Subject: Bioinformatics Table of Contents for 01 March 2018 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 5
 
01 March 2018
 
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DISCOVERY NOTE
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules border= 
 
Luis Sanchez-Pulido; Chris P Ponting; Janet Kelso
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
ARCS: scaffolding genome drafts with linked reads border= 
 
Sarah Yeo; Lauren Coombe; René L Warren; Justin Chu; Inanç Birol ...
 
 
Chromatin accessibility prediction via a hybrid deep convolutional neural network 
 
Qiao Liu; Fei Xia ; Qijin Yin; Rui Jiang; Inanc Birol
 
 
 
SEQUENCE ANALYSIS
 
 
 
Bartender: a fast and accurate clustering algorithm to count barcode reads 
 
Lu Zhao; Zhimin Liu; Sasha F Levy ; Song Wu; Bonnie Berger
 
 
Evaluation of tools for long read RNA-seq splice-aware alignment 
 
Krešimir Križanović; Amina Echchiki; Julien Roux; Mile Šikić; Inanc Birol
 
 
 
 
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening 
 
Alejandro A Schäffer; Eric P Nawrocki ; Yoon Choi; Paul A Kitts; Ilene Karsch-Mizrachi ...
 
 
DEEPre: sequence-based enzyme EC number prediction by deep learning border= 
 
Yu Li; Sheng Wang; Ramzan Umarov; Bingqing Xie ; Ming Fan ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Machine learning accelerates MD-based binding pose prediction between ligands and proteins border= 
 
Kei Terayama; Hiroaki Iwata; Mitsugu Araki; Yasushi Okuno ; Koji Tsuda ...
 
 
Predicting protein'DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver 
 
Yunhui Peng ; Lexuan Sun; Zhe Jia; Lin Li; Emil Alexov ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays 
 
Cynthia A Kalita ; Gregory A Moyerbrailean; Christopher Brown; Xiaoquan Wen; Francesca Luca ...
 
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
Sipros Ensemble improves database searching and filtering for complex metaproteomics 
 
Xuan Guo; Zhou Li ; Qiuming Yao; Ryan S Mueller; Jimmy K Eng ...
 
 
Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates 
 
Bram Thijssen; Tjeerd M H Dijkstra; Tom Heskes; Lodewyk F A Wessels ; Jonathan Wren
 
 
Constructing prediction models from expression profiles for large scale lncRNA'miRNA interaction profiling 
 
Yu-An Huang ; Keith C C Chan; Zhu-Hong You; Ivo Hofacker
 
 
 
DATA AND TEXT MINING
 
 
 
Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques 
 
Jinglong Niu; Yan Shi ; Maolin Cai; Zhixin Cao; Dandan Wang ...
 
 
Drug'drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths border= 
 
Yijia Zhang; Wei Zheng; Hongfei Lin; Jian Wang; Zhihao Yang ...
 
 
Cancer progression models and fitness landscapes: a many-to-many relationship border= 
 
Ramon Diaz-Uriarte; Jonathan Wren
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Quality of biological images, reconstructed using localization microscopy data 
 
Błażej Ruszczycki; Tytus Bernas; Robert Murphy
 
 
A fast fiducial marker tracking model for fully automatic alignment in electron tomography border= 
 
Renmin Han; Fa Zhang ; Xin Gao; Robert Murphy
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks  
 
Markus Hollander; Mohamed Hamed; Volkhard Helms ; Kerstin Neininger; Bonnie Berger
 
 
Mosdepth: quick coverage calculation for genomes and exomes border= 
 
Brent S Pedersen; Aaron R Quinlan; John Hancock
 
 
 
SEQUENCE ANALYSIS
 
 
 
mORCA: sailing bioinformatics world with mobile devices border= 
 
Sergio Díaz-del-Pino; Juan Falgueras; Esteban Perez-Wohlfeil; Oswaldo Trelles; John Hancock
 
 
SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer border= 
 
Marco Beccuti ; Francesca Cordero; Maddalena Arigoni; Riccardo Panero; Elvio G Amparore ...
 
 
Simulating the dynamics of targeted capture sequencing with CapSim 
 
Minh Duc Cao; Devika Ganesamoorthy; Chenxi Zhou ; Lachlan J M Coin; Bonnie Berger
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration 
 
Soundhararajan Gopi; Devanshu Devanshu; Praveen Krishna; Athi N Naganathan; Alfonso Valencia
 
 
LIBRA-WA: a web application for ligand binding site detection and protein function recognition 
 
Daniele Toti ; Le Viet Hung; Valentina Tortosa; Valentina Brandi; Fabio Polticelli ...
 
 
 
GENE EXPRESSION
 
 
 
AEGS: identifying aberrantly expressed gene sets for differential variability analysis 
 
Jinting Guan ; Moliang Chen; Congting Ye; James J Cai; Guoli Ji ...
 
 
Bringing numerous methods for expression and promoter analysis to a public cloud computing service border= 
 
Krzysztof Pola"ski; Bo Gao ; Sam A Mason; Paul Brown; Sascha Ott ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation 
 
Mitchell J Machiela; Stephen J Chanock ; Oliver Stegle
 
 
 
SYSTEMS BIOLOGY
 
 
 
MWASTools: an R/bioconductor package for metabolome-wide association studies border= 
 
Andrea Rodriguez-Martinez; Joram M Posma; Rafael Ayala; Ana L Neves ; Maryam Anwar ...
 
 
SELANSI: a toolbox for simulation of stochastic gene regulatory networks border= 
 
Manuel Pájaro; Irene Otero-Muras; Carlos Vázquez; Antonio A Alonso; Oliver Stegle
 
 
 
DATA AND TEXT MINING
 
 
 
netReg: network-regularized linear models for biological association studies border= 
 
Simon Dirmeier; Christiane Fuchs; Nikola S Mueller; Fabian J Theis ; Jonathan Wren
 
 
 
BIOIMAGE INFORMATICS
 
 
 
FunImageJ: a Lisp framework for scientific image processing border= 
 
Kyle I S Harrington; Curtis T Rueden; Kevin W Eliceiri; Robert Murphy
 
 
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