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  Research Group of Ivan Ovcharenko






Group Members


 



 
Di Huang
Staff Scientist
April 2015 - present
(Previously: Research Fellow, June 2010 - April 2015)

Mapping biological pathways in tissue-specific enhancers
My project is aimed at decoding regulatory pathways underlying the development of specific tissues. An enhancer set driving the development of a specific tissue (e.g., heart) is heterogeneous, regulating different pathways and controlling the development of different sub-tissues. We are developing a method to map enhancers into different pathways, and predict the pathway-specific activity of enhancers. This method will provide novel analytical tools for an in detail characterization of enhancers identified using next-generation sequencing technologies.

    D. Huang, H. Petrykowska, B. Miller, L. Elnitski and I. Ovcharenko
    Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression.
    Genome Research, 29(4):657-667 (2019) PDF

    D. Huang and I. Ovcharenko
    Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia.
    BMC Genomics, 18(1):236-245 (2017)

    Huang D and Ovcharenko I
    Identifying causal regulatory SNPs in ChIP-seq enhancers
    Nucleic Acids Research, 43(1):225-36 (2015) PDF

    Busser BW, Haimovich J, Huang D, Ovcharenko I, Michelson AM
    Integrative analysis of the zinc finger ncer modeling uncovers transcriptional signatures of individual cardiac cell states...
    Nucleic Acids Research, 43(3):1726-39 (2015)

    Busser BW*, Huang D*, Rogacki KR*, ... Bulyk ML, Ovcharenko I, Michelson AM
    Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network
    PNAS, 109(50):20768-73 (2013) (* - co-first authors) PDF

    Ahmad SM*, Busser BW*, Huang D*, ... Bulyk ML, Ovcharenko I, Michelson AM
    Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating
    progenitor cell division and cell fate specification
    Development, 141(4):878-88 (2014) (* - co-first authors) PDF

    Huang D and Ovcharenko I
    Genome-Wide Analysis of Functional and Evolutional Features of Tele-Enhancers
    G3: Genes, Genomes, Genetics, 4(4):579-93 (2014) PDF


 



 
Shan Li
Postdoctoral Fellow
April 2013 - present

Killer Mutations of Transcription Factor Binding Sites
My current project focuses on studying the underlying mechanism by which genetic variants affect transcriptional regulation and phenotype divergence. We identified the "killer mutations" (KMs) in human regulatory elements that have disruptive effects on transcription factor binding, and are currently studying the interplay between disease traits and KMs. We are also investigating how "killer mutations" alter transcription factor binding and gene expression during the course of evolution and the mode in which they co-evolve with each other.

    S. Li, E. Kvon, A. Visel, L. Pennacchio and I. Ovcharenko
    Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.
    Genome Biology, 20(1):140-149 (2019) PDF

    R. Vera Alvarez, S. Li, D. Landsman and I. Ovcharenko
    SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genom.
    Bioinformatics, 34(2):289-291 (2017)

    S. Li, R. Vera Alvarez, R. Sharan, D. Landsman and I. Ovcharenko
    Quantifying deleterious effects of regulatory variants.
    Nucleic Acids Research, 45(5):2307-2317 (2017)

    S. Li and I. Ovcharenko
    Human Enhancers Are Fragile and Prone to Deactivating Mutations.
    Molecular Biology and Evolution, 32(8):2161-2180 (2015) PDF

 



 
Wei Song
Postdoctoral Fellow
January 2017 - present

Heterogeneity of tissue-specific enhancers.
My research interests focus on the heterogeneity of tissue-specific enhancers in mammalian genome, including identification of the primary enhancer and hierarchical structure in a multi-element regulatory program of the target gene, based on either the sequence signatures or the 3D chromatin contacts of the enhancer-gene networks. My current project includes clustering enhancers with a deep learning model to capture the sequence features for each class of enhancers, and applying this model to predicting novel active enhancers across the whole human genome.

    W. Song, R.Sharan and I. Ovcharenko
    The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.
    Genome Biology, 20(1):197-207 (2019) PDF

    W. Song and I. Ovcharenko
    Dichotomy in redundant enhancers points to presence of initiators of gene regulation.
    BMC Genomics, 19(1):947-956 (2018)

 



 
Sanjarbek Hudaiberdiev
Postdoctoral Fellow
March 2018 - present

Development of Deep Learning methods for enhancer identification.
My research interests fall into the broad categories of computational genomics and applied Deep Learning. My main project involves the application of Deep Learning methods to identification and analysis of enhancers in the human genome. To that end, we developed a network comprising of Convolutional Layers and Long-Short Term Memory (LSTM) layers to study and detect the regions within enhancers that demonstrate an increased level of vulnerability to mutations. In addition, we are interested in broadening the scope of the deep-learning-based analysis to study complex diseases, with an aim of developing a tool that will help to identify causal SNPs from the GWAS studies where the data may be too noisy owing to LD blocks.




Alumni


  • Mario Flores, Postdoctoral Fellow from January 2016 to November 2019. Currently a Staff Scientist at St. Jude Children's Research Hospital

        M. Flores and I. Ovcharenko
        Enhancer reprogramming in mammalian genomes.
        BMC Bioinformatics, 19(1):316-324 (2018)

  • Justin Malin, Postdoctoral Fellow from January 2016 to September 2018. Currently a Postdoctoral Fellow at NCI.

  • Irina Hashmi, Postdoctoral Fellow from November 2015 to July 2016. Currently an Assistant Professor at George Mason University.

  • Konnor La, IRTA Postbaccalaureate Fellow from October 2013 to July 2015. Currently a Graduate Student at Cornell University.

  • Alexandra G. Cauer, Postbaccalaureate Fellow from June 2014 to July 2015. Currently a Graduate Student at the University of Washington.

  • Yupeng Wang, Postdoctoral Fellow from May 2013 to March 2015. Currently a Senior Bioinformatics Scientist at Inova Fairfax Hospital.

  • Parsa Hosseini, Visiting Graduate Student from July 2012 to November 2013. IRTA Postdoctoral Fellow from November 2013 to January 2015. Currently a Software Engineer at General Dynamics.

  • Radhouane Aniba, Postdoctoral Fellow from February 2013 to December 2013. Currently a Bioinformatician at the BC Cancer Agency, Canada.

  • Leila Taher, Postdoctoral Fellow from January 2008 to August 2012. Currently a Group Leader at the University of Rostock.

        L. Taher, L. Narlikar, I. Ovcharenko
        Identification and Computational Analysis of Gene Regulatory Elements
        Cold Spring Harbor Protocols, 2015(1):24-51 (2015) PDF

        Visel A, Taher L, ... Ovcharenko I, Pennacchio LA, Rubenstein JL (25 authors)
        A High-Resolution Enhancer Atlas of the Developing Telencephalon
        Cell, (2013) PDF

        G. Burzynski*, X. Reed*, L. Taher*, Z.E. Stine, T. Matsui, I. Ovcharenko, A.S. McCallion
        Systematic elucidation and in vivo validation of the sequence basis of hindbrain transcriptional control
        Genome Research, 22(11):2278-89 (2012) (* - co-first authors) PDF

        BW. Busser*, L. Taher*, Y. Kim, T. Tansey, MJ. Bloom, I. Ovcharenko, AM. Michelson
        A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis
        PLoS Genetics, 8(3):e1002531 (2012) (* - co-first authors) PDF

        L. Taher, L. Narlikar, I. Ovcharenko
        CLARE: Cracking the LAnguage of Regulatory Elements
        Bioinformatics, 28(4):581-3 (2012) PDF

        L. Taher, D.M. McGaughey, S. Maragh, I. Aneas, S.L. Bessling, W. Miller, M.A. Nobrega, A.S. McCallion, I. Ovcharenko
        Genome-wide identification of conserved regulatory function in diverged sequences
        Genome Research, 21(7), 1139-1149 (2011) PDF

        L. Taher, N.M. Collette, D. Murugesh, E. Maxwell, I. Ovcharenko, G.G. Loots
        Global gene expression analysis of murine limb development
        PLoS ONE, 6(12):e28358 (2011)

        Martin D, ... Taher L, ... Ovcharenko I, ... G√≥mez-Skarmeta JL.(22 authors)
        Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.
        Nat Struct Mol Biol. 18(6):708-14 (2011)

        Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M.
        Effects of HMGN variants on the cellular transcription profile.
        Nucleic Acids Res. 39(10):4076-87 (2011)

        Hellsten U, ... Ovcharenko I, ... Taher L, ... Rokhsar DS (48 authors)
        The Genome of the Western Clawed Frog Xenopus tropicalis.
        Science (2010) 328:633-636

        Taher L, Ovcharenko I.
        Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements.
        Bioinformatics (2009) 25(5):578-84

  • Chih-Hao Hsu, Postdoctoral Fellow from August 2010 to August 2012. Currently a Research Fellow at the National Cancer Institute.

        Hsu CH, Ovcharenko I.
        Effects of Gene Regulatory Reprogramming on Gene Expression in Human and Mouse Developing Hearts
        Philosophical Transactions B (2013) 368(1620):20120366

  • Chris Lasher, Postdoctoral Fellow from January 2012 to September 2012. Currently a Bioinformatics Analyst and Software Engineer at 5AM Solutions.
  • Hani Girgis, Postdoctoral Fellow from January 2010 to March 2011. Currently an Assistant Professor at the University of Tulsa

        Visel A, Taher L, Girgis H, ... Ovcharenko I, Pennacchio LA, Rubenstein JL (25 authors)
        A High-Resolution Enhancer Atlas of the Developing Telencephalon
        Cell, (2013) PDF

        Girgis HZ and Ovcharenko I.
        Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.
        BMC Bioinformatics (2012) 13:25

  • Evan Maxwell, Summer Student (2010). Currently a Pre-Doctoral Fellow at NHGRI.
  • Peter Cote, Summer Student (2010). Currently a Graduate Student at the University of Illinois at Urbana-Champaign.
  • Valer Gotea, Ph.D., Postdoctoral Fellow from September 2007 to May 2010. Currently a Postdoctoral Fellow at NHGRI.

        Gotea V, Ovcharenko I.
        DiRE: identifying distant regulatory elements of co-expressed genes.
        Nucleic Acids Res. (2008) 36:W133-9

        Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.
        Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.
        Genome Research. (2010) 20(5):565-77

        Jacox E, Gotea V, Ovcharenko I, Elnitski L.
        Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes.
        PLoS One. (2010) 5(8):e12274.

  • Chao Tian, Ph.D., Postdoctoral Fellow from August 2009 to February 2010. Currently a Senior Scientist at Complete Genomics
  • Leelavati Narlikar, Ph.D., Postdoctoral Fellow from April 2008 to July 2009. Currently a Group Leader at the National Chemical Laboratory in Pune, India.

        L. Taher, L. Narlikar, I. Ovcharenko
        Identification and Computational Analysis of Gene Regulatory Elements
        Cold Spring Harbor Protocols, 2015(1):24-51 (2015) PDF

        Narlikal L, Ovcharenko I.
        Identifying regulatory elements in eukaryotic genomes
        Brief Funct Genomic Proteomic, 2009

        Narlikal L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.
        Genome-wide discovery of human heart enhancers
        Genome Research, 2010

        L. Taher, L. Narlikar, I. Ovcharenko
        CLARE: Cracking the LAnguage of Regulatory Elements
        Bioinformatics, 2012

  • Andrew Heekin, Summer Student (2009). Currently a Research Computational Biologist at USDA ARS.
  • Yevgeniy Gindin, Summer Student (2009). Currently a Graduate Student at Boston University.
  • David Tao, High School Summer Student (2009).
  • Brian Abraham, Summer Student (2008). Currently a Postdoctoral Associate at the Whitehead Institute for Biomedical Research.
  • Ryan Vo, High School Summer Student (2008).



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