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Ramya Raviram, PhD - Publications

Affiliations: 
2017-2020 Ludwig Institute for Cancer Research, San Diego 
Area:
Genomics
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29 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
2023 Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, et al. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proceedings of the National Academy of Sciences of the United States of America. 120: e2210991120. PMID 37155843 DOI: 10.1073/pnas.2210991120  0.746
2020 Raviram R, Raman A, Preissl S, Ning J, Wu S, Deynze K, Chen C, Ren B. EPCO-19. INTEGRATED ANALYSIS OF INTRA-TUMORAL HETEROGENEITY IN GLIOBLASTOMAS THROUGH SINGLE NUCLEI ATAC-SEQ AND RNA-SEQ Neuro-Oncology. 22: ii73-ii73. DOI: 10.1093/neuonc/noaa215.298  0.492
2019 Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. PMID 31748743 DOI: 10.1038/S41586-019-1763-5  0.756
2019 Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Perez-Duran P, Alvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortes JR, et al. Gata3-controlled nucleosome eviction drives Myc enhancer activity in T-cell development and leukemia. Cancer Discovery. PMID 31519704 DOI: 10.1158/2159-8290.Cd-19-0471  0.639
2019 Chowdhry S, Zanca C, Rajkumar U, Koga T, Diao Y, Raviram R, Liu F, Turner K, Yang H, Brunk E, Bi J, Furnari F, Bafna V, Ren B, Mischel PS. NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. PMID 31019297 DOI: 10.1038/S41586-019-1150-2  0.688
2019 Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Plos Computational Biology. 15: e1006982. PMID 30986246 DOI: 10.1371/Journal.Pcbi.1006982  0.571
2019 Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F, Corbett KD. Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nature Structural & Molecular Biology. PMID 30778236 DOI: 10.1038/S41594-019-0187-0  0.546
2018 Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA. Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate. Genome Biology. 19: 216. PMID 30541598 DOI: 10.1186/S13059-018-1598-7  0.763
2018 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. Nature Communications. 9: 3594. PMID 30185805 DOI: 10.1038/S41467-018-05834-W  0.646
2018 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. Molecular Cell. 70: 1149-1162.e5. PMID 29932905 DOI: 10.1016/J.Molcel.2018.05.023  0.74
2018 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. Nature Neuroscience. PMID 29497140 DOI: 10.1038/S41593-018-0114-4  0.474
2018 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. Nature Neuroscience. PMID 29434377 DOI: 10.1038/S41593-018-0079-3  0.574
2018 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, et al. Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies. Plos Genetics. 14: e1007181. PMID 29377931 DOI: 10.1371/Journal.Pgen.1007181  0.581
2018 Belver L, Yang AY, Herranz D, Quinn A, Brundu FG, Perez-Duran P, Alvarez S, Gurung D, Rocha PP, Raviram R, Rashkovan M, Rabadan R, Ferrando AA. Suppression of GATA3 Binding Drives Selective Abrogation of NOTCH1-MYC Enhancer Activity By Nucleosome Invasion in Thymocyte Development and Leukemia Blood. 132: 545-545. DOI: 10.1182/Blood-2018-99-119423  0.601
2017 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, et al. Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. Cell Reports. 21: 1267-1280. PMID 29091765 DOI: 10.1016/J.Celrep.2017.10.009  0.768
2017 Modrek A, Golub D, Khan T, Prado J, Bowman C, Deng J, Zhang G, Rocha P, Raviram R, Lazaris H, Kader M, Dhaliwal J, Chi A, Golfinos J, Tsirigos A, et al. LGG-11. LOW-GRADE ASTROCYTOMA CORE MUTATIONS IN IDH1, P53 AND ATRX COOPERATE TO BLOCK DIFFERENTIATION OF HUMAN NEURAL STEM CELLS VIA EPIGENETIC REPRESSION OF SOX2 Neuro-Oncology. 19: iv35-iv35. DOI: 10.1093/Neuonc/Nox083.144  0.711
2016 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, et al. MED12 Regulates HSC-Specific Enhancers Independently of Mediator Kinase Activity to Control Hematopoiesis. Cell Stem Cell. PMID 27570068 DOI: 10.1016/J.Stem.2016.08.004  0.743
2016 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 Research. PMID 27439714 DOI: 10.1093/Nar/Gkw568  0.781
2016 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 Reports. PMID 27320916 DOI: 10.1016/J.Celrep.2016.05.073  0.757
2016 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 Reports. PMID 27239026 DOI: 10.1016/J.Celrep.2016.04.087  0.729
2016 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. Nature Communications. 7: 11707. PMID 27222091 DOI: 10.1038/Ncomms11707  0.743
2016 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 Computational Biology. 12: e1004780. PMID 26938081 DOI: 10.1371/Journal.Pcbi.1004780  0.754
2016 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. The Journal of Experimental Medicine. 213: 303-12. PMID 26903242 DOI: 10.1084/Jem.20141967  0.778
2016 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 Journal of Experimental Medicine. 213: 303-312. DOI: 10.1084/jem.20141967  0.711
2015 Proudhon C, Hao B, Raviram R, Chaumeil J, Skok JA. Long-Range Regulation of V(D)J Recombination. Advances in Immunology. 128: 123-82. PMID 26477367 DOI: 10.1016/Bs.Ai.2015.07.003  0.665
2015 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, et al. Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms. The Journal of Experimental Medicine. PMID 26438359 DOI: 10.1084/Jem.20151323  0.761
2015 Rocha PP, Raviram R, Bonneau R, Skok JA. Breaking TADs: insights into hierarchical genome organization. Epigenomics. 7: 523-6. PMID 26111025 DOI: 10.2217/Epi.15.25  0.788
2015 Narendra V, Rocha PP, An D, Raviram R, Skok JA, Mazzoni EO, Reinberg D. Transcription. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science (New York, N.Y.). 347: 1017-21. PMID 25722416 DOI: 10.1126/Science.1262088  0.727
2014 Raviram R, Rocha PP, Bonneau R, Skok JA. Interpreting 4C-Seq data: how far can we go? Epigenomics. 6: 455-7. PMID 25431936 DOI: 10.2217/Epi.14.47  0.786
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