Subject: Bioinformatics Table of Contents for 01 August 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 15
 
01 August 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
SeqArray'a storage-efficient high-performance data format for WGS variant calls 
 
Xiuwen Zheng; Stephanie M. Gogarten; Michael Lawrence; Adrienne Stilp; Matthew P. Conomos ...
 
 
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis 
 
Georg Stricker; Alexander Engelhardt ; Daniel Schulz; Matthias Schmid; Achim Tresch ...
 
 
cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data 
 
Maximilian Knoll; J√ľrgen Debus; Amir Abdollahi
 
 
SQC: secure quality control for meta-analysis of genome-wide association studies 
 
Zhicong Huang; Huang Lin; Jacques Fellay; Zolt√°n Kutalik; Jean-Pierre Hubaux
 
 
 
SEQUENCE ANALYSIS
 
 
 
Kart: a divide-and-conquer algorithm for NGS read alignment border= 
 
Hsin-Nan Lin; Wen-Lian Hsu
 
 
 
 
BEESEM: estimation of binding energy models using HT-SELEX data 
 
Shuxiang Ruan; S. Joshua Swamidass; Gary D. Stormo
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
NeBcon: protein contact map prediction using neural network training coupled with na√Įve Bayes classifiers 
 
Baoji He; S. M. Mortuza; Yanting Wang; Hong-Bin Shen; Yang Zhang
 
 
 
GENE EXPRESSION
 
 
 
Enhanced methods to detect haplotypic effects on gene expression 
 
Robert Brown; Gleb Kichaev; Nicholas Mancuso; James Boocock ; Bogdan Pasaniuc
 
 
SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation border= 
 
Hirotaka Matsumoto; Hisanori Kiryu; Chikara Furusawa; Minoru S. H. Ko; Shigeru B. H. Ko ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions border= 
 
Steven H. Wu; Rachel S. Schwartz; David J. Winter; Donald F. Conrad ; Reed A. Cartwright
 
 
 
 
A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests 
 
Maggie Haitian Wang; Haoyi Weng ; Rui Sun; Jack Lee; William Ka Kei Wu ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Deep mining heterogeneous networks of biomedical linked data to predict novel drug'target associations 
 
Nansu Zong; Hyeoneui Kim; Victoria Ngo; Olivier Harismendy
 
 
Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming 
 
Hyun-Seob Song ; Noam Goldberg; Ashutosh Mahajan; Doraiswami Ramkrishna
 
 
 
DATA AND TEXT MINING
 
 
 
CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies 
 
Cheng-Hong Yang; Li-Yeh Chuang; Yu-Da Lin
 
 
A transition-based joint model for disease named entity recognition and normalization 
 
Yinxia Lou; Yue Zhang ; Tao Qian; Fei Li; Shufeng Xiong ...
 
 
Mining heterogeneous causal effects for personalized cancer treatment 
 
Weijia Zhang; Thuc Duy Le; Lin Liu; Zhi-Hua Zhou ; Jiuyong Li
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ViPTree: the viral proteomic tree server 
 
Yosuke Nishimura; Takashi Yoshida; Megumi Kuronishi; Hideya Uehara ; Hiroyuki Ogata ...
 
 
annotatr: genomic regions in context 
 
Raymond G. Cavalcante ; Maureen A. Sartor
 
 
modSaRa: a computationally efficient R package for CNV identification 
 
Feifei Xiao ; Yue Niu; Ning Hao; Yanxun Xu; Zhilin Jin ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials border= 
 
Andrew Fiore-Gartland; Nicholas Kullman; Allan C. deCamp; Graham Clenaghan; Wayne Yang ...
 
 
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive border= 
 
Pedro J. Torres ; Robert A. Edwards; Katelyn A. McNair
 
 
 
PHYLOGENETICS
 
 
 
IcyTree: rapid browser-based visualization for phylogenetic trees and networks border=  
 
Timothy G. Vaughan
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Cpi pe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues 
 
Inanc Soylu; Stefano M. Marino
 
 
 
GENE EXPRESSION
 
 
 
The Tomato Expression Atlas border= 
 
Noe Fernandez-Pozo; Yi Zheng; Stephen I. Snyder; Philippe Nicolas; Yoshihito Shinozaki ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
StrandScript: evaluation of Illumina genotyping array design and strand correction 
 
Jing Wang; David C. Samuels; Yu Shyr; Yan Guo
 
 
EthSEQ: ethnicity annotation from whole exome sequencing data border= 
 
Alessandro Romanel; Tuo Zhang ; Olivier Elemento; Francesca Demichelis
 
 
biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements border= 
 
Matti Pirinen; Christian Benner; Pekka Marttinen; Marjo-Riitta Järvelin ; Manuel A. Rivas ...
 
 
EUPAN enables pan-genome studies of a large number of eukaryotic genomes 
 
Zhiqiang Hu ; Chen Sun; Kuang-chen Lu; Xixia Chu; Yue Zhao ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets border= 
 
Ssmund Flobak; Miguel Vazquez; Astrid Lægreid; Alfonso Valencia
 
 
SynergyFinder: a web application for analyzing drug combination dose'response matrix data border= 
 
Aleksandr Ianevski; Liye He ; Tero Aittokallio; Jing Tang
 
 
Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models border= 
 
Michael Mundy; Helena Mendes-Soares; Nicholas Chia
 
 
 
DATA AND TEXT MINING
 
 
 
MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data 
 
Thomas Naake ; Emmanuel Gaquerel
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data 
 
Nikolas Pontikos; Jing Yu; Ismail Moghul; Lucy Withington; Fiona Blanco-Kelly ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification 
 
Ignacio Arganda-Carreras; Verena Kaynig; Curtis Rueden; Kevin W. Eliceiri; Johannes Schindelin ...
 
 
rMSI: an R package for MS imaging data handling and visualization 
 
Pere Ràfols; Sònia Torres ; Noelia Ramírez; Esteban del Castillo; Oscar Yanes ...
 
 
MESSAGE FROM THE ISCB
 
 
 
The International Society for Computational Biology and WikiProject Computational Biology: celebrating 10Čyears of collaboration towards open access border= 
 
Kieran O'Neill; Vivek Rai; Alastair M. Kilpatrick
 
 
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