Volume 35, Issue 1, January 2019

ORIGINAL PAPERS

GENOME ANALYSIS

GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies

Nilotpal Sanyal and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 1–11, https://doi.org/10.1093/bioinformatics/bty472

• Abstract
• View article
• Supplementary data

SEQUENCE ANALYSIS

The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis

Nelson Gil and Andras Fiser

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 12–19, https://doi.org/10.1093/bioinformatics/bty523

• Abstract
• View article
• Supplementary data

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

Ehsan Haghshenas and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 20–27, https://doi.org/10.1093/bioinformatics/bty544

• Abstract
• View article
• Supplementary data

GENE EXPRESSION

A descriptive marker gene approach to single-cell pseudotime inference

Kieran R Campbell and Christopher Yau

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 28–35, https://doi.org/10.1093/bioinformatics/bty498

• Abstract
• View article
• Supplementary data

Unraveling the role of low-frequency mutated genes in breast cancer

Eleonora Lusito and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 36–46, https://doi.org/10.1093/bioinformatics/bty520

• Abstract
• View article
• Supplementary data

GrandPrix: scaling up the Bayesian GPLVM for single-cell data

Sumon Ahmed and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 47–54, https://doi.org/10.1093/bioinformatics/bty533

• Abstract
• View article
• Supplementary data

Differential coexpression in human tissues and the confounding effect of mean expression levels

Marjan Farahbod and Paul Pavlidis

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 55–61, https://doi.org/10.1093/bioinformatics/bty538

• Abstract
• View article
• Supplementary data

Exploring drivers of gene expression in the Cancer Genome Atlas

Andrea Rau and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 62–68, https://doi.org/10.1093/bioinformatics/bty551

• Abstract
• View article

GENETICS AND POPULATION ANALYSIS

Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees

Christian X Weichenberger and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 69–76, https://doi.org/10.1093/bioinformatics/bty541

• Abstract
• View article
• Supplementary data

SYSTEMS BIOLOGY

Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus

Lei Han and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 77–87, https://doi.org/10.1093/bioinformatics/bty457

• Abstract
• View article
• Supplementary data

A network-based zoning for parallel whole-cell simulation

Barnali Das and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 88–94, https://doi.org/10.1093/bioinformatics/bty530

• Abstract
• View article
• Supplementary data

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

Mohammad Sajjad Ghaemi and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 95–103, https://doi.org/10.1093/bioinformatics/bty537

• Abstract
• View article
• Supplementary data

NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug–target interactions

Fangping Wan and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 104–111, https://doi.org/10.1093/bioinformatics/bty543

• Abstract
• View article
• Supplementary data

DATA AND TEXT MINING

Tightly integrated genomic and epigenomic data mining using tensor decomposition

Jianwen Fang

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 112–118, https://doi.org/10.1093/bioinformatics/bty513

• Abstract
• View article
• Supplementary data

APPLICATIONS NOTES

GENOME ANALYSIS

htsget: a protocol for securely streaming genomic data

Jerome Kelleher and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 119–121, https://doi.org/10.1093/bioinformatics/bty492

• Abstract
• View article
• Supplementary data

Seave: a comprehensive web platform for storing and interrogating human genomic variation

Velimir Gayevskiy and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 122–125, https://doi.org/10.1093/bioinformatics/bty540

• Abstract
• View article
• Supplementary data

ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations

Zhaohui Gu and Charles G Mullighan

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 126–129, https://doi.org/10.1093/bioinformatics/bty546

• Abstract
• View article
• Supplementary data

Matt: Unix tools for alternative splicing analysis

André Gohr and Manuel Irimia

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 130–132, https://doi.org/10.1093/bioinformatics/bty606

• Abstract
• View article
• Supplementary data

Kmer-db: instant evolutionary distance estimation

Sebastian Deorowicz and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 133–136, https://doi.org/10.1093/bioinformatics/bty610

• Abstract
• View article
• Supplementary data

Reproducible and replicable comparisons using SummarizedBenchmark

Patrick K Kimes and Alejandro Reyes

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 137–139, https://doi.org/10.1093/bioinformatics/bty627

• Abstract
• View article
• Supplementary data

WAVES: a web application for versatile enhanced bioinformatic services

Marc Chakiachvili and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 140–142, https://doi.org/10.1093/bioinformatics/bty639

• Abstract
• View article
• Supplementary data

SEQUENCE ANALYSIS

Broom: application for non-redundant storage of high throughput sequencing data

Levent Albayrak and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 143–145, https://doi.org/10.1093/bioinformatics/bty580

• Abstract
• View article
• Supplementary data

Cryfa: a secure encryption tool for genomic data

Morteza Hosseini and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 146–148, https://doi.org/10.1093/bioinformatics/bty645

• Abstract
• View article
• Supplementary data

PHYLOGENETICS

SonicParanoid: fast, accurate and easy orthology inference

Salvatore Cosentino and Wataru Iwasaki

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 149–151, https://doi.org/10.1093/bioinformatics/bty631

• Abstract
• View article
• Supplementary data

STRUCTURAL BIOINFORMATICS

RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs

Maciej Antczak and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 152–155, https://doi.org/10.1093/bioinformatics/bty609

• Abstract
• View article

GENE EXPRESSION

GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution

Jamil Najafov and Ayaz Najafov

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 156–159, https://doi.org/10.1093/bioinformatics/bty623

• Abstract
• View article
• Supplementary data

GENETICS AND POPULATION ANALYSIS

GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data

Shijia Zhu and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 160–163, https://doi.org/10.1093/bioinformatics/bty529

• Abstract
• View article
• Supplementary data

emeraLD: rapid linkage disequilibrium estimation with massive datasets

Corbin Quick and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 164–166, https://doi.org/10.1093/bioinformatics/bty547

• Abstract
• View article
• Supplementary data

SYSTEMS BIOLOGY

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Pierre Salvy and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 167–169, https://doi.org/10.1093/bioinformatics/bty499

• Abstract
• View article
• Supplementary data

DATA AND TEXT MINING

ACDtool: a web-server for the generic analysis of large data sets of counts

Jean-Michel Claverie and Thi Ngan Ta

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 170–171, https://doi.org/10.1093/bioinformatics/bty640

• Abstract
• View article
• Supplementary data

DATABASES AND ONTOLOGIES

BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains

Chuan Jiao and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 172–174, https://doi.org/10.1093/bioinformatics/bty576

• Abstract
• View article
• Supplementary data

PepBDB: a comprehensive structural database of biological peptide–protein interactions

Zeyu Wen and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 175–177, https://doi.org/10.1093/bioinformatics/bty579

• Abstract
• View article

BIOIMAGE INFORMATICS

SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data

Paolo Inglese and others

Bioinformatics, Volume 35, Issue 1, January 2019, Pages 178–180, https://doi.org/10.1093/bioinformatics/bty622

• Abstract
• View article
• Supplementary data