Volume 31, Issue 20, October 2015

REVIEW

STRUCTURAL BIOINFORMATICS

Data Safe Havens in health research and healthcare

Paul R. Burton and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3241–3248, https://doi.org/10.1093/bioinformatics/btv279

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DISCOVERY NOTE

GENE EXPRESSION

A note on the false discovery rate of novel peptides in proteogenomics

Kun Zhang and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3249–3253, https://doi.org/10.1093/bioinformatics/btv340

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ORIGINAL PAPERS

GENOME ANALYSIS

Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans

Steve Oden and Luciano Brocchieri

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3254–3261, https://doi.org/10.1093/bioinformatics/btv339

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SEQUENCE ANALYSIS

Assembling short reads from jumping libraries with large insert sizes

Irina Vasilinetc and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3262–3268, https://doi.org/10.1093/bioinformatics/btv337

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TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins

Castrense Savojardo and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3269–3275, https://doi.org/10.1093/bioinformatics/btv367

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LFQC: a lossless compression algorithm for FASTQ files

Marius Nicolae and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3276–3281, https://doi.org/10.1093/bioinformatics/btv384

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PHYLOGENETICS

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Shiwei Lan and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3282–3289, https://doi.org/10.1093/bioinformatics/btv378

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GENE EXPRESSION

biRte: Bayesian inference of context-specific regulator activities and transcriptional networks

Holger Fröhlich

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3290–3298, https://doi.org/10.1093/bioinformatics/btv379

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SYSTEMS BIOLOGY

Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks

Aditya Pratapa and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3299–3305, https://doi.org/10.1093/bioinformatics/btv352

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TENET: topological feature-based target characterization in signalling networks

Huey Eng Chua and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3306–3314, https://doi.org/10.1093/bioinformatics/btv360

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libRoadRunner: a high performance SBML simulation and analysis library

Endre T. Somogyi and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3315–3321, https://doi.org/10.1093/bioinformatics/btv363

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Investigating microbial co-occurrence patterns based on metagenomic compositional data

Yuguang Ban and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3322–3329, https://doi.org/10.1093/bioinformatics/btv364

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NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data

Meng Zou and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3330–3338, https://doi.org/10.1093/bioinformatics/btv374

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DATABASES AND ONTOLOGIES

IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes

Brice Beinsteiner and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3339–3344, https://doi.org/10.1093/bioinformatics/btv347

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APPLICATIONS NOTES

GENOME ANALYSIS

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements

Kishori M. Konwar and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3345–3347, https://doi.org/10.1093/bioinformatics/btv361

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GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications

Matthew R. Laird and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3348–3349, https://doi.org/10.1093/bioinformatics/btv376

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Bandage: interactive visualization of de novo genome assemblies

Ryan R. Wick and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3350–3352, https://doi.org/10.1093/bioinformatics/btv383

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SEQUENCE ANALYSIS

atSNP: transcription factor binding affinity testing for regulatory SNP detection

Chandler Zuo and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3353–3355, https://doi.org/10.1093/bioinformatics/btv328

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Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data

Namita T. Gupta and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3356–3358, https://doi.org/10.1093/bioinformatics/btv359

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IBS: an illustrator for the presentation and visualization of biological sequences

Wenzhong Liu and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3359–3361, https://doi.org/10.1093/bioinformatics/btv362

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PPUS: a web server to predict PUS-specific pseudouridine sites

Yan-Hui Li and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3362–3364, https://doi.org/10.1093/bioinformatics/btv366

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Chimira: analysis of small RNA sequencing data and microRNA modifications

Dimitrios M. Vitsios and Anton J. Enright

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3365–3367, https://doi.org/10.1093/bioinformatics/btv380

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MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Stephen Nayfach and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3368–3370, https://doi.org/10.1093/bioinformatics/btv382

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damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

Owen J. Marshall and Andrea H. Brand

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3371–3373, https://doi.org/10.1093/bioinformatics/btv386

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STRUCTURAL BIOINFORMATICS

FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures

Leonid B. Pereyaslavets and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3374–3376, https://doi.org/10.1093/bioinformatics/btv369

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Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

Peter Kerpedjiev and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3377–3379, https://doi.org/10.1093/bioinformatics/btv372

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GENE EXPRESSION

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq

Miguel Juliá and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3380–3382, https://doi.org/10.1093/bioinformatics/btv368

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SYSTEMS BIOLOGY

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Nicolas Rodriguez and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3383–3386, https://doi.org/10.1093/bioinformatics/btv341

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REDEMPTION: reduced dimension ensemble modeling and parameter estimation

Yang Liu and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3387–3389, https://doi.org/10.1093/bioinformatics/btv365

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Hyperscape: visualization for complex biological networks

Graham L. Cromar and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3390–3391, https://doi.org/10.1093/bioinformatics/btv385

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DATABASES AND ONTOLOGIES

Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map

Günter Klambauer and others

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3392–3394, https://doi.org/10.1093/bioinformatics/btv373

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AmyLoad: website dedicated to amyloidogenic protein fragments

Pawel P. Wozniak and Malgorzata Kotulska

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3395–3397, https://doi.org/10.1093/bioinformatics/btv375

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BIOIMAGE INFORMATICS

Real-time multi-view deconvolution

Benjamin Schmid and Jan Huisken

Bioinformatics, Volume 31, Issue 20, October 2015, Pages 3398–3400, https://doi.org/10.1093/bioinformatics/btv387

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