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Department of Biomedical Engineering: BME Faculty & Staff
Department of Biomedical Engineering: BME Faculty & Staff
Department of Biomedical Engineering: BME Clear
Department of Biomedical Engineering: BME Clear
Department of Biomedical Engineering: BME clear

Mark Borodovsky Mark Borodovsky, Ph.D.
Director, Center for Bioinformatics and Computational Genomics
Regents' Professor

Chair, Department of Bioinformatics
Faculty of Biological and Medical Physics
Moscow Institute for Physics and Technology, Moscow, Russia

Department of Biomedical Engineering and Computational Science and Engineering Division
Georgia Institute of Technology
Atlanta, GA 30332-0535

Phone: 404-894-8432
Fax: 404-385-0383
Location: GT: BME - 4102 CSE - 1338
E-Mail: borodovsky@gatech.edu
URL: http://exon.gatech.edu/GeneMark/

Google Scholar: CLICK HERE

Areas of Research

    Development and applicaton of new machine learning and pattern recognition methods in bioinformatics and biological systems.

Educational Background

  • Ph.D., Moscow Institute of Physics and Technology, 1976
  • M.S., Moscow Institute of Physics and Technology, 1972

Selected Research Publications

    Books
  • Borodovsky M. and Ekisheva S. Problems and Solutions in Biological Sequence Analysis, Cambridge University Press, 2006 - Book Review
    (published in Russian in 2008)

    Publications

  • Antonov I, P Baranov, M Borodovsky GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences, (2013) Nucleic Acids Research, 41, D152-156. More Info
  • Tang, S., Antonov, I., Borodovsky, M. (2012) MetaGeneTack: Ab Initio detection of frameshifts in metagenomic sequences. Bioinformatics. doi: 10.1093/bioinformatics/ bts636. More Info
  • Li, Y., Hong-Mei, L., Burns, P., Borodovsky, M., Robinson, G., Ma, J. (2012) TrueSight: a new algorithm for splice junction detection using RNA-seq. Nucleic Acids Research, doi: 10.1093/nar/gks1311. More Info
  • Blanc G., I. Agarkova, J. Grimwood, A. Kuo, A. Brueggeman, D. Dunigan, J. Gurnon, I. Ladunga, E. Lindquist, S. Lucas, J. Pangilinan, T. Pröschold , A. Salamov, J. Schmutz, D. Weeks, T. Yamada, A. Lomsadze, M. Borodovsky, J.-M. Claverie, I. Grigoriev and J. Van Etten (2012) The genome of the polar eukaryotic microalga coccomyxa subellipsoidea reveals traits of cold adaptation, Genome Biology, 13 (5), R39. More Info
  • Sharma V., A. Firth, I. Antonov, O. Fayet, J. F. Atkins, M. Borodovsky and P. V. Baranov (2011) A survey of bacterial genes with disrupted ORFs: Profusion of non-triplet decoding via ribosomal frameshifting and transcriptional realignment. Molecular Biology and Evolution, 28(11):3195-211. More Info
  • Wóycicki R., Witkowicz J., Gawroński P., Dąbrowska J., Lomsadze A., Pawełkowicz M., Ewa Siedlecka M., Yagi K., PlÄ…der W., Seroczyńska A., Śmiech M., Gutman W., Niemirowicz-Szczytt K., Bartoszewski G., Tagashira N., Hoshi Y., Borodovsky M., Karpinski S., Malepszy S., and Z. Przybecki (2011) The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants, PLOS One. More Info
  • Xu J., R. Linning, J. Fellers, M. Dickinson, W. Zhu, I. Antonov, T. Eilam, Y. Anikster, B. McCallum, T. Banks, S. Munro, M. Mayo, B. Wynhoven, J. Ali, R. Moore, D. L. Joly, M. E. Donaldson, M. Borodovsky, B. Saville and Guus Bakkeren (2011) Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi.  BMC Genomics, advanced publication, 24/03/11; 0.1186/1471-2164-12-161.
  • Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM. The genome of woodland strawberry (Fragaria vesca) Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26. More Info and Press Release
  • Borodovsky M., Gogarten J.P., Przytycka T.M., S. Rajasekaran, Editors. Proceedings of Bioinformatics Research and Applications, 6th International Symposium, ISBRA 2010, Storrs, CT, USA May 2010; Lecture Notes in Bioinformatics, Springer-Verlag Berlin Heidelberg, 2010
  • Blanc G., G. Duncan, I. Agarkova, M. Borodovsky, D. Brogun, T. Gurnon, M. Kuo, M. E. Lindquist, S. Lucas, J. Pangilinan, J. Polle, A. Salamov, A. Terry, T. Yamada, D. Dunigan, I. Grigoriev, J.-M. Claverie, and J. L. Van Etten. Chlorella sp. NC64 A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses and Cryptic Sex, Plant Cell, (2010) advanced publication; 10.1105/tpc.110.076406. More Info
  • Stajich J.E., S. Wilke, D. Ahren, C-H Au, B. W. Birren, M. Borodovsky, C. Burns, B. Canback, L. A. Casselton, C.K. Cheng, J. Deng, F. S. Dietrichd, D. C. Fargo, M. L. Farman, A. C. Gathman, J. Goldberg, R. Guigo, P. J. Hoegger, J. B. Hooker, A. Huggins, T. Y. James, T. Kamada, S. Kilaru, C. Kodira, U. Kues, D. Kupfer, H.S. Kwan, A. Lomsadze, W. Li, W. W. Lilly, L-J Ma, A. J. Mackey, G. Manning, F. Martin, H. Muraguchi, D. O. Natvig, H. Palmerini, M. A. Ramesh, C. J. Rehmeyer, B. A. Roe, N. Shenoy, M. Stanke, V. Ter-Hovhannisyan, A. Tunlid, R. Velagapudi, T. J. Vision, Q. Zeng, M. E. Zolan, and P. J. Pukkila (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Proceedings of the National Academy of Sciences DOI is 10.1073/pnas.1003391107. (Made the cover of June 29 print issue of PNAS). More Info
  • Zhu W., Lomsadze A. & M. Borodovsky (2010) Ab initio Gene Identification in Metagenomic Sequences Nucleic Acids Research, DOI: 10.1093/nar/gkq275. More Info
  • Antonov I. & M. Borodovsky (2010) Frameshift identification in protein coding sequences by the Viterbi algorithm, Journal of Bioinformatics and Computational Biology, 8, 1-17. More Info
  • Martin J., Zhu W., Passalacqua K., Bergman N. and Borodovsky M. (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics, 11(Suppl 3): S10 DOI:10.1186/1471-2105-11-S3-S10. More Info


  • Please visit http://opal.biology.gatech.edu/GeneMark/references.html for the most updated list of publications.


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