3099–3104, https://doi.org/10.1093/bioinformatics/btv348
SoloDel: a probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3105–3113, https://doi.org/10.1093/bioinformatics/btv358
SEQUENCE ANALYSIS
antaRNA: ant colony-based RNA sequence design
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3114–3121, https://doi.org/10.1093/bioinformatics/btv319
QVZ: lossy compression of quality values
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3122–3129, https://doi.org/10.1093/bioinformatics/btv330
A parallel and sensitive software tool for methylation analysis on multicore platforms
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3130–3138, https://doi.org/10.1093/bioinformatics/btv357
STRUCTURAL BIOINFORMATICS
UniAlign: protein structure alignment meets evolution
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3139–3146, https://doi.org/10.1093/bioinformatics/btv354
GENE EXPRESSION
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3147–3155, https://doi.org/10.1093/bioinformatics/btv316
Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3156–3162, https://doi.org/10.1093/bioinformatics/btv334
Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3163–3171, https://doi.org/10.1093/bioinformatics/btv344
SYSTEMS BIOLOGY
CCLasso: correlation inference for compositional data through Lasso
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3172–3180, https://doi.org/10.1093/bioinformatics/btv349
The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3181–3188, https://doi.org/10.1093/bioinformatics/btv353
BIOIMAGE INFORMATICS
Automated profiling of individual cell–cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING)
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3189–3197, https://doi.org/10.1093/bioinformatics/btv355
EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3198–3206, https://doi.org/10.1093/bioinformatics/btv356
APPLICATIONS NOTES
GENOME ANALYSIS
FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3207–3209, https://doi.org/10.1093/bioinformatics/btv280
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3210–3212, https://doi.org/10.1093/bioinformatics/btv351
SEQUENCE ANALYSIS
IgSimulator: a versatile immunosequencing simulator
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3213–3215, https://doi.org/10.1093/bioinformatics/btv326
ACE: accurate correction of errors using K-mer tries
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3216–3218, https://doi.org/10.1093/bioinformatics/btv332
GeIST: a pipeline for mapping integrated DNA elements
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3219–3221, https://doi.org/10.1093/bioinformatics/btv350
STRUCTURAL BIOINFORMATICS
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3222–3224, https://doi.org/10.1093/bioinformatics/btv333
GENE EXPRESSION
oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3225–3227, https://doi.org/10.1093/bioinformatics/btv342
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3228–3230, https://doi.org/10.1093/bioinformatics/btv343
SYSTEMS BIOLOGY
lpNet: a linear programming approach to reconstruct signal transduction networks
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3231–3233, https://doi.org/10.1093/bioinformatics/btv327
TiQuant: software for tissue analysis, quantification and surface reconstruction
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3234–3236, https://doi.org/10.1093/bioinformatics/btv346
DATABASE AND ONTOLOGIES
RPdb: a database of experimentally verified cellular reprogramming records
Bioinformatics, Volume 31, Issue 19, October 2015, Pages 3237–3239, https://doi.org/10.1093/bioinformatics/btv331
CORRIGENDUM
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
Bioinformatics, Volume 31, Issue 19, October 2015, Page 3240, https://doi.org/10.1093/bioinformatics/btv479
