Subject: Bioinformatics Table of Contents for 01 February 2019 ------=_Part_733667502.1549569374156 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_733667502.1549569374156 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 35 Issue 3
 
01 February 2019
 
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DISCOVERY NOTE
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples 
 
Hua Yu; Lu Lu; Bingke Jiao; Chengzhi Liang
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Re-identification of individuals in genomic data-sharing beacons via allele inference 
 
Nora von Thenen; Erman Ayday; A Ercument Cicek
 
 
 
SEQUENCE ANALYSIS
 
 
 
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes border= 
 
Luca Parca; Bruno Ariano ; Andrea Cabibbo; Marco Paoletti; Annalaura Tamburrini ...
 
 
A parallel computational framework for ultra-large-scale sequence clustering analysis 
 
Wei Zheng; Qi Mao; Robert J Genco; Jean Wactawski-Wende ; Michael Buck ...
 
 
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters 
 
Xinguo Lu; Xin Qian; Xing Li; Qiumai Miao ; Shaoliang Peng
 
 
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC 
 
Xiang Cheng; Wei-Zhong Lin; Xuan Xiao; Kuo-Chen Chou
 
 
Dynamic compression schemes for graph coloring border= 
 
Harun Mustafa; Ingo Schilken; Mikhail Karasikov ; Carsten Eickhoff; Gunnar Rätsch ...
 
 
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics 
 
Chen Sun; Paul Medvedev
 
 
Scaling read aligners to hundreds of threads on general-purpose processors border=  
 
Ben Langmead; Christopher Wilks; Valentin Antonescu ; Rone Charles
 
 
StackDPPred: a stacking based prediction of DNA-binding protein from sequence 
 
Avdesh Mishra; Pujan Pokhrel; Md Tamjidul Hoque
 
 
Effusion: prediction of protein function from sequence similarity networks border=  
 
Jeffrey M Yunes; Patricia C Babbitt
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Automatic recognition of ligands in electron density by machine learning 
 
Marcin Kowiel; Dariusz Brzezinski; Przemyslaw J Porebski; Ivan G Shabalin ; Mariusz Jaskolski ...
 
 
SKEMPI 2.0: an updated benchmark of changes in protein'protein binding energy, kinetics and thermodynamics upon mutation border= 
 
Justina JankauskaitÄ- ; Brian Jiménez-García; Justas DapkÅ«nas; Juan Fernández-Recio; Iain H Moal
 
 
BIPSPI: a method for the prediction of partner-specific protein'protein interfaces border=  
 
Ruben Sanchez-Garcia; C O S Sorzano; J M Carazo ; Joan Segura
 
 
 
GENE EXPRESSION
 
 
 
SMSSVD: SubMatrix Selection Singular Value Decomposition border=  
 
Rasmus Henningsson; Magnus Fontes
 
 
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies 
 
Shiquan Sun; Jiaqiang Zhu; Sahar Mozaffari; Carole Ober; Mengjie Chen ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Random walk with restart on multiplex and heterogeneous biological networks 
 
Alberto Valdeolivas; Laurent Tichit; Claire Navarro; Sophie Perrin ; Gaëlle Odelin ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures border= 
 
Bruce A Corliss; H Clifton Ray ; James T Patrie; Jennifer Mansour; Sam Kesting ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MAVIS: merging, annotation, validation, and illustration of structural variants 
 
Caralyn Reisle; Karen L Mungall; Caleb Choo; Daniel Paulino ; Dustin W Bleile ...
 
 
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations border=  
 
Haiming Tang; Robert D Finn; Paul D Thomas
 
 
 
SEQUENCE ANALYSIS
 
 
 
Simulating Illumina metagenomic data with InSilicoSeq border=  
 
Hadrien Gourlé; Oskar Karlsson-Lindsjö; Juliette Hayer ; Erik Bongcam-Rudloff
 
 
MinIONQC: fast and simple quality control for MinION sequencing data border=  
 
R Lanfear; M Schalamun; D Kainer ; W Wang; B Schwessinger
 
 
 
PHYLOGENETICS
 
 
 
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R 
 
Emmanuel Paradis; Klaus Schliep
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data 
 
Zongxiao He; Lu Wang; Andrew T DeWan; Suzanne M Leal
 
 
 
SYSTEMS BIOLOGY
 
 
 
MoDentify : phenotype-driven module identification in metabolomics networks at different resolutions border= 
 
Kieu Trinh Do; David J N -P Rasp ; Gabi Kastenmüller; Karsten Suhre; Jan Krumsiek
 
 
gMCS: fast computation of genetic minimal cut sets in large networks 
 
Iñigo Apaolaza; Luis Vitores Valcarcel; Francisco J Planes
 
 
 
DATA AND TEXT MINING
 
 
 
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries 
 
Zainab Noor; Jemma X Wu; Dana Pascovici; Abidali Mohamedali; Mark P Molloy ...
 
 
 
CORRIGENDUM
 
 
 
polymapR'linkage analysis and genetic map construction from F1 populations of outcrossing polyploids border= 
 
Peter M Bourke; Geert van Geest ; Roeland E Voorrips; Johannes Jansen; Twan Kranenburg ...
 
 
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