William J Greenleaf

William J Greenleaf

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William J Greenleaf

William J Greenleaf

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Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers.

Cold Spring Harb Perspect Biol 2019 Oct 1;11(10). Epub 2019 Oct 1.

Stanford University Department of Genetics, Stanford, California 94305.

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http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshpersp
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http://dx.doi.org/10.1101/cshperspect.a032300DOI Listing
October 2019

High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2.

Mol Cell 2019 Aug 16;75(4):741-755.e11. Epub 2019 Jul 16.

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

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http://dx.doi.org/10.1016/j.molcel.2019.06.012DOI Listing
August 2019

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.

Proc Natl Acad Sci U S A 2019 Aug 2;116(34):16847-16855. Epub 2019 Aug 2.

Department of Biochemistry, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1901530116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708322PMC
August 2019

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade.

Proc Natl Acad Sci U S A 2019 Jul 21;116(28):14113-14118. Epub 2019 Jun 21.

Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1903520116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628832PMC
July 2019

Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2.

RNA 2019 06 26;25(6):702-712. Epub 2019 Mar 26.

Department of Biochemistry, Stanford University, Stanford, California 94035, USA.

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http://dx.doi.org/10.1261/rna.068585.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521599PMC
June 2019

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.

Mol Cell 2019 06 8;74(5):966-981.e18. Epub 2019 May 8.

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6645366PMC
June 2019

Chromatin accessibility and the regulatory epigenome.

Nat Rev Genet 2019 04;20(4):207-220

Department of Genetics, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41576-018-0089-8DOI Listing
April 2019

Blind tests of RNA-protein binding affinity prediction.

Proc Natl Acad Sci U S A 2019 Apr 8;116(17):8336-8341. Epub 2019 Apr 8.

Biophysics Program, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1819047116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486753PMC
April 2019

Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip.

Mol Cell 2019 03;73(5):1075-1082.e4

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan-Zuckerberg Initiative, Palo Alto, CA 94301, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.02.019DOI Listing
March 2019

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.

Cell 2019 01 20;176(1-2):361-376.e17. Epub 2018 Dec 20.

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329648PMC
January 2019

High-resolution mapping of cancer cell networks using co-functional interactions.

Mol Syst Biol 2018 12 20;14(12):e8594. Epub 2018 Dec 20.

Department of Genetics, Stanford University, Stanford, CA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300813PMC
http://dx.doi.org/10.15252/msb.20188594DOI Listing
December 2018

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

Cell Syst 2018 09 22;7(3):310-322.e4. Epub 2018 Aug 22.

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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http://dx.doi.org/10.1016/j.cels.2018.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347013PMC
September 2018

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

Cell 2018 05 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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http://dx.doi.org/10.1016/j.cell.2018.03.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989727PMC
May 2018

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

Nat Immunol 2018 02 15;19(2):162-172. Epub 2018 Jan 15.

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

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http://dx.doi.org/10.1038/s41590-017-0032-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6049828PMC
February 2018

INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division.

Cell Rep 2018 01;22(3):611-623

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

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http://dx.doi.org/10.1016/j.celrep.2017.12.079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949282PMC
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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http://dx.doi.org/10.1101/gr.226233.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741055PMC
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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http://dx.doi.org/10.1038/nmeth.4401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623146PMC
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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https://linkinghub.elsevier.com/retrieve/pii/S19345909173028
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http://dx.doi.org/10.1016/j.stem.2017.07.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591074PMC
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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http://dx.doi.org/10.1016/j.ccell.2017.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559384PMC
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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http://dx.doi.org/10.1038/ng.3769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357084PMC
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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http://dx.doi.org/10.1126/sciimmunol.aag0192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399889PMC
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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http://dx.doi.org/10.1038/nature20781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526328PMC
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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http://dx.doi.org/10.1186/s13059-016-1133-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259890PMC
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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http://dx.doi.org/10.1038/nmeth.3999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501173PMC
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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http://dx.doi.org/10.1016/j.cell.2016.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004630PMC
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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http://dx.doi.org/10.1038/ng.3471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731297PMC
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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http://dx.doi.org/10.1016/j.tcb.2015.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540433PMC
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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http://dx.doi.org/10.1101/gr.192294.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617971PMC
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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http://dx.doi.org/10.1016/j.tig.2015.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490074PMC
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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http://dx.doi.org/10.1038/nature14590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4685948PMC
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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http://dx.doi.org/10.1016/j.cels.2015.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522940PMC
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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http://dx.doi.org/10.1016/j.ymeth.2014.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412609PMC
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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http://dx.doi.org/10.1002/0471142727.mb2129s109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986PMC
January 2015

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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http://dx.doi.org/10.1016/j.celrep.2014.05.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113058PMC
June 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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http://dx.doi.org/10.1126/science.1251871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108260PMC
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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http://greenleaf.stanford.edu/assets/pdf/buenrostro_2013_nat
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http://dx.doi.org/10.1038/nmeth.2688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959825PMC
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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http://dx.doi.org/10.1038/nmeth.1629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414871PMC
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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http://dx.doi.org/10.1016/S0076-6879(10)75015-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965466PMC
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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http://dx.doi.org/10.1146/annurev.biochem.77.073106.100741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854675PMC
September 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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http://dx.doi.org/10.1126/science.1151298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640945PMC
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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http://dx.doi.org/10.1146/annurev.biophys.36.101106.101451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1945240PMC
August 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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http://dx.doi.org/10.1126/science.1130105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865524PMC
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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http://dx.doi.org/10.1038/nature04268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356566PMC
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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1357091PMC
http://dx.doi.org/10.1103/PhysRevLett.95.208102DOI Listing
November 2005