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Volume 34, Issue 23, December 2018
DISCOVERY NOTE
STRUCTURAL BIOINFORMATICS
The ancestral KH peptide at the root of a domain family with three different folds
Joana Pereira and Andrei N Lupas
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3961–3965, https://doi.org/10.1093/bioinformatics/bty480
ORIGINAL PAPERS
GENOME ANALYSIS
Modelling BioNano optical data and simulation study of genome map assembly
Ping Chen and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3966–3974, https://doi.org/10.1093/bioinformatics/bty456
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile
Yuanfang Guan and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3975–3982, https://doi.org/10.1093/bioinformatics/bty467
Meffil: efficient normalization and analysis of very large DNA methylation datasets
J L Min and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3983–3989, https://doi.org/10.1093/bioinformatics/bty476
SEQUENCE ANALYSIS
SSMART: sequence-structure motif identification for RNA-binding proteins
Alina Munteanu and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3990–3998, https://doi.org/10.1093/bioinformatics/bty404
ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization
Guodong Chen and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 3999–4006, https://doi.org/10.1093/bioinformatics/bty444
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides
Leyi Wei and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4007–4016, https://doi.org/10.1093/bioinformatics/bty451
Predicting clone genotypes from tumor bulk sequencing of multiple samples
Sayaka Miura and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4017–4026, https://doi.org/10.1093/bioinformatics/bty469
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
Johan Bengtsson-Palme and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4027–4033, https://doi.org/10.1093/bioinformatics/bty482
STRUCTURAL BIOINFORMATICS
Prediction of kinetics of protein folding with non-redundant contact information
Luciano Censoni and Leandro Martínez
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4034–4038, https://doi.org/10.1093/bioinformatics/bty478
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks
Jack Hanson and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4039–4045, https://doi.org/10.1093/bioinformatics/bty481
Deep convolutional networks for quality assessment of protein folds
Georgy Derevyanko and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4046–4053, https://doi.org/10.1093/bioinformatics/bty494
GENE EXPRESSION
Estimating pseudocounts and fold changes for digital expression measurements
Florian Erhard
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4054–4063, https://doi.org/10.1093/bioinformatics/bty471
Robust clustering of noisy high-dimensional gene expression data for patients subtyping
Pietro Coretto and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4064–4072, https://doi.org/10.1093/bioinformatics/bty502
GENETICS AND POPULATION ANALYSI
On the power of epigenome-wide association studies using a disease-discordant twin design
Weilong Li and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4073–4078, https://doi.org/10.1093/bioinformatics/bty532
SYSTEMS BIOLOGY
Modelling signalling networks from perturbation data
Mathurin Dorel and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4079–4086, https://doi.org/10.1093/bioinformatics/bty473
DATA AND TEXT MINING
Transfer learning for biomedical named entity recognition with neural networks
John M Giorgi and Gary D Bader
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4087–4094, https://doi.org/10.1093/bioinformatics/bty449
Improved design and analysis of CRISPR knockout screens
Chen-Hao Chen and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4095–4101, https://doi.org/10.1093/bioinformatics/bty450
BIOIMAGE INFORMATICS
The Rényi divergence enables accurate and precise cluster analysis for localization microscopy
Adela D Staszowska and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4102–4111, https://doi.org/10.1093/bioinformatics/bty403
BIOIMAGE INFORMATICS
GENOME ANALYSIS
snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions
Kari Nousiainen and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4112–4114, https://doi.org/10.1093/bioinformatics/bty460
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Katarzyna Z Kedzierska and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4115–4117, https://doi.org/10.1093/bioinformatics/bty485
Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes
Blanca Taboada and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4118–4120, https://doi.org/10.1093/bioinformatics/bty496
PHYLOGENETICS
Nextstrain: real-time tracking of pathogen evolution
James Hadfield and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4121–4123, https://doi.org/10.1093/bioinformatics/bty407
STRUCTURAL BIOINFORMATICS
13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA
A A Icazatti and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4124–4126, https://doi.org/10.1093/bioinformatics/bty470
MolArt: a molecular structure annotation and visualization tool
David Hoksza and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4127–4128, https://doi.org/10.1093/bioinformatics/bty489
SYSTEMS BIOLOGY
GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies
Kun Sun and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4129–4130, https://doi.org/10.1093/bioinformatics/bty524
DATA AND TEXT MINING
GateFinder: projection-based gating strategy optimization for flow and mass cytometry
Nima Aghaeepour and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4131–4133, https://doi.org/10.1093/bioinformatics/bty430
MetQy—an R package to query metabolic functions of genes and genomes
Andrea S Martinez-Vernon and others
Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4134–4137, https://doi.org/10.1093/bioinformatics/bty447
CORRIGENDA
Learned protein embeddings for machine learning
Kevin K Yang and others
Bioinformatics, Volume 34, Issue 23, December 2018, Page 4138, https://doi.org/10.1093/bioinformatics/bty455
Distinguishing prognostic and predictive biomarkers: an information theoretic approach
Konstantinos Sechidis and others
Bioinformatics, Volume 34, Issue 23, December 2018, Page 4139, https://doi.org/10.1093/bioinformatics/bty515
ERRATUM
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes
Rostam M Razban and others
Bioinformatics, Volume 34, Issue 23, December 2018, Page 4140, https://doi.org/10.1093/bioinformatics/bty516
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