Volume 32, Issue 18, September 2016

ORIGINAL PAPERS

GENOME ANALYSIS

Predicting regulatory variants with composite statistic

Mulin Jun Li and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2729–2736, https://doi.org/10.1093/bioinformatics/btw288

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Group-combined P-values with applications to genetic association studies

Xiaonan Hu and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2737–2743, https://doi.org/10.1093/bioinformatics/btw314

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SEQUENCE ANALYSIS

Bayesian nonparametrics in protein remote homology search

Mindaugas Margelevičius

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2744–2752, https://doi.org/10.1093/bioinformatics/btw213

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Top-down analysis of protein samples by de novo sequencing techniques

Kira Vyatkina and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2753–2759, https://doi.org/10.1093/bioinformatics/btw307

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MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data

Vladimir I. Ulyantsev and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2760–2767, https://doi.org/10.1093/bioinformatics/btw312

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TarPmiR: a new approach for microRNA target site prediction

Jun Ding and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2768–2775, https://doi.org/10.1093/bioinformatics/btw318

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Revealing aperiodic aspects of solenoid proteins from sequence information

Thomas Hrabe and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2776–2782, https://doi.org/10.1093/bioinformatics/btw319

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KCMBT: a k-mer Counter based on Multiple Burst Trees

Abdullah-Al Mamun and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2783–2790, https://doi.org/10.1093/bioinformatics/btw345

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STRUCTURAL BIOINFORMATICS

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

Debswapna Bhattacharya and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2791–2799, https://doi.org/10.1093/bioinformatics/btw316

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GENE EXPRESSION

Differential rhythmicity: detecting altered rhythmicity in biological data

Paul F Thaben and Pål O Westermark

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2800–2808, https://doi.org/10.1093/bioinformatics/btw309

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Integrated gene set analysis for microRNA studies

Francisco Garcia-Garcia and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2809–2816, https://doi.org/10.1093/bioinformatics/btw334

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GENETICS AND POPULATION ANALYSIS

pong: fast analysis and visualization of latent clusters in population genetic data

Aaron A. Behr and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2817–2823, https://doi.org/10.1093/bioinformatics/btw327

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SYSTEMS BIOLOGY

Weighted mutual information analysis substantially improves domain-based functional network models

Jung Eun Shim and Insuk Lee

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2824–2830, https://doi.org/10.1093/bioinformatics/btw320

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A knowledge-based approach for predicting gene–disease associations

Hongyi Zhou and Jeffrey Skolnick

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2831–2838, https://doi.org/10.1093/bioinformatics/btw358

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DATA AND TEXT MINING

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

Robert Leaman and Zhiyong Lu

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2839–2846, https://doi.org/10.1093/bioinformatics/btw343

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APPLICATIONS NOTES

GENOME ANALYSIS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

Zuguang Gu and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2847–2849, https://doi.org/10.1093/bioinformatics/btw313

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SEQUENCE ANALYSIS

MetalPredator: a web server to predict iron–sulfur cluster binding proteomes

Yana Valasatava and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2850–2852, https://doi.org/10.1093/bioinformatics/btw238

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STRUCTURAL BIOINFORMATICS

DBSI server: DNA binding site identifier

Shravan Sukumar and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2853–2855, https://doi.org/10.1093/bioinformatics/btw315

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GENE EXPRESSION

compendiumdb: an R package for retrieval and storage of functional genomics data

Umesh K. Nandal and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2856–2857, https://doi.org/10.1093/bioinformatics/btw335

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CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

David J. Arenillas and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2858–2860, https://doi.org/10.1093/bioinformatics/btw337

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GENETICS AND POPULATION ANALYSIS

GHap: an R package for genome-wide haplotyping

Yuri T. Utsunomiya and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2861–2862, https://doi.org/10.1093/bioinformatics/btw356

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SYSTEMS BIOLOGY

MEANS: python package for Moment Expansion Approximation, iNference and Simulation

Sisi Fan and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2863–2865, https://doi.org/10.1093/bioinformatics/btw229

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Combenefit: an interactive platform for the analysis and visualization of drug combinations

Giovanni Y. Di Veroli and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2866–2868, https://doi.org/10.1093/bioinformatics/btw230

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CART—a chemical annotation retrieval toolkit

Samy Deghou and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2869–2871, https://doi.org/10.1093/bioinformatics/btw233

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RANKS: a flexible tool for node label ranking and classification in biological networks

Giorgio Valentini and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2872–2874, https://doi.org/10.1093/bioinformatics/btw235

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MIA: non-targeted mass isotopolome analysis

Daniel Weindl and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2875–2876, https://doi.org/10.1093/bioinformatics/btw317

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R.JIVE for exploration of multi-source molecular data

Michael J. O’Connell and Eric F. Lock

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2877–2879, https://doi.org/10.1093/bioinformatics/btw324

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Rule-based modeling with Virtual Cell

James C. Schaff and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2880–2882, https://doi.org/10.1093/bioinformatics/btw353

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DATA AND TEXT MINING

SETH detects and normalizes genetic variants in text

Philippe Thomas and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2883–2885, https://doi.org/10.1093/bioinformatics/btw234

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HiPub: translating PubMed and PMC texts to networks for knowledge discovery

Kyubum Lee and others

Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2886–2888, https://doi.org/10.1093/bioinformatics/btw511

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CORRIGENDUM

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

Sayoni Das and others

Bioinformatics, Volume 32, Issue 18, September 2016, Page 2889, https://doi.org/10.1093/bioinformatics/btw473

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