Subject: Bioinformatics Table of Contents for 01 September 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 17
 
01 September 2017
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Exploring spatially adjacent TFBS-clustered regions with Hi-C data border= 
 
Hebing Chen; Shuai Jiang; Zhuo Zhang; Hao Li ; Yiming Lu ...
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures 
 
Jens Lichtenberg; Laura Elnitski; David M. Bodine
 
 
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method  
 
Keqin Liu; Dominik Beck; Julie A. I. Thoms ; Liang Liu; Weiling Zhao ...
 
 
EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons 
 
Xinjie Hui; Yueming Hu; Ming-An Sun; Xingsheng Shu; Rongfei Han ...
 
 
An efficient graph kernel method for non-coding RNA functional prediction 
 
Nicolò Navarin; Fabrizio Costa
 
 
 
 
Accounting for tumor purity improves cancer subtype classification from DNA methylation data 
 
Weiwei Zhang; Hao Feng; Hao Wu ; Xiaoqi Zheng
 
 
 
SEQUENCE ANALYSIS
 
 
 
HLA class I binding prediction via convolutional neural networks 
 
Yeeleng S. Vang; Xiaohui Xie
 
 
RIblast: an ultrafast RNA'RNA interaction prediction system based on a seed-and-extension approach border= 
 
Tsukasa Fukunaga; Michiaki Hamada
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
A deep learning framework for improving long-range residue'residue contact prediction using a hierarchical strategy 
 
Dapeng Xiong; Jianyang Zeng ; Haipeng Gong
 
 
EigenTHREADER: analogous protein fold recognition by efficient contact map threading border= 
 
Daniel W. A. Buchan; David T. Jones
 
 
 
 
 
GENE EXPRESSION
 
 
 
Entropy-based consensus clustering for patient stratification 
 
Hongfu Liu; Rui Zhao; Hongsheng Fang; Feixiong Cheng ; Yun Fu ...
 
 
Network module-based model in the differential expression analysis for RNA-seq 
 
Mingli Lei ; Jia Xu; Li-Ching Huang; Lily Wang; Jing Li
 
 
 
SYSTEMS BIOLOGY
 
 
 
Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data 
 
Qianqian Shi ; Chuanchao Zhang; Minrui Peng; Xiangtian Yu; Tao Zeng ...
 
 
 
DATA AND TEXT MINING
 
 
 
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association border= 
 
Jian Ma; Cameron P. Casey; Xueyun Zheng; Yehia M. Ibrahim; Christopher S. Wilkins ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Neuro-symbolic representation learning on biological knowledge graphs border= 
 
Mona Alshahrani; Mohammad Asif Khan; Omar Maddouri; Akira R. Kinjo; Núria Queralt-Rosinach ...
 
 
On patterns and re-use in bioinformatics databases border= 
 
Michael J. Bell ; Phillip Lord
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Assembling draft genomes using contiBAIT border= 
 
Kieran O'Neill; Mark Hills; Mike Gottlieb; Matthew Borkowski ; Aly Karsan ...
 
 
OMSim: a simulator for optical map data border= 
 
Giles Miclotte; Stéphane Plaisance; Stephane Rombauts; Yves Van de Peer; Pieter Audenaert ...
 
 
twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis border= 
 
Anthony Chiu ; Mahmood Ayub; Caroline Dive; Ged Brady; Crispin J. Miller
 
 
 
SEQUENCE ANALYSIS
 
 
 
emMAW: computing minimal absent words in external memory 
 
Alice Héliou ; Solon P. Pissis; Simon J. Puglisi
 
 
rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering 
 
Bo Liu; Tao Jiang; S. M. Yiu; Junyi Li; Yadong Wang
 
 
modlAMP: Python for antimicrobial peptides 
 
Alex T. Müller; Gisela Gabernet; Jan A. Hiss ; Gisbert Schneider
 
 
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles 
 
Jiawei Wang ; Bingjiao Yang; Jerico Revote; André Leier; Tatiana T. Marquez-Lago ...
 
 
KMC 3: counting and manipulating k-mer statistics 
 
Marek Kokot; Maciej DÅ‚ugosz; Sebastian Deorowicz
 
 
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud  
 
Roberto R. Expósito; Jorge Veiga; Jorge González-Domínguez ; Juan Touriño
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta border= 
 
Robert Kleffner; Jeff Flatten; Andrew Leaver-Fay; David Baker ; Justin B. Siegel ...
 
 
MD-TASK: a software suite for analyzing molecular dynamics trajectories border= 
 
David K. Brown; David L. Penkler; Olivier Sheik Amamuddy; Caroline Ross; Ali Rana Atilgan ...
 
 
 
GENE EXPRESSION
 
 
 
veqtl-mapper: variance association mapping for molecular phenotypes 
 
Andrew Anand Brown
 
 
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets border= 
 
Francesco Del Carratore; Andris Jankevics; Rob Eisinga; Tom Heskes; Fangxin Hong ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
FlashPCA2: principal component analysis of Biobank-scale genotype datasets 
 
Gad Abraham ; Yixuan Qiu; Michael Inouye
 
 
PopFly: the Drosophila population genomics browser 
 
Sergi Hervas ; Esteve Sanz; Sònia Casillas; John E. Pool; Antonio Barbadilla
 
 
 
SYSTEMS BIOLOGY
 
 
 
MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization 
 
Katherine Maia McCoy ; Margaret L. Antonio; Tim van Opijnen
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
STOPGAP: a database for systematic target opportunity assessment by genetic association predictions 
 
Judong Shen; Kijoung Song; Andrew J. Slater; Enrico Ferrero ; Matthew R. Nelson
 
 
PROXiMATE: a database of mutant protein'protein complex thermodynamics and kinetics 
 
Sherlyn Jemimah ; K. Yugandhar; M. Michael Gromiha
 
 
CORRIGENDUM
 
 
 
Kollector: transcript-informed, targeted de novo assembly of gene loci border= 
 
Erdi Kucuk; Justin Chu ; Benjamin P. Vandervalk; S. Austin Hammond; René L. Warren ...
 
 
ERRATUM
 
 
 
Molecular signatures that can be transferred across different omics platforms 
 
M. Altenbuchinger; P. Schwarzfischer; T. Rehberg; J. Reinders ; Ch. W. Kohler ...
 
 
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