Subject: Bioinformatics Table of Contents for 15 April 2018 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 8
 
15 April 2018
 
button-issue.png
 
ORIGINAL PAPERS
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks border= 
 
Žiga Avsec; Mohammadamin Barekatain; Jun Cheng; Julien Gagneur
 
 
MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks 
 
Brittney N Keel; Bo Deng; Etsuko N Moriyama
 
 
Identifying functionally informative evolutionary sequence profiles 
 
Nelson Gil; Andras Fiser
 
 
FROGS: Find, Rapidly, OTUs with Galaxy Solution 
 
Frédéric Escudié; Lucas Auer ; Maria Bernard; Mahendra Mariadassou; Laurent Cauquil ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
DeepSF: deep convolutional neural network for mapping protein sequences to folds border= 
 
Jie Hou; Badri Adhikari ; Jianlin Cheng
 
 
 
 
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation border= 
 
Maciej Antczak; Mariusz Popenda; Tomasz Zok; Michal Zurkowski; Ryszard W Adamiak ...
 
 
 
GENE EXPRESSION
 
 
 
ASElux: an ultra-fast and accurate allelic reads counter 
 
Zong Miao ; Marcus Alvarez; Päivi Pajukanta; Arthur Ko
 
 
Meta-analytic principal component analysis in integrative omics application 
 
SungHwan Kim; Dongwan Kang; Zhiguang Huo; Yongseok Park ; George C Tseng
 
 
Classifying next-generation sequencing data using a zero-inflated Poisson model 
 
Yan Zhou ; Xiang Wan; Baoxue Zhang; Tiejun Tong
 
 
Sequential feature selection and inference using multi-variate random forests  
 
Joshua Mayer; Raziur Rahman; Souparno Ghosh; Ranadip Pal
 
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments 
 
Wayne B Hayes ; Nil Mamano
 
 
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach border= 
 
Mehreen Ali; Suleiman A Khan; Krister Wennerberg; Tero Aittokallio
 
 
Model-based design of bistable cell factories for metabolic engineering 
 
Shyam Srinivasan; William R Cluett; Radhakrishnan Mahadevan
 
 
 
DATA AND TEXT MINING
 
 
 
Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations 
 
Ine Melckenbeeck ; Pieter Audenaert; Didier Colle; Mario Pickavet
 
 
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition 
 
Ling Luo; Zhihao Yang; Pei Yang; Yin Zhang ; Lei Wang ...
 
 
LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models 
 
Axel J Soto ; Chrysoula Zerva; Riza Batista-Navarro; Sophia Ananiadou
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
glactools: a command-line toolset for the management of genotype likelihoods and allele counts 
 
Gabriel Renaud
 
 
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles border= 
 
Jasper J Koehorst; Jesse C J van Dam; Edoardo Saccenti; Vitor A P Martins dos Santos; Maria Suarez-Diez ...
 
 
ASAR: visual analysis of metagenomes in R border= 
 
Askarbek N Orakov; Nazgul K Sakenova; Anatoly Sorokin; Igor I Goryanin
 
 
Gene Graphics: a genomic neighborhood data visualization web application 
 
Katherine J Harrison; Valérie de Crécy-Lagard; Rémi Zallot
 
 
Delta: a new web-based 3D genome visualization and analysis platform 
 
Bixia Tang ; Feifei Li; Jing Li; Wenming Zhao; Zhihua Zhang
 
 
 
SEQUENCE ANALYSIS
 
 
 
Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis 
 
Nick Weber ; David Liou; Jennifer Dommer; Philip MacMenamin; Mariam Quiñones ...
 
 
Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data 
 
Osvaldo Graña; Hugo López-Fernández; Florentino Fdez-Riverola ; David González Pisano; Daniel Glez-Peña
 
 
 
GENE EXPRESSION
 
 
 
DaMiRseq'an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification 
 
Mattia Chiesa; Gualtiero I Colombo ; Luca Piacentini
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
SimulaTE: simulating complex landscapes of transposable elements of populations border= 
 
Robert Kofler
 
 
 
SYSTEMS BIOLOGY
 
 
 
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models border= 
 
Thomas S Ligon; Fabian Fröhlich; Oana T Chiş ; Julio R Banga; Eva Balsa-Canto ...
 
 
Reproducible and flexible simulation experiments with ML-Rules and SESSL 
 
T Warnke; T Helms; A M Uhrmacher
 
 
CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis 
 
Lin Wu; Min Li; Jianxin Wang; Fang-Xiang Wu
 
 
 
DATA AND TEXT MINING
 
 
 
Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API border= 
 
Alba Gutiérrez-Sacristán; Romain Guedj; Gabor Korodi; Jason Stedman; Laura I Furlong ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web 
 
Daniel Probst; Jean-Louis Reymond
 
 
Curatr: a web application for creating, curating and sharing a mass spectral library 
 
Andrew Palmer; Prasad Phapale; Dominik Fay; Theodore Alexandrov
 
 
CORRIGENDUM
 
 
 
SimulaTE: simulating complex landscapes of transposable elements of populations border= 
 
Robert Kofler
 
 
ERRATUM
 
 
 
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
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

The content of this email is protected by copyright.
 
oxforde_university.jpg
 
 
 
                                 


This email is intended for bionet@evol.biology.mcmaster.ca.