Ramya Raviram

TitlePostdoctoral Scholar
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0367
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Issuree PD, Day K, Au C, Raviram R, Zappile P, Skok JA, Xue HH, Myers RM, Littman DR. Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development. Nat Commun. 2018 Sep 05; 9(1):3594. PMID: 30185805.
      View in: PubMed
    2. Oksuz O, Narendra V, Lee CH, Descostes N, LeRoy G, Raviram R, Blumenberg L, Karch K, Rocha PP, Garcia BA, Skok JA, Reinberg D. Capturing the Onset of PRC2-Mediated Repressive Domain Formation. Mol Cell. 2018 Jun 21; 70(6):1149-1162.e5. PMID: 29932905.
      View in: PubMed
    3. Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci. 2018 Mar 01. PMID: 29497140.
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    4. Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci. 2018 Mar; 21(3):432-439. PMID: 29434377.
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    5. O'Brien LL, Guo Q, Bahrami-Samani E, Park JS, Hasso SM, Lee YJ, Fang A, Kim AD, Guo J, Hong TM, Peterson KA, Lozanoff S, Raviram R, Ren B, Fogelgren B, Smith AD, Valouev A, McMahon AP. Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies. PLoS Genet. 2018 Jan; 14(1):e1007181. PMID: 29377931.
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    6. Modrek AS, Golub D, Khan T, Bready D, Prado J, Bowman C, Deng J, Zhang G, Rocha PP, Raviram R, Lazaris C, Stafford JM, LeRoy G, Kader M, Dhaliwal J, Bayin NS, Frenster JD, Serrano J, Chiriboga L, Baitalmal R, Nanjangud G, Chi AS, Golfinos JG, Wang J, Karajannis MA, Bonneau RA, Reinberg D, Tsirigos A, Zagzag D, Snuderl M, Skok JA, Neubert TA, Placantonakis DG. Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. Cell Rep. 2017 Oct 31; 21(5):1267-1280. PMID: 29091765.
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    7. Aranda-Orgilles B, Saldaña-Meyer R, Wang E, Trompouki E, Fassl A, Lau S, Mullenders J, Rocha PP, Raviram R, Guillamot M, Sánchez-Díaz M, Wang K, Kayembe C, Zhang N, Amoasii L, Choudhuri A, Skok JA, Schober M, Reinberg D, Sicinski P, Schrewe H, Tsirigos A, Zon LI, Aifantis I. MED12 Regulates HSC-Specific Enhancers Independently of Mediator Kinase Activity to Control Hematopoiesis. Cell Stem Cell. 2016 12 01; 19(6):784-799. PMID: 27570068.
      View in: PubMed
    8. Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Res. 2016 Oct 14; 44(18):8714-8725. PMID: 27439714.
      View in: PubMed
    9. Rocha PP, Raviram R, Fu Y, Kim J, Luo VM, Aljoufi A, Swanzey E, Pasquarella A, Balestrini A, Miraldi ER, Bonneau R, Petrini J, Schotta G, Skok JA. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep. 2016 06 28; 16(1):48-55. PMID: 27320916; PMCID: PMC4927351.
    10. Proudhon C, Snetkova V, Raviram R, Lobry C, Badri S, Jiang T, Hao B, Trimarchi T, Kluger Y, Aifantis I, Bonneau R, Skok JA. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016 06 07; 15(10):2159-2169. PMID: 27239026; PMCID: PMC4899175.
    11. Fu Y, Rocha PP, Luo VM, Raviram R, Deng Y, Mazzoni EO, Skok JA. CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat Commun. 2016 May 25; 7:11707. PMID: 27222091; PMCID: PMC4894952.
    12. Raviram R, Rocha PP, Müller CL, Miraldi ER, Badri S, Fu Y, Swanzey E, Proudhon C, Snetkova V, Bonneau R, Skok JA. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput Biol. 2016 Mar; 12(3):e1004780. PMID: 26938081; PMCID: PMC4777514.
    13. Thomas-Claudepierre AS, Robert I, Rocha PP, Raviram R, Schiavo E, Heyer V, Bonneau R, Luo VM, Reddy JK, Borggrefe T, Skok JA, Reina-San-Martin B. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med. 2016 Mar 07; 213(3):303-12. PMID: 26903242; PMCID: PMC4813673.
    14. Mullenders J, Aranda-Orgilles B, Lhoumaud P, Keller M, Pae J, Wang K, Kayembe C, Rocha PP, Raviram R, Gong Y, Premsrirut PK, Tsirigos A, Bonneau R, Skok JA, Cimmino L, Hoehn D, Aifantis I. Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms. J Exp Med. 2015 Oct 19; 212(11):1833-50. PMID: 26438359; PMCID: PMC4612095.
    15. Proudhon C, Hao B, Raviram R, Chaumeil J, Skok JA. Long-Range Regulation of V(D)J Recombination. Adv Immunol. 2015; 128:123-82. PMID: 26477367; PMCID: PMC4660984.
    16. Narendra V, Rocha PP, An D, Raviram R, Skok JA, Mazzoni EO, Reinberg D. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science. 2015 Feb 27; 347(6225):1017-21. PMID: 25722416; PMCID: PMC4428148.
    17. Rocha PP, Raviram R, Bonneau R, Skok JA. Breaking TADs: insights into hierarchical genome organization. Epigenomics. 2015; 7(4):523-6. PMID: 26111025; PMCID: PMC4624204.
    18. Raviram R, Rocha PP, Bonneau R, Skok JA. Interpreting 4C-Seq data: how far can we go? Epigenomics. 2014; 6(5):455-7. PMID: 25431936; PMCID: PMC4406053.
    19. Harvey BG, Strulovici-Barel Y, Vincent TL, Mezey JG, Raviram R, Gordon C, Salit J, Tilley AE, Chung A, Sanders A, Crystal RG. High correlation of the response of upper and lower lobe small airway epithelium to smoking. PLoS One. 2013; 8(9):e72669. PMID: 24039793; PMCID: PMC3767732.
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