Anton Nekrutenko

According to our database, Anton Nekrutenko authored at least 25 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of four.

2023

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy.

Aysam Guerler, Dannon Baker, Marius van den Beek, Björn A. Grüning, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko

BMC Bioinform., December, 2023

2022

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.

Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs

Nucleic Acids Res., 2022

2021

Fostering accessible online education using Galaxy as an e-learning platform.

Beatriz Serrano-Solano, Melanie Christine Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia D. Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning

PLoS Comput. Biol., 2021

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping.

Gulsum Gudukbay, Jashwant Raj Gunasekaran, Yilin Feng, Mahmut T. Kandemir, Anton Nekrutenko, Chita R. Das, Paul Medvedev, Björn A. Grüning, Nate Coraor, Nathan Roach, Enis Afgan

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021

2020

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update.

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel J. Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko

Nucleic Acids Res., 2020

Family reunion via error correction: an efficient analysis of duplex sequencing data.

Nicholas Stoler, Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D. Makova, Irene Tiemann-Boege, Anton Nekrutenko

BMC Bioinform., 2020

2019

Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage.

Anastasia Tyryshkina, Nate Coraor, Anton Nekrutenko

Bioinform., 2019

2018

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia D. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg

Nucleic Acids Res., 2018

2017

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko

PLoS Comput. Biol., 2017

2016

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

Enis Afgan, Dannon Baker, Marius van den Beek, Daniel J. Blankenberg, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks

Nucleic Acids Res., 2016

A guide and best practices for R/Bioconductor tool integration in Galaxy.

Nitesh Turaga, Mallory Ann Freeberg, Dannon Baker, John Chilton, The Galaxy Team, Anton Nekrutenko, James Taylor

F1000Research, 2016

2015

StructureFold: genome-wide RNA secondary structure mapping and reconstruction <i>in vivo</i>.

Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann

Bioinform., 2015

2014

Wrangling Galaxy's reference data.

Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko

Bioinform., 2014

2013

Ten Simple Rules for Reproducible Computational Research.

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig

PLoS Comput. Biol., 2013

A sustainable national gateway for biological computation.

James Taylor, Anton Nekrutenko, Nathan Coraor, Philip D. Blood, Alex Ropelewski, Zhihui Zhang, Josephine Palencia, Sergiu Sanielevici, Jared Yanovich, Robert Budden

Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013

2012

A reference model for deploying applications in virtualized environments.

Enis Afgan, Dannon Baker, Anton Nekrutenko, James Taylor

Concurr. Comput. Pract. Exp., 2012

Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses.

Jeremy Goecks, The Galaxy Team, Anton Nekrutenko, James Taylor

Proceedings of the 8th IEEE International Conference on E-Science, 2012

2011

Galaxy: A Gateway to Tools in e-Science.

Enis Afgan, Jeremy Goecks, Dannon Baker, Nate Coraor, Anton Nekrutenko, James Taylor

Proceedings of the Guide to e-Science, Next Generation Scientific Research and Discovery, 2011

Making whole genome multiple alignments usable for biologists.

Daniel J. Blankenberg, James Taylor, Anton Nekrutenko

Bioinform., 2011

Integrating diverse databases into an unified analysis framework: a Galaxy approach.

Daniel J. Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko

Database J. Biol. Databases Curation, 2011

2010

Galaxy CloudMan: delivering cloud compute clusters.

Enis Afgan, Dannon Baker, Nathan Coraor, Brad Chapman, Anton Nekrutenko, James Taylor

BMC Bioinform., 2010

Manipulation of FASTQ data with Galaxy.

Daniel J. Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko

Bioinform., 2010

2007

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes.

Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko

PLoS Comput. Biol., 2007

2006

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.

Wen-Yu Chung, Réka Albert, István Albert, Anton Nekrutenko, Kateryna D. Makova

BMC Bioinform., 2006

2003

ETOPE: evolutionary test of predicted exons.

Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li

Nucleic Acids Res., 2003