Brief Bio

Selected Publications [Complete List] - * indicates corresponding author

	Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, and Keji Zhao* Nucleic Acids Research, To appear.
	Differences in evolutionary pressure acting within highly conserved ortholog groups Teresa M Przytycka*, Raja Jothi, L. Aravind, and David J Lipman BMC Evolutionary Biology, To appear.
	Improved approximation algorithms for the single-sink buy-at-bulk network design problem Raja Jothi* and Balaji Raghavachari Journal of Discrete Algorithms, To appear.
	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] [Citations]
	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] [Citations]
	Approximating the k-Traveling Repairman Problem with Repairtimes Raja Jothi* and Balaji Raghavachari Journal of Discrete Algorithms, 5(2), 293-303, 2007 [PDF] [Citations]
	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] [Citations]
	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] [Citations]
	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] [Citations]
	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] [Citations]
	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] [Citations]

Databases & Software Packages

• 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).

Professional Service

• 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, 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 of my drawings
• Some of my GRAPHICS coursework at CLEMSON UNIVERSITY
• Computer Science Conference Rankings
• Problems in Combinatorial Optimization
• A compendium of NP optimization problems
• Puzzles to solve
• How to write proofs
• Journey of Man