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Author Details

Anton Nekrutenko
The Pennsylvania State University, University Park
1998
95
39
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36828587The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.Genome Res2023
37425881Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.bioRxiv2023
35325204Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.Mol Biol Evol2022
35752633Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.Nat Commun2022
36322581RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis.PLoS One2022
35075458RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.bioRxiv2022
35075456Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.bioRxiv2022
34090324Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses.BMC Microbiol2021
33575654Increased yields of duplex sequencing data by a series of quality control tools.NAR Genom Bioinform2021
33791701Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.bioRxiv2021
33709076Erratum: Increased yields of duplex sequencing data by a series of quality control tools.NAR Genom Bioinform2021
33817639Sequencing error profiles of Illumina sequencing instruments.NAR Genom Bioinform2021
33583104Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update.Curr Protoc2021
34588690Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.Nat Biotechnol2021
34505896Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses.Mol Biol Evol2021
34159333Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses.bioRxiv2021
33983944Fostering accessible online education using Galaxy as an e-learning platform.PLoS Comput Biol2021
31504749HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.Mol Biol Evol2020
33079170A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.Gigascience2020
32585001Corrigendum: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update.Nucleic Acids Res2020
32354350In memory of James Taylor: the birth of Galaxy.Genome Biol2020
32131723Family reunion via error correction: an efficient analysis of duplex sequencing data.BMC Bioinformatics2020
32479607The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update.Nucleic Acids Res2020
30698642Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage.Bioinformatics2019
31757848Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees.Proc Natl Acad Sci U S A2019
31539047A High-Resolution View of Adaptive Event Dynamics in a Plasmid.Genome Biol Evol2019
29790989The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.Nucleic Acids Res2018
30232389Child Weight Gain Trajectories Linked To Oral Microbiota Composition.Sci Rep2018
29953864Community-Driven Data Analysis Training for Biology.Cell Syst2018
29953862Practical Computational Reproducibility in the Life Sciences.Cell Syst2018
29688462Biology Needs Evolutionary Software Tools: Let's Build Them Right.Mol Biol Evol2018
28542180Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.PLoS Comput Biol2017
26780094Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.Nat Methods2016
27566673Streamlined analysis of duplex sequencing data with Du Novo.Genome Biol2016
27137889The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.Nucleic Acids Res2016
25655493Online resources for genomic analysis using high-throughput sequencing.Cold Spring Harb Protoc2015
25886980StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.Bioinformatics2015
24641477Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach.Biotechniques2014
25313049Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.Proc Natl Acad Sci U S A2014
25001293Dissemination of scientific software with Galaxy ToolShed.Genome Biol2014
24585771Wrangling Galaxy's reference data.Bioinformatics2014
23758618Web-based visual analysis for high-throughput genomics.BMC Genomics2013
24104757The anatomy of successful computational biology software.Nat Biotechnol2013
24204232Ten simple rules for reproducible computational research.PLoS Comput Biol2013
23913925RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.Genome Res2013
22898652Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.Nat Rev Genet2012
33907528A reference model for deploying applications in virtualized environments.Concurr Comput2012
23138293NGS analyses by visualization with Trackster.Nat Biotechnol2012
22700312Using Galaxy to perform large-scale interactive data analyses.Curr Protoc Bioinformatics2012
21699709Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.Genome Biol2011
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Collaborators

James Taylor
Johns Hopkins University
Co-authored papers 36
Daniel Blankenberg
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
Co-authored papers 23
Sergei L Kosakovsky Pond
Co-authored papers 14
Enis Afgan
Johns Hopkins University
Co-authored papers 10
Jeremy Goecks
Oregon Health & Science University
Co-authored papers 9
Dave Clements
Johns Hopkins University
Co-authored papers 9
Marius van den Beek
Institut Curie, PSL Research University, CNRS UMR 5, INSERM U934
Co-authored papers 7
Ross C Hardison
Co-authored papers 6
John Chilton
The Pennsylvania State University, University Park
Co-authored papers 6
Webb Miller
Co-authored papers 6
Wen-Yu Chung
Co-authored papers 6
Eric S Rasche
Clinical Bioinformatics Group, Erasmus Medical Center
Co-authored papers 5
Wolfgang Maier
University Hospital Bonn
Co-authored papers 4
Jennifer Hillman-Jackson
Co-authored papers 4
Gundula Povysil
Institute for Genomic Medicine, Columbia University Medical Center
Co-authored papers 3
Richard A Gibbs
Baylor College of Medicine
Co-authored papers 3
Belinda Giardine
Co-authored papers 3
Michael C Schatz
Johns Hopkins University
Co-authored papers 3
William James Kent
Co-authored papers 3
Rasmus Nielsen
Co-authored papers 2
Laura Elnitski
National Human Genome Research Institute
Co-authored papers 2
Jordi Rambla
Universitat Pompeu Fabra
Co-authored papers 2
Martin Krzywinski
BC Cancer Research Center
Co-authored papers 2
James T Robinson
University of California San Diego
Co-authored papers 2
Fidel Ram??rez
Max Planck Institute of Immunobiology and Epigenetics
Co-authored papers 2
Peter J Tonellato
University of Missouri School of Medicine
Co-authored papers 2
Philippe Lemey
Rega Institute, Laboratory of Clinical and Evolutionary Virology
Co-authored papers 2
Richard Durbin
University of Cambridge
Co-authored papers 2
Evan E Eichler
University of Washington
Co-authored papers 2
Ross Lazarus
Co-authored papers 2
Release 1.2