Subject: Bioinformatics Table of Contents for 15 July 2018 ------=_Part_1283132528.1531422430760 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1283132528.1531422430760 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 14
 
15 July 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment 
 
Shijia Zhu; Gang Fang
 
 
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms 
 
Zilu Zhou; Weixin Wang; Li-San Wang; Nancy Ruonan Zhang
 
 
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile 
 
Ryuichiro Nakato; Katsuhiko Shirahige
 
 
 
SEQUENCE ANALYSIS
 
 
 
STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts border= 
 
Nicholas K Akers; Eric E Schadt ; Bojan Losic
 
 
Updating the 97% identity threshold for 16S ribosomal RNA OTUs 
 
Robert C Edgar
 
 
PriLive: privacy-preserving real-time filtering for next-generation sequencing 
 
Tobias P Loka; Simon H Tausch ; Piotr W Dabrowski; Aleksandar Radonić; Andreas Nitsche ...
 
 
 
GENE EXPRESSION
 
 
 
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing 
 
Yu Hu; Jennie Lin; Jian Hu; Gang Hu ; Kui Wang ...
 
 
Isoform-level gene expression patterns in single-cell RNA-sequencing data border= 
 
Trung Nghia Vu; Quin F Wills; Krishna R Kalari; Nifang Niu; Liewei Wang ...
 
 
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes border= 
 
Wanseon Lee ; Katharine Plant; Peter Humburg; Julian C Knight
 
 
 
SYSTEMS BIOLOGY
 
 
 
Principal metabolic flux mode analysis border= 
 
Sahely Bhadra; Peter Blomberg; Sandra Castillo; Juho Rousu
 
 
FWER and FDR control when testing multiple mediators 
 
Joshua N Sampson; Simina M Boca ; Steven C Moore; Ruth Heller
 
 
Prediction of potential disease-associated microRNAs using structural perturbation method 
 
Xiangxiang Zeng; Li Liu; Linyuan Lü; Quan Zou
 
 
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework  
 
Nikolaos Tsiantis; Eva Balsa-Canto; Julio R Banga
 
 
Network-based integration of multi-omics data for prioritizing cancer genes border= 
 
Christos Dimitrakopoulos; Sravanth Kumar Hindupur ; Luca Häfliger; Jonas Behr; Hesam Montazeri ...
 
 
 
DATA AND TEXT MINING
 
 
 
A new approach for interpreting Random Forest models and its application to the biology of ageing border=  
 
Fabio Fabris; Aoife Doherty; Daniel Palmer ; João Pedro de Magalhães; Alex A Freitas
 
 
Extrema-weighted feature extraction for functional data 
 
Willem van den Boom; Callie Mao; Rebecca A Schroeder; David B Dunson
 
 
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank 
 
Ronghui You; Zihan Zhang; Yi Xiong ; Fengzhu Sun; Hiroshi Mamitsuka ...
 
 
Exploiting and assessing multi-source data for supervised biomedical named entity recognition border= 
 
Dieter Galea; Ivan Laponogov; Kirill Veselkov
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix border= 
 
Giovanna Ambrosini; Romain Groux; Philipp Bucher
 
 
BPRMeth: a flexible Bioconductor package for modelling methylation profiles border= 
 
Chantriolnt-Andreas Kapourani; Guido Sanguinetti
 
 
 
SEQUENCE ANALYSIS
 
 
 
SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification 
 
Balázs Szalkai ; Vince Grolmusz
 
 
Parallelization of MAFFT for large-scale multiple sequence alignments border= 
 
Tsukasa Nakamura; Kazunori D Yamada; Kentaro Tomii; Kazutaka Katoh
 
 
FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data 
 
Yan-Bo Sun
 
 
AnaCoDa: analyzing codon data with Bayesian mixture models 
 
Cedric Landerer; Alexander Cope; Russell Zaretzki; Michael A Gilchrist
 
 
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences  
 
Zhen Chen; Pei Zhao; Fuyi Li ; André Leier; Tatiana T Marquez-Lago ...
 
 
NeSSie: a tool for the identification of approximate DNA sequence symmetries 
 
Michele Berselli; Enrico Lavezzo; Stefano Toppo
 
 
 
PHYLOGENETICS
 
 
 
NGSphy: phylogenomic simulation of next-generation sequencing data 
 
Merly Escalona; Sara Rocha; David Posada
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
eMolTox: prediction of molecular toxicity with confidence  
 
Changge Ji; Fredrik Svensson; Azedine Zoufir ; Andreas Bender
 
 
 
GENE EXPRESSION
 
 
 
anexVis: visual analytics framework for analysis of RNA expression 
 
Diem-Trang Tran ; Tian Zhang; Ryan Stutsman; Matthew Might; Umesh R Desai ...
 
 
 
DATA AND TEXT MINING
 
 
 
pymzML v2.0: introducing a highly compressed and seekable gzip format  
 
M Kösters; J Leufken; S Schulze ; K Sugimoto; J Klein ...
 
 
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC 
 
Ruidong Li; Han Qu; Shibo Wang; Julong Wei; Le Zhang ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
CarbonylDB: a curated data-resource of protein carbonylation sites 
 
R Shyama Prasad Rao; Ning Zhang ; Dong Xu; Ian Max Møller
 
 
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