Raja jothi's Publications


Copyright Notice: Most of these papers are published, and the copyright has been transferred to the respective publishers. Therefore, the papers cannot be duplicated or disseminated for commercial purposes without the written permission from the respective publishers. All persons copying this information must understand that they adhere to the terms and constraints invoked by each author's and/or publisher's copyright. In particular, these works may not be re-posted without permission from the copyright holders.

Publications (click here for publications in reverse chronological order)

(* indicates corresponding author)

Computational Biology & Bioinformatics

  • Critical requirement of GABPα for normal T cell development
    Shuyang Yu , Dong-Mei Zhao, Raja Jothi, and Hai-Hui Xue*.
    Under review.
  • Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi1,*, S Balaji1, Arthur Wuster, Joshua A Grochow, Jorg Gsponer, Teresa M Przytycka, L Aravind, and M Madan Babu*.
    Molecular Systems Biology, In press. (1Co-first authors)
  • Chromatin poises miRNA and protein-coding genes for expression
    Artem Barski1, Raja Jothi1, Suresh Cuddapah1, Kairong Cui, Tae-Young Roh, Dustin E Schones, and Keji Zhao*.
    Genome Research, In press. (1Co-first authors)
  • Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes
    Eric Kallin, Ru Cao, Raja Jothi, Kai Xia, Kairong Cui, Keji Zhao, and Yi Zhang*.
    PLoS Genetics, Jun;5(6):e1000506, 2009. (1Co-first authors) [Pubmed] [PDF] [Text]
  • An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network
     Lena Ho1, Raja Jothi1, Jehnna L Ronan, Kairong Cui, Keji Zhao, and Gerald R Crabtree*.
    Proc Natl Acad Sci (PNAS)    , 106(13):5187-5191, 2009. (1Co-first authors) [Pubmed] [PDF] [Text]
  • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
     Suresh Cuddapah, Raja Jothi1, Dustin E Schones, Artem Barski, Tae-Young Roh, Kairong Cui, and Keji Zhao
    Genome Research    , 19(1):24-32, 2009. (1Co-first authors) [Text] [PDF]
  • 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]
  • 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, accepted. [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]
  • 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]
  • Predicting Domain-Domain Interactions Using a Parsimony Approach
    Katia Guimares, Raja Jothi, Elena Zotenko, and Teresa Przytycka*,
    Genome Biology    , 7(11):R104, 2006. [PDF]
  • 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,     Vol. 362(4), pages 861-875, Elsevier Press. [PDF] [Suppl. 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]
    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]
  • 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]
    presented at 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, Jun 25-29, 2005.

Algorithms, Graph Theory & Combinatorics

  • Improved approximation algorithms for the single-sink buy-at-bulk network design problem
     Raja Jothi* and Balaji Raghavachari
    Journal of Discrete Algorithms    , 7(2):249-255, 2009.
  • Degree-Bounded Minimum Spanning Trees
     Raja Jothi* and Balaji Raghavachari
    Discrete Applied Mathematics    , 157(5):960-970, 2009.[PDF]
  • Approximating the k-Traveling Repairman Problem with Repairtimes
    Raja Jothi* and Balaji Raghavachari
    Journal of Discrete Algorithms, 5(2), 293-303, 2007 [PDF]
  • 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]
  • 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, 91(4), 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 [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), 336-348, Springer-Verlag LNCS 3111, Humleb�k, Denmark, July 8-10, 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, 423-433, Buenos Aires, Argentina, April 4-9, 2004. Journal version (contains better approximation results) [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]
  • 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]

Networks & Telecommunications

  • Load Balanced Agent Activation for Value Added Network Services
    Chao Gong*, Kamil Sarac, Ovidiu Daescu, Balaji Raghavachari, and Raja Jothi,
    Computer Communications, Vol. 29(11), pages 1905-1916, Elsevier Press, 2006. [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, Vol. 23, No. 10, pages 3111-3124, October 2005. [PDF]
  • 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]
  • 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]
  • 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]
  • 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]