Subject: Bioinformatics Table of Contents for 15 August 2018 ------=_Part_1499975563.1534011844191 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1499975563.1534011844191 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 16
 
15 August 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs 
 
Oana Ursu; Nathan Boley; Maryna Taranova; Y X Rachel Wang; Galip Gurkan Yardimci ...
 
 
ASGART: fast and parallel genome scale segmental duplications mapping 
 
Franklin Delehelle; Sylvain Cussat-Blanc ; Jean-Marc Alliot; Hervé Luga; Patricia Balaresque
 
 
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data 
 
Xiwei Sun; Yi Han; Liyuan Zhou; Enguo Chen ; Bingjian Lu ...
 
 
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease border= 
 
Mariusz Butkiewicz; Elizabeth E Blue; Yuk Yee Leung; Xueqiu Jian; Edoardo Marcora ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Nimbus: a design-driven analyses suite for amplicon-based NGS data border= 
 
R W W Brouwer ; M C G N van den Hout; C E M Kockx; E Brosens; B Eussen ...
 
 
Deep learning improves antimicrobial peptide recognition border= 
 
Daniel Veltri; Uday Kamath ; Amarda Shehu
 
 
FaStore: a space-saving solution for raw sequencing data 
 
ukasz Roguski ; Idoia Ochoa; Mikel Hernaez; Sebastian Deorowicz
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules 
 
Emilie Neveu; Petr Popov; Alexandre Hoffmann; Angelo Migliosi ; Xavier Besseron ...
 
 
 
GENE EXPRESSION
 
 
 
A reference peptide database for proteome quantification based on experimental mass spectrum response curves border= 
 
Wanlin Liu; Lai Wei; Jianan Sun; Jinwen Feng; Gaigai Guo ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
SMMB: a stochastic Markov blanket framework strategy for epistasis detection in GWAS 
 
Clément Niel; Christine Sinoquet ; Christian Dina; Ghislain Rocheleau
 
 
Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr border= 
 
Florian Privé; Hugues Aschard; Andrey Ziyatdinov; Michael G B Blum
 
 
LSMM: a statistical approach to integrating functional annotations with genome-wide association studies 
 
Jingsi Ming; Mingwei Dai; Mingxuan Cai; Xiang Wan; Jin Liu ...
 
 
Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models 
 
Ping Zeng; Xingjie Hao; Xiang Zhou
 
 
 
SYSTEMS BIOLOGY
 
 
 
Kernelized rank learning for personalized drug recommendation border= 
 
Xiao He; Lukas Folkman ; Karsten Borgwardt
 
 
A novel computational approach for drug repurposing using systems biology 
 
Azam Peyvandipour ; Nafiseh Saberian; Adib Shafi; Michele Donato; Sorin Draghici
 
 
The latent geometry of the human protein interaction network border= 
 
Gregorio Alanis-Lobato; Pablo Mier ; Miguel Andrade-Navarro
 
 
 
DATA AND TEXT MINING
 
 
 
Predicting serious rare adverse reactions of novel chemicals border= 
 
Aleksandar Poleksic; Lei Xie
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Efficient population-scale variant analysis and prioritization with VAPr 
 
Amanda Birmingham ; Adam M Mark; Carlo Mazzaferro; Guorong Xu; Kathleen M Fisch
 
 
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle 
 
Simone Rizzetto; David N P Koppstein; Jerome Samir ; Mandeep Singh; Joanne H Reed ...
 
 
 
PHYLOGENETICS
 
 
 
ALPHA: a toolkit for Automated Local PHylogenomic Analyses 
 
R A Leo Elworth; Chabrielle Allen; Travis Benedict; Peter Dulworth; Luay Nakhleh
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
ONETOOL for the analysis of family-based big data border= 
 
Yeunjoo E Song ; Sungyoung Lee; Kyungtaek Park; Robert C Elston; Hyeon-Jong Yang ...
 
 
POPdemog: visualizing population demographic history from simulation scripts 
 
Ying Zhou; Xiaowen Tian; Brian L Browning ; Sharon R Browning
 
 
 
SYSTEMS BIOLOGY
 
 
 
Reactome Pengine: a web-logic API to the Homo sapiens reactome border= 
 
Samuel R Neaves; Sophia Tsoka; Louise A C Millard
 
 
pyNBS: a Python implementation for network-based stratification of tumor mutations 
 
Justin K Huang; Tongqiu Jia; Daniel E Carlin; Trey Ideker
 
 
A comprehensive web tool for toehold switch design 
 
Andrew Ching-Yuet To; David Ho-Ting Chu; Angela Ruoning Wang ; Frances Cheuk-Yau Li; Alan Wai-On Chiu ...
 
 
 
DATA AND TEXT MINING
 
 
 
iterClust: a statistical framework for iterative clustering analysis border= 
 
Hongxu Ding; Wanxin Wang; Andrea Califano
 
 
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles 
 
Zhenjia Wang; Mete Civelek; Clint L Miller ; Nathan C Sheffield; Michael J Guertin ...
 
 
REVIEW
 
 
 
 
GENE EXPRESSION
 
 
 
Understanding sequencing data as compositions: an outlook and review border= 
 
Thomas P Quinn; Ionas Erb; Mark F Richardson; Tamsyn M Crowley
 
 
CORRIGENDUM
 
 
 
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq 
 
Xing Tang; Arunima Srivastava; Huayang Liu; Raghu Machiraju ; Kun Huang ...
 
 
ERRATUM
 
 
 
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems border= 
 
Dennis Pischel ; Kai Sundmacher; Robert J Flassig
 
 
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