Subject: Bioinformatics Table of Contents for 01 December 2018 ------=_Part_1656077337.1543078928123 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1656077337.1543078928123 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 23
 
01 December 2018
 
button-issue.png
 
 
DISCOVERY NOTE
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
The ancestral KH peptide at the root of a domain family with three different folds 
 
Joana Pereira; Andrei N Lupas
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Modelling BioNano optical data and simulation study of genome map assembly border=  
 
Ping Chen; Xinyun Jing; Jian Ren ; Han Cao; Pei Hao ...
 
 
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile 
 
Yuanfang Guan; Tingyang Li; Hongjiu Zhang; Fan Zhu; Gilbert S Omenn
 
 
Meffil: efficient normalization and analysis of very large DNA methylation datasets border=  
 
J L Min; G Hemani; G Davey Smith ; C Relton; M Suderman
 
 
 
SEQUENCE ANALYSIS
 
 
 
SSMART: sequence-structure motif identification for RNA-binding proteins 
 
Alina Munteanu; Neelanjan Mukherjee; Uwe Ohler
 
 
ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization 
 
Guodong Chen; Man Cao; Kun Luo; Lina Wang ; Pingping Wen ...
 
 
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides 
 
Leyi Wei; Chen Zhou; Huangrong Chen; Jiangning Song; Ran Su
 
 
Predicting clone genotypes from tumor bulk sequencing of multiple samples 
 
Sayaka Miura; Karen Gomez; Oscar Murillo; Louise A Huuki ; Tracy Vu ...
 
 
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker border= 
 
Johan Bengtsson-Palme ; Rodney T Richardson; Marco Meola; Christian Wurzbacher; Émilie D Tremblay ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Prediction of kinetics of protein folding with non-redundant contact information 
 
Luciano Censoni; Leandro Martínez
 
 
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks 
 
Jack Hanson; Kuldip Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou
 
 
Deep convolutional networks for quality assessment of protein folds 
 
Georgy Derevyanko; Sergei Grudinin; Yoshua Bengio; Guillaume Lamoureux
 
 
 
GENE EXPRESSION
 
 
 
Estimating pseudocounts and fold changes for digital expression measurements 
 
Florian Erhard
 
 
Robust clustering of noisy high-dimensional gene expression data for patients subtyping 
 
Pietro Coretto; Angela Serra; Roberto Tagliaferri
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
On the power of epigenome-wide association studies using a disease-discordant twin design 
 
Weilong Li; Lene Christiansen; Jacob Hjelmborg; Jan Baumbach; Qihua Tan
 
 
 
SYSTEMS BIOLOGY
 
 
 
Modelling signalling networks from perturbation data 
 
Mathurin Dorel; Bertram Klinger; Torsten Gross; Anja Sieber ; Anirudh Prahallad ...
 
 
 
DATA AND TEXT MINING
 
 
 
Transfer learning for biomedical named entity recognition with neural networks border= 
 
John M Giorgi; Gary D Bader
 
 
Improved design and analysis of CRISPR knockout screens 
 
Chen-Hao Chen; Tengfei Xiao; Han Xu; Peng Jiang ; Clifford A Meyer ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
The Rényi divergence enables accurate and precise cluster analysis for localization microscopy border= 
 
Adela D Staszowska; Patrick Fox-Roberts; Liisa M Hirvonen; Christopher J Peddie; Lucy M Collinson ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions border= 
 
Kari Nousiainen; Kartiek Kanduri ; Isis Ricaño-Ponce; Cisca Wijmenga; Riitta Lahesmaa ...
 
 
SONiCS: PCR stutter noise correction in genome-scale microsatellites  
 
Katarzyna Z Kedzierska; Livia Gerber; Daniele Cagnazzi; Michael Krützen ; Aakrosh Ratan ...
 
 
Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes border=  
 
Blanca Taboada; Karel Estrada; Ricardo Ciria ; Enrique Merino
 
 
 
PHYLOGENETICS
 
 
 
Nextstrain: real-time tracking of pathogen evolution border=  
 
James Hadfield; Colin Megill; Sidney M Bell ; John Huddleston; Barney Potter ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA 
 
A A Icazatti; O A Martin; M Villegas; I Szleifer ; J A Vila
 
 
MolArt: a molecular structure annotation and visualization tool border= 
 
David Hoksza; Piotr Gawron; Marek Ostaszewski ; Reinhard Schneider
 
 
 
SYSTEMS BIOLOGY
 
 
 
GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies 
 
Kun Sun; Jiguang Wang; Huating Wang; Hao Sun
 
 
 
DATA AND TEXT MINING
 
 
 
GateFinder: projection-based gating strategy optimization for flow and mass cytometry 
 
Nima Aghaeepour; Erin F Simonds; David J H F Knapp; Robert V Bruggner; Karen Sachs ...
 
 
MetQy'an R package to query metabolic functions of genes and genomes border=  
 
Andrea S Martinez-Vernon; Frederick Farrell; Orkun S Soyer
 
 
 
CORRIGENDA
 
 
 
Learned protein embeddings for machine learning 
 
Kevin K Yang; Zachary Wu; Claire N Bedbrook; Frances H Arnold
 
 
Distinguishing prognostic and predictive biomarkers: an information theoretic approach border=  
 
Konstantinos Sechidis; Konstantinos Papangelou; Paul D Metcalfe ; David Svensson; James Weatherall ...
 
 
 
ERRATUM
 
 
 
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 ...
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
oxforde_university.jpg
 
 
 
                                 


This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1656077337.1543078928123--