Subject: Briefings in Bioinformatics Table of Contents for September 2018 ------=_Part_500627939.1538415598170 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_500627939.1538415598170 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Briefings in Bioinformatics  
Volume 19 Issue 5
 
September 2018
 
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Papers
 
 
 
GWAS summary-based pathway analysis correcting for the genetic confounding impact of environmental exposures 
 
Qianrui Fan; Feng Zhang; Wenyu Wang; Jiawen Xu ; Jingcan Hao ...
 
 
DNA copy number profiling using single-cell sequencing 
 
Xuefeng Wang; Hao Chen; Nancy R Zhang
 
 
A survey of the approaches for identifying differential methylation using bisulfite sequencing data 
 
Adib Shafi; Cristina Mitrea; Tin Nguyen; Sorin Draghici
 
 
Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome 
 
Shengli Li; Jiwei Zhang; Shenglin Huang; Xianghuo He
 
 
Strategies for processing and quality control of Illumina genotyping arrays 
 
Shilin Zhao; Wang Jing; David C Samuels; Quanghu Sheng ; Yu Shyr ...
 
 
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions 
 
Ciaran Evans; Johanna Hardin; Daniel M Stoebel
 
 
Individualized analysis of differentially expressed miRNAs with application to the identification of miRNAs deregulated commonly in lung cancer tissues 
 
Haidan Yan; Hao Cai; Qingzhou Guan; Jun He ; Juan Zhang ...
 
 
Circular RNA identification based on multiple seed matching 
 
Yuan Gao; Jinyang Zhang; Fangqing Zhao
 
 
Comparison of the general co-expression landscapes between human and mouse 
 
Di Liu; Linna Zhao; Yang Chen; Zhaoyang Wang ; Jing Xu ...
 
 
Review and comparative assessment of sequence-based predictors of protein-binding residues 
 
Jian Zhang; Lukasz Kurgan
 
 
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity 
 
Huilin Wang; Liubin Feng; Geoffrey I Webb; Lukasz Kurgan ; Jiangning Song ...
 
 
Molecular dynamics recipes for genome research 
 
Tommaso Biagini; Giovanni Chillemi; Gianluigi Mazzoccoli; Alessandro Grottesi ; Caterina Fusilli ...
 
 
Detection of drug'drug interactions through data mining studies using clinical sources, scientific literature and social media 
 
Santiago Vilar; Carol Friedman; George Hripcsak
 
 
A review of network-based approaches to drug repositioning 
 
Maryam Lotfi Shahreza; Nasser Ghadiri; Sayed Rasoul Mousavi; Jaleh Varshosaz ; James R Green
 
 
Comparative analysis of de novo assemblers for variation discovery in personal genomes border=  
 
Shulan Tian; Huihuang Yan; Eric W Klee ; Michael Kalmbach; Susan L Slager
 
 
CASH: a constructing comprehensive splice site method for detecting alternative splicing events 
 
Wenwu Wu; Jie Zong; Ning Wei; Jian Cheng ; Xuexia Zhou ...
 
 
Experimental design and data analysis of Ago-RIP-Seq experiments for the identification of microRNA targets 
 
Diana Tichy; Julia Maria Anna Pickl; Axel Benner; Holger Sültmann
 
 
Long noncoding RNA: a crosslink in biological regulatory network 
 
Yuwei Zhang; Yang Tao; Qi Liao
 
 
Row versus column correlations: avoiding the ecological fallacy in RNA/protein expression studies 
 
Jonathon J O'Brien; Harsha P Gunawardena; Bahjat F Qaqish
 
 
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? 
 
Thilo Muth; Bernhard Y Renard
 
 
Identification of differentially expressed peptides in high-throughput proteomics data 
 
Michiel P van Ooijen; Victor L Jong; Marinus J C Eijkemans; Albert J R Heck ; Arno C Andeweg ...
 
 
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges 
 
Sheng-You Huang
 
 
Context-based retrieval of functional modules in protein'protein interaction networks 
 
Maria Pamela Dobay; Silke Stertz; Mauro Delorenzi
 
 
The anatomy of phenotype ontologies: principles, properties and applications border=  
 
Georgios V Gkoutos; Paul N Schofield; Robert Hoehndorf
 
 
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites 
 
Arvind K Chavali; Seung Y Rhee
 
 
Improving data workflow systems with cloud services and use of open data for bioinformatics research border=  
 
Md Rezaul Karim; Audrey Michel; Achille Zappa ; Pavel Baranov; Ratnesh Sahay ...
 
 
Dynamic modeling and network approaches for omics time course data: overview of computational approaches and applications 
 
Yulan Liang; Arpad Kelemen
 
 
 
Software Review
 
 
 
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data 
 
Bingqiang Liu; Jinyu Yang; Yang Li; Adam McDermaid ; Qin Ma
 
 
 
Book Review
 
 
 
Next-generation sequencing data analysis 
 
Christian T K-H Stadtländer
 
 
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