Peter V Kharchenko

Peter V Kharchenko

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Peter V Kharchenko

Peter V Kharchenko

Publications by authors named "Peter V Kharchenko"

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56Publications

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Joint analysis of heterogeneous single-cell RNA-seq dataset collections.

Nat Methods 2019 Aug 15;16(8):695-698. Epub 2019 Jul 15.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41592-019-0466-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684315PMC
August 2019

Cell Kinetics in the Adult Neurogenic Niche and Impact of Diet-Induced Accelerated Aging.

J Neurosci 2019 Apr 8;39(15):2810-2822. Epub 2019 Feb 8.

Department of Preclinical Research, BioChron LLC, Worcester, Massachusetts 01605,

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http://dx.doi.org/10.1523/JNEUROSCI.2730-18.2019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462444PMC
April 2019

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.

Nat Biotechnol 2018 01 11;36(1):70-80. Epub 2017 Dec 11.

Department of Bioengineering, University of California San Diego, La Jolla, California, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4038
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http://dx.doi.org/10.1038/nbt.4038DOI Listing
January 2018

Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate.

J Neurosci 2017 02 13;37(7):1900-1909. Epub 2017 Jan 13.

Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts 02118,

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http://dx.doi.org/10.1523/JNEUROSCI.3222-16.2017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320617PMC
February 2017

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.

Cancer Cell 2016 Nov 3;30(5):750-763. Epub 2016 Nov 3.

Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127278PMC
November 2016

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.

Cell 2016 11;167(5):1310-1322.e17

Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(16)31466-0.pdf
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http://www.cell.com/cms/attachment/2072756198/2068594890/mmc
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http://dx.doi.org/10.1016/j.cell.2016.10.045DOI Listing
November 2016

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.

Cell 2016 Aug;166(5):1147-1162.e15

Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.07.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5248659PMC
August 2016

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.

Proc Natl Acad Sci U S A 2015 Dec 2;112(49):15148-53. Epub 2015 Nov 2.

Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129; Howard Hughes Medical Institute, Chevy Chase, MD 20815; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114;

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http://dx.doi.org/10.1073/pnas.1518008112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679016PMC
December 2015

DAZL regulates Tet1 translation in murine embryonic stem cells.

EMBO Rep 2015 Jul 15;16(7):791-802. Epub 2015 Jun 15.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands Department of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands

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http://dx.doi.org/10.15252/embr.201540538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515119PMC
July 2015

The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains.

Genes Dev 2015 Jul;29(14):1507-23

Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;

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http://dx.doi.org/10.1101/gad.267583.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526735PMC
July 2015

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.

Nat Neurosci 2015 Jan 24;18(1):145-53. Epub 2014 Nov 24.

Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nn.3881DOI Listing
January 2015

Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes.

Proc Natl Acad Sci U S A 2015 Jan 24;112(2):554-9. Epub 2014 Dec 24.

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1422580112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299249PMC
January 2015

BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.

Curr Protoc Mol Biol 2015 Jan 5;109:21.30.1-32. Epub 2015 Jan 5.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/0471142727.mb2130s109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308290PMC
January 2015

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Cancer Cell 2014 Dec;26(6):813-825

Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302418PMC
December 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Bayesian approach to single-cell differential expression analysis.

Nat Methods 2014 Jul 18;11(7):740-2. Epub 2014 May 18.

1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.2967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112276PMC
July 2014

Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs.

Genes Dev 2014 Jul;28(13):1445-60

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;

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http://genesdev.cshlp.org/cgi/doi/10.1101/gad.241950.114
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http://dx.doi.org/10.1101/gad.241950.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083088PMC
July 2014

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.

Proc Natl Acad Sci U S A 2014 Feb 3;111(7):2488-93. Epub 2014 Feb 3.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1400648111
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http://dx.doi.org/10.1073/pnas.1400648111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932854PMC
February 2014

Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A.

Proc Natl Acad Sci U S A 2014 Jan 16;111(1):421-6. Epub 2013 Dec 16.

Department of Medicine, Brigham and Women's Hospital, Program in Virology, Department of Microbiology and Immunobiology, and Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115.

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http://dx.doi.org/10.1073/pnas.1321704111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890834PMC
January 2014

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.

Proc Natl Acad Sci U S A 2013 Nov 28;110(46):18537-42. Epub 2013 Oct 28.

Department of Medicine, Brigham and Women's Hospital, and Department of Microbiology and Immunobiology, Harvard University, Boston, MA 02115.

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http://dx.doi.org/10.1073/pnas.1317608110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832032PMC
November 2013

Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.

Mol Cell Biol 2013 Aug 17;33(16):3274-85. Epub 2013 Jun 17.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1128/MCB.00275-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753906PMC
August 2013

Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila.

Nat Struct Mol Biol 2013 Feb 6;20(2):202-9. Epub 2013 Jan 6.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674866PMC
February 2013

The genomic binding sites of a noncoding RNA.

Proc Natl Acad Sci U S A 2011 Dec 5;108(51):20497-502. Epub 2011 Dec 5.

Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.

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http://dx.doi.org/10.1073/pnas.1113536108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251105PMC
December 2011

Evidence for dosage compensation between the X chromosome and autosomes in mammals.

Nat Genet 2011 Nov 28;43(12):1167-9; author reply 1171-2. Epub 2011 Nov 28.

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http://dx.doi.org/10.1038/ng.991DOI Listing
November 2011

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.

Nature 2011 Mar;471(7336):115-8

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/nature09757
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http://dx.doi.org/10.1038/nature09757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076316PMC
March 2011

Chromatin signatures of the Drosophila replication program.

Genome Res 2011 Feb 22;21(2):164-74. Epub 2010 Dec 22.

Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1101/gr.116038.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032920PMC
February 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Estimating enrichment of repetitive elements from high-throughput sequence data.

Genome Biol 2010 28;11(6):R69. Epub 2010 Jun 28.

Harvard-MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/gb-2010-11-6-r69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911117PMC
November 2010

Analysis of primary structure of chromatin with next-generation sequencing.

Epigenomics 2010 Apr;2(2):187-197

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St., Boston, MA 02115 USA.

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http://dx.doi.org/10.2217/epi.09.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196531PMC
April 2010

A region of the human HOXD cluster that confers polycomb-group responsiveness.

Cell 2010 Jan;140(1):99-110

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

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http://dx.doi.org/10.1016/j.cell.2009.12.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324942PMC
January 2010

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes.

Genome Res 2009 Jun 26;19(6):967-77. Epub 2009 Feb 26.

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.084830.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694475PMC
June 2009

Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Nat Biotechnol 2008 Dec 16;26(12):1351-9. Epub 2008 Nov 16.

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St., Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nbt.1508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597701PMC
December 2008

Nucleosome positioning in human HOX gene clusters.

Genome Res 2008 Oct 22;18(10):1554-61. Epub 2008 Aug 22.

Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.075952.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556261PMC
October 2008