Subject: Bioinformatics Table of Contents for 15 November 2018 ------=_Part_1013863872.1541955830157 Content-Type: text/plain;charset=UTF-8 This email is intended for ------=_Part_1013863872.1541955830157 Content-Type: text/html;charset=UTF-8 Oxford Academic
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Volume 34 Issue 22
15 November 2018
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 ...
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
MASCOT: parameter and state inference under the marginal structured coalescent approximation border= 
Nicola F Müller; David Rasmussen; Tanja Stadler
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 ...
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals 
Ehsan Motazedi; Dick de Ridder; Richard Finkers; Samantha Baldwin; Susan Thomson ...
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
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
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
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
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
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 ...
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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