Subject: Bioinformatics Table of Contents for 01 March 2017 Oxford Academic
 
 
 
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Bioinformatics   International Society for Computational Biology
 
 
New issue alert
 
Bioinformatics  
Volume 33 Issue 5
 
01 March 2017
 
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RECOMB-CG 2016
 
 
 
 
PHYLOGENETICS
 
 
 
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization border= 
 
Pranjal Vachaspati; Tandy Warnow
 
 
Xenolog classification border= 
 
Charlotte A. Darby; Maureen Stolzer; Patrick J. Ropp; Daniel Barker ; Dannie Durand
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data border= 
 
Denye Ogeh; Richard Badge
 
 
 
SEQUENCE ANALYSIS
 
 
 
Statistical significance based on length and position of the local score in a model of i.i.d. sequences 
 
Agnès Lagnoux ; Sabine Mercier; Pierre Vallois
 
 
ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives 
 
Jyun-Rong Wang; Wen-Lin Huang; Ming-Ju Tsai; Kai-Ti Hsu; Hui-Ling Huang ...
 
 
 
 
 
PHYLOGENETICS
 
 
 
Accelerating Bayesian inference for evolutionary biology models border= 
 
Xavier Meyer; Bastien Chopard; Nicolas Salamin
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction 
 
Tong Wang; Yuedong Yang; Yaoqi Zhou ; Haipeng Gong
 
 
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks 
 
Jack Hanson ; Yuedong Yang; Kuldip Paliwal; Yaoqi Zhou
 
 
 
GENE EXPRESSION
 
 
 
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm 
 
Cristóbal Fresno; Germán Alexis González ; Gabriela Alejandra Merino; Ana Georgina Flesia; Osvaldo Luis Podhajcer ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Network-based analysis of omics data: the LEAN method border= 
 
Frederik Gwinner; Gwénola Boulday ; Claire Vandiedonck; Minh Arnould; Cécile Cardoso ...
 
 
 
 
Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface 
 
Steven S. Andrews
 
 
Robust parameter estimation for dynamical systems from outlier-corrupted data 
 
Corinna Maier ; Carolin Loos; Jan Hasenauer
 
 
Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology 
 
Arya A. Das; T. Ajayakumar Darsana; Elizabeth Jacob
 
 
A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases 
 
Xing Chen; Yu-An Huang; Zhu-Hong You; Gui-Ying Yan ; Xue-Song Wang
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data border= 
 
Elizabeth Baskin; Rick Farouni; Ewy A. Mathé
 
 
SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets border= 
 
Hongliang Mao; Hao Wang
 
 
fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets border= 
 
Pedro Madrigal
 
 
 
SEQUENCE ANALYSIS
 
 
 
FUEL-mLoc: feature-unified prediction and explanation of multi-localization of cellular proteins in multiple organisms 
 
Shibiao Wan ; Man-Wai Mak; Sun-Yuan Kung
 
 
SeqLib: a C‰++ API for rapid BAM manipulation, sequence alignment and sequence assembly 
 
Jeremiah Wala; Rameen Beroukhim
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Expanding the toolkit for membrane protein modeling in Rosetta 
 
Julia Koehler Leman; Benjamin K. Mueller; Jeffrey J. Gray
 
 
 
GENE EXPRESSION
 
 
 
ImpulseDE: detection of differentially expressed genes in time series data using impulse models 
 
Jil Sander ; Joachim L. Schultze; Nir Yosef
 
 
GENIUS: web server to predict local gene networks and key genes for biological functions border= 
 
Tomas Puelma; Viviana Araus; Javier Canales; Elena A. Vidal ; Juan M. Cabello ...
 
 
cerebroViz: an R package for anatomical visualization of spatiotemporal brain data border= 
 
Ethan Bahl; Tanner Koomar; Jacob J. Michaelson
 
 
LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering 
 
Alicia T. Specht; Jun Li
 
 
Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud 
 
Andrian Yang; Michael Troup; Peijie Lin; Joshua W. K. Ho
 
 
 
SYSTEMS BIOLOGY
 
 
 
PyBoolNet: a python package for the generation, analysis and visualization of boolean networks 
 
Hannes Klarner ; Adam Streck; Heike Siebert
 
 
MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways border= 
 
Andrea Rodriguez-Martinez; Rafael Ayala; Joram M. Posma; Ana L. Neves ; Dominique Gauguier ...
 
 
CymeR: cytometry analysis using KNIME, docker and R border= 
 
B. Muchmore; M.E. AlarcĂłn-Riquelme
 
 
SPADEVizR: an R package for visualization, analysis and integration of SPADE results border= 
 
Guillaume Gautreau; David Pejoski; Roger Le Grand; Antonio Cosma ; Anne-Sophie Beignon ...
 
 
 
DATA AND TEXT MINING
 
 
 
Calypso: a user-friendly web-server for mining and visualizing microbiome'environment interactions border= 
 
Martha Zakrzewski; Carla Proietti; Jonathan J. Ellis; Shihab Hasan ; Marie-Jo Brion ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
PhagesDB: the actinobacteriophage database 
 
Daniel A. Russell; Graham F. Hatfull
 
 
 
BIOIMAGE INFORMATICS
 
 
 
tranSMART-XNAT Connector tranSMART-XNAT connector'image selection based on clinical phenotypes and genetic profiles 
 
Sijin He; May Yong; Paul M. Matthews; Yike Guo
 
 
SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images 
 
Côme Pasqualin; François Gannier; Angèle Yu; Claire O. Malécot; Pierre Bredeloux ...
 
 
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