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Science ⎜August, 2018

Engineered CRISPR-Cas9 nuclease with expanded targeting space 

Hiroshi Nishimasu, Xi Shi, Soh Ishiguro, Linyi Gao, Seiichi Hirano, Sanae Okazaki, Taichi Noda, Omar O. Abudayyeh, Jonathan S. Gootenberg, Hideto Mori, Seiya Oura, Benjamin Holmes, Mamoru Tanaka, Motoaki Seki, Hisato Hirano, Hiroyuki Aburatani, Ryuichiro Ishitani, Masahito Ikawa, Nozomu Yachie, Feng Zhang & Osamu Nureki 

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Science ⎜February, 2018

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

Jonathan S. Gootenberg, Omar O. Abudayyeh, Max J. Kellner, Julia Joung, James J. Collins & Feng Zhang



Nature Biomedical Engineering ⎜April, 2018

Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons

Halil Tekin, Sean Simmons, Beryl Cummings, Linyi Gao, Xian Adiconis, Cynthia C. Hession, Ayan Ghoshal, Danielle Dionne, Sourav R. Choudhury, Volkan Yesilyurt, Neville E. Sanjana, Xi Shi, Congyi Lu, Matthias Heidenreich, Jen Q. Pan, Joshua Z. Levin & Feng Zhang

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Science ⎜October, 2017

RNA editing with CRISPR-Cas13

David B.T. Cox, Jonathan S. Gootenberg, Omar O. Abudayyeh, Brian Franklin, Max J. Kellner, Julia Joung & Feng Zhang

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Nature ⎜October, 2017

RNA Targeting with CRISPR-Cas13

Omar O. Abudayyeh, Jonathan S. Gootenberg, Patrick Essletzbichler, Shuo Han, Julia Joung, Joseph J. Belanto, Vanessa Verdine, David B. T. Cox, Max J. Kellner, Aviv Regev, Eric S. Lander, Daniel F. Voytas, Alice Y. Ting & Feng Zhang

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Nature Methods ⎜August 2017

Massively parallel single-nucleus RNA-seq with DroNc-seq

Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet , Ellen Gelfand, Kristin Ardlie, David A Weitz, Orit Rozenblatt-Rosen, Feng Zhang & Aviv Regev

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Nature ⎜August 2017

Identification of essential genes for cancer immunotherapy

Shashank J. Patel, Neville E. Sanjana, Rigel J. Kishton, Arash Eidizadeh, Suman K. Vodnala, Maggie Cam, Jared J. Gartner, Li Jia, Seth M. Steinberg, Tori N. Yamamoto, Anand S. Merchant, Gautam U. Mehta, Anna Chichura, Ophir Shalem, Eric Tran, Robert Eil, Madhusudhanan Sukumar, Eva Perez Guijarro, Chi-Ping Day, Paul Robbins, Steve Feldman, Glenn Merlino, Feng Zhang & Nicholas P. Restifo

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Molecular Cell ⎜August, 2017

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1

Akashi Yamano, Bernd Zetsche, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu & Osamu Nureki

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Nature ⎜August, 2017

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

Julia Joung, Jesse M. Engreitz, Silvana Konermann, Omar O. Abudayyeh, Vanessa K. Verdine, Francois Aguet, Jonathan S. Gootenberg, Neville E. Sanjana, Jason B. Wright, Charles P. Fulco, Yuen-Yi Tseng, Charles H. Yoon, Jesse S. Boehm, Eric S. Lander & Feng Zhang

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Nature Medicine ⎜July, 2017

Implications of human genetic variation in CRISPR-based therapeutic genome

David A. Scott & Feng Zhang

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Nature Biotechnology ⎜June, 2017

Engineered Cpf1 variants with altered PAM specificities

Linyi Gao, David B. T. Cox, Winston X. Yan, John C. Manteiga, Martin W. Schneider, Takashi Yamano, Hiroshi Nishimasu, Osamu Nureki, Nicola Crosetto & Feng Zhang

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Molecular Cell ⎜June, 2017

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1

Hiroshi Nishimasu, Takashi Yamano, Linyi Gao, Feng Zhang, Ryuichiro Ishitani & Osamu Nureki

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Nature Communications ⎜May, 2017

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

Winston X. Yan, Reza Mirzazadeh, Silvano Garnerone, David Scott, Martin W. Schneider, Tomasz Kallas, Joaquin Custodio, Erik Wernersson, Yinqing Li, Linyi Gao, Yana Federova, Bernd Zetsche, Feng Zhang, Magda Bienko & Nicola Crosetto

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Science⎜April, 2017

Nucleic acid detection with CRISPR-Cas13a/C2c2

Jonathan S. Gootenberg, Omar O. Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J. Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M. Daringer, Catherine A. Freije, Cameron Myhrvold, Roby P. Bhattacharyya, Jonathan Livny, Aviv Regev, Eugene V. Koonin, Deborah T. Hung, Pardis C. Sabeti, James J. Collins & Feng Zhang

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Cell Reports ⎜April, 2017

Chd8 Mutation Leads to Autistic-like Behaviors and Impaired Striatal Circuits

Randall J. Platt, Yang Zhou, Ian M. Slaymaker, Ashwin S. Shetty, Niels R. Weisbach, Jin-Ah Kim, Jitendra Sharma, Mitul Desai, Sabina Sood, Hannah R. Kempton, Gerald R. Crabtree, Guoping Feng  & Feng Zhang

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Molecular Cell ⎜March, 2017

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems

Mari Yamada, Yuto Watanabe, Jonathan S. Gootenberg, Hisato Hirano, F. Ann Ran, Takanori Nakane, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu & Osamu Nureki

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Nature ⎜March, 2017

Transcription control by the ENL YEATS domain in acute leukaemia

Michael A. Erb, Thomas G. Scott, Bin E. Li, Huafeng Xie, Joshiawa Paulk, Hyuk-Soo Seo, Amanda Souza, Justin M. Roberts, Shiva Dastjerdi, Dennis L. Buckley, Neville E. Sanjana, Ophir Shalem, Behnam Nabet, Rhamy Zeid, Nana K. Offei-Addo, Sirano Dhe-Paganon, Feng Zhang, Stuart H. Orkin, Georg E. Winter & James E. Bradner

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Molecular Cell ⎜January, 2017

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Aaron A. Smargon, David B.T. Cox, Neena K. Pyzocha, Kaijie Zheng, Ian M. Slaymaker, Jonathan S. Gootenberg, Omar A. Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S. Makarova, Eugene V. Koonin  & Feng Zhang

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Nature Biotechnology ⎜December, 2016

Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M DeGennaro, Nerges Winblad, Sourav R. Choudhury, Omar O. Abudayyeh, Jonathan S. Gootenberg, Wen Y. Wu, David A. Scott, Konstantin Severinov, John van der Oost  & Feng Zhang

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Nature Communications ⎜November, 2016

Engineering and optimising deaminase fusions for genome editing

Luhan Yang, Adrian W. Briggs, Wei Leong Chew, Prashant Mali, Marc Guell, John Aach, Daniel Bryan Goodman, David Cox, Yinan Kan, Emal Lesha, Venkataramanan Soundararajan, Feng Zhang & George Church

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Nature Chemical Biology⎜October, 2016

Multidimensional chemical control of CRISPR-Cas9

Basudeb Maji, Christopher L. Moore, Bernd Zetsche, Sara E. Volz, Feng Zhang, Matthew D. Shoulders & Amit Choudhary

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Nature Medicine ⎜July, 2017

High-resolution interrogation of functional elements in the noncoding genome

Neville E. Sanjana, Jason Wright, Kaijie Zheng, Ophir Shalem, Pierre Fontanillas, Julia Joung, Christine Cheng, Aviv Regev  & Feng Zhang

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Science ⎜July, 2016

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

Naomi Habib, Yinqing Li, Matthias Heidenreich, Lukasz Swiech, Inbal Avraham-Davidi, John J. Trombetta, Cynthia Hession, Feng Zhang & Aviv Regev

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Science ⎜June, 2016

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR

Omar O. Abudayyeh, Jonathan S. Gootenberg, Silvana Konermann, Julia Joung, Ian M. Slaymaker, David B.T. Cox, Sergey Shmakov, Kira S. Makarova, Ekaterina Semenova, Leonid Minakhin, Konstantin Severinov, Aviv Regev, Eric S. Lander, Eugene V. Koonin & Feng Zhang

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Scientific Reports ⎜May, 2016

An RNA-aptamer-based two-color CRISPR labeling system

Siyuan Wang, Jun-Han Su, Feng Zhang & Xiaowei Zhuang

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Cell ⎜April, 2016

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

Takashi Yamano, Hiroshi Nishimasu, Bernd Zetsche, Hisato Hirano, Ian M. Slaymaker, Yinqing Li, Iana Fedorova, Takanori Nakane, Kira S. Makarova, Eugene V. Koonin, Ryuichiro Ishitani, Feng Zhang & Osamu Nureki

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Science ⎜February, 2016

Hypoxia as a therapy for mitochondrial disease

Isha H. Jain, Luca Zazzeron, Rahul Goli, Kristen Alexa, Stephanie Schatzman-Bone, Harveen Dhillon, Olga Goldberger, Jun Peng, Ophir Shalem, Neville E. Sanjana, Feng Zhang, Wolfram Goessling, Warren M. Zapol & Vamsi K. Mootha

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Cell⎜February, 2016

Structure and Engineering of Francisella novicida Cas9

Hisato Hirano, Jonathan S. Gootenberg, Takuro Horii, Omar O. Abudayyeh, Mika Kimura, Patrick D. Hsu, Takanori Nakane, Ryuichiro Ishitani, Izuho Hatada, Feng Zhang, Hiroshi Nishimasu & Osamu Nureki

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Science⎜December, 2015

In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy

Christopher E. Nelson, Chady H. Hakim, David G. Ousterout, Pratiksha I. Thakore, Eirik A. Moreb, Ruth M. Castellanos Rivera, Sarina Madhavan, Xiufang Pan, F. Ann Ran, Winston X. Yan, Aravind Asokan, Feng Zhang, Dongsheng Duan & Charles A. Gersbach

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Science⎜December, 2015

In vivo gene editing in dystrophic mouse muscle and muscle stem cells

Mohammadsharif Tabebordbar, Kexian Zhu, Jason K. W. Cheng, Wei Leong Chew, Jeffrey J. Widrick, Winston X. Yan, Claire Maesner, Elizabeth Y. Wu, Ru Xiao, F. Ann Ran, Le Cong, Feng Zhang, Luk H. Vandenberghe, George M. Church & Amy J. Wagers

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Nature Reviews Neuroscience⎜December, 2015

Applications of CRISPR-Cas systems in neuroscience

Matthias Heidenreich & Feng Zhang

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Science⎜December, 2015

Rationally engineered Cas9 nucleases with improved specificity

Ian M. Slaymaker, Linyi Gao, Bernd Zetsche, David A. Scott, Winston X. Yan & Feng Zhang

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Molecular Cell⎜October, 2015

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

Sergey Shmakov, Omar O. Abudayyeh, Kira S. Makarova, Yuri I. Wolf, Jonathan S. Gootenberg, Ekaterina Semenova, Leonid Minakhin, Julia Joung, Silvana Konermann, Konstantin Severinov, Feng Zhang & Eugene V. Koonin

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Nature Biotechnology⎜October, 2015

 

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease

 

James E Dahlman, Omar O Abudayyeh, Julia Joung, Jonathan S. Gootenberg, Feng Zhang & Silvana Konermann

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Cell⎜September, 2015

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Bernd Zetsche, Jonathan S. Gootenberg, Omar O. Abudayyeh, Ian M. Slaymaker, Kira S. Makarova, Patrick Essletzbichler, Sara E. Volz, Julia Joung, John van der Oost, Aviv Regev, Eugene V. Koonin & Feng Zhang

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Nature⎜September, 2015

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Matthew C. Canver, Elenoe C. Smith, Falak Sher, Luca Pinello, Neville E. Sanjana, Ophir Shalem, Diane D. Chen, Patrick G. Schupp, Divya S. Vinjamur, Sara P. Garcia, Sidinh Luc, Ryo Kurita, Yukio Nakamura, Yuko Fujiwara, Takahiro Maeda, Guo-Cheng Yuan, Feng Zhang, Stuart H. Orkin & Daniel E. Bauer

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Cell⎜August, 2015

Crystal Structure of Staphylococcus aureus Cas9

Hiroshi Nishimasu, Le Cong, Winston X. Yan, F. Ann Ran, Bernd Zetsche, Yinqing Li, Arisa Kurabayashi, Ryuichiro Ishitani, Feng Zhang  & Osamu Nureki

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Cell⎜July, 2015

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Oren Parnas, Marko Jovanovic, Thomas M. Eisenhaure, Rebecca H. Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski, Randall J. Platt, Itay Tirosh, Neville E. Sanjana, Ophir Shalem, Rahul Satija, Raktima Raychowdhury, Philipp Mertins, Steven A. Carr, Feng Zhang, Nir Hacohen & Aviv Regev

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Genome Research⎜June, 2015

Sequence determinants of improved CRISPR sgRNA design

Han Xu, Tengfei Xiao, Chen-Hao Chen, Wei Li, Clifford A. Meyer, Qiu Wu, Di Wu, Le Cong, Feng Zhang, Jun S. Liu, Myles Brown & X. Shirley Liu

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Scientific Reports⎜June, 2015

CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus

Vyas Ramanan, Amir Shlomai, David B.T. Cox, Robert E. Schwartz, Eleftherios Michailidis, Ankit Bhatta, David A. Scott, Feng Zhang, Charles M. Rice & Sangeeta N. Bhatia

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Nature Reviews Genetics⎜April, 2015

High-throughput functional genomics using CRISPR-Cas9

Ophir Shalem, Neville E. Sanjana and Feng Zhang

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Nature⎜April, 2015

In vivo genome editing using Staphylococcus aureus Cas9

F. Ann Ran, Le Cong, Winston X. Yan, David A. Scott, Jonathan S. Gootenberg, Andrea J. Kriz, Bernd Zetsche, Ophir Shalem, Xuebing Wu, Kira S. Makarova, Eugene V. Koonin, Phillip A. Sharp & Feng Zhang

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Cell⎜March, 2015

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

Sidi Chen, Neville E. Sanjana, Kaijie Zheng, Ophir Shalem, Kyungheon Lee, Xi Shi, David A. Scott, Jun Song, Jen Q. Pan, Ralph Weissleder, Hakho Lee, Feng Zhang & Phillip A. Sharp

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Nature Medicine⎜February, 2015

Therapeutic genome editing: prospects and challenges

David B. T. Cox, Randall J. Platt & Feng Zhang

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Nature Biotechnology⎜February, 2015

A split-Cas9 architecture for inducible genome editing and transcription modulation

Bernd Zetsche, Sara E. Volz & Feng Zhang

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Nature⎜December, 2014

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Silvana Konermann, Mark D. Brigham, Alexandro E. Trevino, Julia Joung, Omar O. Abudayyeh, Clea Barcena, Patrick D. Hsu, Naomi Habib, Jonathan S. Gootenberg, Hiroshi Nishimasu, Osamu Nureki & Feng Zhang

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Nature Biotechnology⎜October, 2014

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

Lukasz Swiech, Matthias Heidenreich, Abhishek Banerjee, Naomi Habib, Yinqing Li, John Trombetta, Mriganka Sur & Feng Zhang

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Cell⎜September, 2014

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

Randall J. Platt, Sidi Chen, Yang Zhou, Michael J. Yim, Lukasz Swiech, Hannah R. Kempton, James E. Dahlman, Oren Parnas, Thomas M. Eisenhaure, Marko Jovanovic, Daniel B. Graham, Siddharth Jhunjhunwala, Matthias Heidenreich, Ramnik J. Xavier, Robert Langer, Daniel G. Anderson, Nir Hacohen, Aviv Regev, Guoping Feng, Phillip A. Sharp & Feng Zhang

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Nature⎜August, 2014

CRISPR-mediated direct mutation of cancer genes in the mouse liver

Wen Xue, Sidi Chen, Hao Yin, Tuomas Tammela, Thales Papagiannakopoulos, Nikhil S. Joshi, Wenxin Cai, Gillian Yang, Roderick Bronson, Denise G. Crowley, Feng Zhang, Daniel G. Anderson, Phillip A. Sharp & Tyler Jacks

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Cell Reports⎜June, 2014

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

Schraga Schwartz, Maxwell R. Mumbach, Marko Jovanovic, Tim Wang, Karolina Maciag, G. Guy Bushkin, Philipp Mertins, Dmitry Ter-Ovanesyan, Naomi Habib, Davide Cacchiarelli, Neville E. Sanjana, Elizaveta Freinkman, Michael E. Pacold, Rahul Satija, Tarjei S. Mikkelsen, Nir Hacohen, Feng Zhang, Steven A. Carr,
Eric S. Lander & Aviv Regev

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Cell⎜June, 2014

Development and Applications of CRISPR-Cas9 for Genome Engineering

Patrick D. Hsu, Eric S. Lander & Feng Zhang

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Genes & Development⎜May, 2014

Global microRNA depletion suppresses tumor angiogenesis

Sidi Chen, Yuan Xue, Xuebing Wu, Cong Le, Arjun Bhutkar, Eric L. Bell, Feng Zhang, Robert Langer & Phillip A. Sharp

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Nature Biotechnology⎜April, 2014

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

Xuebing Wu, David A Scott, Andrea J Kriz, Anthony C Chiu, Patrick D Hsu, Daniel B Dadon, Albert W Cheng, Alexandro E Trevino, Silvana Konermann, Sidi Chen, Rudolf Jaenisch, Feng Zhang & Phillip A Sharp

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Science⎜March, 2014

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Mark N. Lee, Chun Ye, Alexandra-Chloé Villani, Towfique Raj, Weibo Li, Thomas M. Eisenhaure, Selina H. Imboywa, Portia I. Chipendo, F. Ann Ran, Kamil Slowikowski, Lucas D. Ward, Khadir Raddassi, Cristin McCabe, Michelle H. Lee, Irene Y. Frohlich, David A. Hafler, Manolis Kellis, Soumya Raychaudhuri, Feng Zhang, Barbara E. Stranger, Christophe O. Benoist, Philip L. De Jager, Aviv Regev & Nir Hacohen

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Cell⎜February, 2014

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang & Osamu Nureki

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Science⎜December, 2013

Genome-scale CRISPR-Cas9 knockout screening in human cells

Ophir Shalem, Neville E. Sanjana, Ella Hartenian, Xi Shi, David A. Scott, Tarjei S. Mikkelsen, Dirk Heckl, Benjamin L. Ebert, David E. Root, John G. Doench  & Feng Zhang

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Cell⎜August, 2013

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing

F. Ann Ran, Patrick D. Hsu, Chie-Yu Lin, Jonathan S. Gootenberg, Silvana Konermann, Alexandro E. Trevino, David A. Scott, Azusa Inoue, Shogo Matoba, Yi Zhang & Feng Zhang

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Nature⎜July, 2013

Optical control of mammalian endogenous transcription and epigenetic states

Silvana Konermann, Mark D. Brigham, Alexandro Trevino, Patrick D. Hsu, Matthias Heidenreich, Le Cong, Randall J. Platt, David A. Scott, George M. Church & Feng Zhang

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Nature Biotechnology⎜July, 2013

DNA targeting specificity of RNA-guided Cas9 nucleases

Patrick D. Hsu, David A. Scott, Joshua A. Weinstein, F. Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J. Fine, Xuebing Wu, Ophir Shalem, Thomas J. Cradick, Luciano A. Marraffini, Gang Bao & Feng Zhang

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Cell⎜May, 2013

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

Haoyi Wang, Hui Yang, Chikdu S. Shivalila, Meelad M. Dawlaty, Albert W. Cheng, Feng Zhang & Rudolf Jaenisch

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Nucleic Acids Research⎜June, 2014

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

David Bikard, Wenyan Jiang, Poulami Samai, Ann Hochschild, Feng Zhang & Luciano A. Marraffini

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Nature Biotechnology⎜January, 2013

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

Wenyan Jiang, David Bikard, David Cox, Feng Zhang & Luciano A Marraffini

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Science⎜January, 2013

Multiplex genome engineering using CRISPR/Cas systems

Le Cong, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu, Xuebing Wu, Wenyan Jiang, Luciano A. Marraffini & Feng Zhang

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Nature Communications⎜July, 2012

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains

Le Cong, Ruhong Zhou, Yu-chi Kuo, Margaret Cunniff & Feng Zhang

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Nature Communications⎜January, 2012

A transcription activator-like effector toolbox for genome engineering

Neville E. Sanjana, Le Cong, Yang Zhou, Margaret M. Cunniff, Guoping Feng & Feng Zhang

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Nature Biotechnology⎜January, 2011

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription

Feng Zhang, Le Cong, Simona Lodato, Sriram Kosuri, George M. Church & Paola Arlotta

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