Publications by authors named "Mark Borodovsky"

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Translon: a single term for translated regions.
Michał I Świrski, Jack A S Tierney, M Mar Albà, Dmitry E Andreev, Julie L Aspden, Mark Borodovsky

Nat Methods· October 2025

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GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
Tomáš Brůna, Alexandre Lomsadze, Mark Borodovsky

Genome Res· June 2024

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BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.
Lars Gabriel, Tomáš Brůna, Katharina J Hoff, Matthis Ebel, Alexandre Lomsadze, Mark Borodovsky

Genome Res· June 2024

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A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky

bioRxiv· April 2024

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BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA.
Lars Gabriel, Tomáš Brůna, Katharina J Hoff, Matthis Ebel, Alexandre Lomsadze, Mark Borodovsky

bioRxiv· February 2024

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MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes.
Aaron Pfennig, Alexandre Lomsadze, Mark Borodovsky

J Mol Biol· July 2023

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A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").
Tomáš Brůna, Rishi Aryal, Olga Dudchenko, Daniel James Sargent, Daniel Mead, Mark Borodovsky

G3 (Bethesda)· February 2023

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StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.
Karl Gemayel, Alexandre Lomsadze, Mark Borodovsky

Front Bioinform· December 2021

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TSEBRA: transcript selector for BRAKER.
Lars Gabriel, Katharina J Hoff, Tomáš Brůna, Mark Borodovsky, Mario Stanke

BMC Bioinformatics· November 2021

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GeneMark-HM: improving gene prediction in DNA sequences of human microbiome.
Alexandre Lomsadze, Christophe Bonny, Francesco Strozzi, Mark Borodovsky

NAR Genom Bioinform· June 2021

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BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
Tomáš Brůna, Katharina J Hoff, Alexandre Lomsadze, Mario Stanke, Mark Borodovsky

NAR Genom Bioinform· March 2021

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Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of .
Waleed M M El-Sayed, Alli L Gombolay, Penghao Xu, Taehwan Yang, Youngkyu Jeon, Mark Borodovsky

iScience· January 2021

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Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis.
Katelyn A Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Mark Borodovsky

Parasite· December 2020

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GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.
Tomáš Brůna, Alexandre Lomsadze, Mark Borodovsky

NAR Genom Bioinform· June 2020

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Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine.
Alexandre Lomsadze, Tengguo Li, Mangalathu S Rajeevan, Elizabeth R Unger, Mark Borodovsky

Viruses· June 2020

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Whole-Genome Annotation with BRAKER.
Katharina J Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke

Methods Mol Biol· August 2019

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Consent insufficient for data release-Response.
Rudolf I Amann, Shakuntala Baichoo, Benjamin J Blencowe, Peer Bork, Mark Borodovsky

Science· May 2019

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Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.
Ivan V Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A Medvedeva

Brief Bioinform· March 2019

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Toward unrestricted use of public genomic data.
Rudolf I Amann, Shakuntala Baichoo, Benjamin J Blencowe, Peer Bork, Mark Borodovsky

Science· January 2019

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Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky

Genome Res· July 2018

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The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).
Matteo Buti, Marco Moretto, Elena Barghini, Flavia Mascagni, Lucia Natali, Mark Borodovsky

Gigascience· April 2018

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NCBI prokaryotic genome annotation pipeline.
Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P Nawrocki, Mark Borodovsky

Nucleic Acids Res· August 2016

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BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Katharina J Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke

Bioinformatics· March 2016

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Identification of protein coding regions in RNA transcripts.
Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky

Nucleic Acids Res· July 2015

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Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
Alexandre Lomsadze, Paul D Burns, Mark Borodovsky

Nucleic Acids Res· September 2014

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