Sitemap Feedback Login  
 
 
  Biography Details
 
Dr. Vladimir KUZNETSOV
Principal Investigator
 
Areas of Research Interest
 
  • Study and computational prediction of DNA-protein interactions, complexities of gene and genome architectures, cis-antisense gene pairs, regulatory sequences, transcription regulation networks, and their relevance for phenotypic properties of normal and cancerous cells
 
Biography
 
Dr Vladimir Kuznetsov was appointed Principal Scientist and Head of the Genome and Gene Expression Data Analysis Division at the Bioinformatics Institute (BII), A*STAR in November 2007.

Dr Kuznetsov obtained his degree in Physics at Kyrghyz State University (Kyrghyz Republic, Soviet Union). He went on to obtain a PhD in Biophysics at Moscow State University (Russian Federation, Soviet Union) in 1984. While he was a postgraduate student at the Institute of Molecular Biology (Moscow), Dr Kuznetsov simultaneously worked as a Junior Scientist at the Research Institute of Oncology and Radiology (Kyrghyz Republic) and a lecturer at the Department of Mathematics and Mechanics. In 1992, Dr Kuznetsov received a Doctor of Science degree in Mathematics and Physics at the Technical Union of Russian Academy of Sciences (St. Petersburg, Russian Federation).

In 1992, Dr Kuznetsov was appointed to head a laboratory in the Institute of Chemical Physics (Moscow). In 1995, he was awarded a prestige one year scholar grant by the American Cancer Society/International Union against Cancer. He worked as a researcher scholar at the Laboratory of Molecular Tumor Biology, Centre for Biological Evaluation, FDA (Bethesda, MD, USA), where he made his experimental study and computational modeling of the dynamics of IL-13 receptor subunits expressed in human solid tumor cells. He later worked as an exchange research fellow and a senior research fellow at the National Cancer Institute and the National Institute of Child Health and Human Development of the National Institutes of Health (MD, USA), where he was involved in the NIH Cancer Genome Anatomy Project. He also served as Chief Scientist at the Civilized Software Inc. (Bethesda, MD) and as a Senior Member of the professional staff at System Research Applications International Inc. (Farfax, VA, USA). In 2004, he joined the Genome Institute of Singapore as a Senior Group Leader. Currently, Dr Kuznetsov holds adjunct professor appointments in the Mathematical Department of the National University of Singapore, and in the School of Computing Engineering of Nanyang Technological University, Singapore.

Dr Kuznetsov has made significant contributions to the field of science. In 1994, he was awarded the P.L Kapitsa Silver Medal "To the Author of Scientific Discovery" and elected as a Corresponding Member the Russian Academy of Natural Sciences. Dr Vladimir Kuznetsov has published over 80 research papers and reviews, and is a member of the editorial boards of international journals including Biology Direct and Journal of Integrative Bioinformatics. He is known internationally for his works on basic models of mathematical immunology of cancer, probabilistic models of gene expression analyzed based on SAGE and microarray data, statistical simulation of protein-DNA interaction avidity based on ChIP-PET data, modeling of evolution of protein domains and proteome complexity, stochastic process models leading to Pareto-like scale-dependent evolution dynamics, classification and prognosis of the human cancers. Dr Kuznetsov is an inventor of the pattern recognition algorithm – Statistically Weighed Syndromes voting method. This algorithm allows for the selection of a small number of variables from high dimension (e.g. microarray) data and provides robust individual prediction even if the original data set is noisy, contains missing values and is represented by very limited number of samples.
 
Selected Publications
 
  1. Kuznetsov VA, Orlov YL, Wei CL, Ruan YJ.
    Computational Analysis and Modeling of Genome-scale Avidity Distribution of Transcription Factor Binding Sites in Chip-PET Experiments. (Eds. Ng See-Kiong , Mamitsuka and Wong Limsoon).
    Imperial College Press London-Singapore. 2007. Vol.19: 83-94


  2. Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL.
    Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.
    Cell Stem Cell. 2007 Sep 13;1(3):286-98.
    PMID: 18371363 [PubMed - indexed for MEDLINE]


  3. Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JE, Liu ET, Bergh J, Kuznetsov VA, Miller LD.
    Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer.
    Cancer Res. 2006 Nov 1;66(21):10292-301.
    PMID: 17079448 [PubMed - indexed for MEDLINE]


  4. Liu ET, Kuznetsov VA, Miller LD.
    In the pursuit of complexity: systems medicine in cancer biology.
    Cancer Cell. 2006 Apr;9(4):245-7. Review.
    PMID: 16616330 [PubMed - indexed for MEDLINE


  5. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.
    A global map of p53 transcription-factor binding sites in the human genome.
    Cell. 2006 Jan 13;124(1):207-19.
    PMID: 16413492 [PubMed - indexed for MEDLINE]


  6. Kuznetsov, VA.
    Scale-dependent Statistics of the number of Transcripts and Protein Sequence Encoded in the Genome. In: Computational and Statistical Methods to Genomics. (Eds. Zhang W, Shmulevich I).
    Springer, USA. 2nd edition. 2006: 160-208.


  7. Broët P, Kuznetsov VA, Bergh J, Liu ET, Miller LD.
    Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients.
    Bioinformatics. 2006 Jun 15;22(12):1477-85. Epub 2006 Mar 21.
    PMID: 16551658 [PubMed - indexed for MEDLINE]


  8. Zucchi I, Mento E, Kuznetsov VA, Scotti M, Valsecchi V, Simionati B, Vicinanza E, Valle G, Pilotti S, Reinbold R, Vezzoni P, Albertini A, Dulbecco R.
    Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis.
    Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18147-52. Epub 2004 Dec 17.
    PMID: 15608061 [PubMed - indexed for MEDLINE]


  9. Kuznetsov VA, Knott GD, Bonner RF.
    General statistics of stochastic process of gene expression in eukaryotic cells.
    Genetics. 2002 Jul;161(3):1321-32.
    PMID: 12136033 [PubMed - indexed for MEDLINE]


  10. Belyakov IM, Hel Z, Kelsall B, Kuznetsov VA, Ahlers JD, Nacsa J, Watkins DI, Allen TM, Sette A, Altman J, Woodward R, Markham PD, Clements JD, Franchini G, Strober W, Berzofsky JA.
    Mucosal AIDS vaccine reduces disease and viral load in gut reservoir and blood after mucosal infection of macaques.
    Nat Med. 2001 Dec;7(12):1320-6.
    PMID: 11726972 [PubMed - indexed for MEDLINE]


  11. Orlov YL, Zhou J, Lipovich L, Shahab A, Kuznetsov VA.
    Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis.
    In Silico Biol. 2007;7(3):241-60.
    PMID: 18415975 [PubMed - indexed for MEDLINE]


  12. Kuznetsov, VA.
    Emergence of size-dependent networks on genome scale. In: Lecture Series on Computer and Computational Sciences.
    Brill Acad. Publishers, The Netherlands. 2006. Vol. 7a: 754-757


  13. Chua A L-S, Ivshina AV, Kuznetsov VA.
    Pareto-Gamma Statistics reveals global rescaling in transcriptomes of low and high aggressive breast cancer phenotypes. In : Pattern Recognition in Bioinformatics (PRIB-2006). (Eds. J.C. Ragapakese, L. Wong, R. Acharya)
    Springer-Verlag Berlin-Heidelberg. 2006: 49-59.


  14. Kuznetsov VA, Pickalov VV, Kanapin AA.
    Proteome complexity measures based on counting of domain-to-protein links for replicative and non-replicative domains. In: Bioinformatics of genome regulation and structure- II.(Eds. N. Kolchanov, R. Hofestaedt, L. Milanesi)
    Springer. 2006: 329-341.


  15. Belyakov IM, Kuznetsov VA, Kelsall B, Klinman D, Moniuszko M, Lemon M, Markham PD, Pal R, Clements JD, Lewis MG, Strober W, Franchini G, Berzofsky JA.
    Impact of vaccine-induced mucosal high-avidity CD8+ CTLs in delay of AIDS viral dissemination from mucosa.
    Blood. 2006 Apr 15;107(8):3258-64. Epub 2005 Dec 22.
    PMID: 16373659 [PubMed - indexed for MEDLINE]


  16. Kuznetsov VA, Senko OV, Miller LD, Ivshina Anna V.
    Statistically Weighted Voting Analysis of Microarrays for Molecular Pattern Selection and Discovery Cancer Genotypes.
    Intern J of Computer Sciences and Network Security. 2006. 6(12) 73-83.


  17. Orlov Y, Zhou JT, Chen J., Shahab A., Kuznetsov V.
    APMA Database for Affymetrix target sequences mapping, quality assessment and expression data mining. In: Pattern Recognition in Bioinformatics (JC. Ragapakese, B . Schmidt, and G. Volkert (Eds.)
    Springer-Verlag Berlin-Heidelberg. 2007: 166-177.


  18. Kuznetsov VA.
    Scale-dependent Statistics of the number of Transcripts and Protein Sequence Encoded in the Genome. In: Computational and Statistical Methods to Genomics. (Eds. Zhang W, Shmulevich I).
    Springer, USA. 2nd edition. 2006: 160-208.


  19. Fink J, Gu F, Ling L, Tolfvenstam T, Olfat F, Chin KC, Aw P, George J, Kuznetsov VA, Schreiber M, Vasudevan SG, Hibberd ML.
    Host gene expression profiling of dengue virus infection in cell lines and patients.
    PLoS Negl Trop Dis. 2007 Nov 21;1(2):e86.
    PMID: 18060089 [PubMed - in process]


  20. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET.
    Whole-genome cartography of estrogen receptor alpha binding sites.
    PLoS Genet. 2007 Jun;3(6):e87. Epub 2007 Apr 17.
    PMID: 17542648 [PubMed - indexed for MEDLINE]


  21. Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL.
    Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).
    Genome Res. 2007 Jun;17(6):828-38.
    PMID: 17568001 [PubMed - indexed for MEDLINE]


  22. Hibberd ML, Ling L, Tolfvenstam T, Mitchell W, Wong C, Kuznetsov VA, George J, Ong SH, Ruan Y, Wei CL, Gu F, Fink J, Yip A, Liu W, Schreiber M, Vasudevan SG.
    A genomics approach to understanding host response during dengue infection.
    Novartis Found Symp. 2006;277:206-14; discussion 214-7, 251-3. Review.
    PMID: 17319164 [PubMed - indexed for MEDLINE]


  23. Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL.
    Global mapping of c-Myc binding sites and target gene networks in human B cells.
    Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17834-9. Epub 2006 Nov 8.
    PMID: 17093053 [PubMed - indexed for MEDLINE]


  24. Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH.
    The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.
    Nat Genet. 2006 Apr;38(4):431-40. Epub 2006 Mar 5.
    PMID: 16518401 [PubMed - indexed for MEDLINE]


  25. Kuznetsov, V.A.
    Mathematical analysis and modeling of SAGE transcriptome. In: SAGE: Current Technologies and Applications (Ed. San Ming Wang)
    Horizon Science Press, Rowan House, Hethersett, UK. 2005: 139-179.


  26. Kuznetsov VA, Stepanov VS, Berzofsky JA, Belyakov IM.
    Assessment of the relative therapeutic effects of vaccines on virus load and immune responses in small groups at several time points: efficacy of mucosal and subcutaneous polypeptide vaccines in rhesus macaques exposed to SHIV.
    J Clin Virol. 2004 Dec;31 Suppl 1:S69-82.
    PMID: 15567097 [PubMed - indexed for MEDLINE]


  27. Matzavinos A, Chaplain MA, Kuznetsov VA.
    Mathematical modelling of the spatio-temporal response of cytotoxic T-lymphocytes to a solid tumour.
    Math Med Biol. 2004 Mar;21(1):1-34.
    PMID: 15065736 [PubMed - indexed for MEDLINE]


  28. Kuznetsov VA.
    Family of skewed distributions associated with the gene expression and proteome evolution.
    Signal Processing. 83(4): 889-910
    (Available online 14 Dec., 2002: www.ComputerScienceWeb.com)


  29. Kuznetsov VA., Knott GD.
    Modeling tumor re-growth and immunotherapy.
    Math. Comput. Modeling. 33: 1275-1287


  30. Kuznetsov, VA.
    A stochastic model of evolution of conserved protein coding sequence in the archaeal, bacterial and eukaryotic proteomes.
    Fluctuation and Noise Letters, 2003; 3(3) L295-L324.


  31. Jones MB, Michener CM, Blanchette JO, Kuznetsov VA, Raffeld M, Serrero G, Emmert-Buck MR, Petricoin EF, Krizman DB, Liotta LA, Kohn EC.
    The granulin-epithelin precursor/PC-cell-derived growth factor is a growth factor for epithelial ovarian cancer.
    Clin Cancer Res. 2003 Jan;9(1):44-51.
    PMID: 12538450 [PubMed - indexed for MEDLINE]


  32. Kuznetsov VA, Pickalov VV, Senko OV and Knott GD.
    Analysis of the evolving proteomes: Prediction of the numbers of protein domains in nature and the number of genes in eukaryotic organisms.
    J. Biol. Systems, 2002; 10(4), 381-408.


  33. Belyakov IM, Earl P, Dzutsev A, Kuznetsov VA, Lemon M, Wyatt LS, Snyder JT, Ahlers JD, Franchini G, Moss B, Berzofsky JA.
    Shared modes of protection against poxvirus infection by attenuated and conventional smallpox vaccine viruses.
    Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9458-63. Epub 2003 Jul 17.
    PMID: 12869693 [PubMed - indexed for MEDLINE]


  34. Ivshina AV, Vodeiko GM, Kuznetsov VA, Volokhov D, Taffs R, Chizhikov VI, Levandowski RA, Chumakov KM.
    Mapping of genomic segments of influenza B virus strains by an oligonucleotide microarray method.
    J Clin Microbiol. 2004 Dec;42(12):5793-801.
    PMID: 15583314 [PubMed - indexed for MEDLINE]


  35. Kuznetsov, V.A.
    Stochastic model of evolution of conserved protein coding sequences. In: Unsolved Problems of Noise and Fluctuations (Ed. S. Bezrukov)
    Melville, New-York: Amer. Inst. Physics. 2003: 369-380.


  36. Kuznetsov, VA.
    Distribution associated with stochastic processes of gene expression in a single eukaryotic cell.
    EURASIP J. on Applied Signal Processing. 2001. 4: 285-296.


  37. Kuznetsov, V.A., Knott, G.D.
    A prediction Method for Multi-Class Systems Based on Limited Data. In: Fourteenth IEEE Symposium on Computer-Based Medical Systems.
    Computer Society Los Alamitos etc. 2001: 279-284.


  38. Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, Brown MR, Buetow KH, Chuaqui RF, Cole KA, Duray PH, Englert CR, Gillespie JW, Greenhut S, Grouse L, Hillier LW, Katz KS, Klausner RD, Kuznetzov V, Lash AE, Lennon G, Linehan WM, Liotta LA, Marra MA, Munson PJ, Ornstein DK, Prabhu VV, Prange C, Schuler GD, Soares MB, Tolstoshev CM, Vocke CD, Waterston RH.
    Molecular profiling of clinical tissue specimens: feasibility and applications.
    Am J Pathol. 2000 Apr;156(4):1109-15. Review. No abstract available.
    PMID: 10751334 [PubMed - indexed for MEDLINE]


  39. Jackson AM, Ivshina AV, Senko O, Kuznetsova A, Sundan A, O'Donnell MA, Clinton S, Alexandroff AB, Selby PJ, James K, Kuznetsov VA.
    Prognosis of intravesical bacillus Calmette-Guerin therapy for superficial bladder cancer by immunological urinary measurements: statistically weighted syndrome analysis.
    J Urol. 1998 Mar;159(3):1054-63.
    PMID: 9474231 [PubMed - indexed for MEDLINE]


  40. Kuznetsov VA, Puri RK.
    Kinetic analysis of high affinity forms of interleukin (IL)-13 receptors: suppression of IL-13 binding by IL-2 receptor gamma chain.
    Biophys J. 1999 Jul;77(1):154-72.
    PMID: 10388747 [PubMed - indexed for MEDLINE]


  41. Grossman Z, Feinberg M, Kuznetsov V, Dimitrov D, Paul W.
    HIV infection: how effective is drug combination treatment?
    Immunol Today. 1998 Nov;19(11):528-32. Review.
    PMID: 9818549 [PubMed - indexed for MEDLINE]


  42. Mueller BU, Zeichner SL, Kuznetsov VA, Heath-Chiozzi M, Pizzo PA, Dimitrov DS.
    Individual prognoses of long-term responses to antiretroviral treatment based on virological, immunological and pharmacological parameters measured during the first week under therapy.
    AIDS. 1998 Oct 22;12(15):F191-6.
    PMID: 9814861 [PubMed - indexed for MEDLINE]
 

Please contact us by email if you wish a reprint from any of the selected publications.
 

Bioinformatics Institute, a member of A*STAR's Biomedical Sciences Institutes. 30 Biopolis Street, #07-01 Matrix, S(138671)
Copyright © 2008. All Rights Reserved.
Terms of Use
Feedback Login Site Map