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NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region.

Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R.

Nat Commun. 2019 Jul 11;10(1):3072. doi: 10.1038/s41467-019-10905-7.


Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency.

Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R.

Cell Syst. 2019 May 22;8(5):427-445.e10. doi: 10.1016/j.cels.2019.03.012. Epub 2019 May 8.


GLIS3 Transcriptionally Activates WNT Genes to Promote Differentiation of Human Embryonic Stem Cells into Posterior Neural Progenitors.

Jeon K, Kumar D, Conway AE, Park K, Jothi R, Jetten AM.

Stem Cells. 2019 Feb;37(2):202-215. doi: 10.1002/stem.2941. Epub 2018 Dec 2.


GLIS3 is indispensable for TSH/TSHR-dependent thyroid hormone biosynthesis and follicular cell proliferation.

Kang HS, Kumar D, Liao G, Lichti-Kaiser K, Gerrish K, Liao XH, Refetoff S, Jothi R, Jetten AM.

J Clin Invest. 2017 Dec 1;127(12):4326-4337. doi: 10.1172/JCI94417. Epub 2017 Oct 30.


Intragenic Enhancers Attenuate Host Gene Expression.

Cinghu S, Yang P, Kosak JP, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R.

Mol Cell. 2017 Oct 5;68(1):104-117.e6. doi: 10.1016/j.molcel.2017.09.010.


CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State.

Zheng X, Yang P, Lackford B, Bennett BD, Wang L, Li H, Wang Y, Miao Y, Foley JF, Fargo DC, Jin Y, Williams CJ, Jothi R, Hu G.

Stem Cell Reports. 2016 Nov 8;7(5):897-910. doi: 10.1016/j.stemcr.2016.09.007. Epub 2016 Oct 13.


mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes.

Minard AY, Tan SX, Yang P, Fazakerley DJ, Domanova W, Parker BL, Humphrey SJ, Jothi R, Stöckli J, James DE.

Cell Rep. 2016 Sep 27;17(1):29-36. doi: 10.1016/j.celrep.2016.08.086.


Self-directed learning modules of CT scan images to improve students' perception of gross anatomy.

Kumar PA, Jothi R, Mathivanan D.

Educ Health (Abingdon). 2016 May-Aug;29(2):152-5. doi: 10.4103/1357-6283.188778.


KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis.

Yang P, Patrick E, Humphrey SJ, Ghazanfar S, James DE, Jothi R, Yang JY.

Proteomics. 2016 Jul;16(13):1868-71. doi: 10.1002/pmic.201600068. Epub 2016 May 27.


Functional grouping of similar genes using eigenanalysis on minimum spanning tree based neighborhood graph.

Jothi R, Mohanty SK, Ojha A.

Comput Biol Med. 2016 Apr 1;71:135-48. doi: 10.1016/j.compbiomed.2016.02.007. Epub 2016 Feb 21.


Traumatic transfers: calibration is adversely affected when prediction models are transferred between trauma care contexts in India and the United States.

Gerdin M, Roy N, Felländer-Tsai L, Tomson G, von Schreeb J, Petzold M; Towards Improved Trauma Care Outcomes in India (TITCO) Consortium, Gupta A, Jhakal A, Basak D, Mohamed Ismail D, Yabo D, Jegadeesan K, Kamble J, Saha ML, Nitnaware M, Khajanchi M, Jothi R, Ghosh SN, Bhoi S, Mahindrakar S, Dharap S, Rao S, Kamal V, Kumar V, Tirlotkar S.

J Clin Epidemiol. 2016 Jun;74:177-86. doi: 10.1016/j.jclinepi.2016.01.004. Epub 2016 Jan 15.


The Madras Institute of Neurology, Madras Medical College, Chennai.

Ramesh VG, Bhanu K, Jothi R.

Neurol India. 2015 Nov-Dec;63(6):940-6.


Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates.

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.

Cell Metab. 2015 Nov 3;22(5):922-35. doi: 10.1016/j.cmet.2015.09.001. Epub 2015 Oct 1. Erratum in: Cell Metab. 2015 Nov 3;22(5):948.


Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data.

Yang P, Humphrey SJ, James DE, Yang YH, Jothi R.

Bioinformatics. 2016 Jan 15;32(2):252-9. doi: 10.1093/bioinformatics/btv550. Epub 2015 Sep 22.


Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.

Yang P, Zheng X, Jayaswal V, Hu G, Yang JY, Jothi R.

PLoS Comput Biol. 2015 Aug 7;11(8):e1004403. doi: 10.1371/journal.pcbi.1004403. eCollection 2015 Aug.


DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis.

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.

Nat Commun. 2015 Apr 24;6:6910. doi: 10.1038/ncomms7910.


Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.

Oldfield AJ, Yang P, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R.

Mol Cell. 2014 Sep 4;55(5):708-22. doi: 10.1016/j.molcel.2014.07.005. Epub 2014 Aug 14.


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 Genet. 2014 May 15;10(5):e1004331. doi: 10.1371/journal.pgen.1004331. eCollection 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 B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G.

Cell Stem Cell. 2014 May 1;14(5):575-91. doi: 10.1016/j.stem.2014.02.013.


Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis.

Cinghu S, Yellaboina S, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1581-90. doi: 10.1073/pnas.1318598111. Epub 2014 Apr 7.


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. 2014 Apr 16;33(8):878-89. doi: 10.1002/embj.201386537. Epub 2014 Mar 4.


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. 2014 May;9(5):747-59. doi: 10.4161/epi.28075. Epub 2014 Feb 12.


Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells.

Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, Jothi R, Resnick MA.

Nucleic Acids Res. 2013 Aug;41(15):7286-301. doi: 10.1093/nar/gkt504. Epub 2013 Jun 17.


Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation.

Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE.

Blood. 2013 May 30;121(22):4575-85. doi: 10.1182/blood-2013-01-479451. Epub 2013 Apr 22.


RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo.

Takeda Y, Jothi R, Birault V, Jetten AM.

Nucleic Acids Res. 2012 Sep 1;40(17):8519-35. Epub 2012 Jun 29.


Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation.

Zheng X, Dumitru R, Lackford BL, Freudenberg JM, Singh AP, Archer TK, Jothi R, Hu G.

Stem Cells. 2012 May;30(5):910-22. doi: 10.1002/stem.1070.


Interplay between gene expression noise and regulatory network architecture.

Chalancon G, Ravarani CN, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM.

Trends Genet. 2012 May;28(5):221-32. doi: 10.1016/j.tig.2012.01.006. Epub 2012 Feb 25. Review.


Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity.

Freudenberg JM, Ghosh S, Lackford BL, Yellaboina S, Zheng X, Li R, Cuddapah S, Wade PA, Hu G, Jothi R.

Nucleic Acids Res. 2012 Apr;40(8):3364-77. doi: 10.1093/nar/gkr1253. Epub 2011 Dec 30.


ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Narlikar L, Jothi R.

Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.


Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types.

Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K.

Immunity. 2011 Aug 26;35(2):299-311. doi: 10.1016/j.immuni.2011.08.007.


esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function.

Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R, Crabtree GR.

Nat Cell Biol. 2011 Jul 24;13(8):903-13. doi: 10.1038/ncb2285.


A comparative study on the efficacy, safety, and cost-effectiveness of bimatoprost/timolol and dorzolamide/timolol combinations in glaucoma patients.

Jothi R, Ismail AM, Senthamarai R, Pal S.

Indian J Pharmacol. 2010 Dec;42(6):362-5. doi: 10.4103/0253-7613.71917.


Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells.

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.

Nat Immunol. 2011 Feb;12(2):129-36. doi: 10.1038/ni.1978. Epub 2010 Dec 26.


GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells.

Yu S, Cui K, Jothi R, Zhao DM, Jing X, Zhao K, Xue HH.

Blood. 2011 Feb 17;117(7):2166-78. doi: 10.1182/blood-2010-09-306563. Epub 2010 Dec 7.


DOMINE: a comprehensive collection of known and predicted domain-domain interactions.

Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R.

Nucleic Acids Res. 2011 Jan;39(Database issue):D730-5. doi: 10.1093/nar/gkq1229. Epub 2010 Nov 27.


Critical requirement of GABPalpha for normal T cell development.

Yu S, Zhao DM, Jothi R, Xue HH.

J Biol Chem. 2010 Apr 2;285(14):10179-88. doi: 10.1074/jbc.M109.088740. Epub 2010 Feb 5.


Chromatin poises miRNA- and protein-coding genes for expression.

Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K.

Genome Res. 2009 Oct;19(10):1742-51. doi: 10.1101/gr.090951.109. Epub 2009 Aug 27. Erratum in: Genome Res. 2009 Dec;19(12):2343.


Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.

Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM.

Mol Syst Biol. 2009;5:294. doi: 10.1038/msb.2009.52. Epub 2009 Aug 18.


Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks.

Liu M, Chen XW, Jothi R.

Bioinformatics. 2009 Oct 1;25(19):2492-9. doi: 10.1093/bioinformatics/btp480. Epub 2009 Aug 10.


Genome-wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes.

Kallin EM, Cao R, Jothi R, Xia K, Cui K, Zhao K, Zhang Y.

PLoS Genet. 2009 Jun;5(6):e1000506. doi: 10.1371/journal.pgen.1000506. Epub 2009 Jun 5.


An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network.

Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR.

Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5187-91. doi: 10.1073/pnas.0812888106. Epub 2009 Mar 11.


Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.

Genome Res. 2009 Jan;19(1):24-32. doi: 10.1101/gr.082800.108. Epub 2008 Dec 3.


Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.


Differences in evolutionary pressure acting within highly conserved ortholog groups.

Przytycka TM, Jothi R, Aravind L, Lipman DJ.

BMC Evol Biol. 2008 Jul 17;8:208. doi: 10.1186/1471-2148-8-208.


DOMINE: a database of protein domain interactions.

Raghavachari B, Tasneem A, Przytycka TM, Jothi R.

Nucleic Acids Res. 2008 Jan;36(Database issue):D656-61. Epub 2007 Oct 2.


Predicting protein domain interactions from coevolution of conserved regions.

Kann MG, Jothi R, Cherukuri PF, Przytycka TM.

Proteins. 2007 Jun 1;67(4):811-20.


Predicting domain-domain interactions using a parsimony approach.

Guimarães KS, Jothi R, Zotenko E, Przytycka TM.

Genome Biol. 2006;7(11):R104.

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