Subject: Bioinformatics Table of Contents for 15 September 2018 ------=_Part_502116570.1537205627634 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_502116570.1537205627634 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 18
 
15 September 2018
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
TiSAn: estimating tissue-specific effects of coding and non-coding variants border=  
 
Kévin Vervier; Jacob J Michaelson
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling 
 
Hui Peng; Yi Zheng; Michael Blumenstein; Dacheng Tao ; Jinyan Li
 
 
Identifying differentially methylated sites in samples with varying tumor purity 
 
Antti Häkkinen; Amjad Alkodsi; Chiara Facciotto; Kaiyang Zhang ; Katja Kaipio ...
 
 
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC 
 
Bin Liu; Fan Weng; De-Shuang Huang; Kuo-Chen Chou
 
 
 
SEQUENCE ANALYSIS
 
 
 
Minimap2: pairwise alignment for nucleotide sequences 
 
Heng Li
 
 
MechRNA: prediction of lncRNA mechanisms from RNA'RNA and RNA'protein interactions border=  
 
Alexander R Gawronski; Michael Uhl; Yajia Zhang ; Yen-Yi Lin; Yashar S Niknafs ...
 
 
DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters 
 
Semmy Wellem Taju; Trinh-Trung-Duong Nguyen; Nguyen-Quoc-Khanh Le; Rosdyana Mangir Irawan Kusuma ; Yu-Yen Ou
 
 
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping 
 
Daniele Raimondi; Gabriele Orlando; Yves Moreau; Wim F Vranken
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
TMCrys: predict propensity of success for transmembrane protein crystallization border= 
 
Julia K Varga; Gábor E Tusnády
 
 
RBind: computational network method to predict RNA binding sites 
 
Kaili Wang; Yiren Jian; Huiwen Wang; Chen Zeng ; Yunjie Zhao
 
 
 
GENE EXPRESSION
 
 
 
TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers border= 
 
Florian G Pflug; Arndt von Haeseler
 
 
A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues 
 
Dingge Ying; Mulin Jun Li; Pak Chung Sham; Miaoxin Li
 
 
EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy 
 
Xianxiao Zhou; Minghui Wang; Igor Katsyv; Hanna Irie ; Bin Zhang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization 
 
Sudhir Ghandikota; Gurjit K Khurana Hershey; Tesfaye B Mersha
 
 
 
SYSTEMS BIOLOGY
 
 
 
Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis 
 
Zi Wang; Dali Wang; Chengcheng Li; Yichi Xu ; Husheng Li ...
 
 
BNPMDA: Bipartite Network Projection for MiRNA'Disease Association prediction 
 
Xing Chen; Di Xie; Lei Wang; Qi Zhao ; Zhu-Hong You ...
 
 
Automatic selection of verification tools for efficient analysis of biochemical models border=  
 
Mehmet Emin Bakir; Savas Konur; Marian Gheorghe ; Natalio Krasnogor; Mike Stannett
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields 
 
Sean Robinson; Michael J Courtney
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation 
 
Bastian Pfeifer; Martin J Lercher
 
 
GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor 
 
Pau Puigdevall; Robert Castelo
 
 
miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer 
 
Yin Tong; Beibei Ru; Jiangwen Zhang
 
 
 
PHYLOGENETICS
 
 
 
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss border= 
 
Mukul S Bansal; Manolis Kellis; Misagh Kordi; Soumya Kundu
 
 
 
GENE EXPRESSION
 
 
 
CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones 
 
Sören Müller; Ara Cho; Siyuan J Liu; Daniel A Lim; Aaron Diaz
 
 
PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data 
 
Aimin Yan; Yuguang Ban; Zhen Gao; Xi Chen ; Lily Wang
 
 
DEsingle for detecting three types of differential expression in single-cell RNA-seq data 
 
Zhun Miao; Ke Deng; Xiaowo Wang; Xuegong Zhang
 
 
 
SYSTEMS BIOLOGY
 
 
 
MetaBridge: enabling network-based integrative analysis via direct protein interactors of metabolites 
 
Samuel J Hinshaw; Amy H Y Lee; Erin E Gill; Robert E W Hancock
 
 
 
DATA AND TEXT MINING
 
 
 
comoRbidity: an R package for the systematic analysis of disease comorbidities border=  
 
Alba Gutiérrez-Sacristán; Àlex Bravo; Alexia Giannoula ; Miguel A Mayer; Ferran Sanz ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
GlycoStore: a database of retention properties for glycan analysis 
 
Sophie Zhao; Ian Walsh; Jodie L Abrahams; Louise Royle ; Terry Nguyen-Khuong ...
 
 
MARDy: Mycology Antifungal Resistance Database border= 
 
Anthony Nash; Thomas Sewell; Rhys A Farrer ; Alireza Abdolrasouli; Jennifer M G Shelton ...
 
 
CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies border= 
 
Carles Hernandez-Ferrer; Juan R Gonzalez
 
 
 
BIOIMAGE INFORMATICS
 
 
 
ImagePy: an open-source, Python-based and platform-independent software package for bioimage analysis 
 
Anliang Wang; Xiaolong Yan; Zhijun Wei
 
 
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