Subject: Bioinformatics Table of Contents for 01 September 2018 ------=_Part_1035293570.1536772019655 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1035293570.1536772019655 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 17
 
01 September 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA) 
 
Trevor Cickovski; Giri Narasimhan
 
 
Inference of the human polyadenylation code border= 
 
Michael K K Leung; Andrew Delong; Brendan J Frey
 
 
DeepSimulator: a deep simulator for Nanopore sequencing border= 
 
Yu Li; Renmin Han; Chongwei Bi ; Mo Li; Sheng Wang ...
 
 
BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates 
 
Emily Goren; Peng Liu; Chao Wang; Chong Wang
 
 
 
SEQUENCE ANALYSIS
 
 
 
Leveraging known genomic variants to improve detection of variants, especially close-by Indels 
 
Nam S Vo; Vinhthuy Phan
 
 
De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding 
 
Jiao Chen; Yingchao Zhao; Yanni Sun
 
 
Identification and function of FAR protein family genes from a transcriptome analysis of Aphelenchoides besseyi 
 
Dong-Wei Wang; Chun-Ling Xu; Shan-Wen Ding; Xin Huang ; Xi Cheng ...
 
 
Parapred: antibody paratope prediction using convolutional and recurrent neural networks 
 
Edgar Liberis; Petar Veličković; Pietro Sormanni; Michele Vendruscolo ; Pietro Liò
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships border= 
 
Hannah Verena Meyer ; Ewan Birney
 
 
 
SYSTEMS BIOLOGY
 
 
 
Computation and application of tissue-specific gene set weights border=  
 
H Robert Frost
 
 
VSClust: feature-based variance-sensitive clustering of omics data 
 
Veit Schwämmle; Ole N Jensen
 
 
 
DATA AND TEXT MINING
 
 
 
Generalizing biomedical relation classification with neural adversarial domain adaptation 
 
Anthony Rios; Ramakanth Kavuluru; Zhiyong Lu
 
 
LipidPedia: a comprehensive lipid knowledgebase border= 
 
Tien-Chueh Kuo; Yufeng Jane Tseng
 
 
Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects 
 
Leena Choi; Robert J Carroll; Cole Beck; Jonathan D Mosley; Dan M Roden ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
A sequence family database built on ECOD structural domains 
 
Yuxing Liao; R Dustin Schaeffer; Jimin Pei; Nick V Grishin
 
 
 
BIOIMAGE INFORMATICS
 
 
 
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations 
 
Leonid Andronov; Jonathan Michalon; Khalid Ouararhni; Igor Orlov; Ali Hamiche ...
 
 
Comparative analysis of tissue reconstruction algorithms for 3D histology border=  
 
Kimmo Kartasalo; Leena Latonen; Jorma Vihinen ; Tapio Visakorpi; Matti Nykter ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
scanPAV: a pipeline for extracting presence'absence variations in genome pairs border=  
 
Francesca Giordano; Maximilian R Stammnitz; Elizabeth P Murchison ; Zemin Ning
 
 
Genome-by-genome approach for fast bacterial genealogical relationship evaluation 
 
Ji Zhang; Yanwen Xiong; Lynn Rogers; Glen P Carter ; Nigel French
 
 
SnapperDB: a database solution for routine sequencing analysis of bacterial isolates 
 
Timothy Dallman; Philip Ashton; Ulf Schafer; Aleksey Jironkin ; Anais Painset ...
 
 
IRscope: an online program to visualize the junction sites of chloroplast genomes 
 
Ali Amiryousefi; Jaakko Hyvönen; Peter Poczai
 
 
GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models border=  
 
Thomas H Clarke; Lauren M Brinkac; Granger Sutton ; Derrick E Fouts
 
 
 
SEQUENCE ANALYSIS
 
 
 
pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks border= 
 
Stefan Budach ; Annalisa Marsico
 
 
GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS 
 
Viola Ravasio; Marco Ritelli; Andrea Legati; Edoardo Giacopuzzi
 
 
 
PHYLOGENETICS
 
 
 
PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles 
 
Ngoc-Vinh Tran; Bastian Greshake Tzovaras; Ingo Ebersberger
 
 
 
GENE EXPRESSION
 
 
 
MethylMix 2.0: an R package for identifying DNA methylation genes border=  
 
Pierre-Louis Cedoz; Marcos Prunello; Kevin Brennan ; Olivier Gevaert
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms border= 
 
Kazuki Yoshizoe; Aika Terada ; Koji Tsuda
 
 
 
SYSTEMS BIOLOGY
 
 
 
JAMI: fast computation of conditional mutual information for ceRNA network analysis border= 
 
Andrea Hornakova; Markus List ; Jilles Vreeken; Marcel H Schulz
 
 
CaSiAn: a Calcium Signaling Analyzer tool border= 
 
Mahsa Moein; Kamil Grzyb; Teresa Gonçalves Martins ; Shinya Komoto; Francesca Peri ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Building online genomics applications using BioPyramid 
 
Liam Stephenson; Yoshua Wakeham; Nick Seidenman; Jarny Choi
 
 
Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins 
 
Douglas Tomachewski; Carolina Weigert Galvão; Arion de Campos Júnior; Alaine Margarete Guimarães ; José Carlos Ferreira da Rocha ...
 
 
 
ECCB 2018: EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY PROCEEDINGS
 
 
 
 
ECCB 2018: The 17th European Conference on Computational Biology
 
 
 
ECCB 2018: The 17th European Conference on Computational Biology 
 
Artemis G Hatzigeorgiou; Pantelis Bagos; Panayiotis V Benos; Christoforos Nikolaou ; Yves Moreau ...
 
 
 
ECCB 2018 Organization
 
 
 
ECCB 2018 Organization 
 
 
 
 
GENES
 
 
 
Conditional generative adversarial network for gene expression inference 
 
Xiaoqian Wang; Kamran Ghasedi Dizaji; Heng Huang
 
 
Prioritising candidate genes causing QTL using hierarchical orthologous groups border=  
 
Alex Warwick Vesztrocy; Christophe Dessimoz; Henning Redestig
 
 
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection border=  
 
Ludovic Platon; Farida Zehraoui; Abdelhafid Bendahmane ; Fariza Tahi
 
 
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences border=  
 
Peyton Greenside; Tyler Shimko; Polly Fordyce ; Anshul Kundaje
 
 
A deep neural network approach for learning intrinsic protein-RNA binding preferences 
 
Ilan Ben-Bassat; Benny Chor; Yaron Orenstein
 
 
Bayesian inference on stochastic gene transcription from flow cytometry data border=  
 
Simone Tiberi; Mark Walsh; Massimo Cavallaro ; Daniel Hebenstreit; Bärbel Finkenstädt
 
 
Off-target predictions in CRISPR-Cas9 gene editing using deep learning border=  
 
Jiecong Lin; Ka-Chun Wong
 
 
CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs border=  
 
Zhezhen Wang; John M Cunningham; Xinan H Yang
 
 
 
GENOME
 
 
 
SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error border= 
 
Mohammed El-Kebir
 
 
S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks 
 
Hongwei Yan; Andreas D M Gunawan; Louxin Zhang
 
 
Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts border=  
 
Matteo Togninalli; Damian Roqueiro; Karsten M Borgwardt
 
 
Towards an accurate and efficient heuristic for species/gene tree co-estimation 
 
Yaxuan Wang; Luay Nakhleh
 
 
Fast characterization of segmental duplications in genome assemblies border=  
 
Ibrahim Numanagić; Alim S Gökkaya; Lillian Zhang ; Bonnie Berger; Can Alkan ...
 
 
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples border=  
 
Andreas Andrusch; Piotr W Dabrowski; Jeanette Klenner ; Simon H Tausch; Claudia Kohl ...
 
 
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing 
 
Renmin Han; Yu Li; Xin Gao; Sheng Wang
 
 
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations border= 
 
Alex N Salazar ; Thomas Abeel
 
 
CNEFinder: finding conserved non-coding elements in genomes border= 
 
Lorraine A K Ayad; Solon P Pissis; Dimitris Polychronopoulos
 
 
A fast adaptive algorithm for computing whole-genome homology maps border= 
 
Chirag Jain; Sergey Koren; Alexander Dilthey ; Adam M Phillippy; Srinivas Aluru
 
 
Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions 
 
Hui Peng; Yi Zheng; Zhixun Zhao; Tao Liu ; Jinyan Li
 
 
DREAM-Yara: an exact read mapper for very large databases with short update time 
 
Temesgen Hailemariam Dadi; Enrico Siragusa; Vitor C Piro; Andreas Andrusch ; Enrico Seiler ...
 
 
 
PROTEINS
 
 
 
Learning structural motif representations for efficient protein structure search border= 
 
Yang Liu; Qing Ye ; Liwei Wang; Jian Peng
 
 
Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study 
 
Nastazia Lesgidou; Elias Eliopoulos; George N Goulielmos; Metaxia Vlassi
 
 
Topology independent structural matching discovers novel templates for protein interfaces 
 
Claudio Mirabello; Björn Wallner
 
 
Analysis of single amino acid variations in singlet hot spots of protein'protein interfaces 
 
E Sila Ozdemir; Attila Gursoy; Ozlem Keskin
 
 
Predicting protein'protein interactions through sequence-based deep learning 
 
Somaye Hashemifar; Behnam Neyshabur; Aly A Khan; Jinbo Xu
 
 
iCFN: an efficient exact algorithm for multistate protein design border= 
 
Mostafa Karimi; Yang Shen
 
 
DeepDTA: deep drug'target binding affinity prediction border= 
 
Hakime Öztürk; Arzucan Özgür; Elif Ozkirimli
 
 
Protein pocket detection via convex hull surface evolution and associated Reeb graph 
 
Rundong Zhao; Zixuan Cang; Yiying Tong; Guo-Wei Wei
 
 
 
DATA
 
 
 
MDPbiome: microbiome engineering through prescriptive perturbations border=  
 
Beatriz García-Jiménez; Tomás de la Rosa; Mark D Wilkinson
 
 
piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks 
 
Dimitris V Manatakis; Vineet K Raghu; Panayiotis V Benos
 
 
Ontology-based validation and identification of regulatory phenotypes border=  
 
Maxat Kulmanov; Paul N Schofield; Georgios V Gkoutos ; Robert Hoehndorf
 
 
Quantitative trait loci identification for brain endophenotypes via new additive model with random networks 
 
Xiaoqian Wang; Hong Chen; Jingwen Yan; Kwangsik Nho ; Shannon L Risacher ...
 
 
Liquid-chromatography retention order prediction for metabolite identification 
 
Eric Bach; Sandor Szedmak; Céline Brouard; Sebastian Böcker ; Juho Rousu
 
 
fastp: an ultra-fast all-in-one FASTQ preprocessor border= 
 
Shifu Chen; Yanqing Zhou; Yaru Chen ; Jia Gu
 
 
DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications 
 
Arshdeep Sekhon; Ritambhara Singh; Yanjun Qi
 
 
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes border=  
 
Mona Alshahrani; Robert Hoehndorf
 
 
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets border=  
 
Florian Schmidt; Markus List; Engin Cukuroglu ; Sebastian Köhler; Jonathan Göke ...
 
 
Computational enhancement of single-cell sequences for inferring tumor evolution 
 
Sayaka Miura; Louise A Huuki; Tiffany Buturla; Tracy Vu ; Karen Gomez ...
 
 
 
SYSTEMS
 
 
 
A Boolean network inference from time-series gene expression data using a genetic algorithm 
 
Shohag Barman; Yung-Keun Kwon
 
 
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia border=  
 
Clémence Frioux; Enora Fremy; Camille Trottier ; Anne Siegel
 
 
Higher-order molecular organization as a source of biological function 
 
Thomas Gaudelet; Noël Malod-Dognin; NataÅ¡a Pržulj
 
 
FLYCOP: metabolic modeling-based analysis and engineering microbial communities border=  
 
Beatriz García-Jiménez; José Luis García; Juan Nogales
 
 
Single cell network analysis with a mixture of Nested Effects Models border=  
 
Martin Pirkl; Niko Beerenwinkel
 
 
Hierarchical HotNet: identifying hierarchies of altered subnetworks border=  
 
Matthew A Reyna; Mark D M Leiserson; Benjamin J Raphael
 
 
Understanding the evolution of functional redundancy in metabolic networks border=  
 
Gayathri Sambamoorthy; Karthik Raman
 
 
iTOP: inferring the topology of omics data border= 
 
Nanne Aben; Johan A Westerhuis; Yipeng Song ; Henk A L Kiers; Magali Michaut ...
 
 
Comparative Network Reconstruction using mixed integer programming border= 
 
Evert Bosdriesz; Anirudh Prahallad; Bertram Klinger ; Anja Sieber; Astrid Bosma ...
 
 
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series border=  
 
Christopher A Penfold; Anastasiya Sybirna; John E Reid ; Yun Huang; Lorenz Wernisch ...
 
 
 
AUTHOR INDEX
 
 
 
Author Index 
 
 
 
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