Biography Details
Dr. KUZNETSOV Vladimir
Head of Division
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
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 two books, over 90 research papers and reviews. He is a member of the editorial boards of international journals including BMC Biology Direct, BMC Genomics 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. Grinchuk O, Efthymios Motakis, Yenamandra SP, Ow GS, Jenjaroenpun P, Tang Zhiqun, A. Yarmishyn, Ivshina AV, Kuznetsov VA.
    Sense-antisense gene-pairs in breast cancer and associated pathological pathways.
    Oncotarget 2015 Oct 28. doi: 10.18632/oncotarget.6255. [Epub ahead of print]
    PMID: 26517092

  2. Aswad L, Yenamandra SP, Ow GS, Grinchuk O, Ivshina AV, Kuznetsov VA.
    Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development.
    Oncotarget. 2015 Oct 10. doi:10.18632/oncotarget.5543. [Epub ahead of print]
    PMID: 26474389

  3. Nymoen DA, Hetland Falkenthal TE, Holth A, Ow GS, Ivshina AV, Tropé CG, Kuznetsov VA, Staff AC, Davidson B.
    Expression and clinical role of chemoresponse-associated genes in ovarian serous carcinoma.
    Gynecol Oncol. 2015 Jul 29. pii: S0090-8258(15)30091-3. doi:10.1016/j.ygyno.2015.07.107.

  4. Giannakakis A, Zhang J, Jenjaroenpun P, Nama S, Zainolabidin N, Aau MY, Yarmishyn AA, Vaz C, Ivshina AV, Grinchuk OV, Voorhoeve M, Vardy LA, Sampath P, Kuznetsov VA, Kurochkin IV, Guccione E.
    Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress.
    Sci Reports. 2015 May 29;5:9737. doi: 10.1038/srep09737.
    PMID: 26024509

  5. Lim KW, Jenjaroenpun P, Low ZJ, Khong ZJ, Ng YS, Kuznetsov VA, Phan AT.
    Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study.
    Nucleic Acids Res. 2015 May 9. pii: gkv355. [Epub ahead of print]
    PMID: 25958397

  6. Jenjaroenpun P, Wongsurawat T, Yenamandra SP, Kuznetsov VA.
    QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences.
    Nucleic Acids Res. 2015 Apr 16. pii: gkv344. [Epub ahead of print]
    PMID: 25883153

  7. Batagov AO, Yenamandra SP, Jenjaroenpun P, Ivshina AV, Kuznetsov VA.
    The key role of MECOM complex locus and its products in high-grade ovarian carcinoma pathogenesis and clinical outcomes.
    Cancer Research 75 (15 Supplement), 1990-1990.

  8. Ow GS, Ivshina AV, Fuentes G, Kuznetsov VA.
    CHEK2 mutation is an adverse prognostic survival factor for patients diagnosed with high-grade serous ovarian carcinoma.
    Cancer Research. 74 (19 Supplement), 3815-3815.

  9. Ow GS and Vladimir A Kuznetsov VA.
    Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers.
    BMC Genomics 2015, 16(Suppl 7):S2 doi:10.1186/1471-2164-16-S7-S2.

  10. Jenjaroenpun P, Chew CS, Yong TP, Choowongkomon K, Thammasorn W, Kuznetsov VA.
    The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.
    Nucleic Acids Res. 2015 Jan;43(Database issue):D110-6. doi: 10.1093/nar/gku970. Epub 2014 Oct 16.
    PMID: 25324314; PubMed Central PMCID: PMC4384029.

  11. Yarmishyn AA, Batagov AO, Tan JZ, Sundaram GM, Sampath P, Kuznetsov VA, Kurochkin IV.
    HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome.
    BMC Genomics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2164-15-S9-S7. Epub 2014 Dec 8.
    PMID: 25522241; PubMed Central PMCID: PMC4290621.

  12. Ow GS, Ivshina AV, Fuentes G, Kuznetsov VA.
    Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures.
    Cell Cycle. 2014;13(14):2262-80. doi: 10.4161/cc.29271. Epub 2014 May 30.
    PMID: 24879340; PubMed Central PMCID: PMC4111681.

  13. Kuznetsov Vladimir.
    Gene Networks, tumor subtypes and patient prognogtic signatures associated with ovarian cancer mutations.

  14. Tan A, Low DHP, Giannakakis A, Kuznetsov V, Ferrari C, Guccione E, Bertoletti A.
    Journal of Hepatology, 2014; 60(1), S126, Elsevier.

  15. Yeo AJ, Becherel OJ, Luff JE, Cullen JK, Wongsurawat T, Jenjaroenpoon P, Vladimir A. Kuznetsov, Peter J. McKinnon PJ, Martin F. Lavin MF.
    R-Loops in Proliferating Cells but Not in the Brain: Implications for AOA2 and Other Autosomal Recessive Ataxias.
    PLoS ONE 2014, 9(3): e90219. doi:10.1371/journal.pone.0090219.

  16. Kuznetsov VA.
    Cancer biomarker discovery via integrative medicine and bioinformatics analysis of sequencing, gene expression and clinical oncology data.
    Transl Med 2013, 3:2; 2nd International Conference on Translational & Personalized Medicine. August 05-07, 2013 Holiday Inn Chicago-North Shore, IL, USA;

  17. Z Tang, GS Ow, JP Thiery, AV Ivshina, VA Kuznetsov.
    Meta-analysis of transcriptome reveals let-7b as an unfavorable prognostic biomarker and predicts molecular and clinical sub-classes in high-grade serous ovarian carcinoma.
    International Journal of Cancer. Online: 3 JUL 2013 11:36AM EST | 2014 Jan 15;134(2):306-18. DOI: 10.1002/ijc.28371.

  18. VA Kuznetsov, HK Lee, S Maurer-Stroh, MJ Molnár, S Pongor, B Eisenhaber, F Eisenhaber.
    How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health.
    Health Inf Sci Syst 2013 1 (2); 1-18.

  19. Xin Hui Derryn Chan, Srikanth Nama, Felicia Gopal, Pamela Rizk, Srinivas Ramasamy, Gopinath Sundaram, Ghim Siong Ow, Ivshina Anna Vladimirovna, Vivek Tanavde, Johannes Haybaeck, Vladimir Kuznetsov, and Prabha Sampath.
    Targeting Glioma Stem Cells by Functional Inhibition of a Prosurvival OncomiR-138 in Malignant Gliomas.
    Cell Reports, doi:10.1016/j.celrep.2012.07.012.

  20. Sameer Phalke, Slim Mzoughi, Marco Bezzi, Nancy Jennifer, Wei Chuen Mok, Diana HP Low, Aye Aye Thike, Vladimir A Kuznetsov, Puay Hoon Tan, P Mathijs Voorhoeve, Ernesto Guccione.
    p53-Independent regulation of p21Waf1/Cip1 expression and senescence by PRMT6.
    Nucleic Acids Research. Oct 1;40(19):9534-9542. Epub 2012 Sep 16.

  21. Bard-Chapeau EA, Jeyakani J , Kok Chung H, Muller J, Chua Belind QL, Gunaratne J, Batagov A, Jenjaroenpun P, Kuznetsov VA, Wei CL , D'Andrea RJ. D, Bourque G, Jenkins NA , Copeland NG.
    Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS in invasive tumors.
    PNAS USA, 2012; January 19, 2012, doi:10.1073/pnas.1119229109.

  22. Migliori V, Muller J, Phalke S, Low D, Bezzi M, Mok WC, Sahu SK,Gunaratne J, Capasso P, Bassi C, Cecatiello V, De Marco A, Blackstock V, Kuznetsov VA, Amati B, Mapelli M, and Guccione E.
    Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance.
    Nature Structural Biol. 2012.

  23. Wongsurawat T. Jenjaroenpun P, Kwoh CK, Vladimir Kuznetsov VA.
    Quantitative Model of R-loop Forming Structures Reveals a Novel Level of RNA-DNA Interactome Complexity.
    Nucleic Acids Research, 2011, 25 November, pp.1-15. Doi:10.1093/nar/gkr1075.

  24. Toh Swee Heng, Prathipati Philip, Motakis Efthimios, Keong Kwoh Chee, Yenamandra Surya Pavan and Kuznetsov Vladimir A.
    A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma.
    BMC Genomics, 2011 1471-2164/12/S3/S24.

  25. Batagov A, Kuznetsov VA, Kurochkin I.
    Identification of nucleotide patterns enriched in secreted RNAs as putative cis-acting elements targeting them to exosome nano-vesicles.
    BMC Genomics, 2011 12(Suppl 3):S18.

  26. Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir Kuznetsov, Lim Sai Kiang, Vivek Tanavde.
    Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-y microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha.
    BMC Genomics 2010, Vol. 11 (Suppl 1):S6, doi:10.1186/1471-2164-11-S1-S6

  27. Alexander A Kanapin, Nicola Mulder, Vladimir A Kutznetsov.
    Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity.
    BMC Genomics 2010, Vol. 11 (Suppl 1):S6, doi:10.1186/1471-2164-11-S1-S4

  28. Oleg V Grinchuk, Efthimios Motakis, Vladimir A Kutznetsov.
    Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression.
    BMC Genomics 2010, Vol. 11 (Suppl 1):S6, doi:10.1186/1471-2164-11-S1-S9

  29. Vladimir A Kuznetsov, Onkar Singh, Piroon Jenjaroenpun.
    Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.
    BMC Genomics 2010, Vol. 11 (Suppl 1):S6, doi:10.1186/1471-2164-11-S1-S12

  30. Grinchuk O, Motakis E. and Kuznetsov VA.
    Identification of complex sense-antisense gene's module on 17q11.2 associated with breast cancer aggressiveness and patient's survival.
    In: World Academy of Science,Engineering and Technology(WASET), (Editor-in-Chiff: Cemal Ardil), vol.58, pp.1046-1056. Venice, Italy; October, 2009. ISSN: 2070-3724.

  31. Piroon Jenjaroenpun, Vladimir A Kuznetsov.
    TTS Mapping : integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.
    BMC Genomics 2009, Vol. 10 (Suppl 3) :S9, doi: 10.1186/1471-2164-10-S3-S9

  32. Oleg V. Grinchuk, Piroon Jenjaroenpun, Yuriy L. Orlov, Jiangtao Zhou and Vladimir A. Kuznetsov.
    Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.
    Nucleic Acids Res. 2009, Nov 11. [Epub ahead of print]

  33. Motakis, E. and Kuznetsov, V.A. (2009).
    Genome-scale identification of survival significant genes and gene pairs, Lecture Notes in Engineering and Computer Science.
    (Proc. of World Congress on Engineering and Computer Science, San Francisco, USA, 20-22 Oct., 2009; Eds: S.I Ao, C. Douglas, W.S. Grundfelt & J. Burgstone), IA ENG , Newswood Limited, vol. I: 41-46, 2009. ISBN:978-988-17012-6-8

  34. Motakis E, Ivshina A, Kuznetsov V.
    Data-driven approach to predict survival of cancer patients.
    Engineering in Medicine and Biology Magazine, IEEE. Vol 28, Issue: 4, July-Aug 2009, Pg: 58-66, ISSN 0739-5175, doi: 10.1109/MEMB.2009.932937

  35. Vladimir Kuznetsov.
    Relative Avidity, Specificity, and Sensitivity of Transcription Factor-DNA Binding in Genome-Scale Experiments.
    Methods in Molecular Biology: Protein Networks and Pathway Analysis, 2009, Vol: 563, Pg: 15-50. doi: 10.1007/978-1-60761-175-2_2, ISBN: 978-1-60761-174-5

  36. V. A. Kuznetsov, E. Motakis, A. V. Ivshina.
    Low- and High- Aggressive Genetic Breast Cancer Subtypes and Significant Survival Gene Signatures.
    Proceeding IEEE World Congress on Computational Intelligence, 2008 , June 1-6,Hong Kong, 4150-4155

  37. Vladimir Kuznetsov, Sterling Thomas, and Danail Bonchev.
    Data-driven Networking Reveals 5-Genes Signature for Early Detection of Lung Cancer.
    Proceedings of the International Conference on BioMedical Engineering and Informatics BMEI 2008, May 27-30, Sanya, Hainan, China, Vol. 1, 413-417

  38. 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. Genome Informatics 2007. Vol.19: 83-94

  39. 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

  40. 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

  41. 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.

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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.

  49. 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

  50. 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

  51. 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.

  52. 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.

  53. 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

  54. 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.

  55. 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

  56. 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

  57. 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

  58. 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.

  59. 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

  60. 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

  61. 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

  62. 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

  63. Kuznetsov, VA.
    Hypergeometric Model of Evolution of Conserved Protein Coding Sequences in the Proteomes. 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.

  64. 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

  65. 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.

  66. 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

  67. 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:

  68. 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

  69. 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.

  70. 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

  71. Kuznetsov VA., Knott GD.
    Modeling tumor re-growth and immunotherapy.
    Math. Comput. Modeling. June 2001, 33: 1275-1287

  72. 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.

  73. 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.

  74. 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

  75. 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

  76. VA Kuznetsov, GD Knott, AV Ivshina.
    Artificial immune system based on syndromes-response approach: recognition of the patterns of immune response and prognosis of therapy outcome.
    1998, in: Systems, Man, and Cybernetics, 1998. 1998 IEEE International Conference on. Vol. 4, Pages 3804-3809,IEEE.

  77. 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

  78. 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

  79. 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

  80. Chaplain M.A.J., Kuznetsov V.A., James Z.H., Stepanova L.A.
    Spatio-temporal dynamics of the immune system response to cancer.
    (1998) In: Mathematical Models in Medicine and Health Sciences. (Eds.M.A. Horn, G. Simonett, G. Webb) , Vanderbilt University Press: Vanderbilt, Nashville, TN, pp.1-28.

  81. Borisova L.R., Andreev S.G., Kuznetsov V.A.
    Kinetics of T cell proliferation: a mathematical model and data analysis.
    (1998) Membr. Cell. Biol. 12(1), 111-119.

  82. Borisova L.R., Kuznetsov V.A.
    A mathematical model of T lymphocyte proliferation controlled by Interleukin-2 internalization.
    (1997) Membr. and Cell Biol., 14(2), 212-218.

  83. Kuznetsov V.A.
    Harpoon Model for Cell-Cell Adhesion and Recognition of Target Cells by the Natural Killer Cells.
    (1996) J. Theor. Biology, 108, 321-342.

  84. Kuznetsov V.A., Ivshina A.V., Sen'ko O.V., A.V. Kuznetsova,.
    Syndrome approach for computer recognition of fuzzy systems and its application to immunological diagnostics and prognosis of human cancer.
    (1996) Math. Comput. Modeling, 23(6), 92-112.

  85. Kuznetsov V.A.
    Basic Models of Tumor-Immune System Interactions. Identification, Analysis and Predictions.
    (1996) In: A Survey of Models for Tumor-Immune System Dynamics, (Adam J.A. and Bellomo N., Eds), Boston: Birkhauser, 237-290.

  86. Kuznetsov V. A.
    The mathematical models of nonlinear dynamics of the immune processes during tumor growth.
    (1995) In: Mathematical Population Dynamics: Analysis of Heterogeneity. v. II} (O. Arino, D. Axelrod, M. Kimmel, Eds.), Winnipeg: Wuerz Publishing Ltd., Canada, 297-321.

  87. Kuznetsov V.A., Makalkin I.A., Taylor M. A. Perelson A.S.
    Nonlinear dynamics of immunogenic tumors: Parameter estimation and global bifurcations analysis.
    (1994) Bull. Math. Biology, 56(2), 295-321.

  88. VA Kuznetsov, VP Zhivoglyadov, LA Stepanova.
    Kinetic approach and estimation of the parameters of cellular interaction between the immunity system and a tumor.
    Archivum immunologiae et therapiae experimentalis (Warsz). 1993;41(1):21-31.

  89. VA Kuznetsov.
    Dynamics of Immune Processes During Tumor Growth.
    Nauka Publishing House, Moscow (1992) : 340 pages (in Russian).

  90. Alekseeva EI, Kirzhner VM, Kuznetsov VA.
    Structures and Collective Behaviour.
    Znanie Publishing House (Ser: Math. and Cybernetics.N3,1991), Moscow (1991): 48 pages (in Russian).


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