|
|
|
|
|
 |
Professor, School of Biology Faculty Coordinator, Bioinformatics Masters Degree Program mark@amber.biology.gatech.edu 404.894.8432 |
Ph.D., Moscow Institute of Physics and Technology, 1976
- 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.