Volume 31, Issue 23, December 2015

DISCOVERY NOTE

DATA AND TEXT MINING

Determining conserved metabolic biomarkers from a million database queries

Michael E. Kurczy and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3721–3724, https://doi.org/10.1093/bioinformatics/btv475

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ORIGINAL PAPERS

GENOME ANALYSIS

TIPR: transcription initiation pattern recognition on a genome scale

Taj Morton and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3725–3732, https://doi.org/10.1093/bioinformatics/btv464

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GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

Shunichi Kosugi and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3733–3741, https://doi.org/10.1093/bioinformatics/btv465

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Mutadelic: mutation analysis using description logic inferencing capabilities

Matthew E. Holford and Michael Krauthammer

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3742–3747, https://doi.org/10.1093/bioinformatics/btv467

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SEQUENCE ANALYSIS

SuccFind: a novel succinylation sites online prediction tool via enhanced characteristic strategy

Hao-Dong Xu and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3748–3750, https://doi.org/10.1093/bioinformatics/btv439

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An efficient algorithm for the extraction of HGVS variant descriptions from sequences

Jonathan K. Vis and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3751–3757, https://doi.org/10.1093/bioinformatics/btv443

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BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

Dieter De Witte and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3758–3766, https://doi.org/10.1093/bioinformatics/btv466

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STRUCTURAL BIOINFORMATICS

LoopIng: a template-based tool for predicting the structure of protein loops

Mario Abdel Messih and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3767–3772, https://doi.org/10.1093/bioinformatics/btv438

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Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins

Jing Yang and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3773–3781, https://doi.org/10.1093/bioinformatics/btv459

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Improving protein fold recognition with hybrid profiles combining sequence and structure evolution

Yassine Ghouzam and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3782–3789, https://doi.org/10.1093/bioinformatics/btv462

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GENETICS AND POPULATION ANALYSIS

PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers

Alejandro Q. Nato and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3790–3798, https://doi.org/10.1093/bioinformatics/btv444

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SYSTEMS BIOLOGY

Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data

Karen A. Ryall and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3799–3806, https://doi.org/10.1093/bioinformatics/btv427

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A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)

Franziska Taruttis and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3807–3814, https://doi.org/10.1093/bioinformatics/btv461

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DATA AND TEXT MINING

Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose–response data

John-Patrick Mpindi and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3815–3821, https://doi.org/10.1093/bioinformatics/btv455

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DATABASES AND ONTOLOGIES

OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization

Agne Antanaviciute and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3822–3829, https://doi.org/10.1093/bioinformatics/btv473

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APPLICATIONS NOTES

GENOME ANALYSIS

cgmisc: enhanced genome-wide association analyses and visualization

Marcin Kierczak and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3830–3831, https://doi.org/10.1093/bioinformatics/btv426

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MICC: an R package for identifying chromatin interactions from ChIA-PET data

Chao He and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3832–3834, https://doi.org/10.1093/bioinformatics/btv445

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ERC analysis: web-based inference of gene function via evolutionary rate covariation

Nicholas W. Wolfe and Nathan L. Clark

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3835–3837, https://doi.org/10.1093/bioinformatics/btv454

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SEQUENCE ANALYSIS

Correcting systematic bias and instrument measurement drift with mzRefinery

Bryson C. Gibbons and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3838–3840, https://doi.org/10.1093/bioinformatics/btv437

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AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints

Giuseppe Profiti and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3841–3843, https://doi.org/10.1093/bioinformatics/btv451

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ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy

Vojtech Bystry and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3844–3846, https://doi.org/10.1093/bioinformatics/btv456

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motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites

Simon G. Coetzee and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3847–3849, https://doi.org/10.1093/bioinformatics/btv470

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STRUCTURAL BIOINFORMATICS

HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling

Jinchao Yu and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3850–3852, https://doi.org/10.1093/bioinformatics/btv441

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MEPSA: minimum energy pathway analysis for energy landscapes

Iñigo Marcos-Alcalde and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3853–3855, https://doi.org/10.1093/bioinformatics/btv453

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NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

Francis Gaudreault and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3856–3858, https://doi.org/10.1093/bioinformatics/btv458

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GENE EXPRESSION

aRrayLasso: a network-based approach to microarray interconversion

Adam S. Brown and Chirag J. Patel

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3859–3861, https://doi.org/10.1093/bioinformatics/btv469

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GENETICS AND POPULATION ANALYSIS

NAM: association studies in multiple populations

Alencar Xavier and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3862–3864, https://doi.org/10.1093/bioinformatics/btv448

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SYSTEMS BIOLOGY

stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation

Emmanuel Chaplais and Henri-Jean Garchon

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3865–3867, https://doi.org/10.1093/bioinformatics/btv450

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cyNeo4j: connecting Neo4j and Cytoscape

Georg Summer and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3868–3869, https://doi.org/10.1093/bioinformatics/btv460

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DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism

Jing Yang and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3870–3872, https://doi.org/10.1093/bioinformatics/btv474

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DATA AND TEXT MINING

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

Mario Di Guardo and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3873–3874, https://doi.org/10.1093/bioinformatics/btv446

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Vizardous: interactive analysis of microbial populations with single cell resolution

Stefan Helfrich and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3875–3877, https://doi.org/10.1093/bioinformatics/btv468

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DATABASES AND ONTOLOGIES

SurvCurv database and online survival analysis platform update

Matthias Ziehm and others

Bioinformatics, Volume 31, Issue 23, December 2015, Pages 3878–3880, https://doi.org/10.1093/bioinformatics/btv463

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