Subject: Bioinformatics Table of Contents for 15 November 2018 ------=_Part_1013863872.1541955830157 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1013863872.1541955830157 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 22
 
15 November 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
DeepMirTar: a deep-learning approach for predicting human miRNA targets 
 
Ming Wen; Peisheng Cong; Zhimin Zhang; Hongmei Lu ; Tonghua Li
 
 
Lost in translation: bioinformatic analysis of variations affecting the translation initiation codon in the human genome 
 
Francisco Abad-Navarro; María Eugenia de la Morena-Barrio; Jesualdo Tomás Fernández-Breis ; Javier Corral
 
 
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data 
 
Panisa Treepong; Christophe Guyeux; Alexandre Meunier; Charlotte Couchoud ; Didier Hocquet ...
 
 
Bayesian integrative model for multi-omics data with missingness 
 
Zhou Fang; Tianzhou Ma; Gong Tang; Li Zhu ; Qi Yan ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
An automated method for detecting alternatively spliced protein domains 
 
Vitor Coelho; Michael Sammeth
 
 
RIFRAF: a frame-resolving consensus algorithm 
 
Kemal Eren; Ben Murrell
 
 
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning 
 
Cheng Yang; Longshu Yang; Man Zhou; Haoling Xie ; Chengjiu Zhang ...
 
 
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach 
 
Bin Liu; Kai Li; De-Shuang Huang; Kuo-Chen Chou
 
 
 
PHYLOGENETICS
 
 
 
MASCOT: parameter and state inference under the marginal structured coalescent approximation border= 
 
Nicola F Müller; David Rasmussen; Tanja Stadler
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Knotty: efficient and accurate prediction of complex RNA pseudoknot structures 
 
Hosna Jabbari; Ian Wark; Carlo Montemagno; Sebastian Will
 
 
The size matters? A computational tool to design bivalent ligands border=  
 
Laura Pérez-Benito; Andrew Henry; Minos-Timotheos Matsoukas ; Laura Lopez; Daniel Pulido ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals 
 
Ehsan Motazedi; Dick de Ridder; Richard Finkers; Samantha Baldwin; Susan Thomson ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
deepNF: deep network fusion for protein function prediction border=  
 
Vladimir Gligorijević; Meet Barot; Richard Bonneau
 
 
Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis 
 
Mingyuan Tian; Jennifer L Reed
 
 
 
DATA AND TEXT MINING
 
 
 
LncRNAnet: long non-coding RNA identification using deep learning  
 
Junghwan Baek; Byunghan Lee; Sunyoung Kwon; Sungroh Yoon
 
 
An in silico proteomics screen to predict and prioritize protein'protein interactions dependent on post-translationally modified motifs 
 
Anna M Schmoker; Heather E Driscoll; Stefanie R Geiger ; James J Vincent; Alicia M Ebert ...
 
 
Predicting Cancer Drug Response using a Recommender System 
 
Chayaporn Suphavilai; Denis Bertrand; Niranjan Nagarajan
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data 
 
Braulio Valdebenito-Maturana; Gonzalo Riadi
 
 
SciApps: a cloud-based platform for reproducible bioinformatics workflows border=  
 
Liya Wang; Zhenyuan Lu; Peter Van Buren ; Doreen Ware
 
 
ClusterScan: simple and generalistic identification of genomic clusters 
 
Massimiliano Volpe; Marco Miralto; Stefano Gustincich; Remo Sanges
 
 
 
SEQUENCE ANALYSIS
 
 
 
Axe: rapid, competitive sequence read demultiplexing using a trie  
 
Kevin D Murray; Justin O Borevitz
 
 
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files 
 
Elisha D O Roberson
 
 
PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences 
 
Simon Whelan; Iker Irisarri; Fabien Burki
 
 
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins border=  
 
Sandeep Kumar Dhanda; Randi Vita; Brendan Ha ; Alba Grifoni; Bjoern Peters ...
 
 
Grimon: graphical interface to visualize multi-omics networks border= 
 
Masahiro Kanai; Yuichi Maeda; Yukinori Okada
 
 
ICBdocker: a Docker image for proteome annotation and visualization 
 
Nicola Bordin; Damien P Devos
 
 
PASTA for proteins border= 
 
Kodi Collins; Tandy Warnow
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
BioStructMap: a Python tool for integration of protein structure and sequence-based features border= 
 
Andrew J Guy; Vashti Irani ; Jack S Richards; Paul A Ramsland
 
 
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations 
 
M Eric Irrgang; Jennifer M Hays; Peter M Kasson
 
 
mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling 
 
Joseph Masison; Paul J Michalski; Leslie M Loew; Adam D Schuyler
 
 
 
SYSTEMS BIOLOGY
 
 
 
ggCyto: next generation open-source visualization software for cytometry border=  
 
Phu Van; Wenxin Jiang; Raphael Gottardo ; Greg Finak
 
 
iMetaLab 1.0: a web platform for metaproteomics data analysis 
 
Bo Liao; Zhibin Ning; Kai Cheng; Xu Zhang ; Leyuan Li ...
 
 
 
DATA AND TEXT MINING
 
 
 
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts border= 
 
Teemu D Laajala ; Mika Murtojärvi; Arho Virkki; Tero Aittokallio
 
 
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