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Selected Publications

Systems Biology Group

2008 - present

  1. Cinghu S*, Yang P*, Kosak J, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R. (2017) Intragenic Enhancers Attenuate Host Gene Expression. Molecular Cell (To appear)(*Co-first authors). 
  2. Kang HS, Kumar D, Liao G, Lichti-Kaiser K, Gerrish K, Liao X-H, Refetoff S, Jothi R, Jetten AM. GLIS3 is Indispensable for TSH/TSHR-Dependent Thyroid Hormone Biosynthesis and Follicular Cell Proliferation. Journal of Clinical Investigation (To appear). 
  3. Minard AY, Tan S-X , Yang P, Fazakerley DJ, Domanova W, Parker BL, Humphrey SJ, Jothi R, Stöckli J, James DE. (2016) mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes. Cell Reports 17(1):29-36. [Abstract Minard AY, Tan S-X , Yang P, Fazakerley DJ, Domanova W, Parker BL, Humphrey SJ, Jothi R, Stöckli J, James DE. (2016) mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes. Cell Reports 17(1):29-36.]
  4. 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, Wojtaszewski JF, Richter EA, James DE. (2015) Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabolism 22(5):922-935. [Abstract 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, Wojtaszewski JF, Richter EA, James DE. (2015) Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabolism 22(5):922-935.]
  5. Yang P, Humphrey SJ, James DE, Yang YH, Jothi R. (2015) Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics (Oxford, England) 2016 32(2):252-259. [Abstract Yang P, Humphrey SJ, James DE, Yang YH, Jothi R. (2015) Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics (Oxford, England) 2016 32(2):252-259.]
  6. Yang P, Zheng X, Jayaswal V, Hu G, Yang JY, Jothi R. (2015) Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. PLoS Computational Biology 11(8):e1004403 [Abstract Yang P, Zheng X, Jayaswal V, Hu G, Yang JY, Jothi R. (2015) Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. PLoS Computational Biology 11(8):e1004403]
  7. 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, Prasad PD, Sharma S, Ganapathy V, Jothi R, Thangaraju M. (2015) DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nature communications 6:6910-. [Abstract 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, Prasad PD, Sharma S, Ganapathy V, Jothi R, Thangaraju M. (2015) DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nature communications 6:6910-.]
  8. Oldfield AJ*, Yang P*, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R. (2014) Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors. Molecular Cell 55(5):708-22. (*Co-first authors) [Abstract Oldfield AJ*, Yang P*, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R. (2014) Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors. Molecular Cell 55(5):708-22. (*Co-first authors)]
  9. Cinghu S*, Yellaboina S*, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R . (2014) Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis. Proc Natl Acad Sci 111(16):E1581-E1590. (*Co-first authors) [Abstract Cinghu S*, Yellaboina S*, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R . (2014) Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis. Proc Natl Acad Sci 111(16):E1581-E1590. (*Co-first authors)]
  10. Takeda Y, Kang HS, Freudenberg J, DeGraff LM, Jothi R, Jetten AM. (2014) Retinoic Acid-Related Orphan Receptor γ (RORγ): A Novel Participant in the Diurnal Regulation of Hepatic Gluconeogenesis and Insulin Sensitivity. PLoS Genetics 10(5):e1004331. [Abstract Takeda Y, Kang HS, Freudenberg J, DeGraff LM, Jothi R, Jetten AM. (2014) Retinoic Acid-Related Orphan Receptor γ (RORγ): A Novel Participant in the Diurnal Regulation of Hepatic Gluconeogenesis and Insulin Sensitivity. PLoS Genetics 10(5):e1004331.]
  11. 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. (2014) INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development. Cell Stem Cell 14(5):575-91. [Abstract 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. (2014) INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development. Cell Stem Cell 14(5):575-91.]
  12. 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. (2014) Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO Journal 33(8):878-89. [Abstract 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. (2014) Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO Journal 33(8):878-89.]
  13. 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 2014 9(5):747-59. [Abstract 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 2014 9(5):747-59.]
  14. Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, Jothi R*, Resnick MA*. (2013) Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Research 41(15):7286-7301. (*Co-corresponding authors) [Abstract Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, Jothi R*, Resnick MA*. (2013) Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Research 41(15):7286-7301. (*Co-corresponding authors)]
  15. Li L, Freudenberg JM, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R*, Love PE*. (2013) Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood 121(22):4575-4585. (*Co-corresponding authors) [Abstract Li L, Freudenberg JM, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R*, Love PE*. (2013) Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood 121(22):4575-4585. (*Co-corresponding authors)]
  16. Agarwal SK, Jothi R. (2012) 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(5):e37952-. [Abstract Agarwal SK, Jothi R. (2012) 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(5):e37952-.]
  17. Takeda Y, Jothi R, Birault V, Jetten AM. (2012) RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo. Nucleic Acids Research. 40(17):8519-35. [Abstract Takeda Y, Jothi R, Birault V, Jetten AM. (2012) RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo. Nucleic Acids Research. 40(17):8519-35.]
  18. Chalancon G, Ravarani C, Balaji S, Martinez-Ariez A, Aravind L, Jothi R, M Madan Babu (2012) Interplay between gene expression noise and regulatory network architecture. Trends in Genetics. 28(5):221-32. [Abstract Chalancon G, Ravarani C, Balaji S, Martinez-Ariez A, Aravind L, Jothi R, M Madan Babu (2012) Interplay between gene expression noise and regulatory network architecture. Trends in Genetics. 28(5):221-32.]
  19. Freudenberg JM†, Ghosh S†, Lackford B†, Yellaboina S, Zheng X, Li R, Cuddapah S, Wade PA, Hu G*, Jothi R* (2012) 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(8):3364-77. (†Co-first authors; *Co-corresponding authors) [Abstract Freudenberg JM†, Ghosh S†, Lackford B†, Yellaboina S, Zheng X, Li R, Cuddapah S, Wade PA, Hu G*, Jothi R* (2012) 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(8):3364-77. (†Co-first authors; *Co-corresponding authors)]
  20. Zheng X, Dumitru R*, Lackford B*, Freudenberg JM*, Singh A, Archer T, Jothi R, Hu G (2012) Cnot1, Cnot2, and Cnot3 maintain mouse and human ES cell identity and inhibit extraembryonic differentiation. Stem Cells 30(5):910-22. (*Equal contribution) [Abstract Zheng X, Dumitru R*, Lackford B*, Freudenberg JM*, Singh A, Archer T, Jothi R, Hu G (2012) Cnot1, Cnot2, and Cnot3 maintain mouse and human ES cell identity and inhibit extraembryonic differentiation. Stem Cells 30(5):910-22. (*Equal contribution)]
  21. Narlikar L and Jothi R (2012) Analyzing ChIP-Seq data to identify protein-DNA binding sites. Methods in Molecular Biology 802:305-22. [Abstract Narlikar L and Jothi R (2012) Analyzing ChIP-Seq data to identify protein-DNA binding sites. Methods in Molecular Biology 802:305-22.]  
  22. Wei G, Abraham B, Yagi R, Jothi R, Cui C, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K (2011) Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types. Immunity  35(2):299-311. [Abstract Wei G, Abraham B, Yagi R, Jothi R, Cui C, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K (2011) Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types. Immunity  35(2):299-311.]  
  23. Ho L†, Miller EL, Ronan JL, Ho W, Jothi R†,*, Crabtree GR* (2011) esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function. Nature Cell Biology 13(8):903-913. (*Co-corresponding authors; †Co-first authors). [Abstract Ho L†, Miller EL, Ronan JL, Ho W, Jothi R†,*, Crabtree GR* (2011) esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function. Nature Cell Biology 13(8):903-913. (*Co-corresponding authors; †Co-first authors).]  
  24. Li L, Jothi R, Cui K, Lee JY, Cohen T, Gorivodsky M, Tzhori I, Zhao Y, Hayes SM, Bresnick EH, Zhao K, Westphal H and Love PE (2011) Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells. Nature Immunology 12(2):129-136. [Abstract Li L, Jothi R, Cui K, Lee JY, Cohen T, Gorivodsky M, Tzhori I, Zhao Y, Hayes SM, Bresnick EH, Zhao K, Westphal H and Love PE (2011) Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells. Nature Immunology 12(2):129-136.]  
  25. Yu S*, Cui K*, Jothi R*, Zhao DM, Jing X, Zhao K, and Xue HH (2011) GABP is required for survival of HSCs and constitutes a core component of HSC-specific gene regulatory circuitry. Blood 117(7):2166-2178. (*Co-first authors) [Abstract Yu S*, Cui K*, Jothi R*, Zhao DM, Jing X, Zhao K, and Xue HH (2011) GABP is required for survival of HSCs and constitutes a core component of HSC-specific gene regulatory circuitry. Blood 117(7):2166-2178. (*Co-first authors)]  
  26. Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Research 39(Database issue):D730-735 [Abstract Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Research 39(Database issue):D730-735]  
  27. Yu S, Zhao DM, Jothi R and Xue HH (2010) Critical requirement of GABPα for normal T Cell Development. Journal of Biological Chemistry 285(14): 10179-10188. [Abstract Yu S, Zhao DM, Jothi R and Xue HH (2010) Critical requirement of GABPα for normal T Cell Development. Journal of Biological Chemistry 285(14): 10179-10188.]
  28. Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM (2009). Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Molecular Systems Biology 5:294 [Abstract Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM (2009). Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Molecular Systems Biology 5:294]  
  29. Liu M, Chen XW, and Jothi R (2009) Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics 25(19): 2492-2499. [Abstract Liu M, Chen XW, and Jothi R (2009) Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics 25(19): 2492-2499.]  
  30. Barski A*, Jothi R*, Cuddapah S*, Cui K, Roh TY, Schones DE, and Zhao K (2009) Chromatin poises miRNA- and protein-coding genes for expression. Genome Research 19(10):1742-1751. (*Co-first authors) [Abstract Barski A*, Jothi R*, Cuddapah S*, Cui K, Roh TY, Schones DE, and Zhao K (2009) Chromatin poises miRNA- and protein-coding genes for expression. Genome Research 19(10):1742-1751. (*Co-first authors)]  
  31. Kallin EM, Cao R, Jothi R, Xia K, Cui K, Zhao K, and Zhang Y (2009) Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes. PLoS Genetics 5(6):e1000506. [Abstract Kallin EM, Cao R, Jothi R, Xia K, Cui K, Zhao K, and Zhang Y (2009) Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes. PLoS Genetics 5(6):e1000506.]  
  32. Ho L*, Jothi R*, Ronan JL, Cui K, Zhao K, and Crabtree GR (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci 106(13):5187-5191. (*Co-first authors) [Abstract Ho L*, Jothi R*, Ronan JL, Cui K, Zhao K, and Crabtree GR (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci 106(13):5187-5191. (*Co-first authors)]  
  33. Cuddapah S*, Jothi R*, Schones DE, Roh TY, Cui K, Zhao K (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research 19(1):24-32. (*Co-first authors) [Abstract Cuddapah S*, Jothi R*, Schones DE, Roh TY, Cui K, Zhao K (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research 19(1):24-32. (*Co-first authors)]
  34. Jothi R and Raghavachari B (2009) Improved approximation algorithms for the single-sink buy-at-bulk network design problem. Journal of Discrete Algorithms, 7(2):249-255.  
  35. Jothi R and Raghavachari B (2009) Degree-Bounded Minimum Spanning Trees. Discrete Applied Mathematics 157(5):960-970.  
  36. Jothi R, Cuddapah S, Barski A, Cui K, and Zhao K. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research 36(16):5221-5231. [Abstract Jothi R, Cuddapah S, Barski A, Cui K, and Zhao K. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research 36(16):5221-5231.]  
  37. Przytycka TM, Jothi R, Aravind L, and Lipman DJ (2008) Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evolutionary Biology 8:208. [Abstract Przytycka TM, Jothi R, Aravind L, and Lipman DJ (2008) Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evolutionary Biology 8:208.]  
  38. Raghavachari B, Tasneem A, Przytycka TM, and Jothi R (2008) DOMINE: A database of protein domain interactions. Nucleic Acids Research 36(Database issue):D656-661. [Abstract Raghavachari B, Tasneem A, Przytycka TM, and Jothi R (2008) DOMINE: A database of protein domain interactions. Nucleic Acids Research 36(Database issue):D656-661.]  
  39. Jothi R and Przytycka TM (2008) Computational approaches to predict protein-protein and domain-domain interactions. Bioinformatics Algorithms: Techniques and Applications (Eds: Alexander Zelikovsky and Ion Mandoiu), Wiley, John & Sons.
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