Mark Borodovsky

Personal Home Page

http://www.biology.gatech.edu/faculty/mark-borodovsky/

Articles in Scholarly Journals [Incomplete List]

  1. Control of Streptococcus pyogenes virulence: Modeling of the CovR/S signal transduction system
    Journal of Theoretical Biology, vol. 246, no. 1, pp. 113–128, 2007
  2. Convergence rate estimation for the TKF91 model of biological sequence length evolution
    Mathematical Biosciences, vol. 209, no. 2, pp. 470–485, 2007
  3. Exonization of the LTR transposable elements in human genome
    BMC Genomics, vol. 8, no. 1, p. 291, 2007
  4. BMC Bioinformatics, vol. 7, no. 1, p. 178, 2006
  5. Statistical significance in biological sequence analysis
    Briefings in Bioinformatics, vol. 7, no. 1, pp. 2–24, 2006
  6. The Fifth Georgia Tech--Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology
    Bioinformatics, vol. 21, no. Suppl 3, pp. iii1–iii1, 2005
  7. Sensitivity of hidden Markov models
    Journal of Applied Probability, vol. 42, no. 3, pp. 632–642, 2005
  8. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    Nucleic Acids Research, vol. 33, no. Web Server, pp. W451–W454, 2005
  9. Gene identification in novel eukaryotic genomes by self-training algorithm
    Nucleic Acids Research, vol. 33, no. 20, pp. 6494–6506, 2005
  10. Identification of Proteins Associated with Murine Cytomegalovirus Virions
    Journal of Virology, vol. 78, no. 20, pp. 11187–11197, 2004
  11. Effects of choice of DNA sequence model structure on gene identification accuracy
    Bioinformatics, vol. 20, no. 7, pp. 993–1005, 2004
  12. Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory
    Briefings in Bioinformatics, vol. 5, no. 2, pp. 118–130, 2004
  13. Identification of New Human Cadherin Genes Using a Combination of Protein Motif Search and Gene Finding Methods*1
    Journal of Molecular Biology, vol. 337, no. 2, pp. 307–317, 2004
  14. Three New Isoforms of Caenorhabditis elegans UNC-89 Containing MLCK-like Protein Kinase Domains
    Journal of Molecular Biology, vol. 342, no. 1, pp. 91–108, 2004
  15. The Fourth Georgia Tech--University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA)
    Bioinformatics, vol. 19, no. 15, pp. 1867–1868, 2003
  16. Improving gene annotation of complete viral genomes
    Nucleic Acids Research, vol. 31, no. 23, pp. 7041–7055, 2003
  17. Complete Sequence and Comparative Analysis of the Genome of Herpes B Virus (Cercopithecine Herpesvirus 1) from a Rhesus Monkey
    Journal of Virology, vol. 77, no. 11, pp. 6167–6177, 2003
  18. Titins in C.elegans with Unusual Features: Coiled-coil Domains, Novel Regulation of Kinase Activity and Two New Possible Elastic Regions
    Journal of Molecular Biology, vol. 323, no. 3, pp. 533–549, 2002
  19. Leaderless Transcripts of the Crenarchaeal Hyperthermophile Pyrobaculum aerophilum,
    Journal of Molecular Biology, vol. 309, no. 2, pp. 347–360, 2001
  20. A novel genetic island of meningitic Escherichia coli K1 containing the ibeA invasion gene (GimA): functional annotation and carbon-source-regulated invasion of human brain microvascular endothelial cells
    Functional & Integrative Genomics, vol. 1, no. 5, pp. 312–322, 2001
  21. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    Nucleic Acids Research, vol. 29, no. 12, pp. 2607–2618, 2001
  22. THE THIRD GEORGIA TECH-EMORY INTERNATIONAL CONFERENCE ON BIOINFORMATICS: IN SILICO BIOLOGY; BIOINFORMATICS AFTER HUMAN GENOME (NOVEMBER 15-18, 2001, ATLANTA, GEORGIA, USA)
    Bioinformatics, vol. 17, no. 10, pp. 859–861, 2001
  23. The Vfl1 Protein in Chlamydomonas Localizes in a Rotationally Asymmetric Pattern at the Distal Ends of the Basal Bodies
    The Journal of Cell Biology, vol. 153, no. 1, pp. 63–74, 2001
  24. The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA)
    Bioinformatics, vol. 15, no. 11, pp. 865–866, 1999
  25. Finding prokaryotic genes by the frame-by-frame' algorithm: targeting gene starts and overlapping genes
    Bioinformatics, vol. 15, no. 11, pp. 874–886, 1999
  26. Heuristic approach to deriving models for gene finding
    Nucleic Acids Research, vol. 27, no. 19, pp. 3911–3920, 1999
  27. GeneMark.hmm: new solutions for gene finding
    Nucleic Acids Research, vol. 26, no. 4, pp. 1107–1115, 1998
  28. Genetics in profile
    Trends in Genetics, vol. 14, no. 2, pp. 51–52, 1998
  29. Nature, vol. 389, no. 6649, pp. 412–412, 1997
  30. Nature, vol. 388, no. 6642, pp. 539–547, 1997
  31. cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors
    Proceedings of the National Academy of Sciences, vol. 93, no. 25, pp. 14648–14653, 1996
  32. The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains
    The Journal of Cell Biology, vol. 132, no. 5, pp. 835–848, 1996
  33. Statistical analysis of genemark performance by cross-validation
    Computers & Chemistry, vol. 20, no. 1, pp. 123–133, 1996
  34. Nucleosome DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences
    Journal of Molecular Biology, vol. 262, no. 2, pp. 129–139, 1996
  35. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
    Current Biology, vol. 6, no. 3, pp. 279–291, 1996
  36. Computer Survey for Likely Genes in the One Megabase Contiguous Genomic Sequence Data of Synechocystis sp. Strain PCC6803
    DNA Research, vol. 2, no. 6, pp. 239–246, 1995
  37. Characteristic Features of the Nucleotide Sequences of Yeast Mitochondrial Ribosomal Protein Genes as Analyzed by Computer Program GeneMark
    DNA Research, vol. 1, no. 6, pp. 263–269, 1994
  38. New genes in old sequence: a strategy for finding genes in the bacterial genome
    Trends in Biochemical Sciences, vol. 19, no. 8, pp. 309–313, 1994
  39. Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy
    Computers & Chemistry, vol. 18, no. 3, pp. 259–267, 1994
  40. Recognition of genes in DNA sequence with ambiguities
    Biosystems, vol. 30, no. 1-3, pp. 161–171, 1993