ivan-v-ivanov
Ivan V Ivanov, PhD
Clinical Associate Professor of Veterinary Physiology and Pharmacology

Texas A& M University
Texas, USA
E-mail: iivanov@cvm.tamu.edu

Education

2003-2005 Postdoctoral, Bioinformatics Texas A&M University, USA
2000-2003 Postdoctoral, Mathematics Texas A&M University, USA
1999-2000 Postdoctoral, Mathematics Syracuse University, USA
1999 Ph.D. in Mathematics University of South Florida, USA
1987 MS in Mathematics Sofia University, Bulgaria

Biography

Ivan Ivanov received his M.S. (Mathematics) from the Sofia University “St. Kliment Ohridski”, Bulgaria in 1987 and Ph.D. (Mathematics) from the University of South Florida in 1999. He was a Research Professor at the Mathematics Department of Syracuse University (1999–2000) and Texas A&M University (TAMU) (2000–2003). Dr. Ivanov was a postdoctoral trainee in the Training Program in Bioinformatics, TAMU (2003–2005), and joined the Department of Veterinary Physiology and Pharmacology as a Clinical Assistant Professor in 2005. Dr. Ivanov actively mentors and trains students of all levels. His research focuses in key areas of computational and systems biology and has resulted in over 80 research papers published in peer reviewed journals, and several successful grant applications. He serves as the Director of the Quantitative Biology Core of the Center for Translational and Environmental Health Research (CTEHR). Dr. Ivanov is a member of the Intercollegiate Faculty of Toxicology, the Interdisciplinary Faculty of the Professional Program of Biotechnology and the Institute for Applied Mathematics and Computational Science, TAMU, and an adjunct professor in both ECE and Statistics departments, TAMU.


Research Interest

  • Genomic Signal Processing and Mathematical Modeling of Gene Regulatory Networks
  • Responses of Biological Systems to Environmental and Nutritional Exposure: Predictive Models
  • Compression and Control of Gene Regulatory Networks
  • Integrative Analyses of Multimodal High-Throughput Omics Data

Scientific Activities

Honors & Awards
2014-current Adjunct Faculty, Statistics Department, Texas A&M University, USA
2014-current Director of the Quantitative Biology Core, Center for Translational Environmental Health Research(CTEHR), Texas A&M University, USA
2012-current Member of the Intercollegiate Faculty of the Professional Program of Biotechnology, Texas A&M University, USA
2010-current Application Researcher, Institute of Applied Mathematics and Computational Science, Texas A&M University, USA
2009-current Member of the Intercollegiate Faculty of Toxicology, Texas A&M University, USA
2013-current Clinical Associate Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, USA
2006-current Adjunct Faculty, Department of Electrical and Computer Engineering, Texas A&M University, USA
2005-2013 Clinical Assistant Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, USA
2003-2005 NCI Postdoctoral Trainee, Statistics Department and Department of Electrical Engineering, Texas A&M University, USA
2000-2003 Visiting Assistant Professor, Department of Mathematics, Texas A&M University, USA
1999-2000 Teaching Research Associate, Department of Mathematics, Syracuse University, USA

Publications

  1. R. Zoh, B. Mallick, I. Ivanov, V. Baladandandayuthapani, G. Manyan, R.S. Chapkin, J.W. Lampe, and R.J. Carroll, PCAN: Probabilistic Correlation Analysis of Two Non-normal Data Sets, Biom. Doi:10.1111/biom.12516, 2016.
  2. G. Noratto, B.P. Chew, I. Ivanov, Red raspberry decreases heart biomarkers of cardiac remodeling associated with oxidative and inflammatory stress in obese diabetic db/db mice, Food & Nutrition 7(12), 4944-4955, 2016.
  3. M. Shah, E. Kim, L.A Davidson, J.M Knight, R. Zoh, J. Goldsby, E. Callaway, B. Zhou, I. Ivanov, R.S. Chapkin, Data describing the effects of dietary bioactive agents on colonic stem cell microRNA and mRNA expression. Data in Brief 6, 398-404, 2016.
  4. H. Kim, N. Banerjee, I. Ivanov, C.M. Pfent, K.R. Prudhomme, W.H. Bisson, R.H. Dashwood, S.T. Talcott, S.U. Mertens‐Talcott, Comparison of anti‐inflammatory mechanisms of mango (Mangifera Indica L.) and pomegranate (Punica Granatum L.) in a preclinical model of colitis. Molecular Nutrition & Food Research 3, 2016.
  5. M. Shah, E. Kim, L.A. Davidson, J.M. Knight, R. Zoh, J. Goldsby, E. Callaway, B. Zhou, I. Ivanov, R.S. Chapkin, Comparative effects of diet and carcinogen on microRNA expression in the stem cell niche of the mouse colonic crypt. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1862(1), 121-134, 2016.
  6. J.F. Garcia-Mazcorro, I. Ivanov, D.A. Mills, and G. Noratto, Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice. Peer J., 2016, 15;4:e1702. doi: 10.7717/peerj.1702. eCollection 2016, PMID:26925326.
  7. J.M. Knight, I. Ivanov, K. Triff, R.S. Chapkin and E.R. Dougherty, Detecting multivariate gene interactions in RNA-Seq data using optimal Bayesian classification, (IEEE)/ACM Transactions on Computational Biology and Bioinformatics. 2015, PMID:26441451.
  8. K. Triff, J.M. Knight, I. Ivanov, B. Zhou, R.S. Chapkin, Epigenetic Mechanisms by Which Chemoprotective Natural Compounds Promote RXR/FXR Signaling and Reduce Colon Cancer Progression, The FASEB Journal 29 (1 Supplement), 394.3, 2015.
  9. C. Martin, J. Knight, L. Davidson, D. Herman, J. Goldsby, I. Ivanov, S.M. Donovan, R.S. Chapkin, T7. 4. Noninvasive Nutrigenomic Strategies to Define Intestinal Host Responses in the Preterm Infant, Journal of Human Lactation 31(3) 549, 2015.
  10. S.M. Donovan, M. Monaco, L. Davidson, I. Ivanov, R.S. Chapkin, T5. 4. Modulation of the Intestinal Transcriptome by Human Milk: Data from Sloughed Intestinal Cells, Journal of Human Lactation 31(3) 543-544, 2015.
  11. G. Noratto, E. García-Pérez, I. Ivanov, D. Mills, Whole-Wheat Supplemented Diet Changed Fecal Microbial Ecology of Obese Diabetic Mice. The FASEB Journal 29 (1 Supplement), 385.5, 2015.
  12. M. Wang, M. Li, S. Wu, C.B. Lebrilla, R.S. Chapkin, I. Ivanov, S.M. Donovan, Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed. Journal of pediatric gastroenterology and nutrition 60 (6), 825-833, 2015.
  13. J.M. Knight, I. Ivanov, E.R. Dougherty, MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. BMC bioinformatics 15 (1), 401, 2014. - one of the highly accessed papers in the journal, http://www.biomedcentral.com/1471-2105/15/401?utm_source=twitterfeed&utm_medium=twitter .
  14. J.L. Brannan, P.K. Riggs, P.U. Olafson, I. Ivanov, P.J. Holman, Expression of bovine genes associated with local and systemic immune response to infestation with the Lone Star tick, Amblyomma americanum. Ticks and tick-borne diseases 5 (6), 676-688, 2014.
  15. H. Kim, N. Banerjee, I. Ivanov, S. Talcott, S. Mertens-Talcott, Comparison of anti-inflammatory mechanisms of mango (Mangifera indica L.) and pomegranate (Punica granatum L.) in DSS-induced colitis in rats (372.8). The FASEB Journal 28 (1 Supplement), 372.8, 2014.
  16. J.M. Knight, L.A. Davidson, D. Herman, C.R. Martin, J.S. Goldsby, I.V. Ivanov, S.M. Donovan and R.S. Chapkin, Non-invasive analysis of intestinal development in premature and full term infants using RNA-Sequencing. Scientific Reports Nature 4:5453; DOI:10.1038/srep05453, 2014. PMID:24965658.
  17. S.M. Donovan, M. Wang, M.H. Monaco, C.R. Martin, L.A. Davidson, I. Ivanov, R.S. Chapkin, Noninvasive molecular fingerprinting of host–microbiome interactions in neonates, FEBS Lett., http://dx.doi.org/10.1016/j.febslet.2014.07.008. , 2014.
  18. C.M. McQueen, R. Doan, S.V. Dindot, J.R. Bourquin, Z.Z. Zlatev, M.K. Chaffin, G.P. Blodgett, I. Ivanov, N.D. Cohen, Identification of Genomic Loci Associated with Rhodococcus equi Susceptibility in Foals, PLoS ONE 9(6): e98710. doi:10.1371/journal.pone.0051907, 2014.
  19. K. Triff, K. Konganti, S. Gaddis, B. Zhou, I. Ivanov, and R.S. Chapkin, Genome wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression, Physiological Genomics, Vol. no. , DOI: 10.1152/physiolgenomics.00136.2013.
  20. C. Sayes, P. Smith, and I. Ivanov, A framework for grouping nanoparticles based on their measurable characteristics, International Journal of Nanomedicine, 8:1-12, 2013.
  21. N. Ghaffari, M. Yousefi, C. Jhonson, I. Ivanov, and E.R. Dougherty, Modeling of Next Generation Sequencing Sample Processing Pipeline for the Purposes of Classification, BMC Bioinformatics, 14:307, 2013, PMID: 24118904.
  22. P. Kachroo, I. Ivanov, A. Seabury, M. Liu, B. Chowdhary, and N. Cohen, Age-Related Changes Following in vitro Stimulation with Rhodococcus equi of Peripheral Blood Leukocytes from Neonatal Foals, PLoS One, 2013.
  23. E. Archibong, L. Wang, I. Ivanov, A. Lita, K. Redda, and N. Mateeva, Investigation of the Binding of Dioxin Selective Pentapeptides to a Polyaniline Matrix, Synthetic Metals, 162(13-14):1255-1263, 2012.
  24. J.S. Suchodolski, M.E. Markel, J.F. Garcia-Mazcorro, S. Unterer, R.M. Heilmann, S.E. Dowd, P. Kachroo, I. Ivanov, Y. Minamoto, E.M. Dillman, J.M. Steiner, A.K. Cook, L. Toresson, The Fecal Microbiome in Dogs with Acute Diarrhea and Idiopathic Inflammatory Bowel Disease. PLoS ONE 7(12): e51907. doi:10.1371/journal.pone.0051907, 2012.
  25. S. Schwartz, I. Friedberg, I. Ivanov, L.A. Davidson, J.S. Goldsby, D.B. Dahl, D. Herman, M. Wang, S.M. Donovan, and R. Chapkin, A Metagenomic Study of Diet-Dependent Interaction Between Gut Microflora and Host in Infants Reveals Differences in Developmental and Immune Responses, Genome Biology, 13(4):R32, 2012, PMID: 22546241 . – one of the most accessed papers in the journal: http://genomebiology.com/2012/13/4/r32/about .
  26. J. Qin, X. Liu, B. Laffin, X. Chen, Grace Choy, C.R. Jeter, T. Calhoun-Davis, H. Li, G.S. Palapattu, S. Pang, K. Lin, J. Huang, I. Ivanov, W. Li, M.V. Suraneni, and D.G. Tang, The PSA–/lo Prostate Cancer Cell Population Harbors Self-Renewing Long-Term Tumor-Propagating Cells that Resist Castration, Cell Stem Cell, 10(5):556-569, 2012, PMID: 22560078.
  27. C. Zhao, J. Hua, M.L. Bittner, I. Ivanov, and E.R. Dougherty, Identifying mechanistic similarities in drug responses, Bioinformatics, 28(14):1902-10, 2012, PMID:22592382.
  28. C. Zhao, I. Ivanov, M.L. Bittner, and E.R. Dougherty, Pathway Regulatory Analysis in the Context of Bayesian Networks Using the Coefficient of Determination, Journal of Biological Systems, 19(4):651-682, 2011.
  29. A.A. Romoser, P.L. Chen, J.M. Berg, C. Seabury, I. Ivanov, M.F. Criscitiello, and C.M. Sayes, Quantum dots trigger modulation of the NFkappaB pathway in human skin cells, Molecular Immunology, 48(12-13):1349-59, 2011, PMID: 21481475 .
  30. M. Shah, S. Schwartz, C. Zhao, L.A. Davidson, B. Zhou, J.R. Lupton, I. Ivanov, and R. Chapkin, Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: Effect of a chemo-protective diet, Physiol Genomics, 43(10): 640-654, 2011, PMID: 21406606.
  31. P. Kachroo, I. Ivanov, L.A. Davidson, B.P. Chowdhary, J.R. Lupton, and R.S. Chapkin, Classification of diet-modulated gene signatures at the colon cancer initiation and progression stages, Digestive Diseases and Sciences, 56:2595-2604, 2011, PMCID: PMC3139012.
  32. Q. Jia, I. Ivanov, Z. Z. Zlatev, R.C. Alaniz, B.R. Weeks, E.S. Callaway, J.S. Goldsby, L.A. Davidson, Y-Yi Fan, L. Zhou, J. R. Lupton, D.N. McMurray, and R.S. Chapkin, Fish oil and curcumin combination modulates colonic cytokinetics and gene expression in DSS-treated mice, British Journal of Nutrition, 106:519-529, 2011, PMID: 21401974.
  33. C.M. Sayes and I. Ivanov, Comparative Study of Predictive Computational Models for Nanoparticle-Induced Cytotoxicity, Risk Analysis, 30(11):1723-1734, 2010, PMID: 20561263.
  34. X. Qian, N. Ghaffari, I. Ivanov, and E.R. Dougherty, State Reduction for Network Intervention in Probabilistic Boolean Networks, Bioinformatics, 26(24):3098-3104, 2010.
  35. I. Ivanov, P. Simeonov, N. Ghaffari, X. Qian, and E.R. Dougherty, Selection Policy-Induced Reduction Mappings for Boolean Networks, IEEE Transactions on Signal Processing, 58(9): 4871-4882, 2010.
  36. R.S. Chapkin, C. Zhao, I. Ivanov, L. Davidson, J. Goldsby, J.R. Lupton, R.A. Mathai, M. Siegel, D. Rai, M. Russell, S.M. Donovan, and E.R. Dougherty, Noninvasive stool-based detection of infant gastrointestinal development using gene expression profiles from exfoliated epithelial cells, American Journal of Physiology, Gastrointestinal and Liver Physiology, 298(5):G582-G589, 2010, PMCID: 20203060.
  37. L. Davidson, N. Wang, M.Shah, J.R.Lupton, I. Ivanov, and R. S.Chapkin, n-3 Polyunsaturated fatty acids modulate carcinogen-directed non-coding microRNA signatures in rat colon, Carcinogenesis, 30(12):2077-2084, 2009, PMCID: 2792315.
  38. L. Davidson, N. Wang, I. Ivanov, J. Goldsby, J.R. Lupton, and R.S. Chapkin, Identification of Actively Translated mRNA Transcripts in a Rat Model of Early Stage Colon Carcinogenesis, Cancer Prevention Research, 2(11):984-994, 2009, PMCID: PMC2783859.
  39. X. Qian, I. Ivanov, and E.R. Dougherty, Intervention in Gene Regulatory Networks via Greedy Control Policies Based on Long-Run Behavior, BMC Systems Biology, pp. 3-61, 2009.
  40. C. Zhao, I. Ivanov, E.R. Dougherty, T.J. Hartman, E. Lanza, G. Bobe, N.H. Colburn, J.R. Lupton, L.A. Davidson, and R.S. Chapkin, Noninvasive Detection of Candidate Molecular Biomarkers in Subjects with a History of Insulin Resistance and Colorectal Adenomas, Cancer Prevention Research, 2(6):590-597, 2009, PMCID: PMC2745241.
  41. Ivanov, Boolean model of genomic regulatory networks: reduction mappings, inference, and external control, Current Genomics, 10(6):375-87, 2009.
  42. H. Hosako, G.S. Martin, M. Barrier, A.Y. Chen, I. Ivanov, and P.E. Mirkes, Gene and miRNA Expression in p53-Deficient Day 8.5 Mouse Embryos, Birth Defects Res A Clin Mol Teratol., 85(6):546-555, 2009.
  43. F. Wu, I. Ivanov, R. Xu, and S. Safe, Role of Sp Transcription Factors in Hormone- Dependent Modulation of Genes in MCF-7 Breast Cancer Cells: Microarray and RNA interference studies, Journal of Molecular Endocrinology, 42(1):19-33. 2009.
  44. G. Vahedi, I. Ivanov, and E.R. Dougherty, Inference of Boolean Networks under Constraint on Bidirectional Gene Relationships, IET Systems Biology Journal, 3(3):191-202, 2009.
  45. I. Ivanov, R. Pal, and E.R. Dougherty, Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks, IEEE Transactions on Signal Processing, 55(5):2310-2322, 2007.
  46. I. Ivanov, and E.R. Dougherty, Modeling Genetic Regulatory Networks: Continuous or Discrete?, Journal of Biological Systems, 14(2):219-229, 2006.
  47. R. Pal, I. Ivanov, A. Data, and E.R. Dougherty, Generating Boolean Networks With a Prescribed Attractor Structure, Bioinformatics, 21(21):4021-4025, 2005.
  48. X. Zhou, X. Wang, R. Pal, I. Ivanov, and E.R. Dougherty, A Bayesian Connectivity-based Approach to Constructing Probabilistic Gene Regulatory Networks, Bioinformatics, 20(17):2918-2927, 2004.
  49. I. Ivanov and E.R. Dougherty, Reduction Mappings Between Probabilistic Boolean Networks, Journal of Applied Signal Processing, 4(1):125-131, 2004.
  50. I. Ivanov, B. Shekhtman, Linear Discrete Operators on the Disk Algebra, Proc. Amer. Math. Soc., 129(7):1987-1993, 2001.

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