Anton Nekrutenko

Biochemistry, Genetics and Molecular BiologyDecision SciencesAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 33 papers. Top paper: “Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space”.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Cell Genomics(2022)10.1016/j.xgen.2021.100085

N/A

3.9DataRank · unranked

132 citations

Anthony Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll +95 more

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City

Nature Communications(2022)10.1038/s41467-022-31247-x

N/A

2.1DataRank · unranked

46 citations

Jade Wang, Mindy Leelawong, Darren P. Martin, Jennifer L. Havens, Moinuddin A. Chowdhury +19 more

Ten Simple Rules for Reproducible Computational Research

PLoS Computational Biology(2013)10.1371/journal.pcbi.1003285

N/A

1.0DataRank · unranked

799 citations

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

Complete Khoisan and Bantu genomes from southern Africa

Nature(2010)10.1038/nature08795

N/A

0.932DataRank · unranked

500 citations

Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson +44 more

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

GigaScience(2020)10.1093/gigascience/giaa102

N/A

0.687DataRank · unranked

21 citations

Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramírez +18 more

The anatomy of successful computational biology software

Nature Biotechnology(2013)10.1038/nbt.2721

N/A

0.483DataRank · unranked

24 citations

Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Alexandra P. Lewis +6 more

RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis

PLoS ONE(2022)10.1371/journal.pone.0275623

N/A

0.402DataRank · unranked

10 citations

Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Mei Han +4 more

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.13.620707

N/A

0.366DataRank · unranked

9 citations

Nathan L Clark, Timothy B. Sackton, Spencer V. Muse, Alexander G. Lucaci, Steven Weaver +4 more

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.25.437046

N/A

0DataRank · unranked

10 citations

Simon Bray, Marius van den Beek, Dave Bouvier, Nathaniel Coraor, Milad Miladi +12 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.17.435706

N/A

0DataRank · unranked

0 citations

Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor +5 more

Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.14.448413

N/A

0DataRank · unranked

0 citations

Anton Nekrutenko, Mei Han

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

Nucleic Acids Research(2022)10.1093/nar/gkac247

N/A

0DataRank · unranked

1384 citations

Enis Afgan, Anton Nekrutenko, Björn Grüning, Daniel Blankenberg, Jeremy Goecks +89 more

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Molecular Biology and Evolution(2022)10.1093/molbev/msac061

N/A

0DataRank · unranked

123 citations

Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank +33 more

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.15.476448

N/A

0DataRank · unranked

3 citations

Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Mei Han, Anton Nekrutenko +3 more

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.13.483965

N/A

0DataRank · unranked

3 citations

Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche +6 more

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

BMC Bioinformatics(2023)10.1186/s12859-023-05389-8

N/A

0DataRank · unranked

2 citations

Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor +5 more

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Genome Research(2023)10.1101/gr.276963.122

N/A

0DataRank · unranked

16 citations

John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut +6 more

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.28.546576

N/A

0DataRank · unranked

11 citations

Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo Alba, Björn Grüning, Byung June Ko +32 more

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Nucleic Acids Research(2024)10.1093/nar/gkae410

N/A

0DataRank · unranked

865 citations

Linelle Ann L Abueg, Enis Afgan, Olivier Allart, Ahmed Awan, Wendi Bacon +95 more

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Nature Biotechnology(2024)10.1038/s41587-023-02100-3

N/A

0DataRank · unranked

67 citations

Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo Alba, Björn Grüning, Byung June Ko +36 more

KegAlign: Optimizing pairwise alignments with diagonal partitioning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.02.610839

N/A

0DataRank · unranked

1 citations

Richard Burhans, Robert Harris, Mahmut Kandemir, Maximilian Haeussler, Anton Nekrutenko +1 more

Evaluation of sequencing reads at scale using rdeval

Bioinformatics(2025)10.1093/bioinformatics/btaf416

N/A

0DataRank · unranked

2 citations

Bonhwang Koo, Marco Sollitto, Jennifer Balacco, Nadolina Brajuka, Richard Burhans +9 more

KegAlign: optimizing pairwise alignments with diagonal partitioning

Genome biology(2025)10.1186/s13059-025-03830-0

N/A

0DataRank · unranked

1 citations

Richard Burhans, Robert Harris, Mahmut Kandemir, Maximilian Haeussler, Anton Nekrutenko +1 more

From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.13.682095

N/A

0DataRank · unranked

2 citations

Danielle Callan, Marius van den Beek, Dannon Baker, David J. Rogers, Wolfgang Maier +8 more

Evaluation of sequencing reads at scale using rdeval

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.01.636073

N/A

0DataRank · unranked

1 citations

Bonhwang Koo, Marco Sollitto, Jennifer Balacco, Nadolina Brajuka, Richard Burhans +9 more

MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution

Evolution(2025)10.1093/evolut/qpaf240

N/A

0DataRank · unranked

0 citations

Nathan L Clark, Anton Nekrutenko, Maria Chikina, Sergei L. Kosakovsky Pond, Avery Selberg

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

Nucleic Acids Research(2020)10.1093/nar/gkaa434

N/A

0DataRank · unranked

558 citations

Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks +3 more

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

BMC Bioinformatics(2020)10.1186/s12859-020-3419-8

N/A

0DataRank · unranked

16 citations

Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D. Makova +3 more

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

PLoS Pathogens(2020)10.1371/journal.ppat.1008643

N/A

0DataRank · unranked

34 citations

Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor +13 more

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.21.959973

N/A

0DataRank · unranked

4 citations

Anton Nekrutenko, Sergei L. Kosakovsky Pond, Galaxy and HyPhy developments teams

A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.06.137570

N/A

0DataRank · unranked

3 citations

Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramírez +18 more

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Nature Biotechnology(2021)10.1038/s41587-021-01069-1

N/A

0DataRank · unranked

30 citations

Simon Bray, Marius van den Beek, Dave Bouvier, Nathan Coraor, Milad Miladi +12 more

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

Molecular Biology and Evolution(2021)10.1093/molbev/msab265

N/A

0DataRank · unranked

12 citations

Sergei L. Kosakovsky Pond, Anton Nekrutenko, Mei Han