Raja Jothi's Publications

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Publications

(1 indicates co-first authors; * indicates corresponding author)

2010

  • Critical requirement of GABPα for normal T cell development
    Shuyang Yu , Dong-Mei Zhao, Raja Jothi, and Hai-Hui Xue.
    Journal of Biological Chemistry, 285(14):10179-10188. [Pubmed] [PDF] [Text]
2009

  • Knowledge-Guided Inference of Domain-Domain Interactions from Incomplete Protein-Protein Interaction Networks
    Mei Liu, Xue-Wen Chen, Raja Jothi.
    Bioinformatics, 25: 2492-2499, 2009. [Pubmed] [PDF] [Text]
  • 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, 5:294, 2009. (1Co-first authors) [Pubmed] [PDF] [Text]
  • 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, 19(10):1742-1751, 2009. (1Co-first authors) [Pubmed] [PDF] [Text] [Cover page]
  • 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) [Pubmed] [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    , 36(16):5221-31, 2008. [Pubmed] [PDF] [Text] [Download SISSRs]
  • 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.
    also appeared in Proc. 9th Scandinavian Workshop on Algorithm Theory (SWAT), LNCS 3111, pp. 336-348, 2004.
  • Degree-Bounded Minimum Spanning Trees
     Raja Jothi* and Balaji Raghavachari
    Discrete Applied Mathematics    , 157(5):960-970, 2009.[PDF]
    also appeared in Proc. 16th Canadian Conference on Computational Geometry (CCCG), pp. 192-195, 2004.

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    , 36(16):5221-31, 2008. [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, 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]
    also appeared in Proc. Latin American Theoretical INformatics (LATIN), LNCS 2976, pp. 423-433, 2004.

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, 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, April 2006 [PDF] [Text] .
  • 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, 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, 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, 2005. [PDF] [Website]
    presented at 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 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, 2005. [PDF]
    also appeared in Proc. 31st International Colloquium on Automata, Languages and Programming (ICALP), LNCS 3142, pp. 805-818, 2004.
  • 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]
    also appeared in Proc. IEEE International Conference on Communications (ICC), Vol. 3, pp. 1644-1648, 2004.

2004

  • 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]
  • 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), pp. 334-338, 2004 [PDF]
  • A Note on Altinkemer-Gavish's Algorithm for the Design of Tree Networks
    Raja Jothi*
    in Proc. 7th INFORMS Telecommunications Conference, 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, 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, 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, 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, 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), pp. 883-888, 2003. [PDF]

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, pp. 725-734, 2003. [PDF] 
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