Publications (in reverse chronological order) click here for publications by subject area

Journals and refereed conference proceedings (* indicates corresponding author)

2008

• 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.[PDF] [Text] [Download SISSRs]
• Differences in evolutionary pressure acting within highly conserved ortholog groups
  Teresa M Przytycka, Raja Jothi, L. Aravind, and David J Lipman
  BMC Evolutionary Biology, 8:208, 2008. [PDF] [Text]
• 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, in 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]

2007

• 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]

2006

• 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, Elsevier Press. [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, April 2006 [PDF] [Text]
  also in Proc. Annual RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics, Springer-Verlag LNBI, San Diego, CA, Dec 2-4, 2005.
• COCO-CL: Hierarchical Clustering of Homology Relations Based on Evolutionary Correlations
  Raja Jothi*, Elena Zotenko, Asba Tasneem, and Teresa Przytycka*
  Bioinformatics, 22(7), 779-788, Oxford University Press, 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]

2005

• Predicting Protein-Protein Interaction by Searching Evolutionary Tree Automorphism Space
  Raja Jothi, Maricel Kann, and Teresa Przytycka*
  Bioinformatics, Vol. 21 (Suppl 1), pp. i241-i250, Oxford University Press, 2005. [PDF] [Website]
  presented at 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, Jun 25-29, 2005.
• Approximation Algorithms for the Capacitated Minimum Spanning Tree Problem and its Variants in Network Design
  Raja Jothi* and Balaji Raghavachari,
  ACM Transactions on Algorithms, 1(2), 265-282, ACM Press, 2005. [PDF]
• Dual-Homing Protection in IP-over-WDM Networks
  Jianping Wang, Vinod Vokkarane, Raja Jothi, Xiangtong Qi, Balaji Raghavachari, and Jason Jue*
  IEEE/OSA Journal of Lightwave Technology, 23(10), 3111-3124, 2005. [PDF]

2004 and before

• Load Balancing for Reliable Multicast
  Chao Gong, Ovidiu Daescu, Raja Jothi, Balaji Raghavachari, and Kamil Sarac*
  in Proc. 3rd IASTED Intl. Conference on Communications, Internet, and Information Technology (CIIT), US Virgin Islands, Nov 22-24, 2004.[PDF]
• Degree-Bounded Minimum Spanning Trees
  Raja Jothi* and Balaji Raghavachari*
  in Proc. 16th Canadian Conference on Computational Geometry (CCCG), pp. 192-195, Montreal, Canada, Aug 9-11, 2004. [PDF] Submitted for journal publication. Journal Version [PDF]
• Survivable Network Design: The Capacitated Minimum Spanning Network Problem
  Raja Jothi* and Balaji Raghavachari,
  Information Processing Letters, Vol. 91(4), pp. 183-190, 2004. [PDF]
• Approximation Algorithms for Single-Sink Edge Installation Problems and Other Graph Problems
  Raja Jothi
  Ph.D. Thesis, Department of Computer Science, University of Texas at Dallas, Aug 2004.[PS] [PDF] (or Email me for a copy)
• Approximation Algorithms for the Capacitated Minimum Spanning Tree Problem and its Variants in Network Design
  Raja Jothi* and Balaji Raghavachari*,
  in Proc. 31st International Colloquium on Automata, Languages and Programming (ICALP), pp. 805-818, Springer-Verlag LNCS 3142, Turku, Finland, July 12-16, 2004 Journal version [PDF].
• Improved Approximation Algorithms for the Single-Sink Buy-At-Bulk Network Design Problems
  Raja Jothi* and Balaji Raghavachari*
  in Proc. 9th Scandinavian Workshop on Algorithm Theory (SWAT), pp. 336-348, Springer-Verlag LNCS 3111, Humlebæk, Denmark, July 8-10, 2004. [PDF]
• Dynamic Dual-Homing Protection in WDM Mesh Networks
  Vinod Vokkarane, Jianping Wang, Raja Jothi, Xiangtong Qi, Balaji Raghavachari, and Jason Jue*
  in Proc. IEEE International Conference on Communications (ICC), Vol. 3, pp. 1644-1648, Paris, France, June 20-24, 2004 [PDF]
• Minimum Latency Tours and the k-Traveling Repairman Problem
  Raja Jothi* and Balaji Raghavachari*
  in Proc. Latin American Theoretical INformatics (LATIN), Springer-Verlag LNCS 2976, pp. 423-433, Buenos Aires, Argentina, April 4-9, 2004. Journal version (contains better approximation results) [PDF]
• Optimal Placement of NAK Suppressing Agents for Reliable Multicast: A Partial Deployment Case
  Ovidiu Daescu, Raja Jothi, Balaji Raghavachari, and Kamil Sarac
  in Proc. 19th ACM Symposium on Applied Computing (SAC), Nicosia, Cyprus, March 14-17, pp. 334-338, 2004 [PDF]
• Survivable Network Design: The Capacitated Minimum Spanning Network Problem
  Raja Jothi* and Balaji Raghavachari,
  in Proc. 7th INFORMS Telecommunications Conference (Telecom), Boca Raton, Florida, March 7-10, pp. 50-52, 2004
  Also in Information Processing Letters. [PDF]
• A Note on Altinkemer-Gavish's Algorithm for the Design of Tree Networks
  Raja Jothi*
  in Proc. 7th INFORMS Telecommunications Conference (Telecom), Boca Raton, Florida, March 7-10, pp. 78-80, 2004.[PDF]
• Revisiting Esau-Williams' Algorithm: On the Design of Local Access Networks
  Raja Jothi* and Balaji Raghavachari
  in Proc. 7th INFORMS Telecommunications Conference (Telecom), Boca Raton, Florida, March 7-10, pp. 104-107, 2004 [PDF]
• Threshold-Based Differentiated Intermediate-Node Initiated (TDINI) Signaling for Optical Burst-Switched Networks
  Raja Jothi* and Vinod Vokkarane
  in Proc. 7th INFORMS Telecommunications Conference (Telecom), Boca Raton, Florida, March 7-10, 2004. [PDF]
• Multi-Homing Protection in WDM Mesh Networks
  Khawar Deen, Raja Jothi* and Balaji Raghavachari
  in Proc. 7th INFORMS Telecommunications Conference (Telecom), Boca Raton, Florida, March 7-10, 2004. [PDF]
• Dynamic Capacitated Minimum Spanning Trees
  Raja Jothi* and Balaji Raghavachari*
  in Proc. 3rd IEEE International Conference on Networking (ICN), ISBN 0-86341-326-9, French Caribbean, Feb 29-Mar 4, 2004. [PDF]
• Placement of Proxy Servers to Support Server-Based Reliable Multicast
  Raja Jothi* and Balaji Raghavachari *
  in Proc. 3rd IEEE International Conference on Networking (ICN), ISBN 0-86341-326-9, French Caribbean, Feb 29-Mar 4, 2004.[PDF]
• Design of Local Access Networks (Nominated for the best paper award)
  Raja Jothi* and Balaji Raghavachari*
  in Proc. 15th IASTED Intl. Conf. on Parallel and Distributed Computing and Systems (PDCS), Marina Del Ray, CA, Nov 3-5, pages 883-888, 2003. [PDF]
• Leave No Stone Unturned: Improved Approximation Algorithm for Degree-Bounded Minimum Spanning Trees
  Raja Jothi and Balaji Raghavachari
  DIMACS Workshop on Geometric Optimization, New Brunswick, NJ, May 19-21, 2003.
• A 5/4-Approximation Algorithm for Minimum 2-Edge-Connectivity (Theorem 6.1 is withdrawn)
  Raja Jothi*, Balaji Raghavachari*, and Subramanian Varadarajan*
  in Proc. 14th ACM-SIAM Symposium on Discrete Algorithms (SODA), ACM Press, pages 725-734, Baltimore, MD, Jan 12-14, 2003. [PDF]