Subject: Bioinformatics Table of Contents for 01 November 2018 ------=_Part_1172304908.1540577677229 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1172304908.1540577677229 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 21
 
01 November 2018
 
button-issue.png
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Indexed variation graphs for efficient and accurate resistome profiling border=  
 
Will P M Rowe; Martyn D Winn
 
 
Pathway-structured predictive modeling for multi-level drug response in multiple myeloma 
 
Xinyan Zhang; Bingzong Li; Huiying Han; Sha Song ; Hongxia Xu ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Predicting gene structure changes resulting from genetic variants via exon definition features 
 
William H Majoros; Carson Holt; Michael S Campbell; Doreen Ware; Mark Yandell ...
 
 
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA) 
 
Le Zhang; Ming Xiao; Jingsong Zhou; Jun Yu
 
 
Combining probabilistic alignments with read pair information improves accuracy of split-alignments border=  
 
Anish M S Shrestha; Naruki Yoshikawa; Kiyoshi Asai
 
 
 
PHYLOGENETICS
 
 
 
Exact Bayesian inference for phylogenetic birth-death models 
 
Kris V Parag; Oliver G Pybus
 
 
RecPhyloXML: a format for reconciled gene trees border= 
 
Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau ; Lars Arvestad; Mukul S Bansal ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation border= 
 
Dinara R Usmanova; Natalya S Bogatyreva; Joan Ariño Bernad; Aleksandra A Eremina; Anastasiya A Gorshkova ...
 
 
Quantification of biases in predictions of protein stability changes upon mutations 
 
Fabrizio Pucci; Katrien V Bernaerts; Jean Marc Kwasigroch; Marianne Rooman
 
 
Development and evaluation of a deep learning model for protein'ligand binding affinity prediction border=  
 
Marta M Stepniewska-Dziubinska; Piotr Zielenkiewicz; Pawel Siedlecki
 
 
Bio-knowledge-based filters improve residue'residue contact prediction accuracy 
 
P P Wozniak; J Pelc; M Skrzypecki; G Vriend ; M Kotulska
 
 
 
GENE EXPRESSION
 
 
 
Single cell clustering based on cell-pair differentiability correlation and variance analysis 
 
Hao Jiang; Lydia L Sohn; Haiyan Huang; Luonan Chen
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Detection of multi-dimensional co-exclusion patterns in microbial communities 
 
Levent Albayrak; Kamil Khanipov; George Golovko; Yuriy Fofanov
 
 
 
SYSTEMS BIOLOGY
 
 
 
PyCoTools: a Python toolbox for COPASI border=  
 
Ciaran M Welsh; Nicola Fullard; Carole J Proctor ; Alvaro Martinez-Guimera; Robert J Isfort ...
 
 
 
DATA AND TEXT MINING
 
 
 
The revival of the Gini importance? border=  
 
Stefano Nembrini; Inke R König; Marvin N Wright
 
 
EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery 
 
Patryk Orzechowski; Moshe Sipper; Xiuzhen Huang; Jason H Moore
 
 
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data 
 
Yunchuan Kong; Tianwei Yu
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ConSpeciFix: classifying prokaryotic species based on gene flow 
 
Louis-Marie Bobay; Brian Shin-Hua Ellis; Howard Ochman
 
 
mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies 
 
Donghyun Tae; Junhee Seok
 
 
 
SEQUENCE ANALYSIS
 
 
 
AC-DIAMOND v1: accelerating large-scale DNA'protein alignment 
 
Huijun Mai; Yifan Zhang; Dinghua Li; Henry Chi-Ming Leung ; Ruibang Luo ...
 
 
PEA: an integrated R toolkit for plant epitranscriptome analysis 
 
Jingjing Zhai; Jie Song; Qian Cheng; Yunjia Tang ; Chuang Ma
 
 
LiveKraken''real-time metagenomic classification of illumina data 
 
Simon H Tausch; Benjamin Strauch; Andreas Andrusch; Tobias P Loka ; Martin S Lindner ...
 
 
MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database border= 
 
Matthieu Leray ; Shian-Lei Ho; I-Jeng Lin; Ryuji J Machida
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
NGL viewer: web-based molecular graphics for large complexes 
 
Alexander S Rose; Anthony R Bradley; Yana Valasatava; Jose M Duarte ; Andreas Prlić ...
 
 
MODE-TASK: large-scale protein motion tools border= 
 
Caroline Ross; Bilal Nizami; Michael Glenister ; Olivier Sheik Amamuddy; Ali Rana Atilgan ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
TimeXNet Web: identifying cellular response networks from diverse omics time-course data 
 
Phit Ling Tan; Yosvany López; Kenta Nakai; Ashwini Patil
 
 
Using meshes for MeSH term enrichment and semantic analyses 
 
Guangchuang Yu
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
SoS Notebook: an interactive multi-language data analysis environment border=  
 
Bo Peng; Gao Wang; Jun Ma ; Man Chong Leong; Chris Wakefield ...
 
 
GSCALite: a web server for gene set cancer analysis 
 
Chun-Jie Liu; Fei-Fei Hu; Meng-Xuan Xia; Leng Han ; Qiong Zhang ...
 
 
Exploring drug space with ChemMaps.com 
 
Alexandre Borrel; Nicole C Kleinstreuer; Denis Fourches
 
 
 
BIOIMAGE INFORMATICS
 
 
 
TomoEED: fast edge-enhancing denoising of tomographic volumes 
 
J J Moreno; A Martínez-Sánchez; J A Martínez; E M Garzón ; J J Fernández
 
 
 
CORRIGENDA
 
 
 
DDR: efficient computational method to predict drug'target interactions using graph mining and machine learning approaches border= 
 
Rawan S Olayan ; Haitham Ashoor; Vladimir B Bajic
 
 
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework 
 
Nikolaos Tsiantis; Eva Balsa-Canto; Julio R Banga
 
 
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_1172304908.1540577677229--