Subject: Bioinformatics Table of Contents for 15 November 2017 ------=_Part_1475804730.1510589489289 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/kvotq-clz6me-63so3tc3/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?kvotq--ply5-63so3tc9&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/kvotq-clz6mf-63so3tc4/) 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/kvotq-clz6mg-63so3tc5/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1475804730.1510589489289 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 33 Issue 22
 
15 November 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise border= 
 
José Carbonell-Caballero; Alicia Amadoz; Roberto Alonso; Marta R Hidalgo ; Cankut Çubuk ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties 
 
Wei Chen; Hui Yang; Pengmian Feng; Hui Ding; Hao Lin
 
 
pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites 
 
Xiang Cheng; Shu-Guang Zhao; Wei-Zhong Lin; Xuan Xiao; Kuo-Chen Chou
 
 
Motif independent identification of potential RNA G-quadruplexes by G4RNA screener border= 
 
Jean-Michel Garant; Jean-Pierre Perreault; Michelle S Scott
 
 
SPRINT: an SNP-free toolkit for identifying RNA editing sites border= 
 
Feng Zhang; Yulan Lu ; Sijia Yan; Qinghe Xing; Weidong Tian
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology 
 
Zixuan Cang; Guo-Wei Wei
 
 
 
GENE EXPRESSION
 
 
 
Towards clinically more relevant dissection of patient heterogeneity via survival-based Bayesian clustering 
 
Ashar Ahmad ; Holger Fröhlich
 
 
Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data border= 
 
Carl Brunius; Anders Pedersen; Daniel Malmodin; B Göran Karlsson; Lars I Andersson ...
 
 
Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape border= 
 
Hanjun Dai ; Ramzan Umarov; Hiroyuki Kuwahara; Yu Li; Le Song ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
A robust DF-REML framework for variance components estimation in genetic studies 
 
V M Lourenço ; P C Rodrigues; A M Pires; H -P Piepho
 
 
 
 
TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP'SNP interactions 
 
Yao-Hwei Fang; Jie-Huei Wang; Chao A Hsiung
 
 
 
SYSTEMS BIOLOGY
 
 
 
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models 
 
Siu H J Chan ; Jingyi Cai; Lin Wang; Margaret N Simons-Senftle; Costas D Maranas
 
 
The value of prior knowledge in machine learning of complex network systems 
 
Dana Ferranti; David Krane; David Craft
 
 
Improved prediction of breast cancer outcome by identifying heterogeneous biomarkers 
 
Jonghwan Choi; Sanghyun Park; Youngmi Yoon ; Jaegyoon Ahn
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration border= 
 
Chao Pang; Fleur Kelpin; David van Enckevort; Niina Eklund ; Kaisa Silander ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
gVolante for standardizing completeness assessment of genome and transcriptome assemblies border= 
 
Osamu Nishimura; Yuichiro Hara; Shigehiro Kuraku
 
 
Phylotyper: in silico predictor of gene subtypes border= 
 
Matthew D Whiteside; Victor P J Gannon ; Chad R Laing
 
 
pgRNAFinder: a web-based tool to design distance independent paired-gRNA border= 
 
Yuanyan Xiong; Xiaowei Xie; Yanzhi Wang; Wenbing Ma; Puping Liang ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
ggseqlogo: a versatile R package for drawing sequence logos 
 
Omar Wagih
 
 
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing 
 
Ravi José Tristão Ramos; Allan Cézar de Azevedo Martins ; Gabrielle da Silva Delgado; Crina-Maria Ionescu; Turán Peter Ürményi ...
 
 
LRCstats, a tool for evaluating long reads correction methods 
 
Sean La; Ehsan Haghshenas; Cedric Chauve
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures border= 
 
Joan Segura; Ruben Sanchez-Garcia; Marta Martinez; Jesus Cuenca-Alba; Daniel Tabas-Madrid ...
 
 
FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery 
 
David Lagorce; Lina Bouslama ; Jerome Becot; Maria A Miteva; Bruno O Villoutreix
 
 
DelPhiForce web server: electrostatic forces and energy calculations and visualization 
 
Lin Li; Zhe Jia; Yunhui Peng; Arghya Chakravorty ; Lexuan Sun ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics 
 
Chia-Lang Hsu; Jian-Kai Wang; Pei-Chun Lu; Hsuan-Cheng Huang; Hsueh-Fen Juan
 
 
SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces 
 
Marek KochaĆ"czyk; William S Hlavacek ; Tomasz Lipniacki
 
 
CausalR: extracting mechanistic sense from genome scale data border= 
 
Glyn Bradley; Steven J Barrett
 
 
ComplexViewer: visualization of curated macromolecular complexes border= 
 
Colin W Combe; Marine (Dumousseau) Sivade; Henning Hermjakob; Joshua Heimbach; Birgit H M Meldal ...
 
 
 
DATA AND TEXT MINING
 
 
 
myVCF: a desktop application for high-throughput mutations data management 
 
Alessandro Pietrelli; Luca Valenti
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment border= 
 
Daniel Domingo-Fernández; Alpha Tom Kodamullil; Anandhi Iyappan; Mufassra Naz; Mohammad Asif Emon ...
 
 
MFIB: a repository of protein complexes with mutual folding induced by binding border= 
 
Erzsébet Fichó; István Reményi; István Simon; Bálint Mészáros
 
 
REVIEW
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
An introduction to deep learning on biological sequence data: examples and solutions 
 
Vanessa Isabell Jurtz ; Alexander Rosenberg Johansen; Morten Nielsen; Jose Juan Almagro Armenteros; Henrik Nielsen ...
 
 
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