Subject: Bioinformatics Table of Contents for 1 July 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 13
 
1 July 2017
 
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DISCOVERY NOTES
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Changes associated with Ebola virus adaptation to novel species 
 
Morena Pappalardo; Ian G. Reddin; Diego Cantoni; Jeremy S. Rossman; Martin Michaelis ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells 
 
Pengyi Yang ; Andrew Oldfield; Taiyun Kim; Andrian Yang; Jean Yee Hwa Yang ...
 
 
ORIGINAL PAPERS
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Empirical comparison of web-based antimicrobial peptide prediction tools 
 
Musa Nur Gabere ; William Stafford Noble
 
 
BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone 
 
Bite Yang ; Feng Liu; Chao Ren; Zhangyi Ouyang; Ziwei Xie ...
 
 
Discriminating the reaction types of plant type III polyketide synthases border= 
 
Yugo Shimizu; Hiroyuki Ogata ; Susumu Goto
 
 
 
 
 
GENE EXPRESSION
 
 
 
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis border= 
 
Yun Zhang; David J. Topham; Juilee Thakar; Xing Qiu
 
 
RefBool: a reference-based algorithm for discretizing gene expression data  
 
Sascha Jung; Andras Hartmann; Antonio del Sol
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
A generalized association test based on U statistics 
 
Changshuai Wei; Qing Lu
 
 
Identification of genetic outliers due to sub-structure and cryptic relationships 
 
Daniel Schlauch ; Heide Fier; Christoph Lange
 
 
 
SYSTEMS BIOLOGY
 
 
 
Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway 
 
Sucheendra K. Palaniappan; François Bertaux; Matthieu Pichené; Eric Fabre ; Gregory Batt ...
 
 
 
 
An approach to infer putative disease-specific mechanisms using neighboring gene networks 
 
Sahar Ansari; Michele Donato ; Nafiseh Saberian; Sorin Draghici
 
 
Systematic inference of functional phosphorylation events in yeast metabolism 
 
Yu Chen; Yonghong Wang; Jens Nielsen
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Image-based surrogate biomarkers for molecular subtypes of colorectal cancer 
 
Vlad Popovici; Eva Budinská; Ladislav Dušek ; Michal Kozubek; Fred Bosman
 
 
A multi-scale convolutional neural network for phenotyping high-content cellular images 
 
William J. Godinez; Imtiaz Hossain; Stanley E. Lazic; John W. Davies; Xian Zhang
 
 
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy 
 
Oliver Hilsenbeck; Michael Schwarzfischer ; Dirk Loeffler; Sotiris Dimopoulos; Simon Hastreiter ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MotifMap-RNA: a genome-wide map of RBP binding sites 
 
Yu Liu; Sha Sun ; Timothy Bredy; Marcelo Wood; Robert C. Spitale ...
 
 
SVPV: a structural variant prediction viewer for paired-end sequencing datasets 
 
Jacob E. Munro; Sally L. Dunwoodie; Eleni Giannoulatou
 
 
 
SEQUENCE ANALYSIS
 
 
 
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets border= 
 
Rogan Magee; Phillipe Loher; Eric Londin; Isidore Rigoutsos
 
 
BCFtools/csq: haplotype-aware variant consequences border= 
 
Petr Danecek; Shane A. McCarthy
 
 
ProtVista: visualization of protein sequence annotations border= 
 
Xavier Watkins ; Leyla J. Garcia; Sangya Pundir; Maria J. Martin; the UniProt Consortium
 
 
PeptideMapper: efficient and versatile amino acid sequence and tag mapping 
 
Dominik Kopczynski; Harald Barsnes; Pål R. Njølstad; Albert Sickmann; Marc Vaudel ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
AQUA-DUCT: a ligands tracking tool 
 
Tomasz Magdziarz; Karolina MitusiĹ"ska; Sandra GoĹ‚dowska; Alicja PĹ‚uciennik; MichaĹ‚ Stolarczyk ...
 
 
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank border= 
 
Jianjiong Gao ; Andreas Prlić; Chunxiao Bi; Wolfgang F. Bluhm; Dimitris Dimitropoulos ...
 
 
 
GENE EXPRESSION
 
 
 
Glimma: interactive graphics for gene expression analysis border= 
 
Shian Su; Charity W. Law; Casey Ah-Cann; Marie-Liesse Asselin-Labat; Marnie E. Blewitt ...
 
 
ctsGE'clustering subgroups of expression data 
 
Michal Sharabi-Schwager; Etti Or ; Ron Ophir
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
LASER server: ancestry tracing with genotypes or sequence reads border= 
 
Daniel Taliun; Sonia P. Chothani; Sebastian Schönherr; Lukas Forer ; Michael Boehnke ...
 
 
GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification 
 
Zachary A. Szpiech ; Alexandra Blant; Trevor J. Pemberton
 
 
 
DATA AND TEXT MINING
 
 
 
DeepBlueR: large-scale epigenomic analysis in R border=  
 
Felipe Albrecht; Markus List; Christoph Bock ; Thomas Lengauer
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Pln24NT: a web resource for plant 24-nt siRNA producing loci 
 
Qi Liu; Changjun Ding; Yanguang Chu; Weixi Zhang; Ganggang Guo ...
 
 
Oncopression: gene expression compendium for cancer with matched normal tissues 
 
Jungsul Lee; Chulhee Choi
 
 
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