Publications:

  1. I.S. Gabashvili, B.H. Sokolowski , C.C.Morton, A.B.Giersch "Ion Channel Gene Expression in the Inner Ear", J Assoc Res Otolaryngol. 2007 Sep;8(3):305-28.
    view/download (PDF 1.3M)
    Supplementary Material
     Sequences:   KCNMA1(1)  KCNMA1(2)   Clic4   KCNA2   TRPM3  

  2. M. Peleg, I.S. Gabashvili, R.B. Altman,  "Qualitative knowledge models in Functional Genomics and Proteomics", in: Genomics and Proteomics Engineering in Medicine and Biology (Akay,M., ed), Wiley-IEEE Press, 2007.
    view/download (PDF 1.2M)

  3. I.S. Gabashvili, R. Carter, P. Markstein, A.B. Giersch "Differential Gene Expression in the Auditory System", Lecture Notes in Computer Science, Vol. 3594, 2005, 1-8.
    view/download (PDF 1.5M)

  4. I.S. Gabashvili, M. Whirl-Carrillo, M. Bada, D.R. Banatao and R.B. Altman, "Ribosomal Dynamics Inferred from Variations in Experimental Measurements", RNA, Vol. 9, 2003, 1301-1307.
    view/download (PDF 0.4M)

  5. Peleg M., I.S. Gabashvili and R.B. Altman, "Qualitative models of molecular function: linking genetic polymorphisms of tRNA to their functional sequelae", Proc. of the IEEE, Vol. 90, No. 12, pp. 1875-1886, 2002.
    view/download (PDF 1.35M)

  6. M. Whirl-Carrillo, I.S. Gabashvili, D.R. Banatao, M. Bada and R.B. Altman, "Mining biochemical information: lessons taught by the ribosome", RNA, Vol. 8, No. 3, pp. 279-289, 2002.
    view/download (PDF 0.4M)

  7. I.S. Gabashvili, S.T. Gregory, M. Valle, R. Grassucci, M. Worbs, M.C. Wahl, A.E. Dahlberg, J. Frank, "The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22",  Molecular Cell, Vol. 8, No. 1, pp.181-188, 2001.
    view/download (PDF 0.3M)

  8. I.S. Gabashvili, R.K. Agrawal, C.M.T. Spahn, R. Grassucci, D.I. Svergun, J. Frank, P.A. Penczek, "Solution structure of the E.coli 70S ribosome at 11.5A resolution", Cell, Vol. 100, No. 5, pp. 537-549, 2000.
    view/download (PDF 0.6M)
    PDB coordinates

  9. I.S. Gabashvili, M. Joshi, and M. Fragata, "Structure of polypeptides and biopolymers probed with FT­IR spectroscopy. The tyrosine ring stretching modes in poly (L­tyrosine) and photosystem II", Recent Research Developments in Physical Chemistry, Vol. 4, pp. 83-99, 2000.

  10. M.S. Van Loock, R.K. Agrawal, I.S. Gabashvili, L. Qi, J. Frank, and S.C. Harvey, "Movement of the Decoding Region of the 16S RNA Accompanies tRNA Translocation", Journal of Molecular Biology, Vol. 304, No. 4, pp. 507-515, 2000.

  11. J.A. Ségui, V. Maire, I.S. Gabashvili and M. Fragata, "Oxygen evolution loss and structural transitions in photosystem II induced by low intensity UV-B radiation of 280 nm. wavelength", J. Photochem. Photobiol., B: Biol., Vol. 56, No. 1, pp. 39-47, 2000.
    view/download (PDF 0.3M)

  12. I.S. Gabashvili, R.K. Agrawal, R. Grassucci, C.S. Squires, A.E. Dahlberg, J. Frank, "Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA", EMBO journal, Vol. 18, No. 22, pp. 6501-6507, 1999.
    view/download (PDF 1.35M)

  13. I.S. Gabashvili, R.K. Agrawal, R. Grassucci, J. Frank, "Structure and Structural Variations of the Escherichia coli 30S Ribosomal Subunit as Revealed by Three-Dimensional Cryo-electron Microscopy", Journal of Molecular Biology, Vol. 286, No. 5, pp. 1285-1291, 1999. (Fig.1 from the article used for the cover page illustration) view/download (PDF 1.35M)


  14. A. Khodjakov, I.S. Gabashvili, C.L. Rieder, "Dumb" versus "Smart" Kinetochore Model for Chromosome Congression During Mitosis in Verterbrate Somatic Cells", Cell Motility & the Cytoskeleton, Vol. 43, No. 3, pp. 179-185, 1999. (cover page illustration)
    view/download (PDF 0.1M)

  15. A. Malhotra, P.A. Penczek, R.K. Agrawal, I.S. Gabashvili, R.A. Grassucci, R. Junemann, N. Burkhardt, K.H. Nierhaus and J. Frank, "E.coli 70S Ribosome at 15A Resolution and Localization of Fmet-tRNA(fmet) at the P-site by Cryo-electron Microscopy", Journal of Molecular Biology, Vol. 280, pp. 103-115, 1998. (Fig.6A from the article used for the cover page illustration)
    view/download (PDF 2.4M)

  16. I.S. Gabashvili, A. Menikh, J. Segui, M. Fragata, "Protein structure of photosystem II studied by FT-IR spectroscopy. Effect of digalactosyldiacylglycerol on the tyrosine side chain residues", Journal of Molecular Structure, Vol. 444, pp. 123-133, 1998.

  17. I.S. Gabashvili, S.A. Khan, S.J. Hayes, P. Serwer, "Polymorphism of T7 bacteriophage", Journal of Molecular Biology, Vol. 273, No. 3, pp. 658-667, 1997.
    view/download (PDF 0.3M)

  18. M. Fragata, E.K. Nenonéné, V. Maire, I.S. Gabashvili, "Structure of the Phosphatidylglycerol-photosystem II complex studied by FT-IR Spectroscopy. Mg(II) effect on the polar head group of phosphatidylglycerol", Journal of Molecular Structure, Vol. 405, Nos. 2-3, pp. 151-158, 1997.

  19. R. Dzadzamia, M. Revazishvili, I. Gabashvili, "Accounting Phrasal Dictionary (Georgian-English-Russian, English-Russian-Georgian, Russian-Georgian-English)" Georgian Academy of Sciences, Tbilisi, 1995.

  20. I. Gabashvili, Z. Brelidze, Yu. Stepanov, G. Khachapuridze, "Simulation of the Mechanisms of Cell Genome Stability and Instability", In: "Mathematical Modelling: Methodology, Software Tools and Applications", pp. 79-83 (Popova E.D., ed) DATECS Publish., Sofia, Bulgaria, 1993.

  21. I.S. Gabashvili, A.Yu. Grosberg, "Dynamics of Double-Stranded DNA Reptation from Bacteriophage", Journal of Biomolecular Structure and Dynamics. , Vol. 9, No. 5, pp. 911-920, 1992.
    view/download (PDF 3.9M)

  22. I.S. Gabashvili, A.Yu. Grosberg, "DNA Reptation from Bacteriophage", Biophysics, Vol. 36, pp. 788-793 , 1991.
    (Biofizika,1991,36,788-793:Rus)

  23. I.S. Gabashvili, A.Yu. Grosberg, D.V. Kuznetsov, G.M. Mrevlishvili, "Theoretical Model of DNA Packaging in the Phage Head", Biophysics , Vol. 36, No. 5, pp. 782-789, 1991. (Biofizika,1991,36,780-787:Rus)

              

    Book Reviews:
  24. I.S. Gabashvili, Greg S. Snider. "Introduction to Biomedical Imaging" Annals of Biomedical Engineering, vol. 31, No. 11, p. 1443, 2003.

              

    In revision:
  25. D.Rey Banatao, Teri E. Klein, I.S. Gabashvili, Russ B. Altman,  "Fast search for ion binding sites in complex RNA structures: Mapping the Ribosome", 2008.

  26. R. Carter, I.S. Gabashvili, "The Stack-AND Exact String Matching Algorithm", 2008

    In preparation:
  27. I.S. Gabashvili, A.B.Giersch, "Age-related hearing loss: before the beginning", 2008
    I.S. Gabashvili, C. Allsup, "Nanometer test - the way nature intended", 2008

    HP restricted: Technical Reports and Internal Conference Papers:
  28. "New Genes Worth Hearing About" HPL-2005-47, with Dick Carter and Peter Markstein
  29. "Nanotechnology-Based Fast and inexpensive genome sequencing"HPL-2005-48, with Zhiyong Li, Ken Ward, Wei Wu, Milo Overbay, Robert Seay, S.-Y. Wang, and Stan Williams
  30. "The Stack-AND Genome Search Algorithm", with Dick Carter and Peter Markstein (TechCon'06, April, 2006, Los Angeles, CA)
  31. "Computational applications in genetic oncology", with Dick Carter and Peter Markstein (TechCon'06, April, 2006, Los Angeles, CA)
  32. "Interlinking Genes and Databases", single authorship, paper presented at HP Labs Enterprise Computing and Services Research Workshop. Palo Alto, December 6-7, 2005
  33. "Ion Channel Gene Isoforms of the Auditory System", HPL-2006-62, with Dick Carter, Peter Markstein, Cynthia Morton and Anne Giersch
  34. "Ion Channel Research Supplementary Material", HPL-2006-61, ", with Dick Carter, Peter Markstein, Cynthia Morton and Anne Giersch

              

    SELECTED ABSTRACTS and CONFERENCE PAPERS

  35. Ígor L. Almeida, Adelmo L. Cechin, Cláudia K. Barcellos, Irene S. Gabashvili "A New Methodology for Regulatory Network Inference" 14th Annual Conference on intelligent Systems for Molecular Biology (Fortaleza, Brazil, August 6-10, 2006).
    view

  36. I.S. Gabashvili, "Assessing functional relevance of UTR isoforms of genes" , Advances in Functional Genomics (South San Francisco, CA, April 25-26, 2006)

  37. I.S. Gabashvili, "Interlinking Ion Channels" , 50th Annual Meeting of Biophysical Society. Salt Lake City, Utah, February 18-22, 2006. (Biophys. J., 2006, 90, N 1, 2669-Pos/B336)
    view

  38. I.S. Gabashvili, R. Carter, P. Markstein, A.B. Giersch "EST-based analysis of gene expression in the human cochlea", Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts IEEE 8-11 Aug. 2005, pp. 75-76 view/download (PDF)

  39. I.S. Gabashvili, R. Carter,  P. Markstein,  "Mapping and identification of sequence flips in ESTs" (D110), 13th International Conference on Intelligent Systems for Molecular Biology (Detroit, MI, June 24-29, 2005)

  40. I.S. Gabashvili, R. Carter, P. Markstein, A.B. Giersch " Identifying hearing impairment gene and pathway candidates by EST-based analysis of gene expression", Bio-IT World 2005(Boston, MA, May 17-19, 2005) Poster Display in Research Row: Real-World Studies

  41. I.S. Gabashvili "Ion Channels: Learning from the body electric" QB3 Life Engineering Symposium (San Francisco, CA, August 19-20, 2005)

  42. I.S. Gabashvili, R. Carter,  P. Markstein,  "Identification of drug target candidates by EST analysis", Emerging Technologies for Drug Discovery Conference and Exhibition. South San Francisco, CA, April 5-6, 2005

  43. I.S. Gabashvili, R. Carter,  P. Markstein,  A.B Giersch, "Novel Ion Channels in Human Cochlea" , 49th Annual Meeting of Biophysical Society. Long Beach, CA Feb. 12-16, 2005. (Biophys. J., 2005, 88, N 1, p.547A, Suppl.S)
    view

  44. I.S. Gabashvili, R. Carter,  P. Markstein,  A.B Giersch, "Mechano-sensation genes of hearing", 44th Annual Meeting, The American Society for Cell Biology. Washington, DC, Dec. 4-8, 2004. (Mol.Biol.Cell, 15, 352A, Suppl. S, 2004)

  45. I.S. Gabashvili, "Protein-RNA Interactions: a message from the untranslated region of a gene" , 48th Annual Meeting of Biophysical Society. Baltimore, MD Feb. 14-18, 2004. (Biophys. J., 2004, 86, N 1, part 2, Suppl.S p.352A)
    view

  46. I.S. Gabashvili,  P. Markstein,  Heat-shock related protein-binding regions in untranslated RNA 43rd Annual Meeting, The American Society for Cell Biology. San Francisco, CA, Dec. 13-17, 2003. (Late Abstracts Poster Session, L289).
    view

  47. I.S. Gabashvili, M. Whirl-Carrillo, M. Bada, D.R. Banatao, R.B. Altman, Mining heterogeneous ribosomal structure data. 47th Annual Meeting of Biophysical Society. San Antonio, TX, Mar. 1-5, 2003. (Biophys. J., 2003, 84, N 1, part 2, p.463A)

  48. I.S. Gabashvili, M. Peleg, R.B. Altman, Modeling molecular function and failure: misreading of genetic code by the ribosome. 46th Annual Meeting of Biophysical Society. San Francisco, CA, Feb. 23-27, 2002. (Biophys. J., 2002, 82, N 1, part 2., pp. 167a-168a)

  49. I.S. Gabashvili , M. Peleg, R.B. Altman, Ontology of ribosomal function and failure: the case of translational misreading. Triennial International Conference on the Ribosome. Queenstown, New Zealand, Jan. 27 - Feb. 1, 2002. p. 127.

  50. I.S. Gabashvili, S.T. Gregory, M. Valle, R. Grassucci, M. Wahl, A.E. Dahlberg, J. Frank, Possible role of ribosomal proteins L4 and L22 in gating of the polypeptide tunnel. 45th Annual Meeting of Biophysical Society. Boston, MA, Feb. 17-21, 2001. (Biophys. J., 2001, 80, N 1, Part 2., p. 2555)

  51. I.S. Gabashvili, R.K. Agrawal, C.M.T. Spahn, R. Grassucci, J. Frank, P. Penczek, 11.5A resolution cryo-EM map of the E.coli 70S ribosome: evidence for molecular rearrangements. (oral presentation) The 44th Biophysical Society Annual Meeting. New Orleans, LA, Feb. 12-16, 2000. (Biophys. J., 2000, 78, N 1, p. 2, p. 8A. 44Plat.)

  52. I.S. Gabashvili, R.K. Agrawal, R. Grassucci, C.S. Squires, A.E. Dahlberg, J. Frank, Local switch and global tuning of the decoding ribosome: a cryo-EM story. The 44th Biophysical Society Annual Meeting. New Orleans, LA, Feb. 12-16, 2000. (Biophys. J., 2000, 78, N 1, p. 2, p. 169A.)

  53. I.S. Gabashvili, R. Agrawal, A. Heagle, R. Grassucci, J. Frank, rRNA-based conformational flexibility of the Escherichia coli 30S ribosomal subunit. RNA-99, Edinburgh, Scotland, UK. June 23-27, 1999.

  54. I. Gabashvili, R. Agrawal, A. Heagle, R. Grassucci, J. Frank, Hinge-bent regions in the Escherichia coli 30S ribosomal subunit: a Three-dimensional cryo-electron microscopy study. The Ribosome: Structure, Function, Antibiotics and Cellular Interactions. Snekkersten, Helsingoer, Denmark, June 13-17, 1999.

  55. I.S. Gabashvili, R.K. Agrawal, R.A. Grassucci, and J. Frank, Conformational variations of the Escherichia coli 30S ribosomal subunit. Biophysical Society 43rd Annual Meeting, Baltimore, MD, Feb. 1999. (Biophys. J., 1999, 76, N 1, p. 2, p. A26.)

  56. I. Gabashvili, M. Fragata, Decomposition of the Infrared Spectra of Benzene and Derivatives: a comparative vibrational analysis. Proc. of the 22nd Annual Conference of the Federation of Analytical Chemistry and Spectroscopy Societies, Cincinnati, OH, 1995.

  57. I. Gabashvili, N. Okudzhava, On the Heritability of Polycystic Ovary Syndrome in Families and Populations of Georgia. Abstr. of 10th Workshop on Development and Function of the Reproductive Organs, Huddinge, Sweden, 1995.

  58. I. Gabashvili, Z. Brelidze, G. Khachapuridze, Intellectual Terminal for Geneticists. Proc. of the Intl. Conf. "The Healthcare Computing", p. 803, Harrogate, England, 1994.

  59. I. Gabashvili, Z. Brelidze, G. Khachapuridze, Biomathematics of the Genetic Homeostasis. In MIE'94 (Proc. of the 12th Intl. Congress on Medical Informatics) Lisbon, Portugal, pp. 132-137, 1994.

  60. I. Gabashvili, Z. Brelidze, G. Khachapuridze, Intelligent Computer-Assisted Learning in Genetic Reasoning. Proc. of the 3rd Panhellenic Congress on Medical Informatics. Thessaloniki, Greece, 1994.

  61. I.S. Gabashvili, A.Yu. Grosberg, D.V. Kuznetsov, G.M. Mrevlishvili, Phage DNA Packaging and Reptation from Protein Shell. Abstr. Int. School-Seminar "Modern Problems of Physical Chemistry of Macromolecules" Pushino, USSR, p. 105, 1991.