Subject: Bioinformatics Table of Contents for 15 August 2019 ------=_Part_1823124978.1565981742451 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1823124978.1565981742451 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 35 Issue 16
 
15 August 2019
 
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DISCOVERY NOTE
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit 
 
Justin R Klesmith; Benjamin J Hackel
 
 
Linking sequence patterns and functionality of alpha-helical antimicrobial peptides 
 
Igor E Eliseev; Ivan N Terterov; Anna N Yudenko; Olga V Shamova
 
 
 
SYSTEMS BIOLOGY
 
 
 
The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana 
 
Tamir Tuller; Alon Diament; Avital Yahalom; Assaf Zemach; Shimshi Atar ...
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps 
 
L Carron; J B Morlot; V Matthys; A Lesne ; J Mozziconacci
 
 
Promoter analysis and prediction in the human genome using sequence-based deep learning models 
 
Ramzan Umarov; Hiroyuki Kuwahara; Yu Li; Xin Gao ; Victor Solovyev
 
 
 
SEQUENCE ANALYSIS
 
 
 
The DNA walk and its demonstration of deterministic chaos'relevance to genomic alterations in lung cancer border= 
 
Blake Hewelt; Haiqing Li; Mohit Kumar Jolly; Prakash Kulkarni; Isa Mambetsariev ...
 
 
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization 
 
Jialin Yu; Shaoping Shi; Fang Zhang; Guodong Chen ; Man Cao
 
 
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation 
 
Balachandran Manavalan; Shaherin Basith; Tae Hwan Shin ; Leyi Wei; Gwang Lee
 
 
DeepPhos: prediction of protein phosphorylation sites with deep learning border=  
 
Fenglin Luo; Minghui Wang; Yu Liu ; Xing-Ming Zhao; Ao Li
 
 
MoMo: discovery of statistically significant post-translational modification motifs 
 
Alice Cheng; Charles E Grant; William S Noble; Timothy L Bailey
 
 
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity 
 
Houxiang Zhu; Chun Liang
 
 
DeepCoil'a fast and accurate prediction of coiled-coil domains in protein sequences 
 
Jan Ludwiczak; Aleksander Winski; Krzysztof Szczepaniak; Vikram Alva ; Stanislaw Dunin-Horkawicz
 
 
i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome 
 
Wei Chen; Hao Lv; Fulei Nie; Hao Lin
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment 
 
Mikhail Karasikov; Guillaume Pagès; Sergei Grudinin
 
 
 
GENE EXPRESSION
 
 
 
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning 
 
Xiangtao Li; Shixiong Zhang; Ka-Chun Wong
 
 
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing border=  
 
Jinyan Chan; Xuan Wang; Jacob A Turner ; Nicole E Baldwin; Jinghua Gu
 
 
 
DATA AND TEXT MINING
 
 
 
CSHAP: efficient haplotype frequency estimation based on sparse representation 
 
Yinsheng Zhou; Han Zhang; Yaning Yang
 
 
 
BIOIMAGE INFORMATICS
 
 
 
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model 
 
Yang Yang; Mingyu Zhou; Qingwei Fang; Hong-Bin Shen
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
PINSPlus: a tool for tumor subtype discovery in integrated genomic data 
 
Hung Nguyen; Sangam Shrestha; Sorin Draghici; Tin Nguyen
 
 
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data 
 
Jos B Poell; Matias Mendeville; Daoud Sie; Arjen Brink ; Ruud H Brakenhoff ...
 
 
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing border=  
 
Georgette Tanner; David R Westhead; Alastair Droop ; Lucy F Stead
 
 
 
SEQUENCE ANALYSIS
 
 
 
GfaViz: flexible and interactive visualization of GFA sequence graphs 
 
Giorgio Gonnella; Niklas Niehus; Stefan Kurtz
 
 
MMseqs2 desktop and local web server app for fast, interactive sequence searches border=  
 
Milot Mirdita; Martin Steinegger; Johannes Söding
 
 
BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads 
 
Linfang Jin; Jinhuo Lai; Yang Zhang; Ying Fu ; Shuhang Wang ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Integration of accessibility data from structure probing into RNA'RNA interaction prediction border= 
 
Milad Miladi; Soheila Montaseri ; Rolf Backofen; Martin Raden
 
 
 
GENE EXPRESSION
 
 
 
M3Drop: dropout-based feature selection for scRNASeq border=  
 
Tallulah S Andrews; Martin Hemberg
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species 
 
Paula Tataru; Thomas Bataillon
 
 
 
SYSTEMS BIOLOGY
 
 
 
MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery 
 
Xiaotao Shen; Zheng-Jiang Zhu
 
 
SIAN: software for structural identifiability analysis of ODE models 
 
Hoon Hong; Alexey Ovchinnikov; Gleb Pogudin; Chee Yap
 
 
Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein'protein interaction 
 
Diego A A Morais; Rita M C Almeida; Rodrigo J S Dalmolin
 
 
 
DATA AND TEXT MINING
 
 
 
Multiview: a software package for multiview pattern recognition methods 
 
Samir Kanaan-Izquierdo; Andrey Ziyatdinov; Maria Araceli Burgueño; Alexandre Perera-Lluna
 
 
Curse: building expression atlases and co-expression networks from public RNA-Seq data 
 
Dries Vaneechoutte; Klaas Vandepoele
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
UbiHub: a data hub for the explorers of ubiquitination pathways border=  
 
Lihua Liu; David R Damerell; Leonidas Koukouflis ; Yufeng Tong; Brian D Marsden ...
 
 
 
CORRIGENDUM
 
 
 
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization 
 
Yuan Luo; Chengsheng Mao; Yiben Yang; Fei Wang; Faraz S Ahmad ...
 
 
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