William J Greenleaf

William J Greenleaf

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William J Greenleaf

William J Greenleaf

Publications by authors named "William J Greenleaf"

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59Publications

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A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas.

Cell Syst 2018 Aug 10. Epub 2018 Aug 10.

Department of Developmental Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA. Electronic address:

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August 2018

Unsupervised clustering and epigenetic classification of single cells.

Nat Commun 2018 Jun 20;9(1):2410. Epub 2018 Jun 20.

Department of Statistics, Stanford University, Stanford, CA, 94305, USA.

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June 2018

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Cell 2018 May 26;173(6):1535-1548.e16. Epub 2018 Apr 26.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94025, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

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May 2018

Rapid chromatin repression by Aire provides precise control of immune tolerance.

Nat Immunol 2018 Feb 15;19(2):162-172. Epub 2018 Jan 15.

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

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February 2018

INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division.

Cell Rep 2018 Jan;22(3):611-623

Department of Biology, Stanford University, Stanford, CA 94305, USA. Electronic address:

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January 2018

Chromatin accessibility dynamics reveal novel functional enhancers in .

Genome Res 2017 12 15;27(12):2096-2107. Epub 2017 Nov 15.

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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December 2017

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Nat Methods 2017 Oct 21;14(10):975-978. Epub 2017 Aug 21.

Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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October 2017

Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci.

Cell Stem Cell 2017 09 10;21(3):305-318.e8. Epub 2017 Aug 10.

Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA. Electronic address:

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September 2017

Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.

Cancer Cell 2017 07 15;32(1):27-41.e4. Epub 2017 Jun 15.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2017

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.

Nat Genet 2017 Mar 23;49(3):377-386. Epub 2017 Jan 23.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.

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March 2017

Epigenomics of human CD8 T cell differentiation and aging.

Sci Immunol 2017 Feb 17;2(8). Epub 2017 Feb 17.

Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306.

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February 2017

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping.

Nature 2017 01 26;541(7636):237-241. Epub 2016 Dec 26.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.

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January 2017

Single-cell epigenomic variability reveals functional cancer heterogeneity.

Genome Biol 2017 01 24;18(1):15. Epub 2017 Jan 24.

Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA.

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January 2017

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Nat Methods 2016 Nov 19;13(11):919-922. Epub 2016 Sep 19.

Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.

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November 2016

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.

Cell 2016 Jul 30;166(2):328-342. Epub 2016 Jun 30.

Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2016

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.

Nat Genet 2016 Feb 21;48(2):117-25. Epub 2015 Dec 21.

Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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February 2016

Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool.

Trends Cell Biol 2015 Dec 1;25(12):716-719. Epub 2015 Oct 1.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA. Electronic address:

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December 2015

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

Genome Res 2015 Nov 27;25(11):1757-70. Epub 2015 Aug 27.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Applied Physics, Stanford University, Stanford, California 94305, USA.

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November 2015

Unraveling the 3D genome: genomics tools for multiscale exploration.

Trends Genet 2015 Jul 14;31(7):357-72. Epub 2015 Apr 14.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2015

Single-cell chromatin accessibility reveals principles of regulatory variation.

Nature 2015 Jul 17;523(7561):486-90. Epub 2015 Jun 17.

1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Applied Physics, Stanford University, Stanford, California 94025, USA.

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July 2015

Individuality and variation of personal regulomes in primary human T cells.

Cell Syst 2015 Jul;1(1):51-61

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.

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July 2015

Assaying the epigenome in limited numbers of cells.

Methods 2015 Jan 22;72:51-6. Epub 2014 Oct 22.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States. Electronic address:

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January 2015

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.

Curr Protoc Mol Biol 2015 Jan 5;109:21.29.1-9. Epub 2015 Jan 5.

Department of Genetics, Stanford University School of Medicine, Stanford, California; Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California.

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January 2015

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.

Nat Biotechnol 2014 Jun 13;32(6):562-8. Epub 2014 Apr 13.

Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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June 2014

A conditional system to specifically link disruption of protein-coding function with reporter expression in mice.

Cell Rep 2014 Jun 12;7(6):2078-86. Epub 2014 Jun 12.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305-5456, USA. Electronic address:

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June 2014

Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy.

Neuromuscul Disord 2014 May 10;24(5):431-5. Epub 2014 Feb 10.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Electronic address:

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May 2014

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

Science 2014 May 1;344(6187):1042-7. Epub 2014 May 1.

Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.

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May 2014

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Nat Methods 2013 Dec 6;10(12):1213-8. Epub 2013 Oct 6.

1] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA. [2] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA. [3] Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.

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December 2013

Fluorogenic DNA sequencing in PDMS microreactors.

Nat Methods 2011 Jun 12;8(7):575-80. Epub 2011 Jun 12.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

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June 2011

An optical apparatus for rotation and trapping.

Methods Enzymol 2010 ;475:377-404

Department of Biology, Stanford University, Stanford, California, USA.

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October 2010

Single-molecule studies of RNA polymerase: motoring along.

Annu Rev Biochem 2008 ;77:149-76

Biophysics Program, Stanford University, Stanford, CA 94305, USA.

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September 2008

Applied force reveals mechanistic and energetic details of transcription termination.

Cell 2008 Mar;132(6):971-82

Biophysics Program, Stanford University, Stanford, CA 94305, USA.

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March 2008

Direct observation of hierarchical folding in single riboswitch aptamers.

Science 2008 Feb 3;319(5863):630-3. Epub 2008 Jan 3.

Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.

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February 2008

High-resolution, single-molecule measurements of biomolecular motion.

Annu Rev Biophys Biomol Struct 2007 ;36:171-90

Department of Applied Physics, Stanford University, Stanford, California 94305-5030, USA.

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August 2007

Molecule by molecule, the physics and chemistry of life: SMB 2007.

Nat Chem Biol 2007 Apr;3(4):193-7

Department of Applied Physics, Stanford University, Stanford, California 94305, USA.

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April 2007

Single-molecule, motion-based DNA sequencing using RNA polymerase.

Science 2006 Aug;313(5788):801

Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.

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August 2006

Direct observation of base-pair stepping by RNA polymerase.

Nature 2005 Nov 13;438(7067):460-5. Epub 2005 Nov 13.

Department of Applied Physics, Stanford University, Stanford, California 94305, USA.

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November 2005

Passive all-optical force clamp for high-resolution laser trapping.

Phys Rev Lett 2005 Nov 8;95(20):208102. Epub 2005 Nov 8.

Department of Applied Physics, Stanford University, Stanford, California 94305-5020, USA.

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November 2005