Subject: Bioinformatics Table of Contents for 15 March 2018 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 6
 
15 March 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information 
 
Zaixiang Tang; Yueping Shen; Yan Li; Xinyan Zhang; Jia Wen ...
 
 
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data 
 
Vida Ravanmehr; Minji Kim ; Zhiying Wang; Olgica Milenković; Bonnie Berger
 
 
Machine learning annotation of human branchpoints 
 
Bethany Signal; Brian S Gloss; Marcel E Dinger; Tim R Mercer ; John Hancock
 
 
ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads 
 
Altti Ilari Maarala ; Zurab Bzhalava; Joakim Dillner; Keijo Heljanko; Davit Bzhalava ...
 
 
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations  
 
Clinton L Cario; John S Witte; John Hancock
 
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences 
 
Akshay Kumar Avvaru ; Divya Tej Sowpati; Rakesh Kumar Mishra; John Hancock
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Predicting loop conformational ensembles 
 
Claire Marks; Jiye Shi; Charlotte M Deane ; Alfonso Valencia
 
 
GRASS: semi-automated NMR-based structure elucidation of saccharides 
 
Roman R Kapaev ; Philip V Toukach; Alfonso Valencia
 
 
 
GENE EXPRESSION
 
 
 
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data 
 
M Sanchez-Castillo; D Blanco; I M Tienda-Luna; M C Carrion; Yufei Huang ...
 
 
An exact test for comparing a fixed quantitative property between gene sets 
 
Matthew M Parks ; Ziv Bar-Joseph
 
 
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Estimation of QTL heritability based on pooled sequencing data 
 
Weiqi Tang; Likun Huang; Suhong Bu; Xuzhang Zhang; Weiren Wu ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease border= 
 
Lichy Han; Mateusz Maciejewski; Christoph Brockel; William Gordon; Scott B Snapper ...
 
 
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias border= 
 
M D Luecken ; M J T Page; A J Crosby; S Mason; G Reinert ...
 
 
 
DATA AND TEXT MINING
 
 
 
Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra border= 
 
S Deepaisarn; P D Tar; N A Thacker; A Seepujak; A W McMahon ...
 
 
Unsupervised multiple kernel learning for heterogeneous data integration 
 
Jérôme Mariette; Nathalie Villa-Vialaneix; Jonathan Wren
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes border= 
 
S Castillo-Lara; J F Abril; Janet Kelso
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Identification of topological features in renal tumor microenvironment associated with patient survival 
 
Jun Cheng ; Xiaokui Mo; Xusheng Wang; Anil Parwani; Qianjin Feng ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool border= 
 
Lucas Lochovsky; Jing Zhang; Mark Gerstein; Bonnie Berger
 
 
NanoStringNormCNV: pre-processing of NanoString CNV data 
 
Dorota H Sendorek; Emilie Lalonde; Cindy Q Yao; Veronica Y Sabelnykova; Robert G Bristow ...
 
 
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication border= 
 
Yasuhiro Tanizawa; Takatomo Fujisawa; Yasukazu Nakamura; John Hancock
 
 
TabPath: interactive tables for metabolic pathway analysis 
 
Lauro Ângelo Gonçalves de Moraes; Érica Barbosa Felestrino; Renata de Almeida Barbosa Assis ; Diogo Matos; Joubert de Castro Lima ...
 
 
Myriads: P-value-based multiple testing correction 
 
Antonio Carvajal-Rodríguez; Bonnie Berger
 
 
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data border= 
 
Tong Liu; Zheng Wang; John Hancock
 
 
 
SEQUENCE ANALYSIS
 
 
 
Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains 
 
Antonio Solano-Román; Verónica Alfaro-Arias; Carlos Cruz-Castillo; Allan Orozco-Solano; Alfonso Valencia
 
 
 
PHYLOGENETICS
 
 
 
Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data 
 
Brian D Piccolo; Umesh D Wankhade; Sree V Chintapalli; Sudeepa Bhattacharyya; Luo Chunqiao ...
 
 
Efficient comparative phylogenetics on large trees 
 
Stilianos Louca; Michael Doebeli ; Alfonso Valencia
 
 
SPECTRE: a suite of phylogenetic tools for reticulate evolution border= 
 
Sarah Bastkowski; Daniel Mapleson; Andreas Spillner; Taoyang Wu; Monika BalvočiÅ«tÄ- ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
BEAM web server: a tool for structural RNA motif discovery border= 
 
Marco Pietrosanto; Marta Adinolfi; Riccardo Casula; Gabriele Ausiello; Fabrizio Ferrè ...
 
 
Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers 
 
Andrei L Lomize; Jacob M Hage ; Irina D Pogozheva; Alfonso Valencia
 
 
PREFMD: a web server for protein structure refinement via molecular dynamics simulations 
 
Lim Heo; Michael Feig; Alfonso Valencia
 
 
 
GENE EXPRESSION
 
 
 
DIEGO: detection of differential alternative splicing using Aitchison's geometry border= 
 
Gero Doose; Stephan H Bernhart ; Rabea Wagener; Steve Hoffmann; Ziv Bar-Joseph
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
pedigreejs: a web-based graphical pedigree editor border= 
 
Tim Carver; Alex P Cunningham ; Chantal Babb de Villiers; Andrew Lee; Simon Hartley ...
 
 
ThetaMater: Bayesian estimation of population size parameter theta from genomic data 
 
Richard H Adams; Drew R Schield; Daren C Card ; Andrew Corbin; Todd A Castoe ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins 
 
Sandy S Pineda; Pierre-Alain Chaumeil; Anne Kunert; Quentin Kaas; Mike W C Thang ...
 
 
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1 
 
Jeongbin Park ; Sangsu Bae; Alfonso Valencia
 
 
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