Subject: Bioinformatics Table of Contents for 01 September 2018 ------=_Part_1035293570.1536772019655 Content-Type: text/plain;charset=UTF-8 This email is intended for ------=_Part_1035293570.1536772019655 Content-Type: text/html;charset=UTF-8 Oxford Academic
New issue alert
Volume 34 Issue 17
01 September 2018
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
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
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships border= 
Hannah Verena Meyer ; Ewan Birney
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
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 ...
A sequence family database built on ECOD structural domains 
Yuxing Liao; R Dustin Schaeffer; Jimin Pei; Nick V Grishin
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 ...
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
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
PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles 
Ngoc-Vinh Tran; Bastian Greshake Tzovaras; Ingo Ebersberger
MethylMix 2.0: an R package for identifying DNA methylation genes border=  
Pierre-Louis Cedoz; Marcos Prunello; Kevin Brennan ; Olivier Gevaert
MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms border= 
Kazuki Yoshizoe; Aika Terada ; Koji Tsuda
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 ...
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: 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 
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
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 ...
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
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 ...
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 
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