| Lab members
Postdoctoral Positions Available
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
[ 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)
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)
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)
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)
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.
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)
An embryonic stem cell chromatin remodeling complex,
esBAF, is an essential component of the core pluripotency transcriptional
Ho L1, Jothi R1, Ronan JL, Cui K, Zhao K, Crabtree GR.
Proc Natl Acad Sci (PNAS), 106(13):5187-5191, 2009.
Global analysis of the insulator binding protein
CTCF in chromatin barrier regions reveals demarcation of active and repressive
Cuddapah S1, Jothi R1, Schones DE, Roh TY, Cui K, Zhao K
Genome Research, 19(1):24-32, 2009. (1Co-first authors)
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.
- Genome-wide identification of in vivo
protein-DNA interactions from ChIP-Seq data
- A database of protein domain interactions
- Performs co-evolutionary analysis of domains
in interacting proteins to predict domain pair(s) that is most likely
mediating a given protein-protein interaction
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:
MORPH - Predicts
protein interaction partners between members of two protein families
that are known to interact (for example: Ligands and Receptors).
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.