Stefan Bekiranov


  • BS, University of California, Los Angeles
  • PhD, University of California, Santa Barbara
  • Postdoc, University of Maryland
  • Postdoc, The Rockefeller University

Primary Appointment

  • Associate Professor, Biochemistry and Molecular Genetics


Research Interest(s)

Physical Modeling of Microarray Hybridization; Analysis of Genomic Tiling Array Data; Bioinformatics; Computational Biology; Regulatory Networks

Research Description

My laboratory develops and applies computational statistics methods to functional genomic data with a focus on epigenetic data. Epigenetics is the study of heritable phenotypic traits not coded in the primary DNA sequence, which can be modified by environmental factors and comprise a complex regulatory network that controls a number of processes on DNA including transcription, replication and repair. A central element of this control network is chemical groups (e.g., acetyl or methyl) that are added or removed from DNA and histones, which package DNA in a cell's nucleus. Control of processes such as transcription is achieved by making DNA sequences available or unavailable for factors including General Transcription Factors and Pol II that initiate transcription as well as recruitment of factors that facilitate each stage of transcription (i.e., promotion, elongation, etc.). Similarly, accessibility of DNA regulates the binding of the Origin Recognition Complex and subsequent initiation of DNA replication. Epigenetic factors have been shown to play a fundamental role in regulating cell differentiation, and the dysregulation of epigenetic processes have been implicated in a number of diseases including cancer, diabetes, and neurological disorders.

We are interested in characterizing the complex epigenetic regulatory network of histone modifications and DNA methylation, which exhibits extensive cross-talk. We apply machine-learning methods including Multivariate Regression Splines (MARS) and Bayesian Networks (BN) to epigenomic data in order to uncover this network and understand how it regulates transcription and DNA replication. We analyze both publicly available data sets (e.g., epigenomic data generated by K. Zhao's lab and the ENCODE, modENCODE and Epigenomics Mapping Consortia) as well as data generated by colleagues here at UVa. In our collaborations, we are studying (1) preinitiation complex (PIC) and transcription factor dynamics and their role in regulation of transcription level and precision (2) epigenomic regulation of the epithelial to mesenchymal transition -- a model of how cells are reprogrammed during metastasis (3) origins of DNA replication in the human genome and the epigenetic factors that drive them (4) the role of histone deacetylaces including Sir2 in aging and (5) the impact of chemicals in our environment (e.g., Bisphenol A) on our epigenome and subsequent phenotypic outcomes. An exciting aspect of the collaborative environment at UVa is that we are able to experimentally test our predicted epigenetic regulatory network models at the biochemical and phenotypic level.

Selected Publications

  • Chen X, Poorey K, Carver M, Müller U, Bekiranov S, Auble D, Brow D. Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS genetics. 2017;13(6): e1006863. PMID: 28665995 | PMCID: PMC5513554
  • Zaidi H, Auble D, Bekiranov S. RNA synthesis is associated with multiple TBP-chromatin binding events. Scientific reports. 2017;7 39631. PMID: 28051102 | PMCID: PMC5209698
  • Zaidi H, Hoffman E, Shetty S, Bekiranov S, Auble D. Second-generation method for analysis of chromatin binding with formaldehyde crosslinking kinetics. The Journal of biological chemistry. 2017. PMID: 28972159
  • Anaya J, Reon B, Chen W, Bekiranov S, Dutta A. A pan-cancer analysis of prognostic genes. PeerJ. 2016;3 e1499. PMID: 27047702 | PMCID: PMC4815555
  • Cherepanova O, Gomez D, Shankman L, Swiatlowska P, Williams J, Sarmento O, Alencar G, Hess D, Bevard M, Greene E, Murgai M, Turner S, Geng Y, Bekiranov S, Connelly J, Tomilin A, Owens G. Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. Nature medicine. 2016;22(6): 657-65. PMID: 27183216 | PMCID: PMC4899256
  • True J, Muldoon J, Carver M, Poorey K, Shetty S, Bekiranov S, Auble D. The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. The Journal of biological chemistry. 2016;291(29): 15307-19. PMID: 27226635 | PMCID: PMC4946942
  • Capaldo B, Roller D, Axelrod M, Koeppel A, Petricoin E, Slingluff C, Weber M, Mackey A, Gioeli D, Bekiranov S. Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma. PloS one. 2015;10(9): e0138210. PMID: 26405815 | PMCID: PMC4583389
  • Cieślik M, Bekiranov S. Genome-wide predictors of NF-κB recruitment and transcriptional activity. BioData mining. 2015;8 37. PMID: 26617673 | PMCID: PMC4661973
  • Roller D, Capaldo B, Bekiranov S, Mackey A, Conaway M, Petricoin E, Gioeli D, Weber M. Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas. Oncotarget. 2015;7(3): 2734-53. PMID: 26673621 | PMCID: PMC4823068
  • Wierman M, Matecic M, Valsakumar V, Li M, Smith D, Bekiranov S, Smith J. Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations. Aging. 2015;7(3): 177-94. PMID: 25769345 | PMCID: PMC4394729
  • Cohen J, Tewalt E, Rouhani S, Buonomo E, Bruce A, Xu X, Bekiranov S, Fu Y, Engelhard V. Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment. PloS one. 2014;9(2): e87740. PMID: 24503860 | PMCID: PMC3913631
  • Viswanathan R, Hoffman E, Shetty S, Bekiranov S, Auble D. Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method. Methods (San Diego, Calif.). 2014;70(2): 97-107. PMID: 25448301 | PMCID: PMC4267959
  • Poorey K, Viswanathan R, Carver M, Karpova T, Cirimotich S, McNally J, Bekiranov S, Auble D. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science (New York, N.Y.). 2013;342(6156): 369-72. PMID: 24091704 | PMCID: PMC3997053
  • McCullough S, Xu X, Dent S, Bekiranov S, Roeder R, Grant P. Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7 (SCA7) astrocytes. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(52): 21319-24. PMID: 23236151 | PMCID: PMC3535616
  • Hoang S, Xu X, Bekiranov S. Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications. BMC research notes. 2011;4 288. PMID: 21834981 | PMCID: PMC3170335
  • Smith S, Havaleshko D, Moon K, Baras A, Lee J, Bekiranov S, Burke D, Theodorescu D. Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agents. Neoplasia (New York, N.Y.). 2011;13(1): 72-80. PMID: 21253455 | PMCID: PMC3023847
  • Matecic M, Smith D, Pan X, Maqani N, Bekiranov S, Boeke J, Smith J. A microarray-based genetic screen for yeast chronological aging factors. PLoS genetics. 2010;6(4): e1000921. PMID: 20421943 | PMCID: PMC2858703
  • Xu X, Hoang S, Mayo M, Bekiranov S. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. BMC bioinformatics. 2010;11 396. PMID: 20653935 | PMCID: PMC2928206
  • Kim Y, Bekiranov S, Lee J, Park T. Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. Bioinformatics (Oxford, England). 2009;25(19): 2486-91. PMID: 19667080 | PMCID: PMC2800349
  • Wade S, Poorey K, Bekiranov S, Auble D. The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression. The EMBO journal. 2009;28(19): 2919-31. PMID: 19680226 | PMCID: PMC2760106
  • Park T, Kim Y, Bekiranov S, Lee J. Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays. Nucleic acids research. 2007;35(9): e69. PMID: 17430969 | PMCID: PMC1888820