Volume 34, Issue 6, March 2018

ORIGINAL PAPERS

GENOME ANALYSIS

Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information

Zaixiang Tang and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 901–910, https://doi.org/10.1093/bioinformatics/btx684

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ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data

Vida Ravanmehr and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 911–919, https://doi.org/10.1093/bioinformatics/btx685

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Machine learning annotation of human branchpoints

Bethany Signal and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 920–927, https://doi.org/10.1093/bioinformatics/btx688

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ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads

Altti Ilari Maarala and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 928–935, https://doi.org/10.1093/bioinformatics/btx702

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Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations

Clinton L Cario and John S Witte

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 936–942, https://doi.org/10.1093/bioinformatics/btx709

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SEQUENCE ANALYSIS

PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences

Akshay Kumar Avvaru and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 943–948, https://doi.org/10.1093/bioinformatics/btx721

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STRUCTURAL BIOINFORMATICS

Predicting loop conformational ensembles

Claire Marks and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 949–956, https://doi.org/10.1093/bioinformatics/btx718

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GRASS: semi-automated NMR-based structure elucidation of saccharides

Roman R Kapaev and Philip V Toukach

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 957–963, https://doi.org/10.1093/bioinformatics/btx696

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GENE EXPRESSION

A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data

M Sanchez-Castillo and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 964–970, https://doi.org/10.1093/bioinformatics/btx605

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An exact test for comparing a fixed quantitative property between gene sets

Matthew M Parks

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 971–977, https://doi.org/10.1093/bioinformatics/btx693

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GENETICS AND POPULATION ANALYSIS

Estimation of QTL heritability based on pooled sequencing data

Weiqi Tang and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 978–984, https://doi.org/10.1093/bioinformatics/btx703

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SYSTEMS BIOLOGY

A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease

Lichy Han and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 985–993, https://doi.org/10.1093/bioinformatics/btx651

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CommWalker: correctly evaluating modules in molecular networks in light of annotation bias

M D Luecken and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 994–1000, https://doi.org/10.1093/bioinformatics/btx706

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DATA AND TEXT MINING

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra

S Deepaisarn and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1001–1008, https://doi.org/10.1093/bioinformatics/btx630

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Unsupervised multiple kernel learning for heterogeneous data integration

Jérôme Mariette and Nathalie Villa-Vialaneix

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1009–1015, https://doi.org/10.1093/bioinformatics/btx682

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DATABASES AND ONTOLOGIES

PlanNET: homology-based predicted interactome for multiple planarian transcriptomes

S Castillo-Lara and J F Abril

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1016–1023, https://doi.org/10.1093/bioinformatics/btx738

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BIOIMAGE INFORMATICS

Identification of topological features in renal tumor microenvironment associated with patient survival

Jun Cheng and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1024–1030, https://doi.org/10.1093/bioinformatics/btx723

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APPLICATIONS NOTES

GENOME ANALYSIS

MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool

Lucas Lochovsky and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1031–1033, https://doi.org/10.1093/bioinformatics/btx700

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NanoStringNormCNV: pre-processing of NanoString CNV data

Dorota H Sendorek and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1034–1036, https://doi.org/10.1093/bioinformatics/btx707

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DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Yasuhiro Tanizawa and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1037–1039, https://doi.org/10.1093/bioinformatics/btx713

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TabPath: interactive tables for metabolic pathway analysis

Lauro Ângelo Gonçalves de Moraes and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1040–1042, https://doi.org/10.1093/bioinformatics/btx714

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Myriads: P-value-based multiple testing correction

Antonio Carvajal-Rodríguez

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1043–1045, https://doi.org/10.1093/bioinformatics/btx746

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scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data

Tong Liu and Zheng Wang

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1046–1047, https://doi.org/10.1093/bioinformatics/btx747

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SEQUENCE ANALYSIS

Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains

Antonio Solano-Román and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1048–1049, https://doi.org/10.1093/bioinformatics/btx694

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PHYLOGENETICS

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data

Brian D Piccolo and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1050–1052, https://doi.org/10.1093/bioinformatics/btx686

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Efficient comparative phylogenetics on large trees

Stilianos Louca and Michael Doebeli

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1053–1055, https://doi.org/10.1093/bioinformatics/btx701

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SPECTRE: a suite of phylogenetic tools for reticulate evolution

Sarah Bastkowski and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1056–1057, https://doi.org/10.1093/bioinformatics/btx740

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STRUCTURAL BIOINFORMATICS

BEAM web server: a tool for structural RNA motif discovery

Marco Pietrosanto and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1058–1060, https://doi.org/10.1093/bioinformatics/btx704

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Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers

Andrei L Lomize and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1061–1062, https://doi.org/10.1093/bioinformatics/btx720

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PREFMD: a web server for protein structure refinement via molecular dynamics simulations

Lim Heo and Michael Feig

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1063–1065, https://doi.org/10.1093/bioinformatics/btx726

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GENE EXPRESSION

DIEGO: detection of differential alternative splicing using Aitchison’s geometry

Gero Doose and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1066–1068, https://doi.org/10.1093/bioinformatics/btx690

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GENETICS AND POPULATION ANALYSIS

pedigreejs: a web-based graphical pedigree editor

Tim Carver and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1069–1071, https://doi.org/10.1093/bioinformatics/btx705

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ThetaMater: Bayesian estimation of population size parameter $θ$ from genomic data

Richard H Adams and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1072–1073, https://doi.org/10.1093/bioinformatics/btx733

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DATABASES AND ONTOLOGIES

ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins

Sandy S Pineda and others

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1074–1076, https://doi.org/10.1093/bioinformatics/btx661

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Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1

Jeongbin Park and Sangsu Bae

Bioinformatics, Volume 34, Issue 6, March 2018, Pages 1077–1079, https://doi.org/10.1093/bioinformatics/btx695

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