Subject: Bioinformatics Table of Contents for 01 May 2018 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 9
 
01 May 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Integrating 5hmC and gene expression data to infer regulatory mechanisms 
 
Cristina Mitrea; Priyanga Wijesinghe; Greg Dyson; Adéle Kruger; Douglas M Ruden ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information 
 
Xiang Cheng; Xuan Xiao; Kuo-Chen Chou
 
 
Analyzing large scale genomic data on the cloud with Sparkhit border= 
 
Liren Huang; Jan Krüger; Alexander Sczyrba
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks border= 
 
Badri Adhikari; Jie Hou; Jianlin Cheng
 
 
Computational identification of binding energy hot spots in protein'RNA complexes using an ensemble approach 
 
Yuliang Pan; Zixiang Wang; Weihua Zhan; Lei Deng
 
 
 
 
Protein classification using modified n-grams and skip-grams 
 
S M Ashiqul Islam; Benjamin J Heil; Christopher Michel Kearney; Erich J Baker
 
 
 
GENE EXPRESSION
 
 
 
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates 
 
Scott S Norton; Jorge Vaquero-Garcia; Nicholas F Lahens; Gregory R Grant ; Yoseph Barash
 
 
gene2drug: a computational tool for pathway-based rational drug repositioning 
 
Francesco Napolitano ; Diego Carrella; Barbara Mandriani; Sandra Pisonero-Vaquero; Francesco Sirci ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies 
 
Andriy Derkach ; Haoyu Zhang; Nilanjan Chatterjee
 
 
 
SYSTEMS BIOLOGY
 
 
 
IndeCut evaluates performance of network motif discovery algorithms 
 
Mitra Ansariola; Molly Megraw; David Koslicki
 
 
 
 
An automated benchmarking platform for MHC class II binding prediction methods 
 
Massimo Andreatta; Thomas Trolle; Zhen Yan; Jason A Greenbaum ; Bjoern Peters ...
 
 
 
DATA AND TEXT MINING
 
 
 
Matrix factorization-based data fusion for the prediction of lncRNA'disease associations 
 
Guangyuan Fu; Jun Wang; Carlotta Domeniconi; Guoxian Yu
 
 
DeepSynergy: predicting anti-cancer drug synergy with Deep Learning border= 
 
Kristina Preuer; Richard P I Lewis ; Sepp Hochreiter; Andreas Bender; Krishna C Bulusu ...
 
 
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text border= 
 
Qile Zhu; Xiaolin Li; Ana Conesa; Cécile Pereira
 
 
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations 
 
Zhuxuan Jin; Jian Kang; Tianwei Yu
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny border= 
 
Alan Cleary; Andrew Farmer
 
 
Aether: leveraging linear programming for optimal cloud computing in genomics border= 
 
Jacob M Luber; Braden T Tierney ; Evan M Cofer; Chirag J Patel; Aleksandar D Kostic
 
 
CscoreTool: fast Hi-C compartment analysis at high resolution 
 
Xiaobin Zheng; Yixian Zheng
 
 
DiffGraph: an R package for identifying gene network rewiring using differential graphical models 
 
Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xiaohua Hu ; Hong Yan
 
 
 
SEQUENCE ANALYSIS
 
 
 
TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants 
 
Xuan Ma; Chunyan Liu; Lianfeng Gu; Beixin Mo; Xiaofeng Cao ...
 
 
fMLC: fast multi-level clustering and visualization of large molecular datasets 
 
D Vu; S Georgievska ; S Szoke; A Kuzniar; V Robert
 
 
PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq 
 
Yubang Gao; Huiyuan Wang; Hangxiao Zhang; Yongsheng Wang ; Jinfeng Chen ...
 
 
Mustguseal: a server for multiple structure-guided sequence alignment of protein families 
 
Dmitry A Suplatov ; Kirill E Kopylov; Nina N Popova; Vladimir V Voevodin; Vytas K Å vedas
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PINE-SPARKY.2 for automated NMR-based protein structure research border= 
 
Woonghee Lee; John L Markley
 
 
 
GENE EXPRESSION
 
 
 
myTAI: evolutionary transcriptomics with R border=  
 
Hajk-Georg Drost; Alexander Gabel; Jialin Liu ; Marcel Quint; Ivo Grosse
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data 
 
Khalid Kunji; Ehsan Ullah; Alejandro Q Nato, Jr; Ellen M Wijsman; Mohamad Saad
 
 
 
SYSTEMS BIOLOGY
 
 
 
ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions 
 
Brendan King; Terry Farrah; Matthew A Richards; Michael Mundy; Evangelos Simeonidis ...
 
 
DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization 
 
Min Li; Jie Yang ; Fang-Xiang Wu; Yi Pan; Jianxin Wang
 
 
 
DATA AND TEXT MINING
 
 
 
heatmaply: an R package for creating interactive cluster heatmaps for online publishing border= 
 
Tal Galili; Alan O'Callaghan ; Jonathan Sidi; Carson Sievert
 
 
PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool 
 
Anbo Zhou; Yeting Zhang; Yazhou Sun; Jinchuan Xing
 
 
GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records 
 
Tasnia Tahsin; Davy Weissenbacher; Karen O'Connor ; Arjun Magge; Matthew Scotch ...
 
 
CGManalyzer: an R package for analyzing continuous glucose monitoring studies 
 
Xiaohua Douglas Zhang; Zhaozhi Zhang; Dandan Wang
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
JASPAR RESTful API: accessing JASPAR data from any programming language 
 
Aziz Khan; Anthony Mathelier
 
 
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data 
 
Lin Wei; Zhilin Jin; Shengjie Yang ; Yanxun Xu; Yitan Zhu ...
 
 
DPMIND: degradome-based plant miRNA'target interaction and network database 
 
Yuhan Fei; Rui Wang; Haoyuan Li; Shu Liu; Hongsheng Zhang ...
 
 
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