Volume 31, Issue 18, September 2015

ORIGINAL PAPERS

GENOME ANALYSIS

A novel essential domain perspective for exploring gene essentiality

Yao Lu and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2921–2929, https://doi.org/10.1093/bioinformatics/btv312

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Bayesian mixture analysis for metagenomic community profiling

Sofia Morfopoulou and Vincent Plagnol

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2930–2938, https://doi.org/10.1093/bioinformatics/btv317

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SEQUENCE ANALYSIS

Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning

Raffaele Giancarlo and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2939–2946, https://doi.org/10.1093/bioinformatics/btv295

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Repeat- and error-aware comparison of deletions

Roland Wittler and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2947–2954, https://doi.org/10.1093/bioinformatics/btv304

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Likelihood-based complex trait association testing for arbitrary depth sequencing data

Song Yan and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2955–2962, https://doi.org/10.1093/bioinformatics/btv307

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IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

Leon Kuchenbecker and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2963–2971, https://doi.org/10.1093/bioinformatics/btv309

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When less is more: ‘slicing’ sequencing data improves read decoding accuracy and de novo assembly quality

Stefano Lonardi and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2972–2980, https://doi.org/10.1093/bioinformatics/btv311

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STRUCTURAL BIOINFORMATICS

Computer vision-based automated peak picking applied to protein NMR spectra

Piotr Klukowski and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2981–2988, https://doi.org/10.1093/bioinformatics/btv318

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GENE EXPRESSION

Diffusion maps for high-dimensional single-cell analysis of differentiation data

Laleh Haghverdi and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2989–2998, https://doi.org/10.1093/bioinformatics/btv325

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SYSTEMS BIOLOGY

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

David Henriques and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 2999–3007, https://doi.org/10.1093/bioinformatics/btv314

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Trans-species learning of cellular signaling systems with bimodal deep belief networks

Lujia Chen and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3008–3015, https://doi.org/10.1093/bioinformatics/btv315

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DATA AND TEXT MINING

CAPRI: efficient inference of cancer progression models from cross-sectional data

Daniele Ramazzotti and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3016–3026, https://doi.org/10.1093/bioinformatics/btv296

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DATABASES AND ONTOLOGIES

SpeeDB: fast structural protein searches

David E. Robillard and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3027–3034, https://doi.org/10.1093/bioinformatics/btv274

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GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

Wallace K. B. Chan and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3035–3042, https://doi.org/10.1093/bioinformatics/btv302

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APPLICATIONS NOTES

GENOME ANALYSIS

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data

Bin Wang and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3043–3045, https://doi.org/10.1093/bioinformatics/btv289

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agplus: a rapid and flexible tool for aggregation plots

Kazumitsu Maehara and Yasuyuki Ohkawa

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3046–3047, https://doi.org/10.1093/bioinformatics/btv322

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PopGeV: a web-based large-scale population genome browser

Xinyi Shi and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3048–3050, https://doi.org/10.1093/bioinformatics/btv324

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SEQUENCE ANALYSIS

TRAL: tandem repeat annotation library

Elke Schaper and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3051–3053, https://doi.org/10.1093/bioinformatics/btv306

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GENE EXPRESSION

tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

Antoine Chambaz and Pierre Neuvial

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3054–3056, https://doi.org/10.1093/bioinformatics/btv320

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ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments

Swneke D. Bailey and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3057–3059, https://doi.org/10.1093/bioinformatics/btv321

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SYSTEMS BIOLOGY

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions

Gregory W. Gundersen and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3060–3062, https://doi.org/10.1093/bioinformatics/btv297

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Fast parametric time warping of peak lists

Ron Wehrens and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3063–3065, https://doi.org/10.1093/bioinformatics/btv299

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CoRegNet: reconstruction and integrated analysis of co-regulatory networks

Rémy Nicolle and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3066–3068, https://doi.org/10.1093/bioinformatics/btv305

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DSigDB: drug signatures database for gene set analysis

Minjae Yoo and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3069–3071, https://doi.org/10.1093/bioinformatics/btv313

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pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge

Astrid Wachter and Tim Beißbarth

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3072–3074, https://doi.org/10.1093/bioinformatics/btv323

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DATABASES AND ONTOLOGIES

PsyGeNET: a knowledge platform on psychiatric disorders and their genes

Alba Gutiérrez-Sacristán and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3075–3077, https://doi.org/10.1093/bioinformatics/btv301

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WGE: a CRISPR database for genome engineering

Alex Hodgkins and others

Bioinformatics, Volume 31, Issue 18, September 2015, Pages 3078–3080, https://doi.org/10.1093/bioinformatics/btv308

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