Subject: Bioinformatics Table of Contents for 15 January 2018 ------=_Part_1925044827.1514736731198 Content-Type: text/plain;charset=UTF-8 Oxford Academic [[HeaderAdvertisingToken]] https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxford_logo.jpg?g72331686458 (http://click.skem1.com/click/lpx3j-d656f8-63so3tc1/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?lpx3j--ply5-63so3tc1&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/lpx3j-d656f9-63so3tc2/) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. The content of this email is protected by copyright. https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxforde_university.jpg?g72331733632 (http://click.skem1.com/click/lpx3j-d656fa-63so3tc2/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1925044827.1514736731198 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 2
 
15 January 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases 
 
Gulce Kale; Erman Ayday; Oznur Tastan
 
 
 
SEQUENCE ANALYSIS
 
 
 
DART: a fast and accurate RNA-seq mapper with a partitioning strategy border= 
 
Hsin-Nan Lin; Wen-Lian Hsu
 
 
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction 
 
Jun Ding; Xiaoman Li ; Haiyan Hu
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
In silico identification of rescue sites by double force scanning border= 
 
Matteo Tiberti; Alessandro Pandini; Franca Fraternali; Arianna Fornili
 
 
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments 
 
Dmytro Guzenko; Sergei V Strelkov
 
 
 
 
IntPred: a structure-based predictor of protein'protein interaction sites border= 
 
Thomas C Northey; Anja BareĊĦić ; Andrew C R Martin
 
 
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain 
 
Jing Yang; Hong-Bin Shen
 
 
 
SYSTEMS BIOLOGY
 
 
 
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations 
 
Qiu Xiao; Jiawei Luo; Cheng Liang; Jie Cai; Pingjian Ding
 
 
NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources border= 
 
Yiming Kang; Hien-Haw Liow ; Ezekiel J Maier; Michael R Brent
 
 
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles border= 
 
Nan Papili Gao; S M Minhaz Ud-Dean; Olivier Gandrillon; Rudiyanto Gunawan
 
 
 
 
 
DATA AND TEXT MINING
 
 
 
A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network 
 
Yingli Zhong ; Ping Xuan; Xiao Wang; Tiangang Zhang; Jianzhong Li ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
A novel SCCA approach via truncated â"'1-norm and truncated group lasso for brain imaging genetics 
 
Lei Du ; Kefei Liu; Tuo Zhang; Xiaohui Yao; Jingwen Yan ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts border= 
 
Chris Chatzinakos; Donghyung Lee; Bradley T Webb; Vladimir I Vladimirov; Kenneth S Kendler ...
 
 
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome 
 
Roberto Vera Alvarez; Shan Li ; David Landsman; Ivan Ovcharenko
 
 
 
PHYLOGENETICS
 
 
 
Phandango: an interactive viewer for bacterial population genomics border= 
 
James Hadfield; Nicholas J Croucher; Richard J Goater ; Khalil Abudahab; David M Aanensen ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction border=  
 
Guillaume Brysbaert; Kevin Lorgouilloux; Wim F Vranken ; Marc F Lensink
 
 
Meta-server for automatic analysis, scoring and ranking of docking models 
 
Anastasia A Anashkina ; Yuri Kravatsky; Eugene Kuznetsov; Alexander A Makarov; Alexei A Adzhubei
 
 
 
GENE EXPRESSION
 
 
 
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data 
 
Christopher J Green ; Matthew R Gazzara; Yoseph Barash
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling 
 
Daniel Boloc; Natalia Rodríguez; Patricia Gassó; Josep F Abril ; Miquel Bernardo ...
 
 
LinkageMapView'rendering high-resolution linkage and QTL maps border= 
 
Lisa A Ouellette; Robert W Reid; Steven G Blanchard; Cory R Brouwer
 
 
 
SYSTEMS BIOLOGY
 
 
 
regNet: an R package for network-based propagation of gene expression alterations 
 
Michael Seifert ; Andreas Beyer
 
 
MetExploreViz: web component for interactive metabolic network visualization 
 
Maxime Chazalviel ; Clément Frainay; Nathalie Poupin; Florence Vinson; Benjamin Merlet ...
 
 
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks 
 
Huey Eng Chua; Sourav S Bhowmick; Jie Zheng
 
 
 
DATA AND TEXT MINING
 
 
 
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry border= 
 
Joe Wandy; Yunfeng Zhu; Justin J J van der Hooft; Rónán Daly; Michael P Barrett ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction 
 
Kun-Hsing Yu; Michael R Fitzpatrick; Luke Pappas; Warren Chan; Jessica Kung ...
 
 
HoTResDB: host transcriptional response database for viral hemorrhagic fevers border= 
 
Jonathan Lo ; Deric Zhang; Emily Speranza; Jose A Negron; John H Connor
 
 
LETTER TO THE EDITOR
 
 
 
 
GENOME ANALYSIS
 
 
 
Gearing up to handle the mosaic nature of life in the quest for orthologs border= 
 
Kristoffer Forslund; Cecile Pereira; Salvador Capella-Gutierrez; Alan Sousa da Silva; Adrian Altenhoff ...
 
 
SPECIAL ISSUE: RECOMB-CCB2017
 
 
 
 
GENOME ANALYSIS
 
 
 
Detecting presence of mutational signatures in cancer with confidence 
 
Xiaoqing Huang; Damian Wojtowicz; Teresa M Przytycka
 
 
Identification of copy number variations and translocations in cancer cells from Hi-C data 
 
Abhijit Chakraborty; Ferhat Ay
 
 
 
SEQUENCE ANALYSIS
 
 
 
Identifying simultaneous rearrangements in cancer genomes border= 
 
Layla Oesper; Simone Dantas ; Benjamin J Raphael
 
 
Identifying structural variants using linked-read sequencing data 
 
Rebecca Elyanow ; Hsin-Ta Wu; Benjamin J Raphael
 
 
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