Subject: Bioinformatics Table of Contents for 15 October 2018 ------=_Part_713692245.1539624119284 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_713692245.1539624119284 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 20
 
15 October 2018
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways 
 
Zhi-Kai Yang; Hao Luo; Yanming Zhang; Baijing Wang; Feng Gao
 
 
 
ORIGINAL PAPERS
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Predicting RNA'protein binding sites and motifs through combining local and global deep convolutional neural networks 
 
Xiaoyong Pan; Hong-Bin Shen
 
 
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading 
 
René Rahn; Stefan Budach; Pascal Costanza; Marcel Ehrhardt ; Jonny Hancox ...
 
 
Base-pair resolution detection of transcription factor binding site by deep deconvolutional network 
 
Sirajul Salekin; Jianqiu Michelle Zhang; Yufei Huang
 
 
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes 
 
Raffaele Giancarlo; Simona E Rombo; Filippo Utro
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Efficient flexible backbone protein'protein docking for challenging targets 
 
Nicholas A Marze; Shourya S Roy Burman; William Sheffler; Jeffrey J Gray
 
 
 
GENE EXPRESSION
 
 
 
JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions 
 
Wenping Deng; Kui Zhang; Sanzhen Liu; Patrick X Zhao; Shizhong Xu ...
 
 
Edge-group sparse PCA for network-guided high dimensional data analysis 
 
Wenwen Min; Juan Liu; Shihua Zhang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
geck: trio-based comparative benchmarking of variant calls border=  
 
Péter Kómár; Deniz Kural
 
 
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 ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
REGGAE: a novel approach for the identification of key transcriptional regulators border= 
 
Tim Kehl; Lara Schneider ; Kathrin Kattler; Daniel Stöckel; Jenny Wegert ...
 
 
Application of network smoothing to glycan LC-MS profiling 
 
Joshua Klein; Luis Carvalho; Joseph Zaia
 
 
Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome 
 
Lixin Cheng; Kwong-Sak Leung
 
 
 
DATA AND TEXT MINING
 
 
 
Covariate-adjusted heatmaps for visualizing biological data via correlation decomposition 
 
Han-Ming Wu; Yin-Jing Tien; Meng-Ru Ho; Hai-Gwo Hwu; Wen-chang Lin ...
 
 
D3NER: biomedical named entity recognition using CRF-biLSTM improved with fine-tuned embeddings of various linguistic information 
 
Thanh Hai Dang; Hoang-Quynh Le; Trang M Nguyen; Sinh T Vu
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA'disease association 
 
Yang Yang; Xiaofeng Fu; Wenhao Qu ; Yiqun Xiao; Hong-Bin Shen
 
 
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes 
 
Rostam M Razban; Amy I Gilson; Niamh Durfee; Hendrik Strobelt; Kasper Dinkla ...
 
 
MRMAssayDB: an integrated resource for validated targeted proteomics assays border=  
 
Pallab Bhowmick; Yassene Mohammed; Christoph H Borchers
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
AnnotSV: an integrated tool for structural variations annotation 
 
Véronique Geoffroy; Yvan Herenger; Arnaud Kress; Corinne Stoetzel ; Amélie Piton ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses 
 
Kathrin M Seibt; Thomas Schmidt; Tony Heitkam
 
 
YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU border=  
 
Daniel Quang; Yuanfang Guan; Stephen C J Parker
 
 
bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens 
 
Jiaxing Lin; Jeremy Gresham; Tongrong Wang; So Young Kim ; James Alvarez ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry border= 
 
Joshua M A Bullock; Konstantinos Thalassinos; Maya Topf
 
 
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories border= 
 
Adam Jurcik ; David Bednar; Jan Byska; Sergio M Marques; Katarina Furmanova ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis 
 
William M B Edmands; Josie Hayes; Stephen M Rappaport
 
 
pyABC: distributed, likelihood-free inference 
 
Emmanuel Klinger; Dennis Rickert; Jan Hasenauer
 
 
PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data border=  
 
Cheng Chang; Kaikun Xu; Chaoping Guo ; Jinxia Wang; Qi Yan ...
 
 
 
DATA AND TEXT MINING
 
 
 
Transform-MinER: transforming molecules in enzyme reactions border=  
 
Jonathan D Tyzack; Antonio J M Ribeiro; Neera Borkakoti ; Janet M Thornton
 
 
 
CORRIGENDUM
 
 
 
Snakemake'a scalable bioinformatics workflow engine 
 
Johannes Köster; Sven Rahmann
 
 
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