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Postdoctoral Positions Available
If interested, please email me your CV and the names of at least 3 references.
Scientist magazine ranks NIEHS as the 16th best
workplace for Postdocs, ahead of the National Cancer Institute (NCI),
which is ranked at number 19, and NIH, which came in at 32. NIEHS is located between Raleigh,
Durham, and Chapel Hill, and is within ~12 miles from Duke University,
University of North Carolina-Chapel Hill, and North Carolina State University.
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Research Interests
I am primarily interested in
- understanding how transcription regulators and chromatin modifications control
gene expression during cellular development and differentiation
- development and application of bioinformatics and genomics tools to identify tissue specific gene regulatory elements such as enhancers, silencers, and insulators by integrating heterogeneous genome-scale data, and
- elucidating the dynamics of genes/proteins in biomolecular (gene regulatory & protein-protein interaction) networks and their role in systems behavior.
General areas of interest
Collaborators (in alphabetical order)
Dr. L. Aravind
NCBI, NIH |
Protein/Genome evolution |
Dr. M. Madan Babu
MRC-LMB, Cambridge |
Gene regulatory networks |
Prof. Gerald R Crabtree
HHMI & Stanford University |
Role of esBAF complexes in mouse embryonic stem cell self-renewal and pluripotency |
Dr. Paul Love
NICHD, NIH |
Role of Ldb1 in T cell development |
Dr. Xin-zhuan Su
NIAID, NIH |
Epigenetic mechanisms controling gene expression in different stages of the asexual erythrocytic cycle of Plasmodium falciparum |
Prof. Hai-Hui Xue
University of Iowa |
Role of GABP complex in hematopoietic stem cell self-renewal and long-term survival |
Prof. Yi Zhang
HHMI & UNC-Chapel Hill |
Role of Bmi1 in H2A ubiquitylation |
Dr. Keji Zhao
NHLBI, NIH |
Identification of tissue specific gene regulatory elements |
Selected Publications
[ Complete List ]
[ Pubmed ]
[ DBLP ]
- * indicates corresponding author
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Shuyang Yu , Dong-Mei Zhao, Raja Jothi, and Hai-Hui Xue*.
Critical requirement of GABPα for normal T cell development.
Under review.
[Pubmed] [PDF] [Text] |
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Raja Jothi1,*, S Balaji1, Arthur Wuster, Joshua A Grochow, Jorg Gsponer,
Teresa M Przytycka, L Aravind, and M Madan Babu*.
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.
Molecular Systems Biology, To appear. (1Co-first authors) [Pubmed] [PDF] [Text |
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Artem Barski1, Raja Jothi1, Suresh Cuddapah1, Kairong Cui,
Tae-Young Roh, Dustin E Schones, and Keji Zhao*.
Chromatin Poises miRNA and Protein-coding Genes for Expression.
Genome Research, To appear. (1Co-first authors)
[Pubmed] [PDF] [Text] |
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Eric Kallin, Ru Cao, Raja Jothi, Kai Xia, Kairong Cui,
Keji Zhao, and Yi Zhang*.
Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes.
PLoS Genetics
[Pubmed]
[PDF]
[Text] |
 |
Lena Ho1, Raja Jothi1, Jehnna L Ronan, Kairong Cui,
Keji Zhao, and Gerald R Crabtree*.
An embryonic stem cell chromatin remodeling complex esBAF is an
essential component of the core pluripotency transcriptional network.
Proc Natl Acad of Sci (PNAS), 106(13):5187-5191, 2009 (1Co-first authors)
[Pubmed]
[PDF]
[Text]
|
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Suresh Cuddapah1,Raja Jothi1, Dustin E Schones, Tae-Young Roe, Kairong Cui, and Keji Zhao*.
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation
of active and repressive domains. Genome Research, 19(1):24-32, 2009. (1Co-first authors)
[Pubmed]
[Text]
[PDF]
|
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Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, and
Keji Zhao*. Genome-wide identification
of in vivo protein-DNA binding sites from ChIP-Seq data.
Nucleic Acids Research, 36(16):5221-31, 2008.
[Pubmed]
[PDF]
[Text]
[Download SISSRs]
[Citations] |
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Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and Raja Jothi*.
DOMINE: a database of protein domain interactions.
Nucleic Acids Research, 36(Database issue):D656-61, 2008.
[Pubmed]
[PDF]
[Text]
[Database Website]
[Citations] |
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Raja Jothi*, Praveen F Cherukuri, Asba Tasneem, and Teresa M Przytycka*.
Co-evolutionary analysis of domains in interacting proteins reveals insights into
domain-domain interactions mediating protein-protein interactions.
Journal of Molecular Biology, 362(4), 861-875, 2006.
[Pubmed]
[PDF]
[Text]
[Supplementary Material]
[Citations]
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Resources
-
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
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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).
Bio
| 2009 - |
Principal Investigator (tenure-track) |
NIEHS,
National Institutes of Health |
| 2007 - 2009 |
Research Fellow |
LMI,
National Heart Lung and Blood Institute,
National Institutes of Health |
| 2004 - 2007 |
Research Fellow/Associate |
NCBI,
National Library of Medicine,
National Institutes of Health |
| 2001 - 2004 |
Ph.D. |
Department of Computer Science,
University of Texas at Dallas |
| 2001 - 2004 |
Research/Teaching Assistant |
Department of Computer Science,
University of Texas at Dallas |
| 2000 - 2001 |
Software Engineer |
Westwave Communications |
| 2000 - 2000 |
M.S. |
Department of Computer Science,
University of Texas at Dallas |
| Fall 1999 |
Graduate Coursework |
School of Computing,
Clemson University |
| 1994 - 1998 |
B.Engg. |
University of Madras, Chennai, India |
| 1990 - 1994 |
High School Diploma |
Seventh Day Adventist Higher Secondary School, Chennai, India |
Professional Service
- Program Committee Member -
IEEE International Conference on Bioinformatics
and Biomedicine (BIBM)
2009
- Conference Vice Chair -
IEEE International Conference on Bioinformatics
and Biomedicine (BIBM) 2008
- Program Committee Member -
ISMB & ECCB 2007
- Program Committee Member -
IEEE International Conference on Bioinformatics
and Biomedicine (BIBM)
2007
- Session Chair -
7th INFORMS
Telecommunications Conference, 2004
- Session Chair -
3rd IEEE International Conference on
Networking, 2004
- Session Chair - 15th IASTED International
Conference on Parallel and Distributed Computing and Systems, 2003.
- Reviewer
- Journals -
Nature Methods,
Genome Research,
Genome Biology,
Trends in
Genetics,
Nucleic
Acids Research,
Molecular Biology and Evolution,
Proteins,
Bioinformatics,
BMC
Bioinformatics,
BMC Genomics,
BMC Systems
Biology,
IEEE/ACM Transactions on
Computational Biology and Bioinformatics,
IEEE Transactions on NanoBioscience,
Pattern Recognition
Letters,
Discrete and Computational Geometry,
Networks,
Journal of Graph
Algorithms and Applications
- Conferences -
PSB 2008,
ISMB/ECCB 2007,
PSB 2006,
BIBM
2007,
ISMB 2006,
PSB 2006,
IWBRA 2006,
APPROX 2006,
INFOCOM 2004,
ICC 2004,
FSTTCS 2003,
Globecom 2003
Some Links
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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 June 07, 2009.
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