Subject: Briefings in Bioinformatics Table of Contents for November 2018 ------=_Part_1707178359.1543683392075 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1707178359.1543683392075 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Briefings in Bioinformatics  
Volume 19 Issue 6
 
November 2018
 
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Paper
 
 
 
Mutational signatures and mutable motifs in cancer genomes 
 
Igor B Rogozin; Youri I Pavlov; Alexander Goncearenco; Subhajyoti De ; Artem G Lada ...
 
 
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes 
 
Shun-Long Weng; Kai-Yao Huang; Julia Tzu-Ya Weng; Fang-Yu Hung; Tzu-Hao Chang ...
 
 
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments 
 
James W Marsh; Regan J Hayward; Amol C Shetty; Anup Mahurkar ; Michael S Humphrys ...
 
 
Subcellular locations of potential cell wall proteins in plants: predictors, databases and cross-referencing 
 
Xiaolin Wu; Qinbin Zhang; Zhaokun Wu; Fuju Tai ; Wei Wang
 
 
Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets 
 
Gaston K Mazandu; Emile R Chimusa; Kayleigh Rutherford ; Elsa-Gayle Zekeng; Zoe Z Gebremariam ...
 
 
In silico polypharmacology of natural products 
 
Jiansong Fang; Chuang Liu; Qi Wang; Ping Lin ; Feixiong Cheng
 
 
Advances in computational approaches in identifying synergistic drug combinations 
 
Zhen Sheng; Yi Sun; Zuojing Yin; Kailin Tang ; Zhiwei Cao
 
 
Pioneering topological methods for network-based drug'target prediction by exploiting a brain-network self-organization theory border= 
 
Claudio Durán ; Simone Daminelli; Josephine M Thomas; V Joachim Haupt; Michael Schroeder ...
 
 
Optimizing drug development in oncology by clinical trial simulation: Why and how? 
 
Jocelyn Gal; Gérard Milano; Jean-Marc Ferrero; Esma Saâda-Bouzid ; Julien Viotti ...
 
 
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling 
 
Supreeta Vijayakumar; Max Conway; Pietro Lió; Claudio Angione
 
 
Deep learning for healthcare: review, opportunities and challenges 
 
Riccardo Miotto; Fei Wang; Shuang Wang; Xiaoqian Jiang ; Joel T Dudley
 
 
Power and sample size calculations for high-throughput sequencing-based experiments 
 
Chung-I Li; David C Samuels; Ying-Yong Zhao; Yu Shyr ; Yan Guo
 
 
Nanopore sequencing data analysis: state of the art, applications and challenges 
 
Alberto Magi; Roberto Semeraro; Alessandra Mingrino; Betti Giusti ; Romina D'Aurizio
 
 
ceRNAs in plants: computational approaches and associated challenges for target mimic research 
 
Alexandre Rossi Paschoal; Irma Lozada-Chávez; Douglas Silva Domingues; Peter F Stadler
 
 
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications border=  
 
Silvia Bottini; David Pratella; Valerie Grandjean ; Emanuela Repetto; Michele Trabucchi
 
 
Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data 
 
Ya Cui; Xiaowei Chen; Yiwei Niu; Dongpeng Wang ; Huaxia Luo ...
 
 
CircView: a visualization and exploration tool for circular RNAs 
 
Jing Feng; Yu Xiang; Siyu Xia; Huan Liu ; Jun Wang ...
 
 
Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow 
 
Dongliang Yu; Zhonghai Tang; Chaogang Shao; Xiaoxia Ma ; Taihe Xiang ...
 
 
SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data 
 
Qiong Zhang; Wei Liu; Chunjie Liu; Sheng-Yan Lin ; An-Yuan Guo
 
 
Proper joint analysis of summary association statistics requires the adjustment of heterogeneity in SNP coverage pattern 
 
Han Zhang; William Wheeler; Lei Song; Kai Yu
 
 
A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation border= 
 
Tommi Välikangas ; Tomi Suomi; Laura L Elo
 
 
A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia 
 
Imene Garali; Isaac M Adanyeguh; Farid Ichou; Vincent Perlbarg ; Alexandre Seyer ...
 
 
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data border=  
 
Jingwen Yan; Shannon L Risacher; Li Shen ; Andrew J Saykin
 
 
Mathematical modeling and computational prediction of cancer drug resistance border=  
 
Xiaoqiang Sun; Bin Hu
 
 
Biomedical text mining for research rigor and integrity: tasks, challenges, directions 
 
Halil Kilicoglu
 
 
 
Software Review
 
 
 
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes border= 
 
Sheng-Yong Niu; Jinyu Yang; Adam McDermaid; Jing Zhao; Yu Kang ...
 
 
 
Opinion Note
 
 
 
The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model 
 
Lidan Sun; Mengmeng Sang; Chenfei Zheng; Dongyang Wang; Hexin Shi ...
 
 
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