Subject: Bioinformatics Table of Contents for 01 June 2018 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 11
 
01 June 2018
 
button-issue.png
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling 
 
Joong Chae Na; Jong-Chan Lee; Je-Keun Rhee; Soo-Yong Shin
 
 
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction border= 
 
Paul Deveau ; Leo Colmet Daage; Derek Oldridge; Virginie Bernard; Angela Bellini ...
 
 
A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values border= 
 
Chao Ning; Dan Wang ; Huimin Kang; Raphael Mrode; Lei Zhou ...
 
 
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms 
 
Umberto Ferraro Petrillo; Gianluca Roscigno; Giuseppe Cattaneo; Raffaele Giancarlo
 
 
GTC: how to maintain huge genotype collections in a compressed form 
 
Agnieszka Danek; Sebastian Deorowicz
 
 
 
 
APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data 
 
Congting Ye; Yuqi Long; Guoli Ji; Qingshun Quinn Li; Xiaohui Wu
 
 
 
SEQUENCE ANALYSIS
 
 
 
OPAL: prediction of MoRF regions in intrinsically disordered protein sequences 
 
Ronesh Sharma; Gaurav Raicar; Tatsuhiko Tsunoda; Ashwini Patil ; Alok Sharma
 
 
 
GENE EXPRESSION
 
 
 
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer 
 
Bahman Afsari; Theresa Guo; Michael Considine; Liliana Florea; Luciane T Kagohara ...
 
 
Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data 
 
Jennifer M Franks ; Guoshuai Cai; Michael L Whitfield
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
A distance-based approach for testing the mediation effect of the human microbiome 
 
Jie Zhang; Zhi Wei; Jun Chen
 
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation border= 
 
Irina M Armean ; Kathryn S Lilley; Matthew W B Trotter; Nicholas C V Pilkington; Sean B Holden
 
 
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy  
 
Wei-Feng Guo; Shao-Wu Zhang; Li-Li Liu ; Fei Liu; Qian-Qian Shi ...
 
 
Computational drug repositioning using low-rank matrix approximation and randomized algorithms 
 
Huimin Luo; Min Li; Shaokai Wang; Quan Liu; Yaohang Li ...
 
 
An easy and efficient approach for testing identifiability 
 
Clemens Kreutz
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Toppar: an interactive browser for viewing association study results border= 
 
Thorhildur Juliusdottir; Karina Banasik; Neil R Robertson; Richard Mott; Mark I McCarthy
 
 
iPat: intelligent prediction and association tool for genomic research 
 
Chunpeng James Chen; Zhiwu Zhang
 
 
VIPER: a web application for rapid expert review of variant calls border= 
 
Marius Wöste ; Martin Dugas
 
 
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements 
 
Luca Pinello ; Rick Farouni; Guo-Cheng Yuan
 
 
Sequanix: a dynamic graphical interface for Snakemake workflows border= 
 
Dimitri Desvillechabrol; Rachel Legendre; Claire Rioualen; Christiane Bouchier ; Jacques van Helden ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Primer3_masker: integrating masking of template sequence with primer design software 
 
Triinu Kõressaar; Maarja Lepamets; Lauris Kaplinski; Kairi Raime; Reidar Andreson ...
 
 
JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure border= 
 
Peter V Troshin ; James B Procter; Alexander Sherstnev; Daniel L Barton; Fábio Madeira ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions 
 
Bernhard Knapp ; Marta Alcala; Hao Zhang; Clare E West; P Anton van der Merwe ...
 
 
CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data border= 
 
Alejandro Panjkovich; Dmitri I Svergun
 
 
Optimal water networks in protein cavities with GAsol and 3D-RISM 
 
Lucia Fusani; Ian Wall ; David Palmer; Alvaro Cortes
 
 
G2S: a web-service for annotating genomic variants on 3D protein structures 
 
Juexin Wang; Robert Sheridan; S Onur Sumer; Nikolaus Schultz; Dong Xu ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs 
 
Corinne E Sexton; Hayden Z Smith; Peter D Newell; Angela E Douglas; John M Chaston
 
 
 
SYSTEMS BIOLOGY
 
 
 
DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function 
 
Liang Cheng ; Yang Hu; Jie Sun; Meng Zhou; Qinghua Jiang
 
 
DExSI: a new tool for the rapid quantitation of 13 C-labelled metabolites detected by GC-MS border= 
 
Michael J Dagley; Malcolm J McConville
 
 
ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases 
 
David Amar ; Amir Vizel; Carmit Levy; Ron Shamir
 
 
 
DATA AND TEXT MINING
 
 
 
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+ border= 
 
Andon Tchechmedjiev; Amine Abdaoui ; Vincent Emonet; Soumia Melzi; Jitendra Jonnagaddala ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets 
 
Kim Wong; José Fernández Navarro ; Ludvig Bergenstråhle; Patrik L Ståhl; Joakim Lundeberg
 
 
REVIEW
 
 
 
 
GENE EXPRESSION
 
 
 
Computational deconvolution of transcriptomics data from mixed cell populations 
 
Francisco Avila Cobos; Jo Vandesompele ; Pieter Mestdagh; Katleen De Preter
 
 
CORRIGENDUM
 
 
 
Aligning dynamic networks with DynaWAVE 
 
Vipin Vijayan; Tijana Milenković
 
 
Unsubscribe       Manage email alerts
 
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.
 
oxforde_university.jpg
 
 
 
                                 


This email is intended for bionet@evol.mcmaster.ca.