Subject: Bioinformatics Table of Contents for 1 October 2019 ------=_Part_331496257.1569781681105 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_331496257.1569781681105 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 35 Issue 19
 
1 October 2019
 
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REVIEW
 
 
 
 
GENOME ANALYSIS
 
 
 
Evolution of biosequence search algorithms: a brief survey 
 
Gregory Kucherov
 
 
 
DISCOVERY NOTE
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Is the Bombali virus pathogenic in humans? 
 
Henry J Martell; Stuart G Masterson; Jake E McGreig ; Martin Michaelis; Mark N Wass
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease 
 
Zixiu Li; Feng Zhang; Yukai Wang ; Yue Qiu; Yang Wu ...
 
 
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis 
 
Anna M Plantinga; Jun Chen; Robert R Jenq ; Michael C Wu
 
 
Integration of methylation QTL and enhancer'target gene maps with schizophrenia GWAS summary results identifies novel genes  
 
Chong Wu; Wei Pan
 
 
 
SEQUENCE ANALYSIS
 
 
 
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides 
 
Sherif Farag; Rachel M Bleich; Elizabeth A Shank ; Olexandr Isayev; Albert A Bowers ...
 
 
RECAP reveals the true statistical significance of ChIP-seq peak calls border= 
 
Justin G Chitpin ; Aseel Awdeh; Theodore J Perkins
 
 
Bit-parallel sequence-to-graph alignment border=  
 
Mikko Rautiainen; Veli Mäkinen; Tobias Marschall
 
 
 
PHYLOGENETICS
 
 
 
Choice of species affects phylogenetic stability of deep nodes: an empirical example in Terrabacteria border= 
 
Ashley A Superson ; Doug Phelan; Allyson Dekovich; Fabia U Battistuzzi
 
 
phylostratr: a framework for phylostratigraphy 
 
Zebulun Arendsee; Jing Li; Urminder Singh ; Arun Seetharam; Karin Dorman ...
 
 
 
GENE EXPRESSION
 
 
 
Benefits of dimension reduction in penalized regression methods for high-dimensional grouped data: a case study in low sample size  
 
Soufiane Ajana; Niyazi Acar; Lionel Bretillon ; Boris P Hejblum; Hélène Jacqmin-Gadda ...
 
 
BioMethyl: an R package for biological interpretation of DNA methylation data border= 
 
Yue Wang ; Jennifer M Franks; Michael L Whitfield; Chao Cheng
 
 
SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation 
 
Ruiqing Zheng; Min Li; Zhenlan Liang ; Fang-Xiang Wu; Yi Pan ...
 
 
DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling border= 
 
F J Campos-Laborie ; A Risueño; M Ortiz-Estévez; B Rosón-Burgo; C Droste ...
 
 
Surrogate minimal depth as an importance measure for variables in random forests border= 
 
Stephan Seifert ; Sven Gundlach; Silke Szymczak
 
 
A new computational drug repurposing method using established disease'drug pair knowledge 
 
Nafiseh Saberian; Azam Peyvandipour; Michele Donato ; Sahar Ansari; Sorin Draghici
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes 
 
Aritra Bose; Vassilis Kalantzis; Eugenia-Maria Kontopoulou ; Mai Elkady; Peristera Paschou ...
 
 
A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data border= 
 
Jarno Vanhatalo ; Zitong Li; Mikko J Sillanpää
 
 
VIMCO: variational inference for multiple correlated outcomes in genome-wide association studies 
 
Xingjie Shi; Yuling Jiao; Yi Yang ; Ching-Yu Cheng; Can Yang ...
 
 
Gene-based association tests using GWAS summary statistics 
 
Gulnara R Svishcheva; Nadezhda M Belonogova; Irina V Zorkoltseva ; Anatoly V Kirichenko; Tatiana I Axenovich
 
 
 
SYSTEMS BIOLOGY
 
 
 
Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction border= 
 
Lei Huang ; David Brunell; Clifford Stephan; James Mancuso; Xiaohui Yu ...
 
 
Using association signal annotations to boost similarity network fusion 
 
Peifeng Ruan; Ya Wang; Ronglai Shen ; Shuang Wang
 
 
Functional geometry of protein interactomes 
 
Noël Malod-Dognin; Nata┼ía Pr┼żulj
 
 
Enhancing the prediction of disease'gene associations with multimodal deep learning 
 
Ping Luo; Yuanyuan Li; Li-Ping Tian ; Fang-Xiang Wu
 
 
Dr.VAE: improving drug response prediction via modeling of drug perturbation effects border= 
 
Ladislav Rampá┼íek ; Daniel Hidru; Petr Smirnov; Benjamin Haibe-Kains; Anna Goldenberg
 
 
Interoperable and scalable data analysis with microservices: applications in metabolomics border= 
 
Payam Emami Khoonsari ; Pablo Moreno; Sven Bergmann; Joachim Burman; Marco Capuccini ...
 
 
 
DATA AND TEXT MINING
 
 
 
Response envelope analysis for quantitative evaluation of drug combinations 
 
Di Du; Chia-Hua Chang; Yumeng Wang ; Pan Tong; Wai Kin Chan ...
 
 
Brain annotation toolbox: exploring the functional and genetic associations of neuroimaging results 
 
Zhaowen Liu; Edmund T Rolls; Zhi Liu ; Kai Zhang; Ming Yang ...
 
 
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination 
 
L Perfetto; M L Acencio; G Bradley ; G Cesareni; N Del Toro ...
 
 
Missing value estimation methods for DNA methylation data 
 
Pietro Di Lena; Claudia Sala; Andrea Prodi ; Christine Nardini
 
 
MeSHProbeNet: a self-attentive probe net for MeSH indexing 
 
Guangxu Xun; Kishlay Jha; Ye Yuan ; Yaqing Wang; Aidong Zhang
 
 
VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota 
 
Oksana E Glushchenko; Nikita A Prianichnikov; Evgenii I Olekhnovich ; Alexander I Manolov; Alexander V Tyakht ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers 
 
Mohamad Koohi-Moghadam; Mitesh J Borad; Nhan L Tran ; Kristin R Swanson; Lisa A Boardman ...
 
 
Anduril 2: upgraded large-scale data integration framework 
 
Alejandra Cervera; Ville Rantanen; Kristian Ovaska ; Marko Laakso; Javier Nuñez-Fontarnau ...
 
 
Destin: toolkit for single-cell analysis of chromatin accessibility border= 
 
Eugene Urrutia ; Li Chen; Haibo Zhou; Yuchao Jiang
 
 
GREP: genome for REPositioning drugs border=  
 
Saori Sakaue; Yukinori Okada
 
 
DEFOR: depth- and frequency-based somatic copy number alteration detector 
 
He Zhang; Xiaowei Zhan; James Brugarolas ; Yang Xie
 
 
 
SEQUENCE ANALYSIS
 
 
 
Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences border= 
 
Kirill Kryukov ; Mahoko Takahashi Ueda; So Nakagawa; Tadashi Imanishi
 
 
aphid: an R package for analysis with profile hidden Markov models 
 
Shaun P Wilkinson
 
 
PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences 
 
Rafsanjani Muhammod; Sajid Ahmed; Dewan Md Farid ; Swakkhar Shatabda; Alok Sharma ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Aggrescan3D standalone package for structure-based prediction of protein aggregation properties 
 
Aleksander Kuriata; Valentin Iglesias; Mateusz Kurcinski ; Salvador Ventura; Sebastian Kmiecik
 
 
AutoDock Bias: improving binding mode prediction and virtual screening using known protein'ligand interactions 
 
Juan Pablo Arcon; Carlos P Modenutti; Demian Avendaño ; Elias D Lopez; Lucas A Defelipe ...
 
 
 
GENE EXPRESSION
 
 
 
LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq 
 
Artem Babaian; I Richard Thompson; Jake Lever ; Liane Gagnier; Mohammad M Karimi ...
 
 
deTS: tissue-specific enrichment analysis to decode tissue specificity 
 
Guangsheng Pei; Yulin Dai; Zhongming Zhao ; Peilin Jia
 
 
FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines border= 
 
Lisa-Katrin Turnhoff ; Ali Hadizadeh Esfahani; Maryam Montazeri; Nina Kusch; Andreas Schuppert
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding 
 
Jeremy Ferlic; Jiantao Shi; Thomas O McDonald ; Franziska Michor
 
 
G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation 
 
You Tang; Xiaolei Liu
 
 
ngsLD: evaluating linkage disequilibrium using genotype likelihoods 
 
Emma A Fox; Alison E Wright; Matteo Fumagalli ; Filipe G Vieira
 
 
 
SYSTEMS BIOLOGY
 
 
 
Parameter balancing: consistent parameter sets for kinetic metabolic models border= 
 
Timo Lubitz ; Wolfram Liebermeister
 
 
Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations 
 
Jonathan Naylor; Harold Fellermann; Natalio Krasnogor
 
 
SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight 
 
Chuang Li; Kenli Li; Tao Chen ; Yunping Zhu; Qiang He
 
 
Automated exploration of gene ontology term and pathway networks with ClueGO-REST border= 
 
Bernhard Mlecnik ; Jérôme Galon; Gabriela Bindea
 
 
 
DATA AND TEXT MINING
 
 
 
VHost-Classifier: virus-host classification using natural language processing 
 
Ezra Kitson; Curtis A Suttle
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data 
 
Nathan D Olson; Nidhi Shah; Jayaram Kancherla ; Justin Wagner; Joseph N Paulson ...
 
 
mirtronDB: a mirtron knowledge base border=  
 
Bruno Henrique Ribeiro Da Fonseca; Douglas Silva Domingues ; Alexandre Rossi Paschoal
 
 
 
BIOIMAGE INFORMATICS
 
 
 
SPIM workflow manager for HPC border= 
 
Jan Ko┼żusznik; Petr Bainar ; Jana Klímová; Michal Krumnikl; Pavel Moravec ...
 
 
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