Department of Veterinary Physiology and Pharmacology

Texas A&M University Veterinary Medicine & Biomedical Sciences

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Ivan Ivanov

Clinical Associate Professor

Phone: (979) 739-4328
Email: [email protected]

Research and Scholarly Interests

Predictive computational modeling of complex systems, e.g. gene regulatory networks, for the purposes of intervention and control. High throughput omics data processing and integration. Genomic Signal Processing. Bioinformatics.

About Me

Focus Areas

Research

Teaching

Trainees

Publications

  • MS in Mathematics, Sofia University, Bulgaria, 1987
  • PhD in Mathematics, University of South Florida, USA, 1999
  • Postdoctoral, Mathematics, Syracuse University, USA, 1999-2000
  • Postdoctoral, Mathematics, Texas A&M University, USA, 2000-2003
  • Postdoctoral, Bioinformatics, Texas A&M University, 2003-2005
  • Genomic Signal Processing
  • 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

My training in mathematics, statistics, and bioinformatics provides the skill set needed to analyze complex high dimensional and multimodal datasets. I have made contributions in several key areas of systems and computational biology with a focus specifically on mathematical modeling of gene regulatory networks and more generally, on analyzing the responses of biological systems to various types of treatments. One of the major challenges in the applications of network models of complex systems is the computational complexity of the model. Even for the simplest Boolean settings the state space of the model grows exponentially with the number of participating nodes. Therefore, the issue of model compression that preserves its important properties, e.g. controllability, becomes of prime importance. My students, collaborators, and I have been working on problems related to these issues for the past 14 years and have achieved several key results. Since my time as a Director of the Quantitative Biology Core of the NIEHS-funded Center for Translational Environmental Health Research (CTEHR) (2014 to 2018) I have increasingly become involved in high-throughput heterogeneous omics data interpretation, analysis, and integration.

Ivan Ivanov is not accepting trainees at this time.

    The full list of my publications can be found on Google Scholar.

    Select publications:

      • Hala, J.A. Cullen, B. Hernout, I. Ivanov, In silico predicted transcriptional regulatory control of steroidogenesis in spawning female fathead minnows ( Pimephales promelas ), Journal of Theoretical Biology 455, 179-190, 2018.
      • E. Kim, I. Ivanov, E.R Dougherty, Quantifying the notions of canalizing and master genes in a gene regulatory network-a Boolean network modeling perspective, Bioinformatics, bty665, 2018, https://doi.org/10.1093/bioinformatics/bty665
      •  M. Whitfield-Cargile, N.D. Cohen, K. He, I. Ivanov, J.S. Goldsby, A. Chamoun-Emanuelli, B.R. Weeks, L.A. Davidson, R.S. Chapkin, The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy, Scientific Reports 7(1), 14687, 2017, PMCID: PMC5665873.
      • E. Kim, I. Ivanov, J. Hua, J.W. Lampe, MAJ Hullar, R.S. Chapkin, E.R. Dougherty, The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data, 16, 1-15, 2017, PMCID: PMC5470876.
      • Mason, MPKJ Engelen, I. Ivanov, G.M. Toffolo, NEP Deutz, A four-compartment compartmental model to assess net whole body protein breakdown using a pulse of phenylalanine and tyrosine stable isotopes in humans, American Journal of Physiology-Endocrinology and Metabolism 313(1), E63-E74, 2017, PMID: 28270442.
      • M. Knight, E. Kim, I.Ivanov, L.A. Davidson, J.S. Goldsby, MAJ Hullar, T.W. Randolph, A.M. Kaz, L.Levy, J.W. Lampe, R.S. Chapkin, Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue, Physiological Genomics 48(9), 651-659, 2016, PMCID: PMC5111881.
      • 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, Biometrics 72 (4), 1358-1368, Doi:10.1111/biom.12516, 2016.
      • 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.
      • 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/14712105/15/401?utm_source=twitterfeed&utm_medium=twitter.
      • J.M. Knight, L.A. Davidson, D. Herman, C.R. Martin, J.S. Goldsby, I. 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.
      • 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.
      • 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
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • I. Ivanov, Boolean model of genomic regulatory networks: reduction mappings, inference, and external control, Current Genomics, 10(6):375-87, 2009.
      • 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.
      • I. Ivanov, and E.R. Dougherty, Modeling Genetic Regulatory Networks: Continuous or Discrete?, Journal of Biological Systems, 14(2):219-229, 2006.
      • R. Pal, I. Ivanov, A. Data, and E.R. Dougherty, Generating Boolean Networks With a Prescribed Attractor Structure, Bioinformatics, 21(21):4021-4025, 2005.
      • 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.
      • I. Ivanov and E.R. Dougherty, Reduction Mappings Between Probabilistic Boolean Networks, Journal of Applied Signal Processing, 4(1):125-131, 2004.
      • I. Ivanov, B. Shekhtman, Linear Discrete Operators on the Disk Algebra, Proc. Amer. Math. Soc., 129(7):1987-1993, 2001.
      • I. Ivanov, R. Kovacheva, and J. Gilewicz, Rational Functions of Best Uniform Approximation and Holomorphic Continuation of Functions, Approx. Theory Appl. (N.S.), 12(1):1-9, 1996.
      • I. Ivanov, Best Rational Approximations and Meromorphic Continuation of a Function, (in Russian), Serdica, 16(1):35-41, 1990.