Subject: Bioinformatics Table of Contents for 01 April 2018 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 7
 
01 April 2018
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability border= 
 
Jana 'echová; Jiří Lýsek; Martin Bartas; Václav Brázda
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Cost-effective and accurate method of measuring fetal fraction using SNP imputation 
 
Minjeong Kim; Jai-Hoon Kim; Kangseok Kim; Sunshin Kim
 
 
 
SEQUENCE ANALYSIS
 
 
 
PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine 
 
Reda Rawi ; Raghvendra Mall; Khalid Kunji; Chen-Hsiang Shen; Peter D Kwong ...
 
 
RepLong: de novo repeat identification using long read sequencing data 
 
Rui Guo; Yan-Ran Li; Shan He ; Le Ou-Yang; Yiwen Sun ...
 
 
microRPM: a microRNA prediction model based only on plant small RNA sequencing data 
 
Kuan-Chieh Tseng; Yi-Fan Chiang-Hsieh; Hsuan Pai; Chi-Nga Chow; Shu-Chuan Lee ...
 
 
 
 
Accurate mapping of tRNA reads 
 
Anne Hoffmann; Jörg Fallmann; Elisa Vilardo ; Mario Mörl; Peter F Stadler ...
 
 
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly 
 
Samarth Rangavittal; Robert S Harris; Monika Cechova; Marta Tomaszkiewicz; Rayan Chikhi ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction border= 
 
Saulo H P de Oliveira; Eleanor C Law; Jiye Shi; Charlotte M Deane
 
 
 
GENE EXPRESSION
 
 
 
Detecting hidden batch factors through data-adaptive adjustment for biological effects 
 
Haidong Yi ; Ayush T Raman; Han Zhang; Genevera I Allen; Zhandong Liu
 
 
Semi-supervised network inference using simulated gene expression dynamics 
 
Phan Nguyen; Rosemary Braun
 
 
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing 
 
Peizhou Liao; Glen A Satten ; Yi-Juan Hu
 
 
 
SYSTEMS BIOLOGY
 
 
 
DDR: efficient computational method to predict drug'target interactions using graph mining and machine learning approaches border= 
 
Rawan S Olayan; Haitham Ashoor; Vladimir B Bajic
 
 
Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network 
 
Carlos Ramírez; Luis Mendoza
 
 
The OncoPPi Portal: an integrative resource to explore and prioritize protein'protein interactions for cancer target discovery 
 
Andrei A Ivanov; Brian Revennaugh ; Lauren Rusnak; Valentina Gonzalez-Pecchi; Xiulei Mo ...
 
 
 
DATA AND TEXT MINING
 
 
 
Compound image segmentation of published biomedical figures 
 
Pengyuan Li; Xiangying Jiang; Chandra Kambhamettu ; Hagit Shatkay
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
SATORI: a system for ontology-guided visual exploration of biomedical data repositories border= 
 
Fritz Lekschas; Nils Gehlenborg
 
 
Reactome diagram viewer: data structures and strategies to boost performance border= 
 
Antonio Fabregat; Konstantinos Sidiropoulos; Guilherme Viteri ; Pablo Marin-Garcia; Peipei Ping ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Deep learning for tumor classification in imaging mass spectrometry 
 
Jens Behrmann; Christian Etmann; Tobias Boskamp; Rita Casadonte ; Jörg Kriegsmann ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files 
 
Pierre Lindenbaum; Richard Redon
 
 
GDSCTools for mining pharmacogenomic interactions in cancer border= 
 
Thomas Cokelaer; Elisabeth Chen; Francesco Iorio; Michael P Menden; Howard Lightfoot ...
 
 
shinyCircos: an R/Shiny application for interactive creation of Circos plot 
 
Yiming Yu ; Yidan Ouyang; Wen Yao
 
 
 
SEQUENCE ANALYSIS
 
 
 
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing 
 
Sunguk Shin; Hanna Lee; Hyeonju Son; Soonmyung Paik ; Sangwoo Kim
 
 
bioBakery: a meta'omic analysis environment border= 
 
Lauren J McIver; Galeb Abu-Ali; Eric A Franzosa; Randall Schwager; Xochitl C Morgan ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
3dRPC: a web server for 3D RNA'protein structure prediction 
 
Yangyu Huang; Haotian Li; Yi Xiao
 
 
NGLview'interactive molecular graphics for Jupyter notebooks 
 
Hai Nguyen; David A Case; Alexander S Rose
 
 
 
GENE EXPRESSION
 
 
 
iDINGO'integrative differential network analysis in genomics with Shiny application border= 
 
Caleb A Class; Min Jin Ha ; Veerabhadran Baladandayuthapani; Kim-Anh Do
 
 
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data border= 
 
Caleb Weinreb; Samuel Wolock; Allon M Klein
 
 
 
SYSTEMS BIOLOGY
 
 
 
PEITH(Θ): perfecting experiments with information theory in Python with GPU support border= 
 
Leander Dony; Jonas Mackerodt; Scott Ward; Sarah Filippi; Michael P H Stumpf ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action 
 
Justin Nelson; Scott W Simpkins; Hamid Safizadeh; Sheena C Li; Jeff S Piotrowski ...
 
 
REVIEW
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
Extreme learning machines for reverse engineering of gene regulatory networks from expression time series 
 
M Rubiolo; D H Milone; G Stegmayer
 
 
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