William J. Greenleaf, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
biophysics, single molecules, motor proteins, transcription

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Molecular Cell. PMID 31078383 DOI: 10.1016/j.molcel.2019.04.012  0.64
2017 Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proceedings of the National Academy of Sciences of the United States of America. PMID 28495970 DOI: 10.1073/pnas.1700557114  0.64
2016 Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nature Methods. PMID 27749837 DOI: 10.1038/nmeth.4031  1
2016 Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics. PMID 27526324 DOI: 10.1038/ng.3646  1
2016 Denny SK, Yang D, Chuang CH, Brady JJ, Lim JS, Grüner BM, Chiou SH, Schep AN, Baral J, Hamard C, Antoine M, Wislez M, Kong CS, Connolly AJ, Park KS, ... ... Greenleaf WJ, et al. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility. Cell. PMID 27374332 DOI: 10.1016/j.cell.2016.05.052  1
2015 Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature Genetics. PMID 26691984 DOI: 10.1038/ng.3471  1
2015 Risca VI, Greenleaf WJ. Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool. Trends in Cell Biology. PMID 26437592 DOI: 10.1016/j.tcb.2015.08.004  1
2015 Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Research. PMID 26314830 DOI: 10.1101/gr.192294.115  1
2015 Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY. Individuality and variation of personal regulomes in primary human T cells. Cell Systems. 1: 51-61. PMID 26251845 DOI: 10.1016/j.cels.2015.06.003  1
2015 Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S, Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, et al. Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors. Nature Biotechnology. 33: 769-74. PMID 26098448 DOI: 10.1038/nbt.3270  1
2015 Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 523: 486-90. PMID 26083756 DOI: 10.1038/nature14590  1
2015 Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends in Genetics : Tig. 31: 357-72. PMID 25887733 DOI: 10.1016/j.tig.2015.03.010  1
2015 Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 109: 21.29.1-9. PMID 25559105 DOI: 10.1002/0471142727.mb2129s109  1
2015 Greenleaf WJ. Assaying the epigenome in limited numbers of cells. Methods (San Diego, Calif.). 72: 51-6. PMID 25461774 DOI: 10.1016/j.ymeth.2014.10.010  1
2014 Greenleaf WJ, Sidow A. The future of sequencing: convergence of intelligent design and market Darwinism. Genome Biology. 15: 303. PMID 25000818 DOI: 10.1186/gb4168  1
2014 Chiou SH, Kim-Kiselak C, Risca VI, Heimann MK, Chuang CH, Burds AA, Greenleaf WJ, Jacks TE, Feldser DM, Winslow MM. A conditional system to specifically link disruption of protein-coding function with reporter expression in mice. Cell Reports. 7: 2078-86. PMID 24931605 DOI: 10.1016/j.celrep.2014.05.031  1
2014 Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science (New York, N.Y.). 344: 1042-7. PMID 24789973 DOI: 10.1126/science.1251871  1
2014 Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature Biotechnology. 32: 562-8. PMID 24727714 DOI: 10.1038/nbt.2880  1
2014 Couthouis J, Raphael AR, Siskind C, Findlay AR, Buenrostro JD, Greenleaf WJ, Vogel H, Day JW, Flanigan KM, Gitler AD. Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy. Neuromuscular Disorders : Nmd. 24: 431-5. PMID 24594375 DOI: 10.1016/j.nmd.2014.01.014  1
2013 Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, ... ... Greenleaf WJ, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. American Journal of Human Genetics. 93: 852-64. PMID 24568772 DOI: 10.1016/j.ajhg.2013.10.002  1
2013 Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods. 10: 1213-8. PMID 24097267 DOI: 10.1038/nmeth.2688  1
2012 Men Y, Fu Y, Chen Z, Sims PA, Greenleaf WJ, Huang Y. Digital polymerase chain reaction in an array of femtoliter polydimethylsiloxane microreactors. Analytical Chemistry. 84: 4262-6. PMID 22482776 DOI: 10.1021/ac300761n  1
2011 Sims PA, Greenleaf WJ, Duan H, Xie XS. Fluorogenic DNA sequencing in PDMS microreactors. Nature Methods. 8: 575-80. PMID 21666670 DOI: 10.1038/nmeth.1629  1
2010 Gutiérrez-Medina B, Andreasson JO, Greenleaf WJ, Laporta A, Block SM. An optical apparatus for rotation and trapping. Methods in Enzymology. 475: 377-404. PMID 20627165 DOI: 10.1016/S0076-6879(10)75015-1  1
2008 Herbert KM, Greenleaf WJ, Block SM. Single-molecule studies of RNA polymerase: motoring along. Annual Review of Biochemistry. 77: 149-76. PMID 18410247 DOI: 10.1146/annurev.biochem.77.073106.100741  1
2008 Larson MH, Greenleaf WJ, Landick R, Block SM. Applied force reveals mechanistic and energetic details of transcription termination. Cell. 132: 971-82. PMID 18358810 DOI: 10.1016/j.cell.2008.01.027  1
2008 Greenleaf WJ, Frieda KL, Foster DA, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science (New York, N.Y.). 319: 630-3. PMID 18174398 DOI: 10.1126/science.1151298  1
2007 Block SM, Larson MH, Greenleaf WJ, Herbert KM, Guydosh NR, Anthony PC. Molecule by molecule, the physics and chemistry of life: SMB 2007. Nature Chemical Biology. 3: 193-7. PMID 17372599 DOI: 10.1038/nchembio0407-193  1
2007 Greenleaf WJ, Woodside MT, Block SM. High-resolution, single-molecule measurements of biomolecular motion. Annual Review of Biophysics and Biomolecular Structure. 36: 171-90. PMID 17328679 DOI: 10.1146/annurev.biophys.36.101106.101451  1
2007 Greenleaf WJ, Frieda KL, Abbondanzieri EA, Woodside MT, Block SM. High-resolution, single-molecule optical trapping measurements of transcription with basepair accuracy: Instrumentation and methods Proceedings of Spie - the International Society For Optical Engineering. 6644. DOI: 10.1117/12.739631  1
2006 Greenleaf WJ, Block SM. Single-molecule, motion-based DNA sequencing using RNA polymerase. Science (New York, N.Y.). 313: 801. PMID 16902131 DOI: 10.1126/science.1130105  1
2005 Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM. Passive all-optical force clamp for high-resolution laser trapping. Physical Review Letters. 95: 208102. PMID 16384102 DOI: 10.1103/PhysRevLett.95.208102  1
2005 Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM. Direct observation of base-pair stepping by RNA polymerase. Nature. 438: 460-5. PMID 16284617 DOI: 10.1038/nature04268  1
2000 Marszalek PE, Greenleaf WJ, Li H, Oberhauser AF, Fernandez JM. Atomic force microscopy captures quantized plastic deformation in gold nanowires. Proceedings of the National Academy of Sciences of the United States of America. 97: 6282-6. PMID 10841533 DOI: 10.1073/pnas.97.12.6282  1
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