"writing is hard work and bad for the health." - e.b. white

papers

papers

papers

papers

2020

Ibrahim C. Kurt, Ronghao Zhou, Sowmya Iyer, Sara P. Garcia, Bret R. Miller, Lukas M. Langner, Julian Grünewald, J. Keith Joung. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nature biotechnology (2020) DOI: 10.1038/s41587-020-0609-x

Julian Grünewald, Ronghao Zhou, Caleb A. Lareau, Sara P. Garcia, Sowmya Iyer, Bret R. Miller, Lukas M. Langer, jonathan y. hsu, Martin J. Aryee, J. Keith Joung. A DUAL-Deaminase crispr base editor enables concurrent adenine and cytosine editing. Nature biotchenology (2020) doi: 10.1038/s41587-020-0535-y

Kendell Clement, Jonathan Y. Hsu, Matthew C. Canver, J Keith Joung, Luca Pinello., Technologies and computational analysis strategies for crispr applications. Molecular Cell (2020) doi: 10.1016/j.molcel.2020.06.012.

Peter C. DeWeirdt , Kendall R. Sanson, Annabel K. Sangree, Mudra Hegde, Ruth E. Hanna, Marissa N. Feeley, Audrey L. Griffith, Teng Teng, Samantha M. Borys, Christine Strand, J. Keith Joung, Benjamin P. Kleinstiver, Xuewen Pan, Alan Huang, John G. Doench. Optimization of AsCas12a for combinatorial genetic screens in human cells. Nature Biotechnology (2020) doi: 10.1038/s41587-020-0600-6.

Lilian Cruz, Bence György, Pike See Cheah, Benjamin P Kleinstiver, William A Eimer, Sara P Garcia, Nutan Sharma, Laurie J Ozelius, D Cristopher Bragg, J Keith Joung, Osmar Norberto de Souza, Luis Fernando Saraiva Macedo Timmers, Xandra O Breakefield. Mutant Allele-Specific CRISPR Disruption in DYT1 Dystonia Fibroblasts Restores Cell Function. Molecular Therapy Nucleic Acids (2020) doi: 10.1016/j.omtn.2020.05.009.

 

Jing Zeng, Yuxuan Wu, Chunyan Ren, Jasmine Bonanno, Anne H. Shen, Devlin Shea, Jason M. Gehrke, Kendell Clement, Kevin Luk, Qiuming Yao, Rachel Kim, Scot A. Wolfe, John P. Manis, Luca Pinello, J. Keith Joung, Daniel E. Bauer. Therapeutic base editing of human hematopoietic stem cells. Nature Medicine (2020) doi: 10.1038/s41591-020-0790-y.

 

Steven J. Grzegorski, Zhilian Hu, Yang Liu, Xinge Yu, Allison C. Ferguson, Hasam Madarati, Alexander P. Friedmann, Deepak Reyon, Paul Y. Kim, Colin A. Kretz, J. Keith Joung, Jordan A. Shavit. Disruption of the kringle 1 domain of prothrombin leads to late onset mortality in zebrafish. Scientific Reports (2020) doi: 10.1038/s41598-020-60840-7.

 

Manxiu Ma, Alexandro D. Ramirez, Tong Wang, Rachel L. Roberts, Katherine E. Harmon, David Schoppik, Avirale Sharma, Christopher Kuang, Stephanie L. Goei, James A. Gagnon, Steve Zimmerman, Shengdar Q. Tsai, Deepak Reyon, J. Keith Joung, Emre R. F. Aksay, Alexander F. Schier, Y. Albert Pan. Zebrafish dscaml1 Deficiency Impairs Retinal Patterning and Oculomotor Function. Journal of Neuroscience (2020) doi: 10.1523/JNEUROSCI.1783-19.2019.

2019

Julian Grünewald, Ronghao Zhou, Sara P. Garcia, Sowmya Iyer, Caleb A. Lareau, Martin J. Aryee, J. Keith Joung. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature (2019)

Eric S. Lander, Françoise Baylis, Feng Zhang, Emmanuelle Charpentier, Paul Berg, Catherine Bourgain, Bärbel Friedrich, J. Keith Joung, Jinsong Li, David Liu, Luigi Naldini, Jing-Bao Nie Nie, Renzong Qiu, Bettina Schöne-Seifert, Feng Shao, Sharon Terry, Wensheng  Wei, Ernst-Ludwig Winnacker. Adopt a moratorium on heritable genome editing. Nature (2019)    

Kendell Clement, Holly Rees, Matthew C. Canver, Jason M. Gehrke, Rick Farouni, Jonathan Y. Hsu, Mitchel A. Cole, David R. Liu, J. Keith Joung, Daniel E. Bauer & Luca Pinello. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nature Biotechnology (2019)

Benjamin P. Kleinstiver, Alexander A. Sousa, Russell T. Walton, Y. Esther Tak, Jonathan Y. Hsu, Kendell Clement, Moira M. Welch, Joy E. Horng, Jose Malagon-Lopez, Irene Scarfò, Marcela V. Maus, Luca Pinello, Martin J. Aryee & J. Keith Joung. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature Biotechnology (2019)

2018

Jonathan Y. Hsu, Charles P. Fulco, Mitchel A. Cole, Matthew C. Canver, Danilo Pellin, Falak Sher, Rick Farouni, Kendell Clement, Jimmy A. Guo, Luca Biasco, Stuart H. Orkin, Jesse M. Engreitz, Eric S. Lander, J. Keith Joung, Daniel E. Bauer & Luca Pinello. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nature Methods (2018)      

  

Cicera R. Lazzarotto, Nhu T. Nguyen, Xing Tang, Jose Malagon-Lopez, Jimmy A. Guo, Martin J. Aryee, J. Keith Joung & Shengdar Q. Tsai. Defining CRISPR–Cas9 genome-wide nuclease activities with CIRCLE-seq. Nature Protocols (2018)   

Pinar Akcakaya, Maggie L. Bobbin, Jimmy A. Guo, Jose Malagon-Lopez, Kendell Clement, Sara P. Garcia, Mick D. Fellows, Michelle J. Porritt, Mike A. Firth, Alba Carreras, Tania Baccega, Frank Seeliger, Mikael Bjursell, Shengdar Q. Tsai, Nhu T. Nguyen, Roberto Nitsch, Lorenz M. Mayr, Luca Pinello, Mohammad Bohlooly-Y, Martin J. Aryee, Marcello Maresca & J. Keith Joung. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature (2018)

Jason M Gehrke, Oliver Cervantes, M Kendell Clement, Yuxuan Wu, Jing Zeng, Daniel E Bauer, Luca Pinello & J Keith Joung. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nature Biotechnology (2018)

Caleb A Lareau, Kendell Clement, Jonathan Y Hsu, Vikram Pattanayak, J Keith Joung, Martin J Aryee & Luca Pinello. Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo.  Nature Methods (2018)

Matthew C. Canver, J. Keith Joung, and Luca Pinello. Impact of Genetic Variation on CRISPR-Cas Targeting. The CRISPR Journal (2018)

 

2017

Y Esther Tak, Benjamin P Kleinstiver, James K Nuñez, Jonathan Y Hsu, Joy E Horng, Jingyi Gong, Jonathan S Weissman & J Keith Joung. Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factorsNature Methods (2017)

Janice S. Chen, Yavuz S. Dagdas, Benjamin P. Kleinstiver, Moira M. Welch, Alexander A. Sousa, Lucas B. Harrington, Samuel H. Sternberg, J. Keith Joung, Ahmet Yildiz & Jennifer A. Doudna. Enhanced proofreading governs CRISPR–Cas9 targeting accuracyNature (2017)

Zhilian Hu, Yang Liu, Michael C. Huarng, Marzia Menegatti, Deepak Reyon, Megan S. Rost, Zachary G. Norris, Catherine E. Richter, Alexandra N. Stapleton, Neil C. Chi, Flora Peyvandi, J. Keith Joung and Jordan A. Shavit. Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathwayBlood (2017)

Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee & J Keith Joung. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targetsNature Methods (2017)

Koji Ando,*, Ankur K. Shah,*, Vibhu Sachdev, Benjamin P. Kleinstiver, Julian Taylor-Parker, Moira M. Welch, Yiheng Hu, Ravi Salgia, Forest M. White, Jeffrey D. Parvin, Al Ozonoff, Lucia E. Rameh , J. Keith Joung and Ajit K. Bharti. Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathwayOncotarget (2017)

2016

Benjamin P Kleinstiver*^, Shengdar Q Tsai*, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee & J Keith Joung^. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cellsNature Biotechnology (2016)        

* contributed equally     ^co-corresponding authors

Supriya K. Saha, John D. Gordan, Benjamin P. Kleinstiver, Phuong Vu, Mortada S. Najem, Jia-Chi Yeo, Lei Shi, Yasutaka Kato, Rebecca S. Levin,James T. Webber, Leah J. Damon, Regina K. Egan, Patricia Greninger, Ultan McDermott, Mathew J. Garnett, Roger L. Jenkins,Kimberly M. Rieger-Christ, Travis B. Sullivan, Aram F. Hezel, Andrew S. Liss,Yusuke Mizukami, Lipika Goyal, Cristina R. Ferrone, Andrew X. Zhu,J. Keith Joung, Kevan M. Shokat, Cyril H. Benes & Nabeel Bardeesy. Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma. Cancer Discovery (2016) 6; 727.

Shengdar Q Tsai, Ved V Topkar, J Keith Joung & Martin J Aryee. Open-source guideseq software for analysis of GUIDE-seq dataNature Biotechnology (2016)

Shengdar Q Tsai & J Keith Joung. Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases. Nature Reviews Genetics (2016) 17(5):300-12.

Benjamin P. Kleinstiver*, Vikram Pattanayak*, Michelle S. Prew, Shengdar Q. Tsai, Nhu T. Nguyen, Zongli Zheng & J Keith Joung. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature (2016) 529(7587)490-5.        

* contributed equally

2015

J. Keith Joung, Daniel F. Voytas & Joanne Kamens. Accelerating research through reagent repositories: the genome editing exampleGenome Biology (2015) 16:225.

Benjamin P Kleinstiver^, Michelle S Prew, Shengdar Q Tsai, Nhu T Nguyen, Ved V Topkar, Zongli Zheng & J Keith Joung^. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognitionNature Biotechnology (2015) 33(12):1293-8.     

^co-corresponding authors

Nicolas Wyvekens, Shengdar Tsai, and J Keith Joung. Genome Editing in Human Cells Using CRISPR/Cas Nucleases. Curr Protoc Mol Biol (2015) 112:31.3.1-18. 

Sándor Spisák, Kate Lawrenson, Yanfang Fu, István Csabai, Rebecca T Cottman, Ji-Heui Seo, Christopher Haiman, Ying Han, Romina Lenci, Qiyuan Li, Viktória Tisza, Zoltán Szállási, Zachery T Herbert, Matthew Chabot, Mark Pomerantz, Norbert Solymosi, The GAME-ON/ELLIPSE Consortium, Simon A Gayther, J Keith Joung & Matthew L Freedman. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variantsNature Medicine (2015) 21(11):1357-63.

Basil P Hubbard, Ahmed H Badran, John A Zuris, John P Guilinger, Kevin M Davis, Liwei Chen, Shengdar Q Tsai, Jeffry D Sander, J Keith Joung & David R Liu. Continuous directed evolution of DNA-binding proteins to improve TALEN specificityNature Methods (2015) 12(10):939-42.

J Keith Joung. Unwanted mutations: Standards needed for gene-editing errorsNature (2015) 523(7559):158.

Benjamin P. Kleinstiver, Michelle S. Prew, Shengdar Q. Tsai, Ved V. Topkar, Nhu T. Nguyen, Zongli Zheng, Andrew P. W. Gonzales, Zhuyun Li, Randall T. Peterson, Jing-Ruey Joanna Yeh, Martin J. Aryee & J Keith Joung. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature (2015) 523(7561):481-5.

Nicolas Wyvekens, Ved V. Topkar, Cyd Khayter, J Keith Joung & Shengdar Q Tsai. Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome EditingHum Gene Ther (2015) 26(7):425-31.

Julia M. Rogers, Luis A. Barrera, Deepak Reyon, Jeffry D. Sander, Manolis Kellis, J Keith Joung & Martha L. Bulyk. Context influences on TALE–DNA binding revealed by quantitative profiling. Nature Communications (2015) 6:7440.

Shamim H Rahman, Johannes Kuehle, Christian Reimann, Tafadzwa Mlambo, Jamal Alzubi, Morgan L Maeder, Heimo Riedel, Paul Fisch, Tobias Cantz, Cornelia Rudolph, Claudio Mussolino, J Keith Joung, Axel Schambach & Toni Cathomen. Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease ModelPLoS Genetics (2015) 11(5):e1005239.

Joshua C Black, Elnaz Atabakhsh, Jaegil Kim, Kelly M Biette, Capucine Van Rechem, Brendon Ladd, Paul d Burrowes, Carlos Donado, Hamid Mattoo, Benjamin P Kleinstiver, Bing Song, Grasiella Andriani, J Keith Joung, Othon Iliopoulos, Cristina Montagna, Shiv Pillai, Gad Getz & Johnathan R. Whetstine. Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Genes & Development (2015) 29(10):1018-31.

Woong Y Hwang, Yanfang Fu, Deepak Reyon, Andrew PW Gonzales, J Keith Joung & Jing-Ruey Joanna Yeh. Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided NucleasesMethods in Molecular Biology (2015) 1311:317-34.

[papers missing]

2014

Tsai, Shengdar Q., Nicolas Wyvekens, Cyd Khayter, Jennifer A. Foden, Vishal Thapar, Deepak Reyon, Mathew J. Goodwin, Martin J. Aryee, and J. Keith Joung. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editingNature Biotechnology  (2014).

Sander, Jeffry D., and J. Keith Joung. CRISPR-Cas systems for editing, regulating and targeting genomesNature Biotechnology  32, no. 4 (2014): 347-355.

Guilinger, John P., Vikram Pattanayak, Deepak Reyon, Shengdar Q. Tsai, Jeffry D. Sander, J. Keith Joung, and David R. Liu. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificityNature Methods 11, no. 4 (2014): 429-435.

Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M. & Joung, J. K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotechnology. 32, 279–284 (2014). 

2013

Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D,Bernstein BE, Costello JF, Wilkinson MF, Joung JK. Targeted DNA Demethylation and Endogenous Gene Activation Using Programmable TALE-TET1 FusionsNat Biotechnol., 2013 Oct 9; doi: 10.1038/nbt2726.

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancersNat Biotechnol.2013 Sep 8, doi:10.1038/nbt.2701

Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF.Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases. G3 (Bethesda) 2013 Oct 3; 3(10): 1707-15.

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE,Liu DR, Joung JK. In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sitesNucleic Acids Res. 2013 Oct 1; 41(19):e181.

Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. CRISPR RNA-guided activation of endogenous human genesNat Methods. 2013 Oct; 10 (10): 977-9.

Hwang WY, Fu Y, Reyon D, Maeder ML, Kaini P, Sander JD, Joung JK, Peterson RT, Yeh JR. Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas SystemPLoS One. 2013 Jul9;8(7):e68708.

Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK. Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) AssemblyCurr Protoc Mol Biol. 2013 Jul;Chapter 12:Unit12.16.

Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK*, Sander JD*. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cellsNat Biotechnol. 2013 Sep;31(9):822-6.

*Co-corresponding authors

Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCrayPB Jr, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineeringProc Natl Acad Sci USA. 2013 June 18; 110(25): E2279-87.

Osborn MJ, Starker CG, McElroy AN, Webber BR, Riddle MJ, Xia L, Defeo AP, Gabriel R, Schmidt M, Von Kalle C, Carlson DF, Maeder ML, Joung JK, Wagner JE, Voytas DF, Blazar BR, Tolar J. TALEN-based Gene Correction for Epidermolysis BullosaMol Ther. 2013 Jun;21(6):1151-9.

Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK. Robust, synergistic regulation of human gene expression using TALE activators. Nat Methods. 2013 Mar;10(3): 243-5.

Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR*, Joung JK*. Efficient genome editing in zebrafish using a CRISPR-Cas systemNat Biotechnol. 2013 Mar;31(3):227-9.

*Co-corresponding authors

Tremblay JP, Xiao X, Aartsma-Rus A, Barbas C, Blau HM, Bogdanove AJ, Boycott K, Braun S,Breakefield XO, Bueren JA, Buschmann M, Byrne BJ, Calos M, Cathomen T, Chamberlain J, Chuah M,Cornetta K, Davies KE, Dickson JG, Duchateau P, Flotte TR, Gaudet D, Gersbach CA, Gilbert R, Glorioso J, Herzog RW, High KA, Huang W, Huard J, Joung JK, Liu D, Liu D, Lochmüller H, Lustig L, Martens J, Massie B, Mavilio F, Mendell JR, Nathwani A, Ponder K, Porteus M, Puymirat J, Samulski J, Takeda S, Thrasher A, Vandendriessche T, Wei Y, Wilson JM, Wilton SD, Wolfe JH, Gao G. Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic DiseasesMol Ther. 2013 Feb;21(2):266-268.

2012

Joung JK, Sander JD. TALENs: a widely applicable technology for targeted genome editing, Nat.Rev. Mol. Cell Biol., 2012, 14: 49-55.

Reyon D, Khayter C, Regan MR, Joung JK*, Sander JD*. Engineering Designer Transcription Activator-Like Effector Nucleases (TALENs) by REAL or REAL-Fast AssemblyCurr Protoc Mol Biol. 2012 Oct;Chapter 12:Unit12.15.

*Co-corresponding authors

Hermann M, Maeder ML, Rector K, Ruiz J, Becher B, Bürki K, Khayter C, Aguzzi A, Joung JK, Buch T,Pelczar P. Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse EmbryosPLoS One. 2012; 7(9): e41796.

Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. A synthetic biology framework for programming eukaryotic transcription functionsCell. 2012 Aug3;150(3):647-58.

Cade L, Reyon D, Hwang WY, Tsai SQ, Patel S, Khayter C, Joung JK, Sander JD, Peterson RT, Yeh JR. Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENsNucleic Acids Res. 2012; 40(16):8001-10.

Moore FE, Reyon D, Sander JD, Martinez SA, Blackburn JS, Khayter C, Ramirez CL, Joung JK, Langenau DM. Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs)PLoS One. 2012;7(5):e37877.

Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD*, Joung JK*. FLASH assembly of TALENs for high-throughput genome editingNat Biotechnol. 2012 May; 30(5):460-5.

*Co-corresponding authors

Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, ScharenbergAM, Joung JK. Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effectsNucleic Acids Res. 2012 Jul;40(12):5560-8.

2011

Sander JD, Maeder ML, Joung JK. Engineering designer nucleases with customized cleavage specificitiesCurr Protoc Mol Biol. 2011 Oct;Chapter 12:Unit12.13.

Sander JD, Yeh JR, Peterson RT, Joung JK. Engineering zinc finger nucleases for targeted mutagenesis of zebrafishMethods Cell Biol. 2011;104:51-8.

Sebastiano V, Maeder ML, Angstman JF, Haddad B, Khayter C, Yeo DT, Goodwin MJ, Hawkins JS,Ramirez CL, Batista LF, Artandi SE, Wernig M*, Joung JK*. In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleasesStem Cells. 2011 Nov;29(11):1717-26.

*Co-corresponding authors

Pattanayak V, Ramirez CL, Joung JK, Liu DR. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selectionNat Methods. 2011 Aug 7;8(9):765-70.

Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK*, Yeh JR*. Targeted gene disruption in somatic zebrafish cells using engineered TALENsNat Biotechnol. 2011 Aug 5;29(8):697-8.

*Co-corresponding authors

Lee J, Hirsh AS, Wittner BS, Maeder ML, Singavarapu R, Lang M, Janarthanan S, McDermott U, YajnikV, Ramaswamy S, Joung JK*, Sgroi DC*. Induction of stable drug resistance in human breast cancer cells using a combinatorial zinc finger transcription factor libraryPLoS One.2011;6(7):e21112.

*Co-corresponding authors

Rahman SH, Maeder ML, Joung JK, Cathomen T. Zinc-finger nucleases for somatic gene therapy: the next frontierHum Gene Ther. 2011 Jun 1. [Epub ahead of print]

Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ,Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM. Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases breakthrough technologiesPlant Physiol. 2011Jun;156(2):466-73.

Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR. ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organismsBMC Genomics. 2011 Jan 28;12:83. 

2010

Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS,Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D,Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)Nat Methods. 2010 Dec 12; doi: 10.1038/nmeth.1542.

Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg E, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D. Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequencesBMC Bioinformatics. 2010; 11: 543.

Söllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T. Autonomous zinc-finger nuclease pairs for targeted chromosomal deletionNucleic Acids Res.2010 Aug 16. Epub ahead of print.

Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering toolNucleic Acids Res. 2010 Jul 1;38 Suppl:W462-8.

Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D,Peterson T, Joung JK, Voytas DF. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleasesProc Natl Acad Sci USA. 2010 Jun 29;107(26):12028-33.

Thibodeau-Beganny S, Maeder ML, Joung JK. Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection systemMethods Mol Biol. 2010;649:31-50.

Joung JK, Voytas DF, Cathomen T. Reply to Genome editing with modularly assembled zinc-finger nucleasesNat Methods, 2010, 7: 91-92.

2009

Voytas DF, Joung JK. Plant science. DNA binding made easyScience, 2009, 326: 1491-1492.

Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR. Targeted mutagenesis in zebrafish using customized zinc-finger nucleasesNat Protocols, 2009, 4: 1855-1867.

Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK. Oligomerized Pool ENgineering (OPEN): An "Open-Source" Protocol for Making Customized Zinc Finger ArraysNat Protocols, 2009, 4: 1471-1501.

 

Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou, B-K, Chen G, Ye Z, ParkI-H,  Daley GQ, Porteus MH, Joung JK, Cheng L. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cellsCell Stem Cell, 2009, 5: 97-110.

 

Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF. High Frequency  Modification of Plant Genes Using Engineered Zinc Finger NucleasesNature, 2009, 459:   442-445.

 

Foley JE, Yeh J-R Y, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK. Rapid Mutation of  Endogenous Zebrafish Genes Using Zinc Finger Nucleases Made by Oligomerized Pool  ENgineering (OPEN)PLoS ONE, 2009, 4: e4348.

 

Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D. An affinity-based scoring scheme for  predicting DNA-binding activities of modularly assembled zinc-finger proteinsNucleic Acids Res., 2009, 37: 506-515.

 

Fu F, Sander JD, Maeder ML, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF. Zinc  Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc finger arraysNucleic Acids Res., 2009, 35: D279-D283.

2008

Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Muller-Lerch F, Fu F, Pearlberg J, Gobel C, Dassie J, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T,  Voytas DF, Joung JK. Rapid "open-source" engineering of customized zinc-finger nucleases  for highly efficient gene modificationMol Cell, 2008, 31: 294-301.

 

Ramirez CL, Foley JE, Wright DA, Muller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK. Unexpected failure rates for modular  assembly of engineered zinc fingersNat Methods, 2008, 5: 374-375.

 

Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH. Comparison of Zinc Finger  Nucleases for Use In Gene Targeting in Mammalian CellsMol Ther., 2008, 16: 707-717.

 

Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T. DNA-binding  specificity is a major determinant of the activity and toxicity of zinc-finger nucleasesMol Ther., 2008, 16: 352-8.

2007

Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA. Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method, Nucleic Acids Res., 2007, 35: e81.

 

Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D. Zinc Finger Targeter (ZiFiT): An Engineered  Zinc Finger/Target Site Design ToolNucleic Acids Res., 2007, 35: W599-W605.

2006

Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF, Joung JK. Standardized reagents and protocols for engineering zinc  finger nucleases by modular assemblyNat Protocols, 2006, 1: 1637-1652.

 

Giesecke AV, Fang R, Joung JK. Synthetic protein-protein interaction domains created by  shuffling Cys2His2 zinc fingersMol Sys Biol., 2006, doi: 10.1038/msb4100053

 

Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA. A counter-selectable marker for  bacterial-based interaction trap systemsBiotechniques, 2006, 40: 179-184.

2005

Vallet-Galy I, Donovan KE, Fang R, Joung JK, Dove SL. Repression of phase-variable cupA gene  expression by H-NS-like proteins in Pseudomonas aeruginosaProc. Natl. Acad. Sci. USA,  2005, 102: 11082-11087.

 

Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA. A combined  yeast/bacterial two-hybrid system: development and evaluationMol Cell Proteomics 2005,  4: 819-826.

2004

Nguyen-Hackley DH, Ramm E, Taylor CM, Joung JK, Dervan PB, Pabo CO. Allosteric Inhibition of  Zinc-Finger Binding in the Major Groove of DNA by Minor-Groove Binding Ligands,  Biochemistry 2004; 43: 3880-3890.

 

Thibodeau SA, Fang R, Joung JK. An optimized high-throughput b-galactosidase assay for  bacterial cell-based reporter systemsBiotechniques 2004; 36: 410-415.

2003

Hurt, JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selectionProc. Natl. Acad. Sci. USA 2003; 100: 12271-12276.

J. Keith Joung

Massachusetts General Hospital
149 13th Street, 6th floor
Charlestown, MA 02129

E-mail: jjoung@mgh.harvard.edu

Website created by Joy Horng