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

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

2014

  • Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors
    Oldfield AJ1, Yang P1, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jotih R*.
    Molecular Cell, to appear (1Co-first authors)
  • Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis
    Cinghu S1, Yellaboina S1, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jotih R*.
    Proc. Natl. Acad. Sci., 111(16):E1581-90, 2014. (1Co-first authors)
  • Retinoic Acid-Related Orphan Receptor γ (RORγ): A Novel Participant in the Diurnal Regulation of Hepatic Gluconeogenesis and Insulin Sensitivity
    Takeda Y, Kang HS, Freudenberg J, DeGraff LM, Jothi R, Jetten AM.
    PLoS Genetics, 10(5):e1004331, 2014.
  • INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development
    Wang L, Du Y, Ward JM, Shimbo T, Lackford L, Zheng, X, Miao Y-l, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G.
    Cell Stem Cell, 14(5):575–91, 2014.
  • Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal
    Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y.
    EMBO J., 33(8):878-89, 2014.
  • Fine-tuning of epigenetic regulation with respect to promoter CpG content in a cell type-specific manner
    Li R, Mav D, Grimm SA, Jothi R, Shah R, Wade PA.
    Epigenetics, 9(5) [Epub ahead of print], 2014.

2013

  • Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation
    Li L1, Freudenberg J1, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R*, Love PE*.
    Blood, 121(22):4575-85, 2013. (*Co-corresponding authors; 1Co-first authors) [Pubmed] [PDF] [Text]
  • Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
    Menendez D1, Nguyen TA1, Freudenberg JM1, Mathew VJ, Anderson CW, Jothi R*, Resnick MA*.
    Nucleic Acids Research, 2013 [Epub ahead of print]. (*Co-corresponding authors; 1Co-first authors) [Pubmed] [PDF] [Text]

2012

  • Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors
    Sunita K Agarwal*, Raja Jothi*.
    PLoS ONE, 2012 (In press).
  • Cnot1, Cnot2, and Cnot3 maintain mouse and human ES cell identity and inhibit extraembryonic differentiation
    Xiaofeng Zheng, Raluca Dumitru, Brad L Lackford, Johannes M Freudenberg, Ajeet P Singh, Trevor K Archer, Raja Jothi, Guang Hu.
    Stem Cells, 30(5):910-22, 2012. [Pubmed]
  • Interplay between gene expression noise and regulatory network architecture
    Guilhem Chalancon, Charles Ravarani, Balaji Santhanam, Alfonso Martinez-Arias, L Aravind, Raja Jothi, M. Madan Babu.
    Trends in Genetics, 28:221-32, 2012 (to appear). [Pubmed]
  • Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
    Johannes M Freudenberg1, Swati Ghosh1, Brad L Lackford1, Sailu Yellaboina, Xiaofeng Zheng, Ruifang Li, Suresh Cuddapah, Paul A Wade, Guang Hu*, Raja Jothi*.
    Nucleic Acids Research, 2012. (*Co-corresponding authors; 1Co-first authors) [Pubmed] [PDF] [Text]
  • ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder
    Leelavati Narlikar and Raja Jothi*.
    Methods in Molecular Biology, 802:305-22, 2012. [Pubmed] [PDF]

2011

  • esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function
    Lena Ho, Erik L Miller, Jehnna L Ronan, Wenqi Ho, Raja Jothi*, Gerald R Crabtree*
    Nature Cell Biology, 13(8):903-913, 2011. (*Co-corresponding authors) [Pubmed] [PDF] [Text]
  • Genome-wide analyses of GATA3-mediated gene regulation in distinct T cell types
    Gang Wei1, Brian Abraham1, Ryoji Yagi1, Raja Jothi1, Kairong Cui, Suveena Sharma, Leelavati Narlikar, Daniel Northrup, Qingsong Tang, William Paul, Jinfang Zhu, Keji Zhao.
    Immunity, 35(2):299-311, 2011. (1Co-first authors) [Pubmed] [PDF] [Text]
  • Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells
    LiQi Li, Raja Jothi, Kairong Cui, Jan Y Lee, Tsadok Cohen, Marat Gorivodsky, Itai Tzchori, Yangu Zhao, Sandra M Hayes, Emery H Bresnick, Keji Zhao, Heiner Westphal, and Paul E Love
    Nature Immunology, 12(2):129-136, 2011.
  • DOMINE: a comprehensive collection of known and predicted domain-domain interactions
    Sailu Yellaboina, Asba Tasneem, Dmitri Zaykin, Balaji Raghavachari, and Raja Jothi*
    Nucleic Acids Research, 39(Database issue):D730-735, 2011. [Database Website]
  • GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells
    Shuyang Yu1, Kairong Cui1, Raja Jothi1, Dong-Mei Zhao, Xuefang Jing, Keji Zhao, and Hai-Hui Xue
    Blood 117(7):2166-78, 2011. (1Co-first authors).

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]
eXTReMe Tracker