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Genetics

D-Index
63
Citations
45484
World Ranking
2822
National Ranking
1235

Research.com Recognitions

  • 2020 - Fellow of the International Society for Computational Biology
  • 2019 - Fellow of the Indian National Academy of Engineering (INAE)

Overview

Mark Borodovsky is affiliated with the Georgia Institute of Technology in the United States and has contributed extensively to the fields of Biochemistry, Genetics, and Molecular Biology. Their work primarily focuses on Molecular Biology, with significant contributions also in Plant Science, Ecology, Genetics, and Parasitology.

Their research spans several key topics including:

  • Genomics and Phylogenetic Studies
  • RNA and protein synthesis mechanisms
  • Machine Learning in Bioinformatics
  • Genomics and Chromatin Dynamics
  • Molecular Biology Techniques and Applications
  • Berry genetics and cultivation research
  • Plant Pathogens and Resistance

Among their recent publications are:

  • BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database, 2021, NAR Genomics and Bioinformatics
  • GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins, 2020, NAR Genomics and Bioinformatics
  • BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA, 2024, Genome Research
  • TSEBRA: transcript selector for BRAKER, 2021, BMC Bioinformatics
  • BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA, 2023, bioRxiv (Cold Spring Harbor Laboratory)

Frequent co-authors who have collaborated with Borodovsky include:

  • Alexandre Lomsadze
  • Tomáš Brůna
  • Katharina J. Hoff
  • Mario Stanke
  • Lars Gabriel

Borodovsky's work has been published predominantly in venues such as:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • NAR Genomics and Bioinformatics
  • Genome Research
  • BMC Bioinformatics
  • G3 Genes Genomes Genetics

Recognition for Borodovsky's contributions includes:

  • Fellow of the International Society for Computational Biology, 2020
  • Fellow of the Indian National Academy of Engineering (INAE), 2019

Best Publications

  • NCBI prokaryotic genome annotation pipeline

    Tatiana Tatusova;Michael DiCuccio;Azat Badretdin;Vyacheslav Chetvernin

  • The complete genome sequence of the gastric pathogen Helicobacter pylori

    Jean-F. Tomb;Owen White;Anthony R. Kerlavage;Rebecca A. Clayton

  • cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors.

    Stefano Censini;Christina Lange;Zhaoying Xiang;Jean E. Crabtree

  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

    John Besemer;Alexandre Lomsadze;Mark Borodovsky

  • GeneMark.hmm: New solutions for gene finding

    Alexander V. Lukashin;Mark Borodovsky

  • Ab initio Gene Identification in Metagenomic Sequences

    Wenhan Zhu;Alexandre Lomsadze;Mark Borodovsky

  • The genome of woodland strawberry ( Fragaria vesca )

    Vladimir Shulaev;Daniel J. Sargent;Ross N. Crowhurst;Todd C. Mockler

  • BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

    Tomáš Brůna;Katharina J Hoff;Alexandre Lomsadze;Mario Stanke

  • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

    John Besemer;Mark Borodovsky

  • BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

    Katharina Jasmin Hoff;Simone Lange;Alexandre Lomsadze;Mark Borodovsky

  • GENMARK: Parallel gene recognition for both DNA strands

    Mark Borodovsky;James D. McIninch

  • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

    Vardges Ter-Hovhannisyan;Alexandre Lomsadze;Yury O. Chernoff;Mark Borodovsky

  • Gene identification in novel eukaryotic genomes by self-training algorithm

    Alexandre Lomsadze;Vardges Ter-Hovhannisyan;Yury O. Chernoff;Mark Borodovsky

  • Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

    G Albert Wu;Simon Prochnik;Jerry Jenkins;Jerome Salse

  • Whole-Genome Annotation with BRAKER.

    Katharina J Hoff;Alexandre Lomsadze;Mark Borodovsky;Mark Borodovsky;Mario Stanke

  • The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

    Guillaume Blanc;Garry A. Duncan;Irina Agarkova;Mark Borodovsky

  • Pan genome of the phytoplankton Emiliania underpins its global distribution

    Betsy A. Read;Jessica Kegel;Mary J. Klute;Alan Kuo

  • Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

    Alexandre Lomsadze;Paul D. Burns;Mark Borodovsky

  • Heuristic approach to deriving models for gene finding

    John Besemer;Mark Borodovsky

  • Problems and Solutions in Biological Sequence Analysis

    Mark Borodovsky;Svetlana Ekisheva

Frequent Co-Authors

Eugene V. Koonin
Eugene V. Koonin National Institutes of Health
Mario Stanke
Mario Stanke University of Greifswald
Aidong Zhang
Aidong Zhang University of Virginia
Hans-Peter Klenk
Hans-Peter Klenk Newcastle University
Jean-Michel Claverie
Jean-Michel Claverie Aix-Marseille University
Antoine Danchin
Antoine Danchin Institut Cochin
Jeremy Schmutz
Jeremy Schmutz Lawrence Berkeley National Laboratory
Igor V. Grigoriev
Igor V. Grigoriev Lawrence Berkeley National Laboratory
Claire M. Fraser
Claire M. Fraser University of Maryland, Baltimore
John F. Atkins
John F. Atkins University College Cork

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