Subject: Bioinformatics Table of Contents for 15 September 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 18
 
15 September 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Reliability of algorithmic somatic copy number alteration detection from targeted capture data border= 
 
Nora Rieber; Regina Bohnert; Ulrike Ziehm; Gunther Jansen
 
 
The spike-and-slab lasso Cox model for survival prediction and associated genes detection 
 
Zaixiang Tang; Yueping Shen; Xinyan Zhang ; Nengjun Yi
 
 
E2FM: an encrypted and compressed full-text index for collections of genomic sequences 
 
Ferdinando Montecuollo ; Giovannni Schmid; Roberto Tagliaferri
 
 
GLANET: genomic loci annotation and enrichment tool 
 
Burçak Otlu; Can Firtina; Sündüz Keleş; Oznur Tastan
 
 
A fast and exhaustive method for heterogeneity and epistasis analysis based on multi-objective optimization  
 
Xiong Li
 
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound 
 
Loris Nanni; Sheryl Brahnam
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility 
 
Rhys Heffernan; Yuedong Yang ; Kuldip Paliwal; Yaoqi Zhou
 
 
RNAblueprint: flexible multiple target nucleic acid sequence design border= 
 
Stefan Hammer; Birgit Tschiatschek; Christoph Flamm; Ivo L. Hofacker; Sven Findeiß
 
 
Predicting accurate contacts in thousands of Pfam domain families using PconsC3 
 
Mirco Michel; Marcin J. Skwark ; David Menéndez Hurtado; Magnus Ekeberg; Arne Elofsson
 
 
 
GENE EXPRESSION
 
 
 
Accelerating high-dimensional clustering with lossless data reduction 
 
Bahjat F. Qaqish; Jonathon J. O'Brien; Jonathan C. Hibbard ; Katie J. Clowers
 
 
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing 
 
Jian Xiao; Hongyuan Cao; Jun Chen
 
 
IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies 
 
Mingwei Dai; Jingsi Ming; Mingxuan Cai; Jin Liu ; Can Yang ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study border= 
 
Nicolas Städler; Frank Dondelinger; Steven M. Hill; Rehan Akbani ; Yiling Lu ...
 
 
 
DATA AND TEXT MINING
 
 
 
A method for learning a sparse classifier in the presence of missing data for high-dimensional biological datasets 
 
Kristen A. Severson; Brinda Monian; J. Christopher Love; Richard D. Braatz
 
 
Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests 
 
Trang T. Le; W. Kyle Simmons ; Masaya Misaki; Jerzy Bodurka; Bill C. White ...
 
 
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive border= 
 
Matthew N. Bernstein; AnHai Doan; Colin N. Dewey
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences 
 
Nili Tickotsky ; Tal Sagiv; Jaime Prilusky; Eric Shifrut; Nir Friedman
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Single-cell regulome data analysis by SCRAT border= 
 
Zhicheng Ji; Weiqiang Zhou; Hongkai Ji
 
 
OMTools: a software package for visualizing and processing optical mapping data border= 
 
Alden King-Yung Leung; Nana Jin; Kevin Y. Yip; Ting-Fung Chan
 
 
FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation 
 
Byoungnam Min; Igor V. Grigoriev ; In-Geol Choi
 
 
UpSetR: an R package for the visualization of intersecting sets and their properties border= 
 
Jake R. Conway; Alexander Lex; Nils Gehlenborg
 
 
 
SEQUENCE ANALYSIS
 
 
 
Flexbar 3.0 ' SIMD and multicore parallelization 
 
Johannes T. Roehr; Christoph Dieterich; Knut Reinert
 
 
Spliceman2: a computational web server that predicts defects in pre-mRNA splicing 
 
Kamil Jan Cygan; Clayton Hendrick Sanford ; William Guy Fairbrother
 
 
 
PHYLOGENETICS
 
 
 
PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization 
 
Å ukasz Kreft; Alexander Botzki; Frederik Coppens; Klaas Vandepoele; Michiel Van Bel
 
 
PASTASpark: multiple sequence alignment meets Big Data 
 
José M. Abuín; Tomás F. Pena ; Juan C. Pichel
 
 
 
GENE EXPRESSION
 
 
 
SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer border= 
 
Jiannong Li; Inna Smalley; Michael J. Schell; Keiran S. M. Smalley ; Y. Ann Chen
 
 
chimeraviz: a tool for visualizing chimeric RNA border= 
 
Stian Lågstad; Sen Zhao; Andreas M. Hoff; Bjarne Johannessen; Ole Christian Lingjærde ...
 
 
Phantom: investigating heterogeneous gene sets in time-course data 
 
Jinghua Gu; Xuan Wang ; Jinyan Chan; Nicole E. Baldwin; Jacob A. Turner
 
 
 
SYSTEMS BIOLOGY
 
 
 
HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens border= 
 
Christian Scheeder; Florian Heigwer ; Michael Boutros
 
 
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution 
 
Hyun-Hwan Jeong ; Seon Young Kim; Maxime W. C. Rousseaux; Huda Y. Zoghbi; Zhandong Liu
 
 
SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments 
 
Atis Elsts; Agris Pentjuss; Egils Stalidzans
 
 
MESSAGE FROM THE ISCB
 
 
 
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing border= 
 
Bonnie Berger; Theresa Gaasterland; Thomas Lengauer; Christine A. Orengo; Bruno Gaeta ...
 
 
Message from the ISCB: The 5th ISCB Wikipedia competition: coming to a classroom near you? 
 
Alastair Kilpatrick
 
 
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