Research
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Brief Bio
|
Publications
| Software
| CV
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Drawings
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Links
It really shouldn't matter where I got my education
from, all that should matter is what I did with it - Raja Jothi
Performance is everything, potential is nothing - Bill Parcells
Research Interests
Transcriptional Regulation
Epigenetics and Epigenomics
Protein and Domain Interactions
Systems Biology
Design and Analysis of Algorithms
Network Design & Analysis
Erdös Number: My
Erdös Number
is 3 (colloboration: P. Erdös
→ F. Harary → B. Raghavachari →
R. Jothi)
Brief Bio
|
2007 - |
Research Fellow |
LMI,
National
Heart Lung and Blood Institute,
National Institutes of Health |
|
2007 - 2007 |
Research Fellow |
NCBI,
National Library
of Medicine,
National Institutes of Health |
|
2005 - 2007 |
Research Associate |
NCBI,
National Library
of Medicine,
National Institutes of Health |
|
2004 - 2005
|
Visiting Fellow |
NCBI,
National
Library of Medicine,
National Institutes of Health |
| 2001 - 2004 |
Research/Teaching Assistant |
Department of
Computer Science,
University of Texas at Dallas |
|
2001 - 2004 |
Ph.D. Candidate |
Department of
Computer Science,
University of Texas at Dallas |
|
2000 - 2001 |
Software Engineer |
Westwave Communications |
|
2000 - 2000 |
M.S. Computer Science |
Department of
Computer Science,
University of Texas at Dallas |
|
1994 - 1998 |
B.E. in Computer Science and Engineering |
University of Madras, Chennai,
INDIA |
|
1990 - 1994. |
High School Diploma |
Seventh Day Adventist Higher Secondary
School, Chennai, INDIA |
Recent Publications (
Complete List )
- (* indicates corresponding author)
 |
Degree-Bounded Minimum
Spanning Trees
Raja Jothi and Balaji Raghavachari
Discrete Applied
Mathematics, To appear.[PDF] |
 |
Computational approaches to
predict protein-protein and domain-domain interactions
Raja Jothi and Teresa M. Przytycka
Bioinformatics
Algorithms: Techniques and Applications, (Eds: Mondoiu and A
Zelikovsky), Wiley Press, 2008.[PDF] |
 |
DOMINE: A Database of Protein Domain
Interactions
Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and
Raja Jothi*
Nucleic Acids Research, 2008 [PDF]
[Text] [Database
Website] |
 |
Discovering Functional Linkages and
Uncharacterized Cellular Pathways Using Phylogenetic Profile Comparisons: A
Comprehensive
Assessment
Raja Jothi*, Teresa
M. Przytycka*, and L. Aravind
BMC Bioinformatics, 8:173,
2007. [PDF]
[Text]
 |
 |
Predicting Protein Domain
Interactions from Co-evolution of Conserved Regions
Maricel G. Kann, Raja Jothi, Praveen F. Cherukuri, and Teresa
M. Przytycka*
Proteins, 67(4):811-20, 2007. [PDF] |
 |
Approximating the k-Traveling Repairman Problem with Repairtimes
Raja Jothi* and Balaji Raghavachari
Journal of Discrete Algorithms, 5(2), 293-303, 2007 [PDF] |
 |
Predicting Domain-Domain Interactions Using a Parsimony Approach
Katia Guimares, Raja Jothi, Elena Zotenko, and Teresa Przytycka*,
Genome Biology
7(11): R104, 2006. [PDF]
[Text]
|
 |
Co-evolutionary
analysis of domains in interacting proteins reveals insights into
domain-domain interactions mediating protein-protein interactions
Raja Jothi*,
Praveen F. Cherukuri, Asba Tasneem, and Teresa M. Przytycka*,
Journal of
Molecular Biology, 362(4), 861-875, 2006. [PDF]
[Text] [Supplementary
Material]
 |
 |
Decomposition
of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing
Static and Dynamic Protein
Associations
Elena Zotenko, Katia Guimares, Raja Jothi, and Teresa Przytycka*,
Algorithms for Molecular Biology, 1:2, 2006 [PDF]
[Text] |
 |
COCO-CL: Hierarchical Clustering of Homology Relations Based on
Evolutionary Correlations
Raja Jothi*, Elena Zotenko, Asba Tasneem, and Teresa M. Przytycka*,
Bioinformatics, Vol. 22(7), 779-788, 2006. [PDF]
[Text] [Supplementary
Material] |
 |
Load Balanced Agent Activation for Value Added Network Services
Chao Gong*, Kamil Sarac, Ovidiu Daescu, Balaji Raghavachari, and Raja Jothi,
Computer Communications, 29(11), 1905-1916, Elsevier
Press, 2006. [PDF] |
 |
Predicting Protein-Protein Interaction by Searching Evolutionary Tree
Automorphism Space
Raja Jothi, Maricel G. Kann, and Teresa M. Przytycka*,
Bioinformatics, Vol. 21 (Suppl 1), i241-i250, 2005 [PDF]
[Website]
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Databases & Software
-
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).
Professional Service
- Area 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 -
Genome Research,
Trends in
Genetics,
Nucleic
Acids Research,
Proteins,
Bioinformatics,
BMC
Bioinformatics,
BMC Genomics,
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
Computer
Science Conference Rankings
Problems in
Combinatorial Optimization
A
compendium of NP optimization problems
Puzzles to solve
How to
write proofs
Journey
of Man
This file was last updated on Mar 18, 2007.
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