Subject: Bioinformatics Table of Contents for 15 March 2017 Oxford Academic
 
 
 
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Bioinformatics   International Society for Computational Biology
 
 
New issue alert
 
Bioinformatics  
Volume 33 Issue 6
 
15 March 2017
 
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RECOMB-SEQ/RECOMB-CBB 2016
 
 
 
 
GENOME ANALYSIS
 
 
 
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge 
 
Yang Young Lu; Ting Chen; Jed A. Fuhrman; Fengzhu Sun
 
 
 
SEQUENCE ANALYSIS
 
 
 
Accurate self-correction of errors in long reads using de Bruijn graphs  border= 
 
Leena Salmela; Riku Walve; Eric Rivals; Esko Ukkonen
 
 
Designing robust watermark barcodes for multiplex long-read sequencing 
 
Joaquín Ezpeleta; Flavia J. Krsticevic; Pilar Bulacio; Elizabeth Tapia
 
 
 
SYSTEMS BIOLOGY
 
 
 
WeSME: uncovering mutual exclusivity of cancer drivers and beyond 
 
Yoo-Ah Kim ; Sanna Madan; Teresa M. Przytycka
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
SNP interaction pattern identifier (SIPI): an intensive search for SNP'SNP interaction patterns 
 
Hui-Yi Lin; Dung-Tsa Chen; Po-Yu Huang ; Yung-Hsin Liu; Augusto Ochoa ...
 
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
DACE: a scalable DP-means algorithm for clustering extremely large sequence data 
 
Linhao Jiang; Yichao Dong; Ning Chen; Ting Chen
 
 
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features 
 
Hang Zhou; Yang Yang ; Hong-Bin Shen
 
 
RBPPred: predicting RNA-binding proteins from sequence using SVM 
 
Xiaoli Zhang ; Shiyong Liu
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier 
 
Jiaqi Xia; Zhenling Peng; Dawei Qi; Hongbo Mu ; Jianyi Yang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS 
 
Feng Chen; Shuang Wang; Xiaoqian Jiang; Sijie Ding ; Yao Lu ...
 
 
 
 
Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies 
 
Anand Bhaskar ; Adel Javanmard; Thomas A. Courtade; David Tse
 
 
Exploring the predictive power of polygenic scores derived from genome-wide association studies: a study of 10 complex traits 
 
Hon-Cheong So; Pak C. Sham
 
 
 
SYSTEMS BIOLOGY
 
 
 
Improving flux predictions by integrating data from multiple strains  
 
Matthew R. Long; Jennifer L. Reed
 
 
Predict drug permeability to blood'brain-barrier from clinical phenotypes: drug side effects and drug indications  
 
Zhen Gao; Yang Chen; Xiaoshu Cai ; Rong Xu
 
 
 
DATA AND TEXT MINING
 
 
 
CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort 
 
Jessica S. Yu; Dante A. Pertusi; Adebola V. Adeniran; Keith E. J. Tyo
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
HiLive: real-time mapping of illumina reads while sequencing 
 
Martin S. Lindner ; Benjamin Strauch; Jakob M. Schulze; Simon H. Tausch; Piotr W. Dabrowski ...
 
 
DNABarcodes: an R package for the systematic construction of DNA sample tags 
 
Tilo Buschmann
 
 
 
SEQUENCE ANALYSIS
 
 
 
AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs  
 
Alex V. Kochetov; Jens Allmer; Alexandra I. Klimenko ; Bulat S. Zuraev; Yury G. Matushkin ...
 
 
Training alignment parameters for arbitrary sequencers with LAST-TRAIN border= 
 
Michiaki Hamada; Yukiteru Ono; Kiyoshi Asai; Martin C. Frith
 
 
PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases 
 
Gauri Shende; Harshala Haldankar; Ram Shankar Barai ; Mohammed Husain Bharmal; Vinit Shetty ...
 
 
 
PHYLOGENETICS
 
 
 
node.dating: dating ancestors in phylogenetic trees in R 
 
Bradley R. Jones; Art F. Y. Poon
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
The PPI3D web server for searching, analyzing and modeling protein'protein interactions in the context of 3D structures 
 
Justas Dapkūnas; Albertas Timinskas ; Kliment Olechnovič; Mindaugas Margelevičius; Rytis Dičiūnas ...
 
 
 
GENE EXPRESSION
 
 
 
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data 
 
Riccardo Panero; Antonio Rinaldi; Domenico Memoli ; Giovanni Nassa; Maria Ravo ...
 
 
GE-mini: a mobile APP for large-scale gene expression visualization 
 
Zefang Tang; Chenwei Li; Karena Zhang; Mingyu Yang; Xueda Hu
 
 
 
SYSTEMS BIOLOGY
 
 
 
MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework 
 
Chuang Li ; Tao Chen; Qiang He; Yunping Zhu; Kenli Li
 
 
caspo: a toolbox for automated reasoning on the response of logical signaling networks families border= 
 
Santiago Videla; Julio Saez-Rodriguez ; Carito Guziolowski; Anne Siegel
 
 
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