Ramya Raviram

Ramya Raviram

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Ramya Raviram

Ramya Raviram

Publications by authors named "Ramya Raviram"

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24Publications

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MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.

PLoS Comput Biol 2019 04 15;15(4):e1006982. Epub 2019 Apr 15.

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483256PMC
April 2019

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase.

Nat Struct Mol Biol 2019 Mar 18;26(3):164-174. Epub 2019 Feb 18.

Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41594-019-0187-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403010PMC
March 2019

Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development.

Nat Commun 2018 09 5;9(1):3594. Epub 2018 Sep 5.

The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, 10016, USA.

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http://www.nature.com/articles/s41467-018-05834-w
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http://dx.doi.org/10.1038/s41467-018-05834-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125341PMC
September 2018

Capturing the Onset of PRC2-Mediated Repressive Domain Formation.

Mol Cell 2018 06;70(6):1149-1162.e5

Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.05.023DOI Listing
June 2018

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies.

PLoS Genet 2018 01 29;14(1):e1007181. Epub 2018 Jan 29.

Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805373PMC
January 2018

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;21(5):1267-1280

Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247173142
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http://dx.doi.org/10.1016/j.celrep.2017.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687844PMC
October 2017

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Nucleic Acids Res 2016 Oct 20;44(18):8714-8725. Epub 2016 Jul 20.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA Program of Applied Mathematics, Yale university, New Haven, CT, USA

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http://dx.doi.org/10.1093/nar/gkw568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062970PMC
October 2016

Breaking TADs: insights into hierarchical genome organization.

Epigenomics 2015 ;7(4):523-6

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.2217/epi.15.25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624204PMC
June 2016

CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci.

Nat Commun 2016 05 25;7:11707. Epub 2016 May 25.

Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA.

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http://dx.doi.org/10.1038/ncomms11707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894952PMC
May 2016

Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination.

J Exp Med 2016 Mar 22;213(3):303-12. Epub 2016 Feb 22.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France

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http://dx.doi.org/10.1084/jem.20141967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813673PMC
March 2016

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

PLoS Comput Biol 2016 Mar 3;12(3):e1004780. Epub 2016 Mar 3.

Department of Pathology, New York University School of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777514PMC
March 2016

Long-Range Regulation of V(D)J Recombination.

Adv Immunol 2015 20;128:123-82. Epub 2015 Aug 20.

Department of Pathology, New York University School of Medicine, New York, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.ai.2015.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660984PMC
February 2016

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms.

J Exp Med 2015 Oct 5;212(11):1833-50. Epub 2015 Oct 5.

Howard Hughes Medical Institute, Department of Pathology, and Center for Health Informatics and Bioinformatics, School of Medicine and Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10016 Howard Hughes Medical Institute, Department of Pathology, and Center for Health Informatics and Bioinformatics, School of Medicine and Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10016

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http://dx.doi.org/10.1084/jem.20151323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612095PMC
October 2015

Interpreting 4C-Seq data: how far can we go?

Epigenomics 2014 ;6(5):455-7

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.2217/epi.14.47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406053PMC
July 2015

CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation.

Science 2015 Feb;347(6225):1017-21

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1126/science.1262088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428148PMC
February 2015

High correlation of the response of upper and lower lobe small airway epithelium to smoking.

PLoS One 2013 9;8(9):e72669. Epub 2013 Sep 9.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America ; Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072669PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767732PMC
June 2014