https://greenleaf.stanford.edu/joinus daily 0.75 2025-04-12 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1575426592169-LYOGE1WFGMKPKYQKB6CL/stanford_palm_large.jpg Join Us! https://greenleaf.stanford.edu/home daily 1.0 2024-09-21 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1637101269951-UNQ6O0DC9Y9F0FWGXO15/DSC_0258.jpg Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1696018451498-CIYXAGESKP8Q37ZJGLK2/holding-will.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1725729779640-MYS0VPGYOUZGG1DCO6E0/2024+lab+photo.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1575426039934-MKLFZUXSZPS1QGUE2VW1/tumblr_dna_sequences.gif Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1575426241220-NT63STE6ZNJM70KEB0O7/buenrostro_2014_heatmap-trim.jpg Home - High-throughput Biophysics & Molecular Evolution We are interested in understanding the biophysical basis and evolutionary consequences of sequence-function relationships in biological molecules and their interactions. Towards this goal, we develop ultra-high-throughput methods to quantitatively assay sequence-space in bulk and single-molecule experiments. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572652019643-FDPSZX272F86DUSG8E4W/Corces_2018.png Home - DNA Accessibility & Chromatin Structure We seek to understand the hierarchical folding of genomic DNA into regulated structures, the most basic and important of which is the nucleosome. With this objective in mind, we have developed methods that assay open chromatin, nucleosome positions, and transcription factor binding genome-wide in small populations of cells undergoing dynamic processes such as differentiation or stochastic state switching. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459178906-XKP23Z9P8QIWR9JRLMSV/F1.medium.gif Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459118827-XI7Q8MZ1R76CGK6IE6JV/Yess_PNAS_2019.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459106938-RI01BQJ0RHWA2F8SHS18/Ansu_NBT_2019.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572652078246-VDIDS3XOHIT91WM43LXQ/1-s2.0-S1097276519304459-fx1_lrg.jpg Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459113924-L8205DR97ZI86IN5T1QN/Corces_2018.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459131654-M02PUCN5WSZ5SV3DY404/Sarah_et_al.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459138462-ZPOW4WL6A7BSUX4J8B73/nature20781-f3.jpg Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459148285-3VPR9KRLUYU7OFYZ35EI/nature20781-f1.jpg Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459155851-75M4H5NCFF7HD37WANLQ/mumbach_et_al.png Home https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459164344-T0PFDA5YG5OH361LBTWV/Mezger_2018.png Home https://greenleaf.stanford.edu/research-interests daily 0.75 2025-10-21 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1580760597759-T1U1YOBWSNYCJNCNWKDI/risca_2016_nature_figure3.jpg Overview https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572651983920-6VIJ3C206897FMVZN6UJ/1-s2.0-S1097276519304459-fx1_lrg.jpg Overview https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572652019643-FDPSZX272F86DUSG8E4W/Corces_2018.png Overview https://greenleaf.stanford.edu/contact daily 0.75 2025-04-12 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1570065135044-GED4PS9R5OK1C0B5A41K/image.img.320.high.jpg Contact https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1570139184661-Z0BHW0NYQLARTDZ8R0TO/image.img.320.high.png Contact https://greenleaf.stanford.edu/publications daily 0.75 2026-01-29 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/0dd59714-0bb2-4160-9eab-68af51551191/Schaepe+2025+doodle.jpg Publications - Make it stand out Julia M Schaepe, Torbjörn Fries, Benjamin R Doughty, Vivekanandan Ramalingam, Betty B Liu, Olivia J Crocker, Georgi K Marinov, Michaela M Hinks, Emil Marklund, William J Greenleaf (2025) Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/b419a27b-5d1d-4311-a96a-34d30d1965bd/Doughty+2024.png Publications - Make it stand out Benjamin R. Doughty, Michaela M. Hinks, Julia M. Schaepe, Georgi K. Marinov, Abby R. Thurm, Carolina Rios-Martinez, Benjamin E. Parks, Yingxuan Tan, Emil Marklund, Danilo Dubocanin, Lacramioara Bintu, William J. Greenleaf (2024) Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/0fd9fd6a-f7b1-4586-80fa-17a38965a38d/ke+2025.png Publications - Make it stand out Yuxi Ke, Eesha Sharma, Hannah K Wayment-Steele, Winston R Becker, Anthony Ho, Emil Marklund, William J Greenleaf (2025) Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/702698cb-6505-4c7a-a1c8-9dd6496ad89c/Choe+2025+doodle.webp Publications - Make it stand out Christian A Choe, Johan OL Andreasson, Feriel Melaine, Wipapat Kladwang, Michelle J Wu, Fernando Portela, Roger Wellington-Oguri, John J Nicol, Hannah K Wayment-Steele, Michael Gotrik, Eterna Participants, Purvesh Khatri, William J Greenleaf, Rhiju Das (2025) Nature Chemistry https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/cc797ad6-c4be-4176-b90d-13fee02fec4c/Yost+2025+cancer+chromatin+landscape.png Publications - Make it stand out Kathryn E Yost, Yanding Zhao, King L Hung, Kaiyuan Zhu, Duo Xu, M Ryan Corces, Shadi Shams, Bryan H Louie, Shahab Sarmashghi, Laksshman Sundaram, Jens Luebeck, Stanley Clarke, Ashley S Doane, Jeffrey M Granja, Hani Choudhry, Marcin Imieliński, Andrew D Cherniack, Ekta Khurana, Vineet Bafna, Ina Felau, Jean C Zenklusen, Peter W Laird, Christina Curtis, William J Greenleaf, Howard Y Chang (2025) Nature Genetcs https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/c60fa54c-50ab-4b47-bdb0-2133b2436b12/Marinov+2025+KasAtac.jpg Publications - Make it stand out Georgi K Marinov, William J Greenleaf (2025) Bio-Protocol https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/0bc63813-41a5-4d7c-8387-3af2107d6d45/Marinov+2025+PlosOne.PNG Publications - Make it stand out Georgi K Marinov, Vivekanandan Ramalingam, William J Greenleaf, Anshul Kundaje (2025) PloS One https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/e5921ac6-ac48-4fdd-a3c7-c57203ed36fe/Kim+2024.png Publications - Make it stand out Samuel H. Kim, Georgi K. Marinov, William J. Greenleaf (2024) Genome Research https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/c94777f9-9cfc-465a-bc0c-70205344bffc/Marinov+2024.png Publications - Make it stand out Georgi K. Marinov, Benjamin Doughty, Anshul Kundaje, William J. Greenleaf (2024) Genome Research https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1f944c34-b523-4227-a00f-ab078b6ea8bf/Tang+2024.png Publications - Make it stand out Jun Tang, Natasha E Weiser, Guiping Wang, Sudhir Chowdhry, Ellis J Curtis, Yanding Zhao, Ivy Tsz-Lo Wong, Georgi K Marinov, Rui Li, Philip Hanoian, Edison Tse, Salvador Garcia Mojica, Ryan Hansen, Joshua Plum, Auzon Steffy, Snezana Milutinovic, S Todd Meyer, Jens Luebeck, Yanbo Wang, Shu Zhang, Nicolas Altemose, Christina Curtis, William J Greenleaf, Vineet Bafna, Stephen J Benkovic, Anthony B Pinkerton, Shailaja Kasibhatla, Christian A Hassig, Paul S Mischel, Howard Y Chang (2024) Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/75066554-efa8-4231-97df-cc2401644914/Esplin+2024.png Publications - Make it stand out Edward D Esplin, Casey Hanson, Si Wu, Aaron M Horning, Nasim Barapour, Stephanie A Nevins, Lihua Jiang, Kévin Contrepois, Hayan Lee, Tuhin K Guha, Zheng Hu, Rozelle Laquindanum, Meredith A Mills, Hassan Chaib, Roxanne Chiu, Ruiqi Jian, Joanne Chan, Mathew Ellenberger, Winston R Becker, Bahareh Bahmani, Aziz Khan, Basil Michael, Annika K Weimer, D Glen Esplin, Jeanne Shen, Samuel Lancaster, Emma Monte, Thomas V Karathanos, Uri Ladabaum, Teri A Longacre, Anshul Kundaje, Christina Curtis, William J Greenleaf, James M Ford, Michael P Snyder (2024) Nature Cancer https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/bdab7473-6a8d-489e-b0d5-d2ace51fc8fd/Screen+Shot+2024-11-05+at+2.29.38+PM.png Publications - Make it stand out John H. Shin, Lena M. Cuevas, Rohit Roy, Steve L. Bonilla, Hashim Al-Hashimi, William J Greenleaf, Daniel Herschlag (2024) RNA https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/cd7395bb-ceb1-431a-aa75-8bd8f8f12f2c/Zhu+2024.png Publications - Make it stand out Yizhou Zhu, Hayan Lee, Shannon White, Annika K Weimer, Emma Monte, Aaron Horning, Stephanie A Nevins, Edward D Esplin, Kristina Paul, Gat Krieger, Zohar Shipony, Roxanne Chiu, Rozelle Laquindanum, Thomas V Karathanos, Melissa WY Chua, Meredith Mills, Uri Ladabaum, Teri Longacre, Jeanne Shen, Ariel Jaimovich, Doron Lipson, Anshul Kundaje, William J Greenleaf, Christina Curtis, James M Ford, Michael P Snyder (2024) Nature Cancer https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/3960ed27-7df0-4871-b0e6-87eff9063764/Gamble_2024_fig.png Publications - Make it stand out Noah Gamble, Alexandra Bradu, Jason A. Caldwell, Joshua McKeever, Olubusayo Bolonduro, Ebru Ermis, Caroline Kaiser, YeEun Kim, Benjamin Parks, Sandy Klemm, William J. Greenleaf, Gerald R. Crabtree, Andrew S. Koh (2024) Nature Immunology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/a67670f9-11ba-4f00-ae0d-43511a0afa5c/Marinov_2024_fig.png Publications - Make it stand out Georgi K. Marinov, Xinyi Chen, Matthew P. Swaffer, Tingting Xiang, Arthur R. Grossman, William J. Greenleaf (2024) Genome Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/32ea5ce1-c72f-4632-8e18-219e6de0048d/Moses+2024.png Publications - Make it stand out Eitan Moses, Tehila Atlan, Xue Sun, Roman Franěk, Atif Siddiqui, Georgi K. Marinov, Sagiv Shifman, David M. Zucker, Adi Oron-Gottesman, William J. Greenleaf, Ehud Cohen, Oren Ram, Itamar Harel (2024) Nature Aging https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/039339de-0065-4043-a9b1-534c6c183cc7/Kim_2024_fig.png Publications - Make it stand out YeEun Kim, Ariel A. Calderon, Patricia Favaro, David R. Glass, Albert G. Tsai, Daniel Ho, Luciene Borges, William J. Greenleaf, Sean C. Bendall (2024) Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8f952ece-b653-41b1-8b4b-fce666f33aed/Zhou+2024.png Publications - Make it stand out Bo Zhou, Joseph G Arthur, Hanmin Guo, Taeyoung Kim, Yiling Huang, Reenal Pattni, Tao Wang, Soumya Kundu, Jay XJ Luo, HoJoon Lee, Daniel C Nachun, Carolin Purmann, Emma M Monte, Annika K Weimer, Ping-Ping Qu, Minyi Shi, Lixia Jiang, Xinqiong Yang, John F Fullard, Jaroslav Bendl, Kiran Girdhar, Minsu Kim, Xi Chen, William J Greenleaf, Laramie Duncan, Hanlee P Ji, Xiang Zhu, Giltae Song, Stephen B Montgomery, Dean Palejev, Heinrich Zu Dohna, Panos Roussos, Anshul Kundaje, Joachim F Hallmayer, Michael P Snyder, Wing H Wong, Alexander E Urban (2024) Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/c3111ac1-8110-4bc4-9cee-b11b3e529af8/Metzl-Raz_2023_fig.png Publications - Make it stand out Eyal Metzl-Raz, Samuel H. Kim, Catherine R. Zhang, William J. Greenleaf (2023) Epigenetic Cancer Therapy (book chapter) https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/55a83313-e229-4d01-97f9-05702bbcb179/Screen+Shot+2024-01-25+at+3.56.55+PM.png Publications - Make it stand out Matthew P Swaffer, Georgi K Marinov, Huan Zheng, Lucas Fuentes Valenzuela, Crystal Yee Tsui, Andrew W Jones, Jessica Greenwood, Anshul Kundaje, William J Greenleaf, Rodrigo Reyes-Lamothe, Jan M Skotheim (2023). Cell. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/bc57c9da-b06e-4828-967a-04c8ab03ad28/Screen+Shot+2024-01-25+at+3.45.03+PM.png Publications - Make it stand out Georgi K Marinov, S Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje, William J Greenleaf (2023). Genome Biology. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1cc4d68d-18da-4f65-9d3b-bdc663ca37a3/Screen+Shot+2024-01-25+at+3.31.32+PM.png Publications - Make it stand out Charles Limouse, Owen K Smith, David Jukam, Kelsey A Fryer, William J Greenleaf, Aaron F Straight (2023). Nature Communications. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/64879230-c823-4ba4-9733-d6502eafaf7d/Horton_2023_fig.png Publications - Make it stand out Connor A Horton , Amr M Alexandar , Michael G B Hayes, Emil Marklund, Julia M Schaepe, Arjun K Aditham, Nilay Shah, Peter H Suzuki, Avanti Shrikumar, Ariel Afek, William J Greenleaf, Raluca Gordân, Julia Zeitlinger, Anshul Kundaje, Polly M Fordyce (2023). Science https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/b77832b4-c0fb-42c8-b031-eae4393e5ba4/Chen_2023_fig.png Publications - Make it stand out Shuxiao Chen, Bokai Zhu, Sijia Huang, John W. Hickey, Kevin Z. Lin, Michael Snyder, William J. Greenleaf, Garry P. Nolan, Nancy R. Zhang & Zongming Ma (2023). Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/657193e1-c388-40c2-97c5-f9953eeb908e/Screen+Shot+2024-01-25+at+2.19.05+PM.jpg Publications Florian V De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González-Blas, Domenica Marchese, Ginevra Caratù, Suresh Poovathingal, Orit Rozenblatt-Rosen, Michael Slyper, Wendy Luo, Christoph Muus, Fabiana Duarte, Rojesh Shrestha, S Tansu Bagdatli, M Ryan Corces, Lira Mamanova, Andrew Knights, Kerstin B Meyer, Ryan Mulqueen, Akram Taherinasab, Patrick Maschmeyer, Jörn Pezoldt, Camille Lucie Germaine Lambert, Marta Iglesias, Sebastián R Najle, Zain Y Dossani, Luciano G Martelotto, Zach Burkett, Ronald Lebofsky, José Ignacio Martin-Subero, Satish Pillai, Arnau Sebé-Pedrós, Bart Deplancke, Sarah A Teichmann, Leif S Ludwig, Theodore P Braun, Andrew C Adey, William J Greenleaf, Jason D Buenrostro, Aviv Regev , Stein Aerts, Holger Heyn (2023). Nature Biotechnology. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8bcc56e7-0415-4369-ab92-4d85a96d3d3d/Screen+Shot+2023-07-28+at+3.45.14+PM.png Publications - Make it stand out Benjamin Ober-Reynolds, Chen Wang, Justin M. Ko, Eon J. Rios, Sumaira Z. Aasi, Mark M. Davis, Anthony E. Oro, William J. Greenleaf (2023). Nature Genetics. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/bde56c87-ad72-416a-b03a-2ae1141b11e7/Screen+Shot+2023-07-24+at+3.55.48+PM.png Publications - Make it stand out John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, Bei Wei, Roxanne Chiu, Derek C. Chen, Daniel L. Cotter, Edward D. Esplin, Annika K. Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M. Schürch, Sarah Black, Maria Brbić, Kaidi Cao, Shuxiao Chen, Weiruo Zhang, Emma Monte, Nancy R. Zhang, Zongming Ma, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K. Plevritis, Yiing Lin, Garry P. Nolan, William J. Greenleaf, Michael Snyder (2023). Nature. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/cd56be1c-69d0-42ed-8f1b-43940307fcca/Screen+Shot+2023-05-12+at+2.43.49+PM.png Publications - Make it stand out Jimena Andersen, Nicholas Thom, Jennifer L. Shadrach, Xiaoyu Chen, Massimo Mario Onesto, Neal D. Amin, Se-Jin Yoon, Li Li, William J. Greenleaf, Fabian Müller, Anca M. Pașca, Julia A. Kaltschmidt, Sergiu P. Pașca (2023). Nature Neuroscience. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/fd60a613-39f0-47e1-9b04-b996e5a44617/Screen+Shot+2023-05-12+at+2.47.12+PM.png Publications - Make it stand out Georgi K. Marinov, Samuel H. Kim, S. Tansu Bagdatli, Soon Il Higashino, Alexandro E. Trevino, Josh Tycko, Tong Wu, Lacramioara Bintu, Michael C. Bassik, Chuan He, Anshul Kundaje, William J. Greenleaf (2023). Genome Biology. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/a86e8c39-5d16-495e-97e4-1fe01c4ace22/Screen+Shot+2023-05-12+at+2.49.37+PM.png Publications - Make it stand out YeEun Kim, William J Greenleaf, Sean C Bendall (2023). Current Opinion in Immunology. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/ae7bddea-89b7-4bc0-b2be-785e6673ede4/Screen+Shot+2023-05-12+at+2.51.25+PM.png Publications - Make it stand out John H. Shin, Steve L. Bonilla, Sarah K. Denny, William J. Greenleaf, Daniel Herschlag (2023). PNAS. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/7adc1887-f419-4cf9-9437-357fdee7b260/Screen+Shot+2023-03-01+at+2.58.09+PM.png Publications - Make it stand out Stephano S. Mello, Brittany M. Flowers, Pawel K. Mazur, James J. Lee, Fabian Müller, Sarah K. Denny, Sofia Ferreira, Kathryn Hanson, Seung K. Kim, William J. Greenleaf, Laura D. Wood, and Laura D. Attardi (2023). PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/24285fce-534a-43f9-ae42-256ca74cae14/Screen+Shot+2023-02-14+at+7.35.17+PM.png Publications - Make it stand out Emil Marklund, Yuxi Ke, William J. Greenleaf (2023). Nature Reviews Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/bf526360-74dd-4e75-ad2d-72b108e730a4/Screen+Shot+2023-03-01+at+3.10.26+PM.png Publications - Make it stand out Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, William J. Greenleaf (2023). Methods in Molecular Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/bf7a9903-21d0-42ad-9705-242b2778393f/Screen+Shot+2023-03-01+at+3.45.53+PM.png Publications - Make it stand out Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D. Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C. Wu, Jesse M. Engreitz, Kyle Farh, Ioannis Karakikes, Kevin C. Wang, Thomas Quertermous, William J. Greenleaf, Anshul Kundaje (2022). Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/44d134b5-8fca-49e9-9fd8-980969e017e0/Screen+Shot+2022-11-03+at+5.40.30+PM.png Publications - Make it stand out King L. Hung, Jens Luebeck, Siavash R. Dehkordi, Caterina I. Colón, Rui Li, Ivy Tsz-Lo Wong, Ceyda Coruh, Prashanthi Dharanipragada, Shirley H. Lomeli, Natasha E. Weiser, Gatien Moriceau, Xiao Zhang, Chris Bailey, Kathleen E. Houlahan, Wenting Yang, Rocío Chamorro González, Charles Swanton, Christina Curtis, Mariam Jamal-Hanjani, Anton G. Henssen, Julie A. Law, William J. Greenleaf, Roger S. Lo, Paul S. Mischel, Vineet Bafna, Howard Y. Chang (2022) Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/83d7125b-52b2-415c-9354-0068b00c472c/Screen+Shot+2023-03-01+at+3.17.22+PM.png Publications - Make it stand out Michaela Hinks, Georgi K. Marinov, Anshul Kundaje, Lacramioara Bintu, William J. Greenleaf (2022). Methods in Molecular Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8c1597c2-5088-4005-a7a0-40fd301b2e13/Screen+Shot+2023-03-01+at+3.24.50+PM.png Publications - Make it stand out Samuel H. Kim, Georgi K. Marinov, S. Tansu Bagdatli, Soon Il Higashino, Zohar Shipony, Anshul Kundaje, William J. Greenleaf (2022). Methods in Molecular Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/650bd3a7-6396-49b3-bd00-2bf86212b630/Screen+Shot+2022-10-11+at+2.50.44+PM.png Publications - Make it stand out Masao Hashimoto, Koichi Araki, Maria A. Cardenas, Peng Li, Rohit R. Jadhav, Haydn T. Kissick, William H. Hudson, Donald J. McGuire, Rebecca C. Obeng, Andreas Wieland, Judong Lee, Daniel T. McManus, James L. Ross, Se Jin Im, Junghwa Lee, Jian-Xin Lin, Bin Hu, Erin E. West, Christopher D. Scharer, Gordon J. Freeman, Arlene H. Sharpe, Suresh S. Ramalingam, Alex Pellerin, Volker Teichgräber, William J. Greenleaf, Christian Klein, Jorg J. Goronzy, Pablo Umaña, Warren J. Leonard, Kendall A. Smith, Rafi Ahmed (2022) Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/15c43431-26aa-47f7-b5c8-b962224d5464/Screen+Shot+2022-10-11+at+2.45.50+PM.png Publications - Make it stand out Christoph Sadée, Lauren D. Hagler, Winston R. Becker, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, Sarah K. Denny, William J. Greenleaf, Daniel Herschlag (2022) Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/de857162-c10a-4fc2-bce9-55eddb6638af/Screen+Shot+2022-10-11+at+2.42.46+PM.png Publications - Make it stand out Jacob W. Freimer, Oren Shaked, Sahin Naqvi, Nasa Sinnott-Armstrong, Arwa Kathiria, Christian M. Garrido, Amy F. Chen, Jessica T. Cortez, William J. Greenleaf, Jonathan K. Pritchard, Alexander Marson (2022) Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8de8b0b1-17ef-47b8-851a-3faf8427b4c2/Screen+Shot+2022-06-21+at+11.26.48+AM.png Publications - Make it stand out Winston R. Becker, Stephanie A. Nevins, Derek C. Chen, Roxanne Chiu, Aaron M. Horning, Tuhin K. Guha, Rozelle Laquindanum, Meredith Mills, Hassan Chaib, Uri Ladabaum, Teri Longacre, Jeanne Shen, Edward D. Esplin, Anshul Kundaje, James M. Ford, Christina Curtis, Michael P. Snyder, William J. Greenleaf (2022) Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/46016c13-6906-4330-83be-ac8ef2b89d41/Screen+Shot+2022-05-27+at+4.03.46+PM.png Publications - Make it stand out Amy F. Chen, Benjamin Parks, Arwa S. Kathiria, Benjamin Ober-Reynolds, Jorg J. Goronzy, William J. Greenleaf (2022) Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/a4fa279d-6e1b-45e6-8a12-9a998ef7f431/Screen+Shot+2022-04-28+at+11.34.25+AM.png Publications - Make it stand out Johan O. L. Andreasson, Michael R. Gotrik, Michelle J. Wu, Hannah K. Wayment-Steele, Wipapat Kladwang, Fernando Portela, Roger Wellington-Oguri, Eterna Participants, Rhiju Das, William J. Greenleaf (2022) PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/d2d8271e-7556-4074-99d2-040b4331394a/Screen+Shot+2022-04-13+at+3.35.46+PM.png Publications - Make it stand out Eyal Metzl-Raz, Nike Bharucha, Jennifer Arthur Ataam, Alexandra A. Gavidia, William J. Greenleaf, Ioannis Karakikes (2022) Stem Cell Research https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8df8b1a6-b001-4904-92ff-33ddc48524de/Screen+Shot+2022-03-25+at+1.56.48+PM.png Publications - Make it stand out Reema Baskar, Amy F. Chen, Patricia Favaro, Warren Reynolds, Fabian Mueller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William J. Greenleaf, Sean C. Bendall (2022) Cell Reports Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/b7584690-b722-4d70-a849-0fc2bf645f31/Screen+Shot+2022-03-25+at+1.57.11+PM.png Publications - Make it stand out Benjamin Ober-Reynolds, Winston R. Becker, Karina Jouravleva, Samson M. Jolly, Phillip D. Zamore, William J. Greenleaf (2022) Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/0ece1aa6-b226-4798-a532-cb9d3a9f1f7c/Screen+Shot+2022-03-15+at+3.31.29+PM.png Publications - Make it stand out Georgi K. Marinov, Xinyi Chen, Tong Wu, Chuan He, Arthur R. Grossman, Anshul Kundaje, William James Greenleaf (2022) Genome Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/dbb469cb-66f0-4402-971d-9edb67b03413/Screen+Shot+2022-03-15+at+3.30.41+PM.png Publications - Make it stand out Rohit R. Jadhav, Bin Hu, Zhongde Ye, Khushboo Sheth, Xuanying Li, William J .Greenleaf, Cornelia M.Weyand, Jörg J.Goronzy (2022) eBioMedicine https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/660c6a1b-3da3-4878-8f2a-69b3442beac9/Screen+Shot+2022-03-15+at+3.29.51+PM.png Publications - Make it stand out Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, William J. Greenleaf (2022) Chromatin https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/015038da-e454-4fbb-b799-b7d3df3c8f46/Zhang_2022_fig.png Publications - Make it stand out Huimin Zhang, Rohit R. Jadhav, Wenqiang Cao, Isabel N. Goronzy, Tuantuan V. Zhao, Jun Jin, Shozo Ohtsuki, Zhaolan Hu, Jose Morales, William J. Greenleaf, Cornelia M. Weyand, Jörg J. Goronzy (2022) Nature Immunology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8d3ad8dd-7065-4047-bb47-80928759ea56/Screen+Shot+2021-12-17+at+2.34.18+PM.png Publications - Make it stand out Matthew P. Swaffer, Jacob Kim, Devon Chandler-Brown, Maurice Langhinrichs, Georgi K. Marinov, William J. Greenleaf, Anshul Kundaje, Kurt M. Schmoller, Jan M. Skotheim (2021) Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/b9a0e0fe-a91b-4b7c-95fa-8f182527e38d/Screen+Shot+2021-12-03+at+3.03.58+PM.png Publications - Make it stand out Chiung-Ying Chang, Zohar Shipony, Sherry G Lin, Ann Kuo, Xiaochen Xiong, Kyle M Loh, William J Greenleaf, Gerald R Crabtree (2021) Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1634594351267-SD6QV7UXN8N1A7SUOWJO/Screen+Shot+2021-10-18+at+2.59.02+PM.png Publications - Make it stand out Daniel S. Kim, Viviana I. Risca, David L. Reynolds, James Chappell, Adam J. Rubin, Namyoung Jung, Laura K. H. Donohue, Vanessa Lopez-Pajares, Arwa Kathiria, Minyi Shi, Zhixin Zhao, Harsh Deep, Mahfuza Sharmin, Deepti Rao, Shin Lin, Howard Y. Chang, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Paul A. Khavari (2021) Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1634593756175-06BSV8HULTAT68E4FIOP/Screen+Shot+2021-10-18+at+2.48.58+PM.png Publications - Make it stand out Hamish W. King, Kristen L. Wells, Zohar Shipony, Arwa S. Kathiria, Lisa E. Wagar, Caleb Lareau, Nara Orban, Robson Capasso, Mark M. Davis, Lars M. Steinmetz, Louisa K. James, William J. Greenleaf (2021) Science Immunology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/5e241daa-0fda-46d7-832b-01fe666d7087/Screen+Shot+2021-12-03+at+3.11.30+PM.png Publications - Make it stand out Maya Maor-Nof, Zohar Shipony, Georgi K Marinov, William J Greenleaf, Aaron D Gitler (2021) STAR Protocols https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1630623338184-DUEJXLVOH4H7JFCBJ70G/Screen+Shot+2021-09-02+at+3.55.28+PM.png Publications - Make it stand out Alexandro E. Trevino, Fabian Muller, Jimena Andersen, Laksshman Sundaram, Arwa Kathiria, Anna Shcherbina, Kyle Farh, Howard Y. Chang, Anca M. Pașca, Anshul Kundaje, Sergiu P. Pașca, William J. Greenleaf (2021) Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1630622840729-VGPCG7FTIP2PP2K1141R/Screen+Shot+2021-09-02+at+3.46.54+PM.png Publications - Make it stand out Sarah E. Pierce, Jeffrey M. Granja, M. Ryan Corces, Jennifer J. Brady, Min K. Tsai, Aubrey B. Pierce, Rui Tang, Pauline Chu, David M. Feldser, Howard Y. Chang, Michael C. Bassik, William J. Greenleaf, Monte M. Winslow (2021) Nature Cell Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/8966aa30-160b-47cf-8746-2986fe815bfb/Screen+Shot+2021-11-17+at+1.27.42+PM.png Publications - Make it stand out David G. Gennert, Rachel C. Lynn, Jeff M. Granja, Evan W. Weber, Maxwell R. Mumbach, Yang Zhao, Zhana Duren, Elena Sotillo, William J. Greenleaf, Wing H. Wong, Ansuman T. Satpathy, Crystal L. Mackall, Howard Y. Chang. (2021) PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1624388018075-05QFYL0XK0CSUSBZDSI7/Screen+Shot+2021-06-22+at+11.53.13+AM.png Publications - Make it stand out Aaron J. Wilk, Madeline J. Lee, Bei Wei, Benjamin Parks, Ruoxi Pi, Giovanny J. Martínez-Colón, Thanmayi Ranganath, Nancy Q. Zhao, Shalina Taylor, Winston Becker, Stanford COVID-19 Biobank, David Jimenez-Morales, Andra L. Blomkalns, Ruth O’Hara, Euan A. Ashley, Kari C. Nadeau, Samuel Yang, Susan Holmes, Marlene Rabinovitch, Angela J. Rogers, William J. Greenleaf, Catherine A. Blish (2021) Journal of Experimental Medicine https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1622236509993-0T0XNIUM5GTQK8A520KN/Screen+Shot+2021-05-28+at+2.13.31+PM.png Publications - Make it stand out Sarah E. Pierce, Jeffrey M. Granja, William J. Greenleaf (2021) Nature Communications. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1620239929443-XEVVXT74YUQYPYC6IFZA/Screen+Shot+2021-05-05+at+11.38.32+AM.png Publications Georgi K. Marinov, Alexandro E. Trevino, Tingting Xiang, Anshul Kundaje, Arthur R. Grossman, William J. Greenleaf (2021) Nature Genetics. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1614626243110-Y21U5IZJ12VQ4UOHVK1G/Screen+Shot+2021-03-01+at+11.09.22+AM.png Publications Jeffrey M. Granja, M. Ryan Corces, Sarah E. Pierce, S. Tansu Bagdatli, Hani Choudhry, Howard Y. Chang, William J. Greenleaf (2021) Nature Genetics. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1614037945027-GOUFVYVAEXHYHYNFP6G4/image-asset.png Publications Evan A. Boyle, Winston R. Becker, Hua B. Bai, Janice S. Chen, Jennifer A. Doudna, William J. Greenleaf (2021) Science Advances https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/5a713ad9-cbfa-4931-9c64-ae324c6b2230/Blum_2021_fig.png Publications Jacob A. Blum, Sandy Klemm, Jennifer L. Shadrach, Kevin A. Guttenplan, Lisa Nakayama, Arwa Kathiria, Phuong T. Hoang, Olivia Gautier, Julia A. Kaltschmidt, William J. Greenleaf, Aaron D. Gitler (2021) Nature Neuroscience https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/25f6f844-7447-4a7a-8482-7bd6604a6b9d/Screen+Shot+2021-11-17+at+12.40.38+PM.png Publications - Make it stand out Maya Maor-Nof, Zohar Shipony, RodrigoLopez-Gonzalez, Lisa Nakayama, Yong-Jie Zhang, Julien Couthouis, Jacob A. Blum, Patricia A. Castruita, Gabriel R. Linares, Kai Ruan, Gokul Ramaswami, David J. Simon, Aviv Nof, Manuel Santana, Kyuho Han, Nasa Sinnott-Armstrong, Michael C. Bassik, Daniel H. Geschwind, Aaron D. Gitler. (2021) Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617403543204-0T5S7LTFA5LMH25I7OZ6/Screen+Shot+2021-04-02+at+3.45.30+PM.png Publications Orit Rozenblatt-Rosen, Jay W. Shin, Jennifer E. Rood, Anna Hupalowska, Human Cell Atlas Standards and Technology Working Group, Aviv Regev, Holger Heyn (2021) “Building a high-quality Human Cell Atlas” Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617831796916-YEVS6SBV7NA9327LFAIP/dna-2789567_1280.png Publications Sarah E Pierce, Samuel H Kim, William J Greenleaf (2021) “Finding needles in a haystack: dissecting tumor heterogeneity with single-cell transcriptomic and chromatin accessibility profiling” Current Opinion in Genetics & Development https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/58d217ae-1d9b-4136-b2f7-f435a98dd39c/Corces_2020_fig.jpg Publications M. Ryan Corces, Anna Shcherbina, Soumya Kundu, Michael J. Gloudemans, Laure Frésard, Jeffrey M. Granja, Bryan H. Louie, Tiffany Eulalio, Shadi Shams, S. Tansu Bagdatli, Maxwell R. Mumbach, Boxiang Liu, Kathleen S. Montine, William J. Greenleaf, Anshul Kundaje, Stephen B. Montgomery, Howard Y. Chang, Thomas J. Montine (2020) “Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1588608535296-MBSLTXV3T0XEMUGGFGT7/Screen+Shot+2020-05-04+at+8.34.55+AM.png Publications Johan O. L. Andreasson, Andrew Savinov, Steven M. Block, William J. Greenleaf (2020) “Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme” Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1582072305569-EHB9XE8LEAYPLP8QCSCO/Screen+Shot+2020-02-18+at+4.31.28+PM.png Publications Zohar Shipony, Georgi K. Marinov, Matthew P. Swaffer, Nicholas A. Sinnott-Armstrong, Jan M. Skotheim, Anshul Kundaje, William J. Greenleaf (2020) “Long-range single-molecule mapping of chromatin accessibility in eukaryotes” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1579895089223-5CW8G2GJ4K23YL630KDQ/Screen+Shot+2020-01-24+at+11.44.16+AM.png Publications Alexandro E. Trevino, Nasa Sinnott-Armstrong, Jimena Andersen, Se-Jin Yoon, Nina Huber, Jonathan K. Pritchard, Howard Y. Chang, William J. Greenleaf, Sergiu P. Pașca (2020) “Chromatin accessibility dynamics in a model of human forebrain development” Science https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1576108186165-OEICI7TULQTWIRWIWQ4H/Screen+Shot+2019-12-11+at+3.49.28+PM.png Publications Jeffrey M. Granja, Sandy Klemm, Lisa M. McGinnis, Arwa S. Kathiria, Anja Mezger, M. Ryan Corces, Benjamin Parks, Eric Gars, Michaela Liedtke, Grace X. Y. Zheng, Howard Y. Chang, Ravindra Majeti, and William J. Greenleaf (2019) “Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia” Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/c0e6d253-985d-42bc-a926-be98c5bb1de9/Screen+Shot+2021-11-16+at+2.13.22+PM.png Publications - Make it stand out Keren I Hilgendorf, Carl T Johnson, Anja Mezger, Selena L Rice, Alessandra M Norris, Janos Demeter, William J Greenleaf, Jeremy F Reiter, Daniel Kopinke, Peter K Jackson. (2019) “Omega-3 Fatty Acids Activate Ciliary FFAR4 to Control Adipogenesis” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1603148000428-TBJ2M23QL780FQSSM6UD/Screen+Shot+2020-10-19+at+3.52.57+PM.png Publications Diego Calderon, Michelle L. T. Nguyen, Anja Mezger, Arwa Kathiria, Fabian Müller, Vinh Nguyen, Ninnia Lescano, Beijing Wu, John Trombetta, Jessica V. Ribado, David A. Knowles, Ziyue Gao, Franziska Blaeschke, Audrey V. Parent, Trevor D. Burt, Mark S. Anderson, Lindsey A. Criswell*, William J. Greenleaf*, Alexander Marson*, and Jonathan K. Pritchard* (2020) “Landscape of stimulation-responsive chromatin across diverse human immune cells” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1618268538728-8TM340A2YZVTHX7ZDAHO/Screen+Shot+2021-04-12+at+4.02.09+PM.png Publications Josh Tycko, Michael Wainberg, Georgi K. Marinov, Oana Ursu, Gaelen T. Hess, Braeden K. Ego, Aradhana, Amy Li, Alisa Truong, Alexandro E. Trevino, Kaitlyn Spees, David Yao, Irene M. Kaplow, Peyton G. Greenside, David W. Morgens, Douglas H. Phanstiel, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Michael C. Bassik (2019) “Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements” Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571693879562-KBUIS2RBOQOK6611BR09/Yess_PNAS_2019.png Publications Joseph D. Yesselman, Sarah K. Denny, Namita Bisaria, Daniel Herschlag, William J. Greenleaf, and Rhiju Das (2019) “ Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation ” PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571694238995-IV0D25K49TNXSPXOZ77X/Ansu_NBT_2019.png Publications Ansuman T. Satpathy, Jeffrey M. Granja, Kathryn E. Yost, Yanyan Qi, Francesca Meschi, Geoffrey P. McDermott, Brett N. Olsen, Maxwell R. Mumbach, Sarah E. Pierce, M. Ryan Corces, Preyas Shah, Jason C. Bell, Darisha Jhutty, Corey M. Nemec, Jean Wang, Li Wang, Yifeng Yin, Paul G. Giresi, Anne Lynn S. Chang, Grace X. Y. Zheng, William J. Greenleaf & Howard Y. Chang (2019) “ Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion ” Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571694376227-S4BMDVLRNU53N2U99LTO/Winston_molcell.png Publications Winston R. Becker, Benjamin Ober-Reynolds, Karina Jouravleva, Samson M. Jolly, Phillip D. Zamore, William J. Greenleaf, (2019) “ High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2 ” Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/717a3186-9382-4f33-8146-2d449cd2bfa6/Screen+Shot+2021-11-16+at+2.05.47+PM.png Publications - Make it stand out Rohit R. Jadhav, Se Jin Im, Bin Hu, Masao Hashimoto, Peng Li, Jian-Xin Lin, Warren J. Leonard, William J. Greenleaf, Rafi Ahmed, Jorg J. Goronzy. (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” PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571694416522-D982CDGKDMHSLJ9EIZ19/Max_nm_2019.png Publications Maxwell R. Mumbach, Jeffrey M. Granja, Ryan A. Flynn, Caitlin M. Roake, Ansuman T. Satpathy, Adam J. Rubin, Yanyan Qi, Zhaozhao Jiang, Shadi Shams, Bryan H. Louie, Jimmy K. Guo, David G. Gennert, M. Ryan Corces, Paul A. Khavari, Maninjay K. Atianand, Steven E. Artandi, Katherine A. Fitzgerald, William J. Greenleaf & Howard Y. Chang (2019) “ HiChIRP reveals RNA-associated chromosome conformation ” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571770451999-7Z770PRPABYMDHQNMT4C/Winston_RNA.png Publications Winston R. Becker, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf and Daniel Herschlag (2019) “ Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2 ” RNA https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571770547954-34Y64U36PF4H5AHW4YL6/Denny_2019.png Publications Inga Jarmoskaite, Sarah K. Denny, Pavanapuresan P. Vaidyanathan, Winston R. Becker, Johan O.L. Andreasson, Curtis J. Layton, Kalli Kappe, Varun Shivashankar, Raashi Sreenivasan, Rhiju Das, William J.Greenleaf, Daniel Herschlag (2019) “ A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins ” Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571770639834-8OPMBTHQRIK4LE8WSB6S/Layton_2019.png Publications Curtis J.Layton, Peter L. McMahon, William J.Greenleaf (2019) “ Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip ” Molecular Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571770746409-KVRQTAAW2QDCPB7HX9N2/Klemm_2019.png Publications Sandy L. Klemm, Zohar Shipony & William J. Greenleaf (2019) “ Chromatin accessibility and the regulatory epigenome ” Nature Reviews Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/26e39842-6d22-4d5d-8c94-78ae75602c15/Screen+Shot+2021-11-16+at+1.56.39+PM.png Publications - Make it stand out Adam J. Rubin, Kevin R. Parker, Ansuman T. Satpathy, Yanyan Qi, Beijing Wu, Alvin J. Ong, Maxwell R. Mumbach, Andrew L. Ji, Daniel S. Kim, Seung Woo Cho, Brian J. Zarnegar, William J. Greenleaf, Howard Y. Chang, Paul A. Khavari. (2019) “Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1571770816653-EPN5EP5BKETYWN975E0Z/Evan_2018.png Publications Evan A Boyle , Jonathan K Pritchard & William J Greenleaf (2018) “ High‐resolution mapping of cancer cell networks using co‐functional interactions ” Molecular Systems Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/4790d69f-ac14-48ba-9b75-62569ffbbd77/Screen+Shot+2021-11-16+at+1.47.31+PM.png Publications - Make it stand out Michael S. Haney, Christopher J. Bohlen, David W. Morgens, James A. Ousey, Amira A. Barkal, C. Kimberly Tsui, Braeden K. Ego, Roni Levin, Roarke A. Kamber, Hannah Collins, Andrew Tucker, Amy Li, Daan Vorselen, Lorenzo Labitigan, Emily Crane, Evan Boyle, Lihua Jiang, Joanne Chan, Esther Rincón, William J. Greenleaf, Billy Li, Michael P. Snyder, Irving L. Weissman, Julie A. Theriot, Sean R. Collins, Ben A. Barres, Michael C. Bassik. (2018) “Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572397567110-UX6SNNBYHBKECS1KKB2Z/Corces_2018.png Publications M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Analysis Network, William J. Greenleaf, Howard Y. Chang (2018) “ The chromatin accessibility landscape of primary human cancers ” Science https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572397695837-6KH2EGVGAUSQ3LJKUJWA/Mezger_2018.png Publications Anja Mezger, Sandy Klemm, Ishminder Mann, Kara Brower, Alain Mir, Magnolia Bostick, Andrew Farmer, Polly Fordyce, Sten Linnarsson & William Greenleaf (2018) “ High-throughput chromatin accessibility profiling at single-cell resolution. ” Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572397806724-CIN436NLB7RAK2G0E72F/Sarah_et_al.png Publications Sarah Knight Denny, William James Greenleaf (2018) “ Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers .” Cold Spring Harbor Perspectives in Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459421983-FX44NYCDON8IGI75HOL0/Sarah_et_al_2018.png Publications Sarah Knight Denny, Namita Bisaria, Joseph David Yesselman, Rhiju Das, Daniel Herschlag, William James Greenleaf (2018) “ High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding .” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459516797-I4V21EARVKZC9P53K2YJ/Jason_cell_2018.png Publications Jason D.Buenrostro, Ryan Corces, Caleb A.Lareau, Beijing Wu, Alicia N.Schep, Martin J.Aryee, Ravindra Majeti, Howard Y.Chang, William J.Greenleaf (2018) “Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572459612900-9PVBJU7EOXQA5F0WH7RY/Aggeli_et_al.png Publications Dimitra Aggeli, Vlad O Karas, Nicholas A Sinnott-Armstrong, Vici Varghese, Robert W Shafer, William J Greenleaf, Gavin Sherlock (2018) “Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery.” Nucleic Acids Research https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572460134742-H34966TVLOPBFDS0F2TS/ino80.png Publications Graeme J. Gowans, Alicia N. Schep, Ka Man Wong, Devin A. King, William J. Greenleaf, Ashby J. Morrison (2018) “INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division.” Cell Reports https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572460708756-RQKT16L2RANTW66G8LYV/mumbach_et_al.png Publications Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R Kazane, Yuning Wei, Trieu Nguyen, Peyton G Greenside, M Ryan Corces, Josh Tycko, Dimitre R Simeonov, Nabeela Suliman, Rui Li, Jin Xu, Ryan A Flynn, Anshul Kundaje, Paul A Khavari, Alexander Marson, Jacob E Corn, Thomas Quertermous, William J Greenleaf & Howard Y Chang (2017) “Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572460802321-AEQAOWHMQLJGBFE5LBUO/Simeonov_et_al.png Publications Dimitre R. Simeonov, Benjamin G. Gowen, Mandy Boontanrart, Theodore L. Roth, John D. Gagnon, Maxwell R. Mumbach, Ansuman T. Satpathy, Youjin Lee, Nicolas L. Bray, Alice Y. Chan, Dmytro S. Lituiev, Michelle L. Nguyen, Rachel E. Gate, Meena Subramaniam, Zhongmei Li, Jonathan M. Woo, Therese Mitros, Graham J. Ray, Gemma L. Curie, Nicki Naddaf, Julia S. Chu, Hong Ma, Eric Boyer, Frederic Van Gool, Hailiang Huang, Ruize Liu, Victoria R. Tobin, Kathrin Schumann, Mark J. Daly, Kyle K. Farh, K. Mark Ansel, Chun J. Ye, William J. Greenleaf, Mark S. Anderson, Jeffrey A. Bluestone, Howard Y. Chang, Jacob E. Corn & Alexander Marson (2017) “Discovery of stimulation-responsive immune enhancers with CRISPR activation.” Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572460978337-WWXL395JM9E77YCYKQ1M/Corces_et_al_NM.png Publications M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu, Arwa Kathiria, Seung Woo Cho, Maxwell R Mumbach, Ava C Carter, Maya Kasowski, Lisa A Orloff, Viviana I Risca, Anshul Kundaje, Paul A Khavari, Thomas J Montine, William J Greenleaf & Howard Y Chang (2017) “An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572630555753-TIHHG3213M0XHV6NFILL/Schep_et_al.png Publications Alicia N Schep, Beijing Wu, Jason D Buenrostro & William J Greenleaf (2017) “chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572630633434-M0EY5LQQVKI3QJYTH6WI/Rubin_et_al.png Publications Adam J Rubin, Brook C Barajas, Mayra Furlan-Magaril, Vanessa Lopez-Pajares, Maxwell R Mumbach, Imani Howard, Daniel S Kim, Lisa D Boxer, Jonathan Cairns, Mikhail Spivakov, Steven W Wingett, Minyi Shi, Zhixin Zhao, William J Greenleaf, Anshul Kundaje, Michael Snyder, Howard Y Chang, Peter Fraser & Paul A Khavari. (2017) “Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation.” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572630704029-48V9ZR41LXQ5HAFLPY7M/Forrest_et_al_CTC.png Publications Marc P. Forrest, Hanwen Zhang, Winton Moy, Heather McGowan, Catherine Leites, Leonardo E. Dionisio, Zihui Xu, Jianxin Shi, Alan R. Sanders, William J. Greenleaf, Chad A. Cowan, Zhiping P. Pang, Pablo V. Gejman, Peter Penzes, Jubao Duan. (2017) “Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci..” Cell Stem Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572630803324-B24KDQZKTVHJDCIC2M2Q/Qu_et_al_Cancer_Cell.png Publications Kun Qu, Lisa C. Zaba, Ansuman T. Satpathy, Paul G. Giresi, Rui Li, Yonghao Jin, Randall Armstrong, Chen Jin, Nathalie Schmitt, Ziba Rahbar, Hideki Ueno, William J. Greenleaf, Youn H. Kim, Howard Y. Chang. (2017) “Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.” Cancer Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572639292703-30HYJC4IQ4FZK8TR56K0/Morgens_et_al.png Publications David W. Morgens,*, Michael Wainberg,*, Evan A. Boyle, Oana Ursu, Carlos L. Araya, C. Kimberly Tsui, Michael S. Haney, Gaelen T. Hess, Kyuho Han, Edwin E. Jeng, Amy Li, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje & Michael C. Bassik.(2017) “Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screen” Nature Communications https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572639364377-E8QMTPJ872KQYN8GKTXP/Boyle_et_al.png Publications Evan A. Boyle, Johan O. L. Andreasson, Lauren M. Chircus, Samuel H. Sternberg, Michelle J. Wue, Chantal K. Guegler, Jennifer A. Doudna, and William J. Greenleaf.(2017) “High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding.” PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572640059486-YZGKHE9D4T57F6Y72SQS/She_PNAS_2017_F1.jpg Publications She R*, Chakravarty AK*, Layton CJ*, Chircus LM, Andreasson JOL, Damaraju N, McMahon PL, Buenrostro JD, Jarosz DF§, and Greenleaf WJ§. (2017) “Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genom” PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572640129677-XX8TY7U0C9Y9JA8C9F6U/Moskowitz_Tcell_F8.jpg Publications Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ§, and Goronzy JJ§ (2017) “Epigenomics of human CD8 T cell differentiation and aging” Science Immunology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572640468561-L7F5CILSHEYZO4M28DZC/ezgif.com-webp-to-png.png Publications Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, and Chang HY (2017) “Single-cell epigenomic variability reveals functional cancer heterogeneity” Genome Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572640723180-CDDR947PBZ6LK51DUTGJ/ng.3769-F1.jpg Publications Xu J, Carter AC, Gendrel A, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, and Chang HY (2017) “Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572640966815-DOML1LBK234LD2OC7V49/risca_2016_nature_figure3.jpg Publications Risca VI, Denny SK, Straight AF, and Greenleaf WJ (2017) “Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping” Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1575328526644-X2WPXGT0T33X2L8CPPN1/Screen+Shot+2019-12-02+at+3.14.57+PM.png Publications 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, and Chang HY (2016) “ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572641076460-XSCRQXWMBBDCFPCFG2EG/mumbach_2016_figure2.jpg Publications Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, and Chang HY (2016) “HiChIP: efficient and sensitive analysis of protein-directed genome architecture” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572641167061-LKREZS18EDOVMZWMJD5C/corces_2016_fig4.jpg Publications Corces MR*, Buenrostro JD*, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R§, Chang HY§ (2016) “Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution” Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572641277393-OBFOXLDEB435XYX6J9YN/SCLC_Cell.jpg Publications Denny SK*, Yang D*, Chuang C-H, Brady JJ, Lim JS, Grüner BM, Chiou S-H, Schep AN, Baral J, Hamard C, Antoine M., Wislez M, Kong CS, Connolly AJ, Park K-S, Sage J, Greenleaf WJ§, Winslow MM§ (2016) “Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572641510589-Z7OMWRGX6I9OQA9OLRF1/araya_2015_nature_genetics_figX.jpg Publications Araya CL*, Cenik C*, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. (2015) "Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations." Nature Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617834806682-MQVQK1737MVV9YRBETP5/Screen+Shot+2021-04-07+at+3.32.44+PM.png Publications Viviana I. Risca, William J. Greenleaf (2015) “Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool” Trends in Cell Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572641622696-UVOADTHIWPCBA35MNTJY/schep_2015_genome_research_fig3.jpg Publications Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. (2015) "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions." Genome Research https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1583280178366-5R12JRUE0Z8UIE2LCV6V/Screen+Shot+2020-03-03+at+4.02.45+PM.png Publications Kun Qu, Lisa C. Zaba, Paul G. Giresi, Rui Li, Michelle Longmire, Youn H. Kim, William J. Greenleaf, Howard Y. Chang (2015) “Individuality and Variation of Personal Regulomes in Primary Human T Cells“ Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1581623859328-A7PR3NHR8SEQ7M45BWRQ/Screen+Shot+2020-02-13+at+11.57.25+AM.png Publications Itay Maza, Inbal Caspi, Asaf Zviran, Elad Chomsky, Yoach Rais, Sergey Viukov, Shay Geula, Jason D Buenrostro, Leehee Weinberger, Vladislav Krupalnik, Suhair Hanna, Mirie Zerbib, James R Dutton, William J Greenleaf, Rada Massarwa, Noa Novershtern, Jacob H Hanna (2015) “Transient acquisition of pluripotency during somatic cell transdifferentiation with iPsC reprogramming factors” Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572642649326-2SCBI5LP4BIUY9NEBLGB/buenrostro_2015_nature_fig3.jpg Publications Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. (2015) "Single-cell chromatin accessibility reveals principles of regulatory variation." Nature https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572642729845-1HZ4I68F6W6194ZQAP43/risca_2015_trends_in_genetics_fig1.jpg Publications Risca VI, Greenleaf WJ. (2015) "Unraveling the 3D genome: genomics tools for multiscale exploration." Trends in Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617831850351-VI9J4YTGUF1QRFJJ5YYV/dna-2789567_1280.png Publications Jason D. Buenrostro, Beijing Wu, Howard Y. Chang, William J. Greenleaf (2015) “ATAC-seq: A Method for Assaying UNIT 21.29 Chromatin Accessibility Genome-Wide” Current Protocols in Molecular Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1580416534049-NYT2G4616P8U70XSEIRS/Screen+Shot+2020-01-30+at+12.34.47+PM.png Publications William J. Greenleaf (2015). “Assaying the epigenome in limited numbers of cells” Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617834457931-XLHLMKQKNJDT7IFX0UAW/Screen+Shot+2021-04-07+at+3.27.13+PM.png Publications Shin-Heng Chiou, Caroline Kim-Kiselak, Viviana I. Risca, Megan K. Heimann, Chen-Hua Chuang, Aurora A. Burds, William J. Greenleaf, Tyler E. Jacks, David M. Feldser, Monte M. Winslow (2014) “A Conditional System to Specifically Link Disruption of Protein-Coding Function with Reporter Expression in Mice” Cell Reports https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572643629490-U5MK5D980X9SRWIHIPNZ/larson_2014_science_fig2.jpg Publications Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ*, Landick R*, Weissman JS*. (2014) "A Pause Sequence Enriched at Translation Start Sites Drives Transcription Dynamics in Vivo." Science https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572644045095-75Y92CSR7DCK8F0L2OO9/buenrostro_2014_nature_biotechnology_fig2.jpg Publications Buenrostro JD*, Araya CL*, Chircus LM, Layton CJ, Chang HY, Snyder MP, and Greenleaf WJ. (2014) "Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes." Nature Biotechnology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1578616723983-WML8H7Z2KHOE12PTZX9J/Screen+Shot+2020-01-09+at+4.38.28+PM.png Publications Julien Couthouis, Alya R. Raphael, Carly Siskind, Andrew R. Findlay, Jason D. Buenrostro, William J. Greenleaf, Hannes Vogel, John W. Day, Kevin M. Flanigan, Aaron D. Gitler. (2014) “Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy” Neuromuscular Disorders https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617831882612-S0TKOWEYVL5121FHTBXW/dna-2789567_1280.png Publications William J Greenleaf, Arend Sidow (2014) “The future of sequencing: convergence of intelligent design and market Darwinism” Genome Biology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617834153284-IP6WWUDBG31FQ0MK325E/Screen+Shot+2021-04-07+at+3.21.46+PM.png Publications Meredith L. Carpenter, Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen, Simon Gravel, Sonia Guillén, Georgi Nekhrizov, Krasimir Leshtakov, Diana Dimitrova, Nikola Theodossiev, Davide Pettener, Donata Luiselli, Karla Sandoval, Andre´s Moreno-Estrada, Yingrui Li, Jun Wang, M. Thomas P. Gilbert, Eske Willerslev, William J. Greenleaf, Carlos D. Bustamante (2013) “Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries” American Journal of Human Genetics https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572644550526-WJOEHLXPNUMCCSIJHDEG/buenrostro_2013_nature_methods_fig1.jpg Publications Buenrostro JD, Giresi PG, Zaba LC, Chang HY, and Greenleaf WJ. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1582589540007-5NIXBPALPUOV8FVVGTZ1/Screen+Shot+2020-02-24+at+4.12.01+PM.png Publications Yongfan Men, Yusi Fu, Zitian Chen, Peter A. Sims, William J. Greenleaf, Yanyi Huang (2012) “Digital Polymerase Chain Reaction in an Array of Femtoliter Polydimethylsiloxane Microreactors” Analytical Chemistry https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1578619787417-S2DKO3NH15EAVSO1L5UV/Screen+Shot+2020-01-09+at+5.29.26+PM.png Publications Peter A Sims, William J Greenleaf, Haifeng Duan, X Sunney Xie. (2011) “Fluorogenic DNA sequencing in PDMS microreactors” Nature Methods https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1617833874748-5KZJM0YNS9TB7ZCCXDT0/Screen+Shot+2021-04-07+at+3.17.30+PM.png Publications Braulio Gutiérrez-Medina, Johan O.L. Andreasson, William J. Greenleaf, Arthur LaPorta, Steven M.Block (2010) “An Optical Apparatus for Rotation and Trapping” Methods in Enzymology https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572645025282-UMO28M15E7T93UVF92RV/greenleaf_2008_science_fig1.jpg Publications Greenleaf WJ*, Frieda KL, Foster, DAN, Woodside MT*, and Block SM. (2008) “Direct observation of hierarchical folding in single riboswitch aptamers.” Science, 319:630-633. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1580757308075-CFEOWH4K6FIY2O659QSG/Screen+Shot+2020-02-03+at+11.14.46+AM.png Publications Matthew H. Larson, William J. Greenleaf, Robert Landick, Steven M. Block (2008) “Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination” Cell https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1580504277819-C26GGXJKEKWMW3SPX5HE/Screen+Shot+2020-01-31+at+12.57.44+PM.png Publications Kristina M. Herbert, William J. Greenleaf, Steven M. Block (2008). “Single-Molecule Studies of RNA Polymerase: Motoring Along” Annual Review Biochemistry https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1579736095277-8IBDIMRH7TDIMDFPN3KF/Screen+Shot+2020-01-22+at+3.34.37+PM.png Publications William J. Greenleaf, Michael T. Woodside, Steven M. Block (2007) “High-Resolution, Single-Molecule Measurements of Biomolecular Motion” Annual Review Biochemistry https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572646447105-M39TUZABIEIS69U3ASSW/greenleaf_2006_science_fig1.jpg Publications Greenleaf WJ, and Block SM. (2006) “Single-molecule, motion-based DNA sequencing using RNA polymerase.” Science 313:801. https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1572646615415-LQ3WJRVQ8CBL5CJ8OXPW/abbondanzieri_2005_nature_fig4.jpg Publications Abbondanzieri EA*, Greenleaf WJ*, Shaevitz JW, Landick R, Block, SM (2005) “Direct observation of basepair stepping by RNA polymerase.” Nature 438(7067):460-465 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1579649068486-5S6TGVDM3Z72VSWLAQZG/Screen+Shot+2020-01-21+at+3.24.13+PM.png Publications William J. Greenleaf*, Michael T. Woodside*, Elio A. Abbondanzieri, Steven M. Block (2005) “Passive All-Optical Force Clamp for High-Resolution Laser Trapping” Physical Review Letters https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1580871188070-6WDVHY1A7VVD7Z8YP0K7/Screen+Shot+2020-02-04+at+6.52.52+PM.png Publications Piotr E. Marszalek, William J. Greenleaf, Hongbin Li, Andres F. Oberhauser, Julio M. Fernandez (2000) “Atomic force microscopy captures quantized plastic deformation in gold nanowires” PNAS https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1578680477411-1LC49P0IT2PLVWQNYDEO/Screen+Shot+2020-01-10+at+10.20.52+AM.png Publications William J. Greenleaf, Mark E. Bolander, Gobinda Sarkar, Mary B. Goldring, and James F. Greenleaf. (1998) “Artifical cavitation nuclei significantly enhance acoustically induced cell transfection” World Federation for Ultrasound in Medicine & Biology https://greenleaf.stanford.edu/lab-fun daily 0.75 2025-07-09 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085283414-GNF0XR27385K38ZFM9SU/IMG_2625-2.jpg Lab Fun - 2025 https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085306813-5GGSP3012YPD58AAFYZS/IMG_2624.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085239474-MHKWPDO374QUAFFLQ5C8/IMG_3113.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085236938-8KKZXDKSPPXBS2ZQJYNA/IMG_3114.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085255452-2JOZ9FAWTB4LICZC5JBY/IMG_3115.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085256099-727H5SZNIU1FB41LZ98B/IMG_3119.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085322973-87FIH20ZUYXW2TPJFPQH/IMG_2627-2.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085336429-MFS5EJ4IEL696OA47H0X/IMG_2638-2.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1752085012228-OULOU27OOE2QFB0S3YGS/IMG_2644-2.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779918149-3LNSXYO58NN4IHBN2RAJ/IMG_5587.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779947114-03SQO2RDNYX5AZ5H44CU/DSC_0522.JPG Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779940130-S51UYCM06Z0T8QG4TLQE/000095020010.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779956255-Y872A4Q8429YBLTWH68A/000095020013.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779949536-KS7DJ1JB534ZPC1XPNE6/000095020012.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779958983-MMSYKX8WM96WPY2RB35N/000095020014.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779964608-FHKGAEQQVYO5WO4ZSFFS/000095020022.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779970640-NGYV0WHHM699QVMS44BG/IMG_6264.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779972541-YJLAFV2NJBOJEXFHHSWQ/Genetic_Retreat_2025_ZL-16.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779899999-V1AJOJ6TI2YZ5TQV6W3A/Genetic_Retreat_2025_ZL-27.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779900579-075SRVD81DRN9A8E5P51/Genetic_Retreat_2025_ZL-28.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779979984-YDOENQXWBX8D4D2GP2RS/Genetic_Retreat_2025_ZL-29.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779979459-YN8G4PPT0DPSK5D2L5CQ/Genetic_Retreat_2025_ZL.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779911478-5VK93N94D3EAE707D5PN/Genetic_Retreat_2025_ZL-34.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779927075-FEE7XMLZ13RCI16SUXGF/Genetic_Retreat_2025_ZL-42.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779908604-VGHP2Y8HGVFFTU72O43Y/Genetic_Retreat_2025_ZL-41.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1758779931853-EFJGP2KK21JV7SA9I2UZ/Genetic_Retreat_2025_ZL-43.jpg Lab Fun https://images.squarespace-cdn.com/content/v1/5d93d88fcd5ddb320534ef42/1696018451498-CIYXAGESKP8Q37ZJGLK2/holding-will.png Lab Fun - 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