Raja Jothi, Ph.D. - Publications

Affiliations: 
2004 University of Texas at Dallas, Richardson, TX, United States 
Area:
Computer Science, Operations Research

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Hoffman NJ, Parker BL, Chaudhuri R, Fisher-Wellman KH, Kleinert M, Humphrey SJ, Yang P, Holliday M, Trefely S, Fazakerley DJ, Stöckli J, Burchfield JG, Jensen TE, Jothi R, Kiens B, et al. Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabolism. PMID 26437602 DOI: 10.1016/J.Cmet.2015.09.001  0.32
2015 Yang P, Zheng X, Jayaswal V, Hu G, Yang JY, Jothi R. Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. Plos Computational Biology. 11: e1004403. PMID 26252020 DOI: 10.1371/Journal.Pcbi.1004403  0.32
2015 Pathania R, Ramachandran S, Elangovan S, Padia R, Yang P, Cinghu S, Veeranan-Karmegam R, Arjunan P, Gnana-Prakasam JP, Sadanand F, Pei L, Chang CS, Choi JH, Shi H, Manicassamy S, ... ... Jothi R, et al. DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nature Communications. 6: 6910. PMID 25908435 DOI: 10.1038/Ncomms7910  0.32
2015 Hoffman NJ, Parker BL, Chaudhuri R, Fisher-Wellman KH, Kleinert M, Humphrey SJ, Yang P, Holliday M, Trefely S, Fazakerley DJ, Stöckli J, Burchfield JG, Jensen TE, Jothi R, Kiens B, et al. Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates Cell Metabolism. 22: 922-935. DOI: 10.1016/j.cmet.2015.10.004  0.32
2014 Oldfield A, Yang P, Conway A, Cinghu S, Freudenberg J, Yellaboina S, Jothi R. Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors Molecular Cell. 55: 708-722. PMID 25132174 DOI: 10.1016/J.Molcel.2014.07.005  0.32
2014 Takeda Y, Kang HS, Freudenberg J, DeGraff LM, Jothi R, Jetten AM. Retinoic acid-related orphan receptor γ (RORγ): a novel participant in the diurnal regulation of hepatic gluconeogenesis and insulin sensitivity. Plos Genetics. 10: e1004331. PMID 24831725 DOI: 10.1371/Journal.Pgen.1004331  0.32
2014 Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G. INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. Cell Stem Cell. 14: 575-91. PMID 24792115 DOI: 10.1016/J.Stem.2014.02.013  0.32
2014 Cinghu S, Yellaboina S, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R. Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis. Proceedings of the National Academy of Sciences of the United States of America. 111: E1581-90. PMID 24711389 DOI: 10.1073/Pnas.1318598111  0.32
2014 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. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. The Embo Journal. 33: 878-89. PMID 24596251 DOI: 10.1002/Embj.201386537  0.32
2014 Li R, Mav D, Grimm SA, Jothi R, Shah R, Wade PA. Fine-tuning of epigenetic regulation with respect to promoter CpG content in a cell type-specific manner. Epigenetics. 9: 747-59. PMID 24521667 DOI: 10.4161/Epi.28075  0.32
2013 Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, Jothi R, Resnick MA. Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Research. 41: 7286-301. PMID 23775793 DOI: 10.1093/Nar/Gkt504  0.32
2013 Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE. Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood. 121: 4575-85. PMID 23610375 DOI: 10.1182/Blood-2013-01-479451  0.32
2012 Takeda Y, Jothi R, Birault V, Jetten AM. RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo. Nucleic Acids Research. 40: 8519-35. PMID 22753030 DOI: 10.1093/Nar/Gks630  0.32
2012 Agarwal SK, Jothi R. Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors. Plos One. 7: e37952. PMID 22666422 DOI: 10.1371/Journal.Pone.0037952  0.32
2012 Zheng X, Dumitru R, Lackford BL, Freudenberg JM, Singh AP, Archer TK, Jothi R, Hu G. Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation. Stem Cells (Dayton, Ohio). 30: 910-22. PMID 22367759 DOI: 10.1002/Stem.1070  0.32
2012 Chalancon G, Ravarani CN, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM. Interplay between gene expression noise and regulatory network architecture. Trends in Genetics : Tig. 28: 221-32. PMID 22365642 DOI: 10.1016/J.Tig.2012.01.006  0.32
2012 Freudenberg JM, Ghosh S, Lackford BL, Yellaboina S, Zheng X, Li R, Cuddapah S, Wade PA, Hu G, Jothi R. Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity. Nucleic Acids Research. 40: 3364-77. PMID 22210859 DOI: 10.1093/Nar/Gkr1253  0.32
2012 Narlikar L, Jothi R. ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder. Methods in Molecular Biology (Clifton, N.J.). 802: 305-22. PMID 22130889 DOI: 10.1007/978-1-61779-400-1_20  0.32
2011 Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity. 35: 299-311. PMID 21867929 DOI: 10.1016/J.Immuni.2011.08.007  0.32
2011 Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R, Crabtree GR. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nature Cell Biology. 13: 903-13. PMID 21785422 DOI: 10.1038/Ncb2285  0.32
2011 Li L, Jothi R, Cui K, Lee JY, Cohen T, Gorivodsky M, Tzchori I, Zhao Y, Hayes SM, Bresnick EH, Zhao K, Westphal H, Love PE. Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells. Nature Immunology. 12: 129-36. PMID 21186366 DOI: 10.1038/Ni.1978  0.32
2011 Yu S, Cui K, Jothi R, Zhao DM, Jing X, Zhao K, Xue HH. GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells. Blood. 117: 2166-78. PMID 21139080 DOI: 10.1182/Blood-2010-09-306563  0.32
2011 Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R. DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Research. 39: D730-5. PMID 21113022 DOI: 10.1093/Nar/Gkq1229  0.32
2010 Yu S, Zhao DM, Jothi R, Xue HH. Critical requirement of GABPalpha for normal T cell development. The Journal of Biological Chemistry. 285: 10179-88. PMID 20139079 DOI: 10.1074/Jbc.M109.088740  0.32
2009 Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Chromatin poises miRNA- and protein-coding genes for expression. Genome Research. 19: 1742-51. PMID 19713549 DOI: 10.1101/Gr.090951.109  0.32
2009 Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Molecular Systems Biology. 5: 294. PMID 19690563 DOI: 10.1038/Msb.2009.52  0.32
2009 Kallin EM, Cao R, Jothi R, Xia K, Cui K, Zhao K, Zhang Y. Genome-wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes. Plos Genetics. 5: e1000506. PMID 19503595 DOI: 10.1371/Journal.Pgen.1000506  0.32
2009 Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proceedings of the National Academy of Sciences of the United States of America. 106: 5187-91. PMID 19279218 DOI: 10.1073/Pnas.0812888106  0.32
2009 Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research. 19: 24-32. PMID 19056695 DOI: 10.1101/Gr.082800.108  0.32
2009 Jothi R, Raghavachari B. Improved approximation algorithms for the single-sink buy-at-bulk network design problems Journal of Discrete Algorithms. 7: 249-255. DOI: 10.1016/J.Jda.2008.12.003  0.32
2009 Jothi R, Raghavachari B. Degree-bounded minimum spanning trees Discrete Applied Mathematics. 157: 960-970. DOI: 10.1016/J.Dam.2008.03.037  0.32
2009 Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Chromatin poises miRNA- and protein-coding genes for expression (Genome Research (2009) 19 (1742-1751)) Genome Research. 19: 2343.  0.32
2008 Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research. 36: 5221-31. PMID 18684996 DOI: 10.1093/Nar/Gkn488  0.32
2008 Przytycka TM, Jothi R, Aravind L, Lipman DJ. Differences in evolutionary pressure acting within highly conserved ortholog groups. Bmc Evolutionary Biology. 8: 208. PMID 18637201 DOI: 10.1186/1471-2148-8-208  0.32
2008 Raghavachari B, Tasneem A, Przytycka TM, Jothi R. DOMINE: a database of protein domain interactions. Nucleic Acids Research. 36: D656-61. PMID 17913741 DOI: 10.1093/Nar/Gkm761  0.32
2007 Jothi R, Przytycka TM, Aravind L. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. Bmc Bioinformatics. 8: 173. PMID 17521444 DOI: 10.1186/1471-2105-8-173  0.32
2007 Kann MG, Jothi R, Cherukuri PF, Przytycka TM. Predicting protein domain interactions from coevolution of conserved regions. Proteins. 67: 811-20. PMID 17357158 DOI: 10.1002/Prot.21347  0.32
2007 Jothi R, Raghavachari B. Approximating the k-traveling repairman problem with repairtimes Journal of Discrete Algorithms. 5: 293-303. DOI: 10.1016/J.Jda.2006.03.023  0.32
2007 Jothi R, Przytycka TM. Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions Bioinformatics Algorithms: Techniques and Applications. 465-491. DOI: 10.1002/9780470253441.ch21  0.32
2006 Guimarães KS, Jothi R, Zotenko E, Przytycka TM. Predicting domain-domain interactions using a parsimony approach. Genome Biology. 7: R104. PMID 17094802 DOI: 10.1186/Gb-2006-7-11-R104  0.32
2006 Jothi R, Cherukuri PF, Tasneem A, Przytycka TM. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. Journal of Molecular Biology. 362: 861-75. PMID 16949097 DOI: 10.1016/J.Jmb.2006.07.072  0.32
2006 Zotenko E, Guimarães KS, Jothi R, Przytycka TM. Decomposition of overlapping protein complexes: a graph theoretical method for analyzing static and dynamic protein associations. Algorithms For Molecular Biology : Amb. 1: 7. PMID 16722537 DOI: 10.1186/1748-7188-1-7  0.32
2006 Jothi R, Zotenko E, Tasneem A, Przytycka TM. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics (Oxford, England). 22: 779-88. PMID 16434444 DOI: 10.1093/Bioinformatics/Btl009  0.32
2006 Gong C, Sarac K, Daescu O, Raghavachari B, Jothi R. Load-balanced agent activation for value-added network services Computer Communications. 29: 1905-1916. DOI: 10.1016/J.Comcom.2005.10.035  0.32
2005 Jothi R, Kann MG, Przytycka TM. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics (Oxford, England). 21: i241-50. PMID 15961463 DOI: 10.1093/Bioinformatics/Bti1009  0.32
2005 Wang J, Vokkarane VM, Jothi R, Qi X, Raghavachari B, Jue JP. Dual-homing protection in IP-over-WDM networks Journal of Lightwave Technology. 23: 3111-3124. DOI: 10.1109/Jlt.2005.856321  0.32
2004 Jothi R, Raghavachari B. Approximation algorithms for the capacitated minimum spanning tree problem and its variants in network design Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3142: 805-818. DOI: 10.1145/1103963.1103967  0.32
2004 Jothi R, Raghavachari B. Survivable network design: The capacitated minimum spanning network problem Information Processing Letters. 91: 183-190. DOI: 10.1016/J.Ipl.2004.04.007  0.32
2004 Daescu O, Jothi R, Raghavachari B, Sarac K. Optimal placement of NAK-suppressing agents for reliable multicast: A partial deployment case Proceedings of the Acm Symposium On Applied Computing. 1: 334-338.  0.32
2004 Gong C, Daescu O, Jothi R, Raghavachari B, Sarac K. Load balancing for reliable multicast 433-121 Proceedings of the Third Iasted International Conference On Communications, Internet, and Information Technology. 86-91.  0.32
2004 Jothi R, Raghavachari B. Minimum latency tours and the k-traveling repairmen problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2976: 423-433.  0.32
2004 Vokkarane VM, Wang J, Qi X, Jothi R, Raghavachari B, Jue JP. Dynamic dual-homing protection in WDM mesh networks Ieee International Conference On Communications. 3: 1644-1648.  0.32
2003 Jothi R, Raghavachari B. Design of local access networks Proceedings of the Iasted International Conference On Parallel and Distributed Computing and Systems. 15: 883-888.  0.32
2003 Jothi R, Raghavachari B, Varadarajan S. A 5/4-approximation algorithm for minimum 2-edge-connectivity Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 725-734.  0.32
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