Professor, School of Biology
Faculty Coordinator, Bioinformatics Masters Degree Program


Ph.D., Moscow Institute of Physics and Technology, 1976

Research Interests

- Developing machine learning algorithms, computational techniques and tools for nucleic acid and protein sequence interpretation
- Discovering biomolecular structure-function relationships
- Gene finding in prokaryotic and eukaryotic DNA
- Genome analysis by probabilistic modeling, particularly, by using Markov and Hidden Markov models

Select Publications  (list last updated 05.11.99)

Hayes W., and M. Borodovsky (1998)
How to interpret anonymous genome? Machine learning approach to gene identification.
Nucleic Acids Research, 8, 1154-1171.

Lukashin A.V. and M. Borodovsky (1998)
GeneMark.hmm: new solutions for gene finding.
Nucleic Acids Research, 26, 1107-1115.

Hayes W. S. and M. Borodovsky (1998)
Deriving Ribosome Binding Site (RBS) statistical models fromunannotated DNA sequences and the use of the RBS model for N-terminal prediction in Proceedings of Pacific Symposium on Biocomputing 1998.
World Scientific, 279-290.

Tomb J-F., White O., Kerlavage A., Clayton R., Sutton G., Fleischmann R., Ketchum K., Klenk H.P., Gill S., Dougherty B., Nelson K., Quackenbush J., Zhou L., Kirkness E.F., Peterson S., Loftus B., Richardson D., Dodson R., Khalak H., Glodek A., McKenney K., Fitzegerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne, Utterback T.R., Peterson J., Kelley J., Cotton M., Weidman J.M., Fujii C.F., Bowman C., Watthey L., Wallin E., Hayes W., Borodovsky M., Karp P., Smith H.O., Fraser C.M. and J.C. Venter. (1997)
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Nature, 388, 539-547.

Hirosawa M., Isono K., Hayes W. S. and M. Borodovsky (1997)
Gene Identification and Classification in the Synechocystis Genomic Sequence by Recursive GeneMark Analysis, DNA sequence, 8, 17-30

Martindale C., Gusein-Zade S., McKenzie D. and M.Borodovsky (1997)
Comparison of Equations Describing the Ranked Frequency Distributions of Graphems and Phonems, J. of Quantitative Linguistics, 3, 106-112

Ioshikhes I., Bolshoy A., Derenshteyn K., Borodovsky M.and E. Trifonov (1996)
Nucleosomal DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally
Mapped Sequences, Journal of Molecular Biology, 262, 129-139.

Censini S. Lange C., Xiang Z., Crabtree J.E., Ghiara P., Borodovsky M., Rappioly R. & A. Covacci (1996) Cag, a pathogenicity island of Helicobacter Pylori, encodes type I-specific and disease-associated virulence factors, Proc. Natl. Acad. Sci. USA, 93, 14648-14653

Bult, C.J., O. White, G.J. Olsen, L. Zhou, R.D. Fleischmann, G.G. Sutton, J.A. Blake, L.M. FitzGerald,
R.A. Clayton, J.D. Gocayne, A.R. Kerlavage, B.A. Dougherty, J.F. Tomb, M.D. Adams, C.I. Reich, R.
Overbeek, E.F. Kirkness, K.G. Weinstock, J.M. Merrick, A. Glodek, J.L. Scott, N.S.M. Geoghagen, J.F. Weidman, J.L. Fuhrmann, D. Nguyen, T.R. Utterback, J.M. Kelley, J.D. Peterson, P.W. Sadow, M.C. Hanna, M.D. Cotton, K.M. Roberts, M.A. Hurst, B.P. Kaine, M. Borodovsky, H.P. Klenk, C.M. Fraser, H.O. Smith, C.R. Woese, and J.C. Venter. (1996.)
Complete Genome Sequence of the Methanogenic Archaeon Methanococcus jannaschii. Science 273: 058-1073.

McIninch, J., W. Hayes, and M. Borodovsky. (1996)
Applications of GeneMark in Multispecies Environments. ISMB '96 Proceedings 176-188.

Benian, G., T.L. Tinley, X. Tang, and M. Borodovsky.(1996)
The C. elegans Gene unc-89, Required for Muscle M-line Assembly, Encodes a Giant Modular Protein
Composed of Ig and Signal Transduction Domains. Journal of Cell Biology 6: 835-848.

Kleffe, J., K. Hermann, and M. Borodovsky. (1996)
Statistical Analysis of GeneMark Performance by Cross-validation. Computers & Chemistry 20: 123-134.

Tatusov, R.L., A.R. Mushegian, P. Bork, N.P. Brown, W. Hayes, M. Borodovsky, K.E. Rudd, and E.V. Koonin. (1996)
Metabolism and Evolution of H. influenzae Deduced from Whole Genome Comparison to E. coli.Current Biology 6: 279-291.

Hirosawa, M., T. Kaneko, S. Tabata, J. McIninch, W. Hayes, M. Borodovsky, and K. Isono. (1995) Prediction of the Coding Regions in a Contiguous 1MB Sequence of the Genome of Synechocystis sp. Strain PCC6803. DNA Research 2: 239-246.

Borodovsky, M., J. McIninch, E. Koonin, K. Rudd, C. Medigue, and A. Danchin. (1995)
Detection of New Genes in the Bacterial Genome Using Markov Models for Three Gene Classes. Nucleic Acids Research 23: 3554-3562.

Borodovsky, M., K. Rudd, and E. Koonin. (1994)
Intrinsic and Extrinsic Approaches for Detecting Genes in a Bacterial Genome. Nucleic Acids Research 22: 4756-4767.

Borodovsky, M., E. Koonin, and K. Rudd. (1994).
New Genes in Old Sequences: A Strategy for Finding Genes in a Bacterial Genome. Trends in Biochemical Sciences 19:309-313.

Borodovsky, M. and A. Peresetsky.( 1994)
Deriving Non-homogeneous Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy. Computers & Chemistry 18: 259-268.

Borodovsky, M. and J. McIninch. (1993)
GeneMark: Parallel Gene Recognition for both DNA Strands.Computers & Chemistry 17: 123-133.