Selected Publications
Zhang lab members indicated with italics
Equal contributions indicated with asterisk*
Corresponding author(s) indicated with bold
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Victoria Madigan*, Yugang Zhang*, Rumya Raghavan*, Max Wilkinson, Guilhem Faure, Elena Puccio, Michael Segel, Blake Lash, Rhiannon Macrae & Feng Zhang
PNAS. 2024 Mar 4; doi.org/10.1073/pnas.230781212
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Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering
Han Altae-Tran*, Soumya Kannan*, Anthony Suberski, Kepler Mears, Esra Demircioglu, Lukas Moeller, Selin Kocalar, Rachel Oshiro, Kira Makarova, Rhiannon Macrae, Eugene Koonin & Feng Zhang
Science. 2023 Nov 23; doi: 10.1126/science.adi191
Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12
Han Altae-Tran, Sergey Shmakov, Kira Makarova, Yuri Wolf, Soumya Kannan, Feng Zhang & Eugene Koonin
PNAS. 2023 Nov 20; doi: 10.1073/pnas.230822412
Drug delivery systems for CRISPR-based genome editors
Victoria Madigan, Feng Zhang & James Dahlman
Nature Reviews Drug Discovery. 2023 Sep 18; doi.org/10.1038/s41573-023-00762-x
Cell Type-specific Delivery by Modular Envelope Design
Daniel Strebinger, Chris Frangieh, Mirco Friedrich, Guilhem Faure, Rhiannon Macrae & Feng Zhang
Nature Communications. 2023 Aug 23; doi.org/10.1038/s41467-023-40788-8
Fanzor Is a eukaryotic programmable RNA-guided endonuclease
Makoto Saito*, Peiyu Xu*, Guilhem Faure, Samantha Maguire, Soumya Kannan, Han Altae-Tran, Sam Vo, AnAn Desimone, Rhiannon Macrae & Feng Zhang
Nature. 2023 Jun 28; doi.org/10.1038/s41586-023-06356-2
The transposon-encoded protein TnpB processes its own mRNA into ωRNA for guided nuclease activity
Suchita Nety, Han Altae-Tran, Soumya Kannan, Esra Demircioglu, Guilhem Faure, Seiichi Hirano, Kepler Mears, Yugang Zhang, Rhiannon Macrae & Feng Zhang
The CRISPR Journal. 2023. Jun 1; doi.org/10.1089/crispr.2023.0015
Modularity and diversity of target selectors in Tn7 transposons
Guilhem Faure*, Makoto Saito*, Sean Benler*, Iris Peng*, Yuri Wolf, Jonathan Strecker, Han Altae-Tran, Edwin Neumann, David Li, Kira Makarova, Rhiannon Macrae, Eugene Koonin & Feng Zhang
Molecular Cell. 2023 Jun 1; doi: 10.1016/j.molcel.2023.05.013
Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription
Max Wilkinson, Chris Frangieh, Rhiannon Macrae & Feng Zhang
Science. 2023 Apr 6; DOI: 10.1126/science.adg7883
Programmable protein delivery with a bacterial contractile injection system
Joseph Kreitz, Mirco Friedrich, Akash Guru, Blake Lash, Makoto Saito, Rhiannon Macrae & Feng Zhang
Nature. 2023 Mar 29; doi.org/10.1038/s41586-023-05870-7
A transcription factor atlas of directed differentiation
Julia Joung, Sai Ma*, Tristan Tay*, Kathryn Geiger-Schuller*, Paul Kirchgatterer, Vanessa Verdine, Baolin Guo, Mario Arias-Garcia, William Allen, Ankita Singh, Olena Kuksenko, Omar Abudayyeh, Jonathan Gootenberg, Zhanyan Fu, Rhiannon Macrae, Jason Buenrostro, Aviv Regev & Feng Zhang
Cell. 2023 Jan 5;186(1):209-229.e26. doi: 10.1016/j.cell.2022.11.026
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RNA-activated protein cleavage with a CRISPR-associated endopeptidase
Jonathan Strecker*, Esra Demircioglu*, David Li, Guilhem Faure, Max Wilkinson, Jonathan Gootenberg, Omar Abudayyeh, Hiroshi Nishimasu, Rhiannon Macrae & Feng Zhang
Science. 2022 Nov 25;378(6622):874-881. doi: 10.1126/science.add7450. Epub 2022 Nov 3.
Naiwen Cui, Guilhem Faure, Ankita Singh, Rhiannon Macrae & Feng Zhang
CRISPR J. 2022 Oct;5(5):677-684. doi: 10.1089/crispr.2022.0054. Epub 2022 Oct 7.
Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA
Seiichi Hirano*, Kalli Kappel*, Han Altae-Tran, Guilhem Faure, Max Wilkinson, Soumya Kannan, Esra Demircioglu, Rui Yan, Momoko Shiozaki, Zhiheng Yu, Kira Makarova, Eugene Koonin, Rhiannon Macrae & Feng Zhang
Nature. 2022 Oct;610(7932):575-581. doi: 10.1038/s41586-022-05324-6. Epub 2022 Oct 12.
Prokaryotic innate immunity through pattern recognition of conserved viral proteins
Linyi Alex Gao*, Max Wilkinson*, Jonathan Strecker*, Kira Makarova, Rhiannon Macrae, Eugene Koonin & Feng Zhang
Science. 2022 Aug 12;377(6607):eabm4096. doi: 10.1126/science.abm4096. Epub 2022 Aug 12.
Julia Joung, Paul Kirchgatterer, Ankita Singh, Jang Cho, Suchita Nety, Rebecca Larson, Rhiannon Macrae, Rebecca Deasy, Yuen-Yi Tseng, Marcela Maus & Feng Zhang
Nat Commun. 2022 Mar 25;13(1):1606. doi: 10.1038/s41467-022-29205-8.
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The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases
Han Alta-Tran*, Soumya Kannan*, Esra Demircioglu, Rachel Oshiro, Suchita Nety, Luke McKay, Mensur Dlakić, William Inskeep, Kira Makarova, Rhiannon Macrae, Eugene Koonin & Feng Zhang
Science. 2021 Oct;374(6563):57-65. doi: 10.1126/science.abj6856. Epub 2021 Sep 9.
Compact RNA editors with small Cas13 proteins
Soumya Kannan*, Han Altae-Tran*, Xin Jin, Victoria Madigan, Rachel Oshiro, Kira Makarova, Eugene Koonin & Feng Zhang
Nat Biotechnol. 2022 Feb;40(2):194-197. doi: 10.1038/s41587-021-01030-2. Epub 2021 Aug 30.
Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine Liu, Xin Jin, Sergei Mekhedov, Rhiannon Macrae, Eugene Koonin & Feng Zhang
Science. 2021 Aug 20;373(6557):882-889. doi: 10.1126/science.abg6155.
Dual modes of CRISPR-associated transposon homing
Makoto Saito*, Alim Ladha*, Jonathan Strecker*, Guilhem Faure*, Edwin Neumann, Han Altae-Tran, Rhiannon Macrae & Feng Zhang
Cell. 2021 Apr 29;184(9):2441-2453.e18. doi: 10.1016/j.cell.2021.03.006. Epub 2021 Mar 25.
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In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes
Xin Jin, Sean Simmons, Amy Guo, Ashwin Shetty, Michelle Ko, Lan Nguyen, Vahbiz Jokhi, Elise Robinson, Paul Oyler, Nathan Curry, Giulio Deangeli, Simona Lodato, Joshua Levin, Aviv Regev, Feng Zhang & Paola Arlotta
Science. 2020 Nov 27;370(6520):eaaz6063. doi: 10.1126/science.aaz6063.
Computational Identification of Repeat-Containing Proteins and Systems
Han Altae-Tran*, Linyi Gao*, Jonathan Strecker, Rhiannon Macrae & Feng Zhang
QRB Discovery. 2020 Oct 20;1, E10. doi:10.1017/qrd.2020.14
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing
Julia Joung*, Alim Ladha*, Makoto Saito, Nam-Gyun Kim, Ann Woolley, Michael Segel, Robert Barretto, Amardeep Ranu, Rhiannon Macrae, Guilhem Faure, Eleonora Ioannidi, Rohan Krajeski, Robert Bruneau, Meei-Li Huang, Xu Yu, Jonathan Li, Bruce Walker, Deborah Hung, Alexander Greninger, Keith Jerome, Jonathan Gootenberg, Omar Abudayyeh & Feng Zhang
N Engl J Med. 2020 Oct 8;383(15):1492-1494. doi: 10.1056/NEJMc2026172. Epub 2020 Sep 16.
Diverse enzymatic activities mediate antiviral immunity in prokaryotes
Linyi Gao, Han Altae-Tran, Francisca Böhning, Kira Makarova, Michael Segel, Jonathan Schmid-Burgk, Jeremy Koob, Yuri Wolf, Eugene Koonin & Feng Zhang
Science. 2020 Aug 28;369(6507):1077-1084. doi: 10.1126/science.aba0372.
Highly Parallel Profiling of Cas9 Variant Specificity
Jonathan Schmid-Burgk*, Linyi Gao*, David Li*, Zachary Gardner, Jonathan Strecker, Blake Lash & Feng Zhang
Mol Cell. 2020 May 21;78(4):794-800.e8. doi: 10.1016/j.molcel.2020.02.023. Epub 2020 Mar 17.
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Optical Pooled Screens in Human Cells
David Feldman*, Avtar Singh*, Jonathan Schmid-Burgk, Rebecca Carlson, Anja Mezger, Anthony Garrity, Feng Zhang & Paul Blainey
Cell. 2019 Oct 17;179(3):787-799.e17. doi: 10.1016/j.cell.2019.09.016.
A cytosine deaminase for programmable single-base RNA editing
Omar Abudayyeh*, Jonathan Gootenberg*, Brian Franklin, Jeremy Koob, Max Kellner, Alim Ladha, Julia Joung, Paul Kirchgatterer, David Cox & Feng Zhang
Science. 2019 Jul 26;365(6451):382-386. doi: 10.1126/science.aax7063. Epub 2019 Jul 11.
DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction
Joshua Weinstein, Aviv Regev & Feng Zhang
Cell. 2019 Jun 27;178(1):229-241.e16. doi: 10.1016/j.cell.2019.05.019. Epub 2019 Jun 20.
RNA-guided DNA insertion with CRISPR-associated transposases
Jonathan Strecker, Alim Ladha, Zachary Gardner, Jonathan Schmid-Burgk, Kira Makarova, Eugene Koonin & Feng Zhang
Science. 2019 Jul 5;365(6448):48-53. doi: 10.1126/science.aax9181. Epub 2019 Jun 6.
Development of CRISPR-Cas systems for genome editing and beyond
Feng Zhang
QRB. 2019 Jun 13;52 E6. doi:10.1017/S0033583519000052
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage
Ian Slaymaker, Pablo Mesa, Max Kellner, Soumya Kannan, Edward Brignole, Jeremy Koob, Patricia Feliciano, Stefano Stella, Omar Abudayyeh, Jonathan Gootenberg, Jonathan Strecker, Guillermo Montoya & Feng Zhang
Cell Rep. 2019 Mar 26;26(13):3741-3751.e5. doi: 10.1016/j.celrep.2019.02.094.
Engineering of CRISPR-Cas12b for human genome editing
Jonathan Strecker, Sara Jones, Balwina Koopal, Jonathan Schmid-Burgk, Bernd Zetsche, Linyi Gao, Kira Makarova, Eugene Koonin & Feng Zhang
Nat Commun. 2019 Jan 22;10(1):212. doi: 10.1038/s41467-018-08224-4.
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Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6
Jonathan Gootenberg*, Omar Abudayyeh*, Max Kellner, Julia Joung, James Collins & Feng Zhang
Science. 2018 Apr 27;360(6387):439-444. doi: 10.1126/science.aaq0179. Epub 2018 Feb 15.
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David Cox*, Jonathan Gootenberg*, Omar Abudayyeh*, Brian Franklin, Max Kellner, Julia Joung & Feng Zhang
Science. 2017 Nov 24;358(6366):1019-1027. doi: 10.1126/science.aaq0180. Epub 2017 Oct 25.
RNA targeting with CRISPR–Cas13
Omar Abudayyeh*, Jonathan Gootenberg*, Patrick Essletzbichler, Shuo Han, Julia Joung, Joseph Belanto, Vanessa Verdine, David Cox, Max Kellner, Aviv Regev, Eric Lander, Daniel Voytas, Alice Ting & Feng Zhang
Nature. 2017 Oct 12;550(7675):280-284. doi: 10.1038/nature24049. Epub 2017 Oct 4.
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood
Julia Joung, Jesse Engreitz, Silvana Konermann, Omar Abudayyeh, Vanessa Verdine, Francois Aguet, Jonathan Gootenberg, Neville Sanjana, Jason Wright, Charles Fulco, Yuen-Yi Tseng, Charles Yoon, Jesse Boehm, Eric Lander & Feng Zhang
Nature. 2017 Aug 17;548(7667):343-346. doi: 10.1038/nature23451. Epub 2017 Aug 11.
Nucleic acid detection with CRISPR-Cas13a/C2c2
Jonathan Gootenberg*, Omar Abudayyeh*, Jeong Wook Lee, Patrick Essletzbichler, Aaron Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole Daringer, Catherine Freije, Cameron Myhrvold, Roby Bhattacharyya, Jonathan Livny, Aviv Regev, Eugene Koonin, Deborah Hung, Pardis Sabeti, James Collins & Feng Zhang
Science. 2017 Apr 28;356(6336):438-442. doi: 10.1126/science.aam9321. Epub 2017 Apr 13.
Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening
Julia Joung*, Silvana Konermann*, Jonathan Gootenberg, Omar Abudayyeh, Randall Platt, Mark Brigham, Neville Sanjana & Feng Zhang
Nat Protoc. 2017 Apr;12(4):828-863. doi: 10.1038/nprot.2017.016. Epub 2017 Mar 23.
Aaron Smargon*, David Cox*, Neena Pyzocha*, Kaijie Zheng, Ian Slaymaker, Jonathan Gootenberg, Omar Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira Makarova, Eugene Koonin & Feng Zhang
Mol Cell. 2017 Feb 16;65(4):618-630.e7. doi: 10.1016/j.molcel.2016.12.023. Epub 2017 Jan 5.
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Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array
Bernd Zetsche*, Matthias Heidenreich*, Prarthana Mohanraju*, Iana Fedorova, Jeroen Kneppers, Ellen DeGennaro, Nerges Winblad, Sourav Choudhury, Omar Abudayyeh, Jonathan Gootenberg, Wen Wu, David Scott, Konstantin Severinov, John van der Oost & Feng Zhang
Nat Biotechnol. 2017 Jan;35(1):31-34. doi: 10.1038/nbt.3737. Epub 2016 Dec 5.
High-resolution interrogation of functional elements in the noncoding genome
Neville Sanjana*, Jason Wright*, Kaijie Zheng, Ophir Shalem, Pierre Fontanillas, Julia Joung, Christine Cheng, Aviv Regev & Feng Zhang
Science. 2016 Sep 30;353(6307):1545-1549. doi: 10.1126/science.aaf7613.
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 Trombetta, Cynthia Hession, Feng Zhang & Aviv Regev
Science. 2016 Aug 26;353(6302):925-8. doi: 10.1126/science.aad7038. Epub 2016 Jul 28.
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
Omar Abudayyeh*, Jonathan Gootenberg*, Silvana Konermann*, Julia Joung, Ian Slaymaker, David Cox, Sergey Shmakov, Kira Makarova, Ekaterina Semenova, Leonid Minakhin, Konstantin Severinov, Aviv Regev, Eric Lander, Eugene Koonin & Feng Zhang
Science. 2016 Aug 5;353(6299):aaf5573. doi: 10.1126/science.aaf5573. Epub 2016 Jun 2.
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA
Takashi Yamano*, Hiroshi Nishimasu*, Bernd Zetsche, Hisato Hirano, Ian Slaymaker, Yinqing Li, Iana Fedorova, Takanori Nakane, Kira Makarova, Eugene Koonin, Ryuichiro Ishitani, Feng Zhang & Osamu Nureki
Cell. 2016 May 5;165(4):949-62. doi: 10.1016/j.cell.2016.04.003. Epub 2016 Apr 21.
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Rationally engineered Cas9 nucleases with improved specificity
Ian Slaymaker*, Linyi Gao*, Bernd Zetsche, David Scott, Winston Yan & Feng Zhang
Science. 2016 Jan 1;351(6268):84-8. doi: 10.1126/science.aad5227. Epub 2015 Dec 1.
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Sergey Shmakov*, Omar Abudayyeh*, Kira Makarova, Yuri Wolf, Jonathan Gootenberg, Ekaterina Semenova, Leonid Minakhin, Julia Joung, Silvana Konermann, Konstantin Severinov, Feng Zhang & Eugene Koonin
Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015 Oct 22.
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease
James Dahlman, Omar Abudayyeh, Julia Joung, Jonathan Gootenberg, Feng Zhang & Silvana Konermann
Nat Biotechnol. 2015 Nov;33(11):1159-61. doi: 10.1038/nbt.3390.
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Bernd Zetsche*, Jonathan Gootenberg*, Omar Abudayyeh, Ian Slaymaker, Kira Makarova, Patrick Essletzbichler, Sara Volz, Julia Joung, John van der Oost, Aviv Regev, Eugene Koonin & Feng Zhang
Cell. 2015 Oct 22;163(3):759-71. doi: 10.1016/j.cell.2015.09.038. Epub 2015 Sep 25.
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
Matthew Canver*, Elenoe Smith*, Falak Sher*, Luca Pinello*, Neville Sanjana*, Ophir Shalem, Diane Chen, Patrick Schupp, Divya Vinjamur, Sara Garcia, Sidinh Luc, Ryo Kurita, Yukio Nakamura, Yuko Fujiwara, Takahiro Maeda, Guo-Cheng Yuan, Feng Zhang, Stuart Orkin & Daniel Bauer
Nature. 2015 Nov 12;527(7577):192-7. doi: 10.1038/nature15521. Epub 2015 Sep 16.
Crystal Structure of Staphylococcus aureus Cas9
Hiroshi Nishimasu, Le Cong, Winston Yan, F. Ann Ran, Bernd Zetsche, Yinqing Li, Arisa Kurabayashi, Ryuichiro Ishitani, Feng Zhang & Osamu Nureki
Cell. 2015 Aug 27;162(5):1113-26. doi: 10.1016/j.cell.2015.08.007.
In vivo genome editing using Staphylococcus aureus Cas9
F. Ann Ran*, Le Cong*, Winston Yan*, David Scott, Jonathan Gootenberg, Andrea Kriz, Bernd Zetsche, Ophir Shalem, Xuebing Wu, Kira Makarova, Eugene Koonin, Phillip Sharp & Feng Zhang
Nature. 2015 Apr 9;520(7546):186-91. doi: 10.1038/nature14299. Epub 2015 Apr 1.
Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis
Sidi Chen*, Neville Sanjana*, Kaijie Zheng, Ophir Shalem, Kyungheon Lee, Xi Shi, David Scott, Jun Song, Jen Pan, Ralph Weissleder, Hakho Lee, Feng Zhang & Phillip Sharp
Cell. 2015 Mar 12;160(6):1246-60. doi: 10.1016/j.cell.2015.02.038. Epub 2015 Mar 5.
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Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Silvana Konermann*, Mark Brigham*, Alexandro Trevino, Julia Joung, Omar Abudayyeh, Clea Barcena, Patrick Hsu, Naomi Habib, Jonathan Gootenberg, Hiroshi Nishimasu, Osamu Nureki & Feng Zhang
Nature. 2015 Jan 29;517(7536):583-8. doi: 10.1038/nature14136. Epub 2014 Dec 10.
CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling
Randall Platt, Sidi Chen*, Yang Zhou, Michael Yim, Lukasz Swiech, Hannah Kempton, James Dahlman, Oren Parnas, Thomas Eisenhaure, Marko Jovanovic, Daniel Graham, Siddharth Jhunjhunwala, Matthias Heidenreich, Ramnik Xavier, Robert Langer, Daniel Anderson, Nir Hacohen, Aviv Regev, Guoping Feng, Phillip Sharp & Feng Zhang
Cell. 2014 Oct 9;159(2):440-55. doi: 10.1016/j.cell.2014.09.014. Epub 2014 Sep 25.
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA
Hiroshi Nishimasu, F. Ann Ran, Patrick Hsu, Silvana Konermann, Soraya Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang & Osamu Nureki
Cell. 2014 Feb 27;156(5):935-49. doi: 10.1016/j.cell.2014.02.001. Epub 2014 Feb 13.
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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
Ophir Shalem*, Neville Sanjana*, Ella Hartenian, Xi Shi, David Scott, Tarjei Mikkelsen, Dirk Heckl, Benjamin Ebert, David Root, John Doench & Feng Zhang
Science. 2014 Jan 3;343(6166):84-87. doi: 10.1126/science.1247005. Epub 2013 Dec 12.
Optical control of mammalian endogenous transcription and epigenetic states
Silvana Konermann*, Mark Brigham*, Alexandro Trevino, Patrick Hsu, Matthias Heidenreich, Le Cong, Randall Platt, David Scott, George Church & Feng Zhang
Nature. 2013 Aug 22;500(7463):472-476. doi: 10.1038/nature12466. Epub 2013 Aug 23.
DNA targeting specificity of RNA-guided Cas9 nucleases
Patrick Hsu*, David Scott*, Joshua Weinstein, F. Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli Fine, Xuebing Wu, Ophir Shalem, Thomas Cradick, Luciano Marraffini, Gang Bao & Feng Zhang
Nat Biotechnol. 2013 Sep;31(9):827-32. doi: 10.1038/nbt.2647. Epub 2013 Jul 21.
Multiplex Genome Engineering Using CRISPR/Cas Systems
Le Cong*, F. Ann Ran*, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick Hsu, Xuebing Wu, Wenyan Jiang, Luciano Marraffini & Feng Zhang
Science. 2013 Feb 15;339(6121):819-23. doi: 10.1126/science.1231143. Epub 2013 Jan 3.