Subject: Bioinformatics Table of Contents for 01 October 2018 ------=_Part_1552118802.1538250012259 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1552118802.1538250012259 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 19
 
01 October 2018
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code 
 
Eli Goz; Zohar Zafrir; Tamir Tuller
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation 
 
Marlena Maziarz; Ruth M Pfeiffer; Yunhu Wan; Mitchell H Gail
 
 
Modeling one thousand intron length distributions with fitild border= 
 
Osamu Gotoh
 
 
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis 
 
Laraib Malik; Fatemeh Almodaresi; Rob Patro
 
 
 
SEQUENCE ANALYSIS
 
 
 
In silico read normalization using set multi-cover optimization border=  
 
Dilip A Durai; Marcel H Schulz
 
 
LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification 
 
Gleb Filatov; Bruno Bauwens; Attila Kertész-Farkas
 
 
PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence 
 
Sumaiya Iqbal; Md Tamjidul Hoque
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
GapRepairer: a server to model a structural gap and validate it using topological analysis 
 
Aleksandra I Jarmolinska; Michal Kadlof; Pawel Dabrowski-Tumanski ; Joanna I Sulkowska
 
 
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features 
 
David T Jones; Shaun M Kandathil
 
 
Applying graph theory to protein structures: an Atlas of coiled coils border=  
 
Jack W Heal; Gail J Bartlett; Christopher W Wood ; Andrew R Thomson; Derek N Woolfson
 
 
MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers 
 
Shintaro Minami; Kengo Sawada; Motonori Ota; George Chikenji
 
 
 
GENE EXPRESSION
 
 
 
RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines 
 
Amrita Basu; Ritwik Mitra; Han Liu; Stuart L Schreiber; Paul A Clemons
 
 
Two-phase differential expression analysis for single cell RNA-seq 
 
Zhijin Wu; Yi Zhang; Michael L Stitzel; Hao Wu
 
 
Bayesian negative binomial regression for differential expression with confounding factors 
 
Siamak Zamani Dadaneh; Mingyuan Zhou; Xiaoning Qian
 
 
 
SYSTEMS BIOLOGY
 
 
 
Prediction of lncRNA'disease associations based on inductive matrix completion 
 
Chengqian Lu; Mengyun Yang; Feng Luo; Fang-Xiang Wu ; Min Li ...
 
 
 
DATA AND TEXT MINING
 
 
 
Distinguishing prognostic and predictive biomarkers: an information theoretic approach border= 
 
Konstantinos Sechidis; Konstantinos Papangelou; Paul D Metcalfe; David Svensson; James Weatherall ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Cluster Locator, online analysis and visualization of gene clustering 
 
Flavio Pazos Obregón; Pablo Soto; José Luis Lavín; Ana Rosa Cortázar ; Rosa Barrio ...
 
 
Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer 
 
Jayendra Shinde; Quentin Bayard; Sandrine Imbeaud; Théo Z Hirsch ; Feng Liu ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs border= 
 
Matthew B Stocks; Irina Mohorianu; Matthew Beckers; Claudia Paicu; Simon Moxon ...
 
 
Correcting mistakes in predicting distributions border= 
 
Valérie Marot-Lassauzaie; Michael Bernhofer; Burkhard Rost
 
 
hts-nim: scripting high-performance genomic analyses 
 
Brent S Pedersen; Aaron R Quinlan
 
 
PROBE: analysis and visualization of protein block-level evolution 
 
Arnaud Kress; Odile Lecompte; Olivier Poch; Julie D Thompson
 
 
Improved enzyme annotation with EC-specific cutoffs using DETECT v2 
 
Nirvana Nursimulu; Leon L Xu; James D Wasmuth; Ivan Krukov ; John Parkinson
 
 
MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data 
 
Waqasuddin Khan; Ganapathi Varma Saripella; Thomas Ludwig; Tania Cuppens ; Florian Thibord ...
 
 
 
PHYLOGENETICS
 
 
 
Two C++ libraries for counting trees on a phylogenetic terrace border=  
 
R Biczok; P Bozsoky; P Eisenmann ; J Ernst; T Ribizel ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids 
 
Julien Dorier; Dimos Goundaroulis; Fabrizio Benedetti; Andrzej Stasiak
 
 
 
GENE EXPRESSION
 
 
 
NGScloud: RNA-seq analysis of non-model species using cloud computing 
 
Fernando Mora-Márquez; José Luis Vázquez-Poletti; Unai López de Heredia
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs border= 
 
Gregor Gorjanc; John M Hickey
 
 
VarExp: estimating variance explained by genome-wide GxE summary statistics 
 
Vincent Laville; Amy R Bentley; Florian Privé; Xiaofeng Zhu ; Jim Gauderman ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
lncFunTK: a toolkit for functional annotation of long noncoding RNAs 
 
Jiajian Zhou; Yile Huang; Yingzhe Ding; Jie Yuan ; Huating Wang ...
 
 
MetaboDiff: an R package for differential metabolomic analysis border= 
 
Andreas Mock; Rolf Warta; Steffen Dettling ; Benedikt Brors; Dirk Jäger ...
 
 
canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit 
 
Baohong Zhang; Shanrong Zhao; Isaac Neuhaus
 
 
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