Volume 33, Issue 19, October 2017

DISCOVERY NOTE

STRUCTURAL BIOINFORMATICS

The interfacial character of antibody paratopes: analysis of antibody–antigen structures

Minh N Nguyen and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 2971–2976, https://doi.org/10.1093/bioinformatics/btx389

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ORIGINAL PAPERS

GENOME ANALYSIS

Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma

Sylvain Mareschal and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 2977–2985, https://doi.org/10.1093/bioinformatics/btx309

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DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes

Milos Pavlovic and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 2986–2994, https://doi.org/10.1093/bioinformatics/btx316

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A multi-scenario genome-wide medical population genetics simulation framework

Jacquiline W Mugo and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 2995–3002, https://doi.org/10.1093/bioinformatics/btx369

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SEQUENCE ANALYSIS

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding

Wenxiu Ma and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3003–3010, https://doi.org/10.1093/bioinformatics/btx336

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M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic

Cristian Zambrano-Vega and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3011–3017, https://doi.org/10.1093/bioinformatics/btx338

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DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

Hao Peng and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3018–3027, https://doi.org/10.1093/bioinformatics/btx357

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MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences

Ka-Chun Wong

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3028–3035, https://doi.org/10.1093/bioinformatics/btx381

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STRUCTURAL BIOINFORMATICS

DeepSite: protein-binding site predictor using 3D-convolutional neural networks

J Jiménez and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3036–3042, https://doi.org/10.1093/bioinformatics/btx350

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ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design

Christopher W Wood and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3043–3050, https://doi.org/10.1093/bioinformatics/btx352

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Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank

Sang-Jun Park and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3051–3057, https://doi.org/10.1093/bioinformatics/btx358

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GENE EXPRESSION

Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data

Dimitrios V Vavoulis and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3058–3064, https://doi.org/10.1093/bioinformatics/btx355

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SYSTEMS BIOLOGY

Computational modeling of immune system of the fish for a more effective vaccination in aquaculture

Alice Madonia and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3065–3071, https://doi.org/10.1093/bioinformatics/btx341

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Moran’s I quantifies spatio-temporal pattern formation in neural imaging data

Christoph Schmal and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3072–3079, https://doi.org/10.1093/bioinformatics/btx351

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JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data

Jiadong Ji and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3080–3087, https://doi.org/10.1093/bioinformatics/btx360

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APPLICATIONS NOTES

GENOME ANALYSIS

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data

Bernat Gel and Eduard Serra

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3088–3090, https://doi.org/10.1093/bioinformatics/btx346

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MoDMaps3D: an interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences

Rallis Karamichalis and Lila Kari

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3091–3093, https://doi.org/10.1093/bioinformatics/btx367

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GfaPy: a flexible and extensible software library for handling sequence graphs in Python

Giorgio Gonnella and Stefan Kurtz

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3094–3095, https://doi.org/10.1093/bioinformatics/btx398

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SEQUENCE ANALYSIS

CWDPRNP: a tool for cervid prion sequence analysis in program R

William L Miller and W David Walter

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3096–3097, https://doi.org/10.1093/bioinformatics/btx333

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Protein–Sol: a web tool for predicting protein solubility from sequence

Max Hebditch and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3098–3100, https://doi.org/10.1093/bioinformatics/btx345

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COMPASS: the COMPletely Arbitrary Sequence Simulator

Andrew Low and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3101–3103, https://doi.org/10.1093/bioinformatics/btx347

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omiXcore: a web server for prediction of protein interactions with large RNA

Alexandros Armaos and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3104–3106, https://doi.org/10.1093/bioinformatics/btx361

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runBNG: a software package for BioNano genomic analysis on the command line

Yuxuan Yuan and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3107–3109, https://doi.org/10.1093/bioinformatics/btx366

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CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens

Preeti Bais and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3110–3112, https://doi.org/10.1093/bioinformatics/btx375

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WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Clovis Galiez and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3113–3114, https://doi.org/10.1093/bioinformatics/btx383

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kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies

Jochen Kruppa and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3115–3116, https://doi.org/10.1093/bioinformatics/btx385

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STRUCTURAL BIOINFORMATICS

Structurexplor: a platform for the exploration of structural features of RNA secondary structures

Jean-Pierre Séhi Glouzon and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3117–3120, https://doi.org/10.1093/bioinformatics/btx323

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BreakPoint Surveyor: a pipeline for structural variant visualization

Matthew A Wyczalkowski and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3121–3122, https://doi.org/10.1093/bioinformatics/btx362

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GENE EXPRESSION

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

Vincent Gardeux and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3123–3125, https://doi.org/10.1093/bioinformatics/btx337

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ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data

Jason T Serviss and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3126–3128, https://doi.org/10.1093/bioinformatics/btx393

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GENETICS AND POPULATION ANALYSIS

rqt: an R package for gene-level meta-analysis

Ilya Y Zhbannikov and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3129–3130, https://doi.org/10.1093/bioinformatics/btx395

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SYSTEMS BIOLOGY

CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization

Taosheng Xu and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3131–3133, https://doi.org/10.1093/bioinformatics/btx378

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GraphSpace: stimulating interdisciplinary collaborations in network biology

Aditya Bharadwaj and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3134–3136, https://doi.org/10.1093/bioinformatics/btx382

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DATA AND TEXT MINING

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Joseph Brown and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3137–3139, https://doi.org/10.1093/bioinformatics/btx373

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TIminer: NGS data mining pipeline for cancer immunology and immunotherapy

Elias Tappeiner and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3140–3141, https://doi.org/10.1093/bioinformatics/btx377

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matter: an R package for rapid prototyping with larger-than-memory datasets on disk

Kylie A Bemis and Olga Vitek

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3142–3144, https://doi.org/10.1093/bioinformatics/btx392

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BIOIMAGE INFORMATICS

Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections

Christopher Churas and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3145–3147, https://doi.org/10.1093/bioinformatics/btx376

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POPULATION GENETICS

fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample

Emil Jørsboe and others

Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3148–3150, https://doi.org/10.1093/bioinformatics/btx474

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