Subject: Bioinformatics Table of Contents for 15 September 2019 ------=_Part_470458676.1568940308272 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_470458676.1568940308272 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 35 Issue 18
 
15 September 2019
 
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EDITORIAL
 
 
 
 
DATA AND TEXT MINING
 
 
 
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention border= 
 
Jonathan D Wren ; Alfonso Valencia; Janet Kelso
 
 
 
DISCOVERY NOTE
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients  
 
V Marie; M Gordon
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Predicting the optimal growth temperatures of prokaryotes using only genome derived features 
 
David B Sauer; Da-Neng Wang
 
 
Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers border= 
 
Tahmid F Mehdi ; Gurdeep Singh; Jennifer A Mitchell; Alan M Moses
 
 
DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis  border= 
 
Yang Yang; Timothy M Walker ; A Sarah Walker; Daniel J Wilson; Timothy E A Peto ...
 
 
Aligning optical maps to de Bruijn graphs 
 
Kingshuk Mukherjee; Bahar Alipanahi; Tamer Kahveci ; Leena Salmela; Christina Boucher
 
 
mCSEA: detecting subtle differentially methylated regions 
 
Jordi Martorell-Marugán; Víctor González-Rumayor; Pedro Carmona-Sáez
 
 
SUBSTRA: Supervised Bayesian Patient Stratification 
 
Sahand Khakabimamaghani; Yogeshwar D Kelkar; Bruno M Grande ; Ryan D Morin; Martin Ester ...
 
 
Using local alignment to enhance single-cell bisulfite sequencing data efficiency 
 
Peng Wu; Yan Gao; Weilong Guo ; Ping Zhu
 
 
 
SEQUENCE ANALYSIS
 
 
 
Haplotype assembly of autotetraploid potato using integer linear programing border= 
 
Enrico Siragusa ; Niina Haiminen; Richard Finkers; Richard Visser; Laxmi Parida
 
 
Finding de novo methylated DNA motifs 
 
Vu Ngo; Mengchi Wang; Wei Wang
 
 
Biological sequence modeling with convolutional kernel networks 
 
Dexiong Chen; Laurent Jacob; Julien Mairal
 
 
 
PHYLOGENETICS
 
 
 
Rapid alignment-free phylogenetic identification of metagenomic sequences 
 
Benjamin Linard; Krister Swenson; Fabio Pardi
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Protein model quality assessment using 3D oriented convolutional neural networks 
 
Guillaume Pagès; Benoit Charmettant; Sergei Grudinin
 
 
refineD: improved protein structure refinement using machine learning based restrained relaxation 
 
Debswapna Bhattacharya
 
 
DeepAffinity: interpretable deep learning of compound'protein affinity through unified recurrent and convolutional neural networks 
 
Mostafa Karimi; Di Wu; Zhangyang Wang ; Yang Shen
 
 
 
GENE EXPRESSION
 
 
 
Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis 
 
Rachel Jeitziner; Mathieu Carrière; Jacques Rougemont ; Steve Oudot; Kathryn Hess ...
 
 
NEMO: cancer subtyping by integration of partial multi-omic data border= 
 
Nimrod Rappoport ; Ron Shamir
 
 
Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes border= 
 
Holger Weishaupt ; Patrik Johansson; Anders Sundström; Zelmina Lubovac-Pilav; Björn Olsson ...
 
 
ChimeraUGEM: unsupervised gene expression modeling in any given organism 
 
Alon Diament; Iddo Weiner; Noam Shahar ; Shira Landman; Yael Feldman ...
 
 
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana  border= 
 
Kimon Froussios; Nick J Schurch ; Katarzyna Mackinnon; Marek Gierli┼"ski; Céline Duc ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Modeling cell proliferation in human acute myeloid leukemia xenografts border= 
 
Marco S Nobile ; Thalia Vlachou; Simone Spolaor; Daniela Bossi; Paolo Cazzaniga ...
 
 
A unified approach for sparse dynamical system inference from temporal measurements border= 
 
Yannis Pantazis ; Ioannis Tsamardinos
 
 
Gsmodutils: a python based framework for test-driven genome scale metabolic model development border= 
 
James Gilbert ; Nicole Pearcy; Rupert Norman; Thomas Millat; Klaus Winzer ...
 
 
Compositional data network analysis via lasso penalized D-trace loss 
 
Huili Yuan; Shun He; Minghua Deng
 
 
Comparison of six breast cancer classifiers using qPCR 
 
Evi Berchtold; Martina Vetter; Melanie Gündert ; Gergely Csaba; Christine Fathke ...
 
 
Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants border= 
 
Joseph J Muldoon ; Jessica S Yu; Mohammad-Kasim Fassia; Neda Bagheri
 
 
ST-Steiner: a spatio-temporal gene discovery algorithm 
 
Utku Norman; A Ercument Cicek
 
 
Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease 
 
Jing Ma; the CRIC and the CPROBE study investigators; Alla Karnovsky ; the CRIC and the CPROBE study investigators; Farsad Afshinnia ...
 
 
 
DATA AND TEXT MINING
 
 
 
Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage 
 
Anastasia Tyryshkina; Nate Coraor; Anton Nekrutenko
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Structured crowdsourcing enables convolutional segmentation of histology images border= 
 
Mohamed Amgad ; Habiba Elfandy; Hagar Hussein; Lamees A Atteya; Mai A T Elsebaie ...
 
 
Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data 
 
Ismail M Khater; Fanrui Meng; Ivan Robert Nabi ; Ghassan Hamarneh
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Assembly Graph Browser: interactive visualization of assembly graphs 
 
Alla Mikheenko; Mikhail Kolmogorov
 
 
KOnezumi: a web application for automating gene disruption strategies to generate knockout mice border= 
 
Akihiro Kuno ; Seiya Mizuno; Satoru Takahashi
 
 
Bacterial Feature Finder (BaFF)'a system for extracting features overrepresented in sets of prokaryotic organisms 
 
Javier López-Ibáñez; Laura T Martín; Mónica Chagoyen ; Florencio Pazos
 
 
rMETL: sensitive mobile element insertion detection with long read realignment 
 
Tao Jiang; Bo Liu; Junyi Li ; Yadong Wang
 
 
Explore, edit and leverage genomic annotations using Python GTF toolkit 
 
F Lopez; G Charbonnier; Y Kermezli ; M Belhocine; Q Ferré ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra 
 
Diogo B Lima; André R F Silva; Mathieu Dupré ; Marlon D M Santos; Milan A Clasen ...
 
 
IGLOSS: iterative gapless local similarity search 
 
Braslav Rabar; Maja Zagor┼í─Źak; Strahil Ristov ; Martin Rosenzweig; Pavle Goldstein
 
 
G4Hunter web application: a web server for G-quadruplex prediction border= 
 
Václav Brázda ; Jan Kolomazník; Ji┼Öí Lýsek; Martin Bartas; Miroslav Fojta ...
 
 
 
PHYLOGENETICS
 
 
 
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution 
 
Soumya Kundu; Mukul S Bansal
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions border= 
 
Judemir Ribeiro ; Carlos Ríos-Vera; Francisco Melo; Andreas Schüller
 
 
NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data 
 
Nagarajan Raju; Ian Setliff; Ivelin S Georgiev
 
 
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces border= 
 
Laura Orellana ; Johan Gustavsson; Cathrine Bergh; Ozge Yoluk; Erik Lindahl
 
 
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) 
 
Tharindu Senapathi; Simon Bray; Christopher B Barnett ; Björn Grüning; Kevin J Naidoo
 
 
Finding enzyme cofactors in Protein Data Bank border=  
 
Abhik Mukhopadhyay; Neera Borkakoti; Luká┼í Pravda; Jonathan D Tyzack; Janet M Thornton ...
 
 
3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations border= 
 
Joan Segura ; Ruben Sanchez-Garcia; C O S Sorzano; J M Carazo
 
 
 
GENE EXPRESSION
 
 
 
ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies border= 
 
Danyue Dong ; Yuan Tian; Shijie C Zheng; Andrew E Teschendorff
 
 
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes border= 
 
Nikolaos Papadopoulos ; Parra R Gonzalo; Johannes Söding
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GRIMM: GRaph IMputation and matching for HLA genotypes 
 
Martin Maiers; Michael Halagan; Loren Gragert ; Pradeep Bashyal; Jason Brelsford ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Miso: an R package for multiple isotope labeling assisted metabolomics data analysis 
 
Yonghui Dong; Liron Feldberg; Asaph Aharoni
 
 
Temporal network alignment via GoT-WAVE 
 
David Aparício; Pedro Ribeiro; Tijana Milenkovi─ç ; Fernando Silva
 
 
 
DATA AND TEXT MINING
 
 
 
Comorbidity4j: a tool for interactive analysis of disease comorbidities over large patient datasets 
 
Francesco Ronzano; Alba Gutiérrez-Sacristán; Laura I Furlong
 
 
PMC text mining subset in BioC: about three million full-text articles and growing 
 
Donald C Comeau; Chih-Hsuan Wei; Rezarta Islamaj Do─čan ; Zhiyong Lu
 
 
GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays 
 
Akul Y Mehta; Richard D Cummings
 
 
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings 
 
Mehdi Ali; Charles Tapley Hoyt; Daniel Domingo-Fernández ; Jens Lehmann; Hajira Jabeen
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
RiboD: a comprehensive database for prokaryotic riboswitches 
 
Sumit Mukherjee; Sukhen Das Mandal; Nikita Gupta ; Matan Drory-Retwitzer; Danny Barash ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Multispectral tracing in densely labeled mouse brain with nTracer border= 
 
Douglas H Roossien ; Benjamin V Sadis; Yan Yan; John M Webb; Lia Y Min ...
 
 
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