News
Bioinform Oct 3, 2008
Article
Georgia Tech article
Science Daily article
Books
Borodovsky M. and Ekisheva S.
Problems and Solutions in Biological Sequence Analysis
Cambridge University Press, 2006
Publisher | DOI | Amazon | Review | Review 2 | Russian Translation
Gene Finding
GeneMark-ES version 2
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M.
"Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training."
Genome Research, 2008, Dec 18(12):1979-90
Medline | Article | Supplemental Materials
GeneMark.hmm-ES
Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M.
"Gene identification in novel eukaryotic genomes by self-training algorithm."
Nucleic Acids Research, 2005, Vol. 33, No. 20, 6494-6506
Medline | Article
GeneMark Web server
Besemer J. and Borodovsky M.
"GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses."
Nucleic Acids Research, 2005, Vol. 33, Web Server Issue, pp. W451-454
Medline | Article
VIOLIN
Mills R., Rozanov M., Lomsadze A., Tatusova T. and Borodovsky M.
"Improving gene annotation in complete viral genomes."
Nucleic Acids Research, 2003, Vol. 31, No. 23, 7041-7055
Medline | Article
GeneMarkS
Besemer J., Lomsadze A. and Borodovsky M.
"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications
for finding sequence motifs in regulatory regions."
Nucleic Acids Research, 2001, Vol. 29, No. 12, 2607-2618
Medline | Article
Heuristic Models
Besemer J. and Borodovsky M.
"Heuristic approach to deriving models for gene finding."
Nucleic Acids Research, 1999, Vol. 27, No. 19, pp. 3911-3920
Medline | Article
GeneMark-Genesis
Hayes W. and Borodovsky M.
"How to interpret an anonymous bacterial genome: machine learning approach to gene identification."
Genome Research, 1998, Vol. 8, No. 11, pp. 1154-1171
Medline | Article
GeneMark.hmm
Lukashin A. and Borodovsky M.
"GeneMark.hmm: new solutions for gene finding."
Nucleic Acids Research, 1998, Vol. 26, No. 4, pp. 1107-1115
Medline | Article
GeneMark
Borodovsky M. and McIninch J.
"GeneMark: parallel gene recognition for both DNA strands."
Computers & Chemistry, 1993, Vol. 17, No. 19, pp. 123-133
Abstract | Article
Borodovsky M.Yu., McIninch J.
"Recognition of genes in DNA sequence with ambiguities"
Biosystems. , 1993;Vol 30(1-3), pp.161-71
Medline | Article
Borodovsky M.Yu., Sprizhitskii Y.A., Golovanov E.I., and Aleksandrov A.A.
"Statistical Patterns in Primary Structures of the Functional Regions of the Genome in Escherichia Coli."
Molekular Biology, 1986, Vol. 20, pp. 826-833, 833-840, 1144-1150
Article
DNA, proteins and cell systems modeling and analysis back to top
Svetlana Ekisheva and Mark Borodovsky
"Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences."
Methodology and Computing in Applied Probability, 2009 Feb; 10.1007/s11009-009-9125-7
Publisher | Article
Mitrophanov A.Yu. and Borodovsky M.
"Convergence rate estimation for the TKF91 model of biological sequence length evolution"
Math Biosci., 2007 Oct;209(2):470-85. Epub 2007 Mar 13.
Medline | Article
Piriyapongsa J., Polavarapu N., Borodovsky M. and McDonald J.
"Exonization of the LTR transposable elements in human genome"
BMC Genomics, 2007 Aug 28;8:291.
Medline | Article
Mitrophanov A.Yu., Churchward G. and Borodovsky M.
"Control of Streptococcus pyogenes virulence: Modeling of the CovR/S signal transduction system"
J Theor Biol., 2007 May 7;246(1):113-28. Epub 2006 Nov 21.
Medline | Article
Aydin Z., Altunbasak Y. and Borodovsky M.
"Protein secondary structure prediction for a single-sequence using hidden semi-Markov models."
BMC Bioinformatics, 2006 Mar 30;7:178
Medline | Article
Kim S.B., Tsui K. and Borodovsky M.
"Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets"
Int. J. Bioinformatics Research and Applications, 2006, Vol. 2, No. 2, pp 193-217
Article
Ekisheva S. and Borodovsky M.
"Probabilistic models for biological sequences:
selection and Maximum Likelihood estimation"
Int. J. Bioinformatics Research and Applications, 2006, Vol. 2, No. 3, pp 305-324
Article
Mitrophanov A.Yu. and Borodovsky M.
"Statistical significance in biological sequence analysis."
Briefings in Bioinformatics, 2006, Vol. 7, No.1, pp. 2-24
Abstract | Article
Mitrophanov A.Yu., Lomsadze A. and Borodovsky M.
"Sensitivity of hidden Markov models."
Journal of Applied Probability, 2005, Vol. 42, pp. 632-642
Abstract | Article
Kattenhorn L.M., Mills R., Wagner M., Lomsadze A., Makeev V., Borodovsky M., Ploegh H.L. and Kessler B.M
"Identification of Proteins Associated with Murine Cytomegalovirus Virions."
Journal of Virology, 2004, Vol. 78, No. 20, pp. 11187-11197
Medline | Article
Azad R.K. and Borodovsky M.Y.
"Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory."
Briefings in Bioinformatics, 2004, Vol. 5, No. 2, pp. 118-130
Medline | Article
Azad R.K. and Borodovsky M.
"Effects of choice of DNA sequence model structure on gene identification accuracy."
Bioinformatics, 2004, Vol. 20, No. 7, pp. 993-1005
Medline | Article
Shmatkov A.M., Melikyan A.A., Chernousko F.L. and Borodovsky M.
"Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes."
Bioinformatics, 1999, Vol. 15, No. 11, pp. 874-886
Medline | Article
Kleffe J. and Borodovsky M.
"First and second moment of counts of words in random texts generated by Markov chains"
Comput. Appl. Biosci., 1992, Vol. 8, No. 5, pp. 433-441
Medline | Article |