Volume 31, Issue 24, December 2015

ORIGINAL PAPERS

GENOME ANALYSIS

Fast and accurate approximate inference of transcript expression from RNA-seq data

James Hensman and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3881–3889, https://doi.org/10.1093/bioinformatics/btv483

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A hybrid bayesian approach for genome-wide association studies on related individuals

A. Yazdani and D. B. Dunson

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3890–3896, https://doi.org/10.1093/bioinformatics/btv496

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SEQUENCE ANALYSIS

LncRNA-ID: Long non-coding RNA IDentification using balanced random forests

Rujira Achawanantakun and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3897–3905, https://doi.org/10.1093/bioinformatics/btv480

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RASER: reads aligner for SNPs and editing sites of RNA

Jaegyoon Ahn and Xinshu Xiao

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3906–3913, https://doi.org/10.1093/bioinformatics/btv505

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STRUCTURAL BIOINFORMATICS

Pairwise RNA secondary structure alignment with conserved stem pattern

Jimmy Ka Ho Chiu and Yi-Ping Phoebe Chen

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3914–3921, https://doi.org/10.1093/bioinformatics/btv471

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An integrated structure- and system-based framework to identify new targets of metabolites and known drugs

Hammad Naveed and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3922–3929, https://doi.org/10.1093/bioinformatics/btv477

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Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6

Virginie Y. Martiny and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3930–3937, https://doi.org/10.1093/bioinformatics/btv486

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GENE EXPRESSION

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

Katharina E. Hayer and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3938–3945, https://doi.org/10.1093/bioinformatics/btv488

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GENETICS AND POPULATION ANALYSIS

Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations

Marc Pybus and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3946–3952, https://doi.org/10.1093/bioinformatics/btv493

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Learning directed acyclic graphical structures with genetical genomics data

Bin Gao and Yuehua Cui

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3953–3960, https://doi.org/10.1093/bioinformatics/btv513

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SYSTEMS BIOLOGY

CoD: inferring immune-cell quantities related to disease states

Amit Frishberg and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3961–3969, https://doi.org/10.1093/bioinformatics/btv498

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DATA AND TEXT MINING

Discovering hospital admission patterns using models learnt from electronic hospital records

Ognjen Arandjelović

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3970–3976, https://doi.org/10.1093/bioinformatics/btv508

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Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach

Xingjie Shi and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3977–3983, https://doi.org/10.1093/bioinformatics/btv518

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APPLICATIONS NOTES

GENOME ANALYSIS

GenomeLaser: fast and accurate haplotyping from pedigree genotypes

Wenzhi Li and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3984–3987, https://doi.org/10.1093/bioinformatics/btv452

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EPGA2: memory-efficient de novo assembler

Junwei Luo and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3988–3990, https://doi.org/10.1093/bioinformatics/btv487

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glmgraph: an R package for variable selection and predictive modeling of structured genomic data

Li Chen and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3991–3993, https://doi.org/10.1093/bioinformatics/btv497

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SEQUENCE ANALYSIS

svviz: a read viewer for validating structural variants

Noah Spies and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3994–3996, https://doi.org/10.1093/bioinformatics/btv478

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msa: an R package for multiple sequence alignment

Ulrich Bodenhofer and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 3997–3999, https://doi.org/10.1093/bioinformatics/btv494

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Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences

Haisi Yi and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4000–4002, https://doi.org/10.1093/bioinformatics/btv501

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BigBWA: approaching the Burrows–Wheeler aligner to Big Data technologies

José M. Abuín and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4003–4005, https://doi.org/10.1093/bioinformatics/btv506

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BS-SNPer: SNP calling in bisulfite-seq data

Shengjie Gao and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4006–4008, https://doi.org/10.1093/bioinformatics/btv507

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NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

Thorfinn Sand Korneliussen and Ida Moltke

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4009–4011, https://doi.org/10.1093/bioinformatics/btv509

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ABIF Manager: simple reading and editing of ABIF formatted files

Pavel Beran and Ivan Mraz

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4012–4013, https://doi.org/10.1093/bioinformatics/btv512

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Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

Jeongbin Park and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4014–4016, https://doi.org/10.1093/bioinformatics/btv537

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STRUCTURAL BIOINFORMATICS

BiopLib and BiopTools—a C programming library and toolset for manipulating protein structure

Craig T. Porter and Andrew C.R. Martin

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4017–4019, https://doi.org/10.1093/bioinformatics/btv482

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LIBRA: LIgand Binding site Recognition Application

Le Viet Hung and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4020–4022, https://doi.org/10.1093/bioinformatics/btv489

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InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite

Christian D. Schenkelberg and Christopher Bystroff

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4023–4025, https://doi.org/10.1093/bioinformatics/btv492

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GENE EXPRESSION

HiXCorr: a portable high-speed X_Corr engine for high-resolution tandem mass spectrometry

Hyunwoo Kim and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4026–4028, https://doi.org/10.1093/bioinformatics/btv490

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GENETICS AND POPULATION ANALYSIS

An interactive genome browser of association results from the UK10K cohorts project

Matthias Geihs and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4029–4031, https://doi.org/10.1093/bioinformatics/btv491

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SYSTEMS BIOLOGY

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes

Mariano J. Alvarez and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4032–4034, https://doi.org/10.1093/bioinformatics/btv499

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DATA AND TEXT MINING

database.bio: a web application for interpreting human variations

Min Ou and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4035–4037, https://doi.org/10.1093/bioinformatics/btv500

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DATABASES AND ONTOLOGIES

RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets

Zhengyu Guo and others

Bioinformatics, Volume 31, Issue 24, December 2015, Pages 4038–4040, https://doi.org/10.1093/bioinformatics/btv503

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