Jesse R Dixon

Jesse R Dixon

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Jesse R Dixon

Jesse R Dixon

Publications by authors named "Jesse R Dixon"

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18Publications

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Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation.

Proc Natl Acad Sci U S A 2019 Jul 24;116(28):14011-14018. Epub 2019 Jun 24.

Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1901423116
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http://dx.doi.org/10.1073/pnas.1901423116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628819PMC
July 2019

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.

Cell Syst 2019 Jun;8(6):494-505.e14

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706282PMC
June 2019

A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells.

Nat Commun 2018 12 3;9(1):5139. Epub 2018 Dec 3.

Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-018-07528-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277444PMC
December 2018

Allelic reprogramming of 3D chromatin architecture during early mammalian development.

Nature 2017 07;547(7662):232-235

Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1038/nature23263DOI Listing
July 2017

Chromatin Domains: The Unit of Chromosome Organization.

Mol Cell 2016 06;62(5):668-80

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371509PMC
June 2016

Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.

BMC Genomics 2015 Nov 5;16:900. Epub 2015 Nov 5.

Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1186/s12864-015-1949-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636068PMC
November 2015

CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.

PLoS One 2014 8;9(12):e114485. Epub 2014 Dec 8.

Ludwig Institute for Cancer Research, San Diego, California, United States of America; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114485PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259346PMC
August 2015

A CRISPR Connection between Chromatin Topology and Genetic Disorders.

Cell 2015 May;161(5):955-957

Ludwig Institute for Cancer Research, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0653.

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http://dx.doi.org/10.1016/j.cell.2015.04.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478077PMC
May 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Chromatin architecture reorganization during stem cell differentiation.

Nature 2015 Feb;518(7539):331-6

1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.

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http://www.nature.com/articles/nature14222
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http://dx.doi.org/10.1038/nature14222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515363PMC
February 2015

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.

Proc Natl Acad Sci U S A 2014 Jan 13;111(3):996-1001. Epub 2013 Dec 13.

Department of Cell Biology, Biophysical Genomics, Department of Cell Biology, Center for Biomics, Cancer Genomics Center, Erasmus Medical Center, 3015 GE, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1317788111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903193PMC
January 2014

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.

Nat Biotechnol 2013 Dec 3;31(12):1111-8. Epub 2013 Nov 3.

1] Ludwig Institute for Cancer Research, La Jolla, California, USA. [2] Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA. [3].

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http://dx.doi.org/10.1038/nbt.2728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180835PMC
December 2013

A high-resolution map of the three-dimensional chromatin interactome in human cells.

Nature 2013 Nov 20;503(7475):290-4. Epub 2013 Oct 20.

1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA [2].

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http://dx.doi.org/10.1038/nature12644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838900PMC
November 2013

Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Nature 2012 Apr 11;485(7398):376-80. Epub 2012 Apr 11.

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature11082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356448PMC
April 2012