Raja Jothi, Ph.D.
Principal Investigator
National Institute of Environmental Health Sciences (NIEHS)
National Institutes of Health (NIH)
111 T.W. Alexander Drive, MD A3-03
Research Triangle Park, NC 27709
Phone: (919) 316-4557
Email: jothi [AT] mail.nih.gov

Performance is everything, potential is nothing - Bill Parcells

There is winning and there is misery - Bill Parcells

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Postdoctoral Positions Available

Research Interests

The laboratory's overall goal is to elucidate mechanisms of gene regulation. In particular, we are interested in understanding how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation. We use a combination of systems biology and functional genomics approaches to map and characterize regulatory elements and epigenomes in stem cells.

Current Lab Members

  • Senthilkumar Cinghu, Ph.D. (University of Madras)
    Postdoctoral Fellow (2011 - )
  • Andrew J Oldfield, Ph.D. (Universite Paris VI Pierre & Marie Curie)
    Postdoctoral Fellow (2012 - )
  • Pengyi Yang, Ph.D. (University of Sydney)
    Postdoctoral Fellow (2013 - )
  • Amanda E Conway, Ph.D. (Duke University)
    Postdoctoral Fellow (2013 - )
  • Justin Kosak, M.S. (University of Pennsylvania)
    Biologist (2013 - )

Past Lab Members

  • Sailu Yellaboina, Ph.D. (University of Hyderabad)
    Next Position: Associate Professor, CR Rao Institute, Hyderabad, India
  • Johannes Freudenberg, Ph.D. (University of Cincinnati)
    Next Position: Scientific Investigator, GlaxoSmithKline, USA
  • Swati Ghosh, Ph.D. (Banaras Hindu University)
    Next Position:Postdoctoral Fellow, NIEHS
  • Viju Mathew, Enloe High School (Summer Intern)
    Next Position: Undergraduate student, Duke University, USA

Selected Publications [ Complete List ] [ Pubmed ] [ DBLP ] - * indicates corresponding author

  • Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors
    Oldfield AJ1, Yang P1, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jotih R*.
    Molecular Cell, 55(5):708-22. (1Co-first authors) [Pubmed]
  • Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis
    Cinghu S1, Yellaboina S1, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jotih R*.
    Proc. Natl. Acad. Sci., 111(16):E1581-90, 2014. (1Co-first authors) [Pubmed]
  • Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
    Freudenberg JM1, Ghosh S1, Lackford BL1, Yellaboina S, Zheng X, Li R, Cuddapah S, Wade PA, Hu G, Jothi R*.
    Nucleic Acids Research, 2011. (*Co-corresponding authors; 1Co-first authors) [Pubmed] [PDF] [Text]
  • esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function
    Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R*, Crabtree GR*
    Nature Cell Biology, 13(8):903-913, 2011. (*Co-corresponding authors) [Pubmed] [PDF] [Text]
  • DOMINE: a comprehensive collection of known and predicted domain-domain interactions
    Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R*.
    Nucleic Acids Research, 39(Database issue):D730-735, 2011. [Database Website] [Pubmed] [PDF] [Text]
  • Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Jothi R*, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM*.
    Molecular Systems Biology, 5:294, 2009. (*Co-corresponding authors) [Pubmed] [PDF] [Text]
  • An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network
    Ho L1, Jothi R1, Ronan JL, Cui K, Zhao K, Crabtree GR.
    Proc Natl Acad Sci (PNAS)
    , 106(13):5187-5191, 2009. (1Co-first authors) [Pubmed] [PDF] [Text]
  • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    Cuddapah S1, Jothi R1, Schones DE, Roh TY, Cui K, Zhao K
    Genome Research
    , 19(1):24-32, 2009. (1Co-first authors) [Pubmed] [Text] [PDF]
  • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Jothi R, Cuddapah S, Barski A, Cui K, Zhao K
    Nucleic Acids Research
    , 36(16):5221-31, 2008. [Pubmed] [PDF] [Text] [Download SISSRs]


  • SISSRs - Genome-wide identification of in vivo protein-DNA interactions from ChIP-Seq data
  • DOMINE - A database of protein domain interactions
  • RCDP - Performs co-evolutionary analysis of domains in interacting proteins to predict domain pair(s) that is most likely mediating a given protein-protein interaction
  • COCO-CL - Identifies orthologous set of genes. Can also be used to perform hierarchical clustering of orthologous (or homologous) genes to identify out-paralogs from automatically generated set of ortholgous genes (eg: COGs).
  • MORPH - Predicts protein interaction partners between members of two protein families that are known to interact (for example: Ligands and Receptors).

Some Links

Disclaimer: The views and opinions expressed on this website do not state or reflect those of the U.S. Government, DHHS, NIH, or NIEHS.

This file was last updated on Dec 10, 2013.
Copyright 2006-2013, Raja Jothi. All rights reserved.
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