Subject: Bioinformatics Table of Contents for 15 October 2017 Oxford Academic
 
 
 
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Bioinformatics  
Volume 33 Issue 20
 
15 October 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array 
 
Yu-Jia Shiah; Michael Fraser; Robert G. Bristow; Paul C. Boutros
 
 
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data 
 
Elena D. Stavrovskaya; Tejasvi Niranjan; Elana J. Fertig ; Sarah J. Wheelan; Alexander V. Favorov ...
 
 
BPP: a sequence-based algorithm for branch point prediction 
 
Qing Zhang; Xiaodan Fan; Yejun Wang; Ming-an Sun; Jianlin Shao ...
 
 
Partitioned learning of deep Boltzmann machines for SNP data 
 
Moritz Hess; Stefan Lenz ; Tamara J. Blätte; Lars Bullinger; Harald Binder
 
 
 
SEQUENCE ANALYSIS
 
 
 
Succinct colored de Bruijn graphs 
 
Martin D. Muggli; Alexander Bowe; Noelle R. Noyes ; Paul S. Morley; Keith E. Belk ...
 
 
 
 
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads 
 
Antoine Recanati ; Thomas BrĂĽls; Alexandre d'Aspremont
 
 
Matrix completion with side information and its applications in predicting the antigenicity of influenza viruses 
 
Li Huang; Xianhong Li; Pengfei Guo; Yuhua Yao; Bo Liao ...
 
 
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria 
 
Marc G. Chevrette; Fabian Aicheler; Oliver Kohlbacher; Cameron R. Currie; Marnix H. Medema
 
 
 
GENE EXPRESSION
 
 
 
Model-based branching point detection in single-cell data by K-branches clustering border= 
 
Nikolaos K. Chlis; F. Alexander Wolf ; Fabian J. Theis
 
 
Integrative analysis of multiple genomic variables using a hierarchical Bayesian model 
 
Martin Schäfer ; Hans-Ulrich Klein; Holger Schwender
 
 
 
 
Sparse redundancy analysis of high-dimensional genetic and genomic data 
 
Attila Csala ; Frans P. J. M. Voorbraak; Aeilko H. Zwinderman; Michel H. Hof
 
 
Identification of transcript regulatory patterns in cell differentiation 
 
Arief Gusnanto; John Paul Gosling; Christopher Pope
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Panoptes: web-based exploration of large scale genome variation data 
 
Paul Vauterin ; Ben Jeffery; Alistair Miles; Roberto Amato; Lee Hart ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules 
 
Xiaohui Yao ; Jingwen Yan; Kefei Liu; Sungeun Kim; Kwangsik Nho ...
 
 
 
DATA AND TEXT MINING
 
 
 
Detecting and removing multiplicative spatial bias in high-throughput screening technologies 
 
Iurie Caraus ; Bogdan Mazoure; Robert Nadon; Vladimir Makarenkov
 
 
EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features 
 
Yu He; Ting Wang
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
HEROD: a human ethnic and regional specific omics database  
 
Xian Zeng; Lin Tao; Peng Zhang ; Chu Qin; Shangying Chen ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies border= 
 
Ludovic Mallet; Tristan Bitard-Feildel ; Franck Cerutti; Hélène Chiapello
 
 
BioQueue: a novel pipeline framework to accelerate bioinformatics analysis 
 
Li Yao; Heming Wang; Yuanyuan Song; Guangchao Sui
 
 
 
SEQUENCE ANALYSIS
 
 
 
CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data border= 
 
Changlin Wan; Jianing Gao; Huan Zhang; Xiaohua Jiang; Qiguang Zang ...
 
 
EDEN: evolutionary dynamics within environments border= 
 
Philipp C. Münch ; Bärbel Stecher; Alice C. McHardy
 
 
TeachEnG: a Teaching Engine for Genomics  
 
Minji Kim; Yeonsung Kim; Lei Qian; Jun S. Song
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT 
 
Kathryn A. Porter ; Bing Xia; Dmitri Beglov; Tanggis Bohnuud; Nawsad Alam ...
 
 
 
GENE EXPRESSION
 
 
 
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data 
 
Igor Mandric ; Yvette Temate-Tiagueu; Tatiana Shcheglova; Sahar Al Seesi; Alex Zelikovsky ...
 
 
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments 
 
Alexey Uvarovskii; Christoph Dieterich
 
 
TSIS: an R package to infer alternative splicing isoform switches for time-series data border= 
 
Wenbin Guo; Cristiane P.G. Calixto ; John W. S. Brown; Runxuan Zhang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
VariantTools: an extensible framework for developing and testing variant callers border=  
 
Michael Lawrence; Robert Gentleman
 
 
 
DATA AND TEXT MINING
 
 
 
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential 
 
Xianwen Meng ; Qi Chen; Peijing Zhang; Ming Chen
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Pheno4J: a gene to phenotype graph database 
 
Sajid Mughal; Ismail Moghul; Jing Yu ; UKIRDC; Tristan Clark ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
NucliTrack: an integrated nuclei tracking application border= 
 
Sam Cooper; Alexis R. Barr; Robert Glen; Chris Bakal
 
 
REVIEW
 
 
 
 
GENOME ANALYSIS
 
 
 
Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning 
 
Mikhail G. Dozmorov
 
 
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