Anton Nekrutenko
Dorothy Foher Huck and J. Lloyd Huck Chair in Genomics, Professor of Biochemistry and Molecular Biology
-
505 Wartik Laboratory
University Park, PA 16802 - aun1@psu.edu
- 814-865-4752
Research Summary
Evolution of overlapping reading frames in eukaryotic genomes.
Huck Affiliations
Links
Most Recent Publications
Evaluation of sequencing reads at scale using rdeval.
G Formenti, B Koo, M Sollitto, J Balacco, N Brajuka, R Burhans, E Duarte, A Giani, K McCaffrey, J Medico, E Myers, P Smeds, Anton Nekrutenko, E Jarvis, 2025, bioRxiv : the preprint server for biology
Minus the Error: Estimating d (N)/d (S) and Testing for Natural Selection in the Presence of Residual Alignment Errors.
A Selberg, M Chikina, T Sackton, S Muse, A Lucaci, S Weaver, Anton Nekrutenko, N Clark, Pond SLK, 2024, bioRxiv : the preprint server for biology
KegAlign: Optimizing pairwise alignments with diagonal partitioning.
A Gulhan, R Burhans, R Harris, M Kandemir, M Haeussler, Anton Nekrutenko, 2024, bioRxiv : the preprint server for biology
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
Linelle Ann L. Abueg, Enis Afgan, Olivier Allart, Ahmed H. Awan, Wendi A. Bacon, Dannon Baker, Madeline Bassetti, Bérénice Batut, Matthias Bernt, Daniel James Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine J. Bromhead, Melissa L. Burke, Patrick K. Capon, Martin Čech, María Chavero-Díez, John M. Chilton, Tyler J. Collins, Frederik Coppens, Nate Coraor, Gianmauro Cuccuru, Fabio Cumbo, John Davis, Paul F. De Geest, Willem de Koning, Martin Demko, Assunta DeSanto, José Manuel Domínguez Begines, Maria A. Doyle, Bert Droesbeke, Anika Erxleben-Eggenhofer, Melanie C. Föll, Giulio Formenti, Anne Fouilloux, Rendani Gangazhe, Tanguy Genthon, Jeremy Goecks, Alejandra N. Gonzalez Beltran, Nuwan A. Goonasekera, Nadia Goué, Timothy J. Griffin, Björn A. Grüning, Aysam Guerler, Sveinung Gundersen, Ove Johan Ragnar Gustafsson, Christina Hall, Thomas W. Harrop, Helge Hecht, Alireza Heidari, Tillman Heisner, Florian Heyl, Saskia Hiltemann, Hans Rudolf Hotz, Cameron J. Hyde, Pratik D. Jagtap, Julia Jakiela, James E. Johnson, Jayadev Joshi, Marie Jossé, Khaled Jum’ah, Matúš Kalaš, Katarzyna Kamieniecka, Tunc Kayikcioglu, Markus Konkol, Leonid Kostrykin, Natalie Kucher, Anup Kumar, Mira Kuntz, Delphine Lariviere, Ross Lazarus, Yvan Le Bras, Gildas Le Corguillé, Justin Lee, Simone Leo, Leandro Liborio, Romane Libouban, David López Tabernero, Lucille Lopez-Delisle, Laila S. Los, Alexandru Mahmoud, Igor Makunin, Pierre Marin, Subina Mehta, Winnie Mok, Pablo A. Moreno, François Morier-Genoud, Stephen Mosher, Teresa Müller, Engy Nasr, Anton Nekrutenko, Tiffanie M. Nelson, Asime J. Oba, Alexander Ostrovsky, Polina V. Polunina, Krzysztof Poterlowicz, Elliott J. Price, Gareth R. Price, Helena Rasche, Bryan Raubenolt, Coline Royaux, Luke Sargent, Michelle T. Savage, Volodymyr Savchenko, Denys Savchenko, Michael C. Schatz, Pauline Seguineau, Beatriz Serrano-Solano, Nicola Soranzo, Sanjay Kumar Srikakulam, Keith Suderman, Anna E. Syme, Marco Antonio Tangaro, Jonathan A. Tedds, Mehmet Tekman, Wai Cheng Thang, Anil S. Thanki, Michael Uhl, Marius van den Beek, Deepti Varshney, Jenn Vessio, Pavankumar Videm, Greg Von Kuster, Gregory R. Watson, Natalie Whitaker-Allen, Uwe Winter, Martin Wolstencroft, Federico Zambelli, Paul Zierep, Rand Zoabi, 2024, Nucleic Acids Research on p. W83-W94
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D Larivière, L Abueg, N Brajuka, C Gallardo-Alba, B Grüning, B Ko, A Ostrovsky, M Palmada-Flores, B Pickett, K Rabbani, A Antunes, J Balacco, Chaisson MJP, Mark J.P. Chaisson, H Cheng, J Collins, M Couture, A Denisova, O Fedrigo, G Gallo, A Giani, G Gooder, K Horan, N Jain, C Johnson, H Kim, C Lee, T Marques-Bonet, Brian O’Toole, B O'Toole, A Rhie, S Secomandi, M Sozzoni, T Tilley, M Uliano-Silva, M van den Beek, R Williams, R Waterhouse, A Phillippy, E Jarvis, M Schatz, Anton Nekrutenko, G Formenti, 2024, Nature Biotechnology on p. 367-370
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko, 2023, BMC Bioinformatics
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
Simon Bray, Martin Cech, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J.A. Cock, Björn Grüning, Anton Nekrutenko, 2023, Genome Research on p. 261-268
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Joel O. Wertheim, Jade C. Wang, Mindy Leelawong, Darren P. Martin, Jennifer L. Havens, Moinuddin A. Chowdhury, Jonathan E. Pekar, Helly Amin, Anthony Arroyo, Gordon A. Awandare, Hoi Yan Chow, Edimarlyn Gonzalez, Elizabeth Luoma, Collins M. Morang’a, Anton Nekrutenko, Stephen D. Shank, Stefan Silver, Peter K. Quashie, Jennifer L. Rakeman, Victoria Ruiz, Lucia V. Torian, Tetyana I. Vasylyeva, Sergei L. Kosakovsky Pond, Scott Hughes, 2022, Nature Communications
RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis
Alexander G. Lucaci, Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P. Martin, Sergei L. Kosakovsky Pond, 2022, PLoS One
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.
A Lucaci, J Zehr, S Shank, D Bouvier, H Mei, Anton Nekrutenko, D Martin, S Kosakovsky Pond, 2022, bioRxiv : the preprint server for biology
Most-Cited Papers
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 Ech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg, 2018, Nucleic Acids Research on p. W537-W544
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks, 2016, Nucleic Acids Research on p. W3-W10
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Martin Cech, Enis Afgan, Delphine Lariviere, Anton Nekrutenko, Bjórn A. Grüning, Daniel Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anton Nekrutenko, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Björn A. Grüning, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel James Blankenberg, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. De Lima Morais, D. L. Tabernero, Delphine Lariviere, Engy Nasr, Enis Afgan, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Greg Von Kuster, Gulsum Gudukbay Akbulut, Helena Rasche, Hotz Hans-Rudolf, Ignacio Eguinoa, Igor Makunin, Isuru J. Ranawaka, James P. Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, Jeremy Goecks, John M. Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Le Bras Yvan, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius Van Den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie C. Föll, Michael C. Schatz, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan A. 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 Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Vandenbrouck Yves, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem De Koning, Wolfgang Maier, Peter J. Briggs, 2022, Nucleic Acids Research on p. W345--W351
HyPhy 2.5 - A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Sergei L. Kosakovsky Pond, Art F.Y. Poon, Ryan Velazquez, Steven Weaver, N. Lance Hepler, Ben Murrell, Stephen D. Shank, Brittany Rife Magalis, Dave Bouvier, Anton Nekrutenko, Sadie Wisotsky, Stephanie J. Spielman, Simon D.W. Frost, Spencer V. Muse, 2020, Molecular Biology and Evolution on p. 295-299
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko, 2020, Nucleic Acids Research on p. W395--W402
Sequencing error profiles of Illumina sequencing instruments
Nicholas Stoler, Anton Nekrutenko, 2021, NAR Genomics and Bioinformatics
Community-Driven Data Analysis Training for Biology
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning, 2018, Cell Systems on p. 752-758.e1
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
Linelle Ann L. Abueg, Enis Afgan, Olivier Allart, Ahmed H. Awan, Wendi A. Bacon, Dannon Baker, Madeline Bassetti, Bérénice Batut, Matthias Bernt, Daniel James Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine J. Bromhead, Melissa L. Burke, Patrick K. Capon, Martin Čech, María Chavero-Díez, John M. Chilton, Tyler J. Collins, Frederik Coppens, Nate Coraor, Gianmauro Cuccuru, Fabio Cumbo, John Davis, Paul F. De Geest, Willem de Koning, Martin Demko, Assunta DeSanto, José Manuel Domínguez Begines, Maria A. Doyle, Bert Droesbeke, Anika Erxleben-Eggenhofer, Melanie C. Föll, Giulio Formenti, Anne Fouilloux, Rendani Gangazhe, Tanguy Genthon, Jeremy Goecks, Alejandra N. Gonzalez Beltran, Nuwan A. Goonasekera, Nadia Goué, Timothy J. Griffin, Björn A. Grüning, Aysam Guerler, Sveinung Gundersen, Ove Johan Ragnar Gustafsson, Christina Hall, Thomas W. Harrop, Helge Hecht, Alireza Heidari, Tillman Heisner, Florian Heyl, Saskia Hiltemann, Hans Rudolf Hotz, Cameron J. Hyde, Pratik D. Jagtap, Julia Jakiela, James E. Johnson, Jayadev Joshi, Marie Jossé, Khaled Jum’ah, Matúš Kalaš, Katarzyna Kamieniecka, Tunc Kayikcioglu, Markus Konkol, Leonid Kostrykin, Natalie Kucher, Anup Kumar, Mira Kuntz, Delphine Lariviere, Ross Lazarus, Yvan Le Bras, Gildas Le Corguillé, Justin Lee, Simone Leo, Leandro Liborio, Romane Libouban, David López Tabernero, Lucille Lopez-Delisle, Laila S. Los, Alexandru Mahmoud, Igor Makunin, Pierre Marin, Subina Mehta, Winnie Mok, Pablo A. Moreno, François Morier-Genoud, Stephen Mosher, Teresa Müller, Engy Nasr, Anton Nekrutenko, Tiffanie M. Nelson, Asime J. Oba, Alexander Ostrovsky, Polina V. Polunina, Krzysztof Poterlowicz, Elliott J. Price, Gareth R. Price, Helena Rasche, Bryan Raubenolt, Coline Royaux, Luke Sargent, Michelle T. Savage, Volodymyr Savchenko, Denys Savchenko, Michael C. Schatz, Pauline Seguineau, Beatriz Serrano-Solano, Nicola Soranzo, Sanjay Kumar Srikakulam, Keith Suderman, Anna E. Syme, Marco Antonio Tangaro, Jonathan A. Tedds, Mehmet Tekman, Wai Cheng Thang, Anil S. Thanki, Michael Uhl, Marius van den Beek, Deepti Varshney, Jenn Vessio, Pavankumar Videm, Greg Von Kuster, Gregory R. Watson, Natalie Whitaker-Allen, Uwe Winter, Martin Wolstencroft, Federico Zambelli, Paul Zierep, Rand Zoabi, 2024, Nucleic Acids Research on p. W83-W94
Practical Computational Reproducibility in the Life Sciences
Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor, 2018, Cell Systems on p. 631-635
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O.Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O'Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, Alexander Baumann, Andrew Rula, Anton Kovalsy, Clare Bernard, Derek Caetano-Anollés, Geraldine A. Van der Auwera, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, John Chilton, 2022, Cell Genomics
News Articles Featuring Anton Nekrutenko
Feb 29, 2024
Anton Nekrutenko named Huck Chair in Genomics
Anton Nekrutenko, professor of biochemistry and molecular biology in the Eberly College of Science at Penn State, has been appointed as the first Dorothy Foher Huck and J. Lloyd Huck Chair in Genomics.
Full Article
Feb 05, 2024
Researchers assemble 51 animal genomes using publicly accessible workflows
Using a new set of tools, an international research collaboration including scientists from Penn State, Rockefeller University and Johns Hopkins University have reconstructed genetic blueprints for 51 species.
Full Article
Sep 21, 2018
Mouth bacteria in toddlers may predict obesity, study says
Bacteria in a toddler's mouth might help predict later obesity, new research suggests. Scientists at Penn State University found the composition of microorganisms in the mouths of 2-year-olds offers clues to the child's future weight.
Full Article
Sep 19, 2018
Child Weight Gain Trajectories Linked To Oral Microbiota Composition
Gut and oral microbiota perturbations have been observed in obese adults and adolescents; less is known about their influence on weight gain in young children.
Full Article