Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway.

Hu Z, Liu Y, Huarng MC, Menegatti M, Reyon D, Rost MS, Norris ZG, Richter CE, Stapleton AN, Chi NC, Peyvandi F, Joung JK, Shavit JA
Blood. 2017;:ePub - PMID: 28576875

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.

Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK
Nat Methods. 2017;14(6):607-614 - PMID: 28459458

Nucleic acid detection with CRISPR-Cas13a/C2c2.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F
Science. 2017;356(6336):438-442 - PMID: 28408723

Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway.

Ando K, Shah AK, Sachdev V, Kleinstiver BP, Taylor-Parker J, Welch MM, Hu Y, Salgia R, White FM, Parvin JD, Ozonoff A, Rameh LE, Joung JK, Bharti AK
Oncotarget. 2017;:ePub - PMID: 28415827

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.

Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T
Mol Ther. 2016;16(2):352-358 - PMID: 28178540

Genome Editing Technologies: Defining a Path to Clinic: Genomic Editing: Establishing Preclinical Toxicology Standards, Bethesda, Maryland 10 June 2014.

Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH
Mol Ther. 2016;23(5):796-806 - PMID: 28142000

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK
Nat Biotechnol. 2016;34(8):869-874 - PMID: 27347757 - PMCID: PMC4980201

Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.

Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N
Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737

Open-source guideseq software for analysis of GUIDE-seq data.

Tsai SQ, Topkar VV, Joung JK, Aryee MJ
Nat Biotechnol. 2016;34(5):483 - PMID: 27153277

Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.

Tsai SQ, Joung JK
Nat Rev Genet. 2016;17(5):300-12 - PMID: 27087594

Accelerating research through reagent repositories: the genome editing example.

Joung JK, Voytas DF, Kamens J
Genome Biol. 2015;16(1):255 - PMID: 26585970 - PMCID: PMC4653914

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition.

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK
Nat Biotechnol. 2015;33(12):1293-1298 - PMID: 26524662 - PMCID: PMC4689141

Genome Editing in Human Cells Using CRISPR/Cas Nucleases.

Wyvekens N, Tsai SQ, Joung JK
Curr Protoc Mol Biol. 2015;112:31.3.1-31.3.18 - PMID: 26423589 - PMCID: PMC4852847

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.

Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, , Gayther SA, Joung JK, Freedman ML
Nat Med. 2015;21(11):1357-1363 - PMID: 26398868 - PMCID: PMC4746056

Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.

Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM, Chen L, Tsai SQ, Sander JD, Joung JK, Liu DR
Nat Methods. 2015;12(10):939-942 - PMID: 26258293 - PMCID: PMC4589463

Unwanted mutations: Standards needed for gene-editing errors.

Joung JK
Nature. 2015;523(7559):158 - PMID: 26156364

Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JJ, Aryee MJ, Joung JK
Nature. 2015;523(7561):481-5 - PMID: 26098369 - PMCID: PMC4540238

Dimeric CRISPR RNA-guided FokI-dCas9 nucleases (RFNs) directed by truncated gRNAs for highly specific genome editing.

Wyvekens N, Topkar VV, Khayter C, Joung JK, Tsai SQ
Hum Gene Ther. 2015;26(7):425-431 - PMID: 26068112 - PMCID: PMC4509490

Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model.

Rahman SH, Kuehle J, Reimann C, Mlambo T, Alzubi J, Maeder ML, Riedel H, Fisch P, Cantz T, Rudolph C, Mussolino C, Joung JK, Schambach A, Cathomen T
PLoS Genet. 2015;11(5):e1005239 - PMID: 26000857 - PMCID: PMC4441453

Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided Nucleases.

Hwang WY, Fu Y, Reyon D, Gonzales AP, Joung JK, Yeh JR
Methods Mol Biol. 2015;1311:317-34 - PMID: 25981483

Genome editing technologies: defining a path to clinic.

Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH
Mol Ther. 2015;23(5):796-806 - PMID: 25943494 - PMCID: PMC4427885

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.

Black JC, Atabakhsh E, Kim J, Biette KM, Van Rechem C, Ladd B, Burrowes PD, Donado C, Mattoo H, Kleinstiver BP, Song B, Andriani G, Joung JK, Iliopoulos O, Montagna C, Pillai S, Getz G, Whetstine JR
Genes Dev. 2015;29(10):1018-31 - PMID: 25995187 - PMCID: PMC4441050

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A
Nat Genet. 2015;47(5):469-78 - PMID: 25822089 - PMCID: PMC4414868

Chromatin regulation at the frontier of synthetic biology.

Keung AJ, Joung JK, Khalil AS, Collins JJ
Nat Rev Genet. 2015;16(3):159-71 - PMID: 25668787 - PMCID: PMC4846386

Fanconi Anemia Gene Editing by the CRISPR/Cas9 System.

Osborn MJ, Gabriel R, Webber BR, DeFeo AP, McElroy AN, Jarjour J, Starker CG, Wagner JE, Joung JK, Voytas DF, von Kalle C, Schmidt M, Blazar BR, Tolar J
Hum Gene Ther. 2014;26(2):114-26 - PMID: 25545896 - PMCID: PMC4326027

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.

Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK
Nat Biotechnol. 2014;33(2):187-197 - PMID: 25513782 - PMCID: PMC4320685

A Zebrafish Model of Myelodysplastic Syndrome Produced Through tet2 Genomic Editing.

Gjini E, Mansour MR, Sander JD, Moritz N, Nguyen AT, Kesarsing M, Gans E, He S, Chen S, Ko M, Kuang YY, Yang S, Zhou Y, Rodig S, Zon LI, Joung JK, Rao A, Look AT
Mol Cell Biol. 2014;35(5):789-804 - PMID: 25512612 - PMCID: PMC4323485

Targeted genome editing in human cells using CRISPR/Cas nucleases and truncated guide RNAs.

Fu Y, Reyon D, Joung JK
Methods Enzymol. 2014;546:21-45 - PMID: 25398334

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo.

Zuris JA, Thompson DB, Shu Y, Guilinger JP, Bessen JL, Hu JH, Maeder ML, Joung JK, Chen ZY, Liu DR
Nat Biotechnol. 2014;33(1):73-80 - PMID: 25357182 - PMCID: PMC4289409

Genome editing: a tool for research and therapy: towards a functional understanding of variants for molecular diagnostics using genome editing.

Tsai SQ, Iafrate AJ, Joung JK
Nat Med. 2014;20(10):1103-4 - PMID: 25295940

Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage.

Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM
Genes Dev. 2014;28(17):1957-75 - PMID: 25184681 - PMCID: PMC4197947

I?B kinase ? (IKBKB) mutations in lymphomas that constitutively activate canonical nuclear factor ?B (NF?B) signaling.

Kai X, Chellappa V, Donado C, Reyon D, Sekigami Y, Ataca D, Louissaint A, Mattoo H, Joung JK, Pillai S
J Biol Chem. 2014;289(39):26960-72 - PMID: 25107905 - PMCID: PMC4175336

What's changed with genome editing?

Tsai SQ, Joung JK
Cell Stem Cell. 2014;15(1):3-4 - PMID: 24996161

Targeted mutagenesis of zebrafish antithrombin III triggers disseminated intravascular coagulation and thrombosis, revealing insight into function.

Liu Y, Kretz CA, Maeder ML, Richter CE, Tsao P, Vo AH, Huarng MC, Rode T, Hu Z, Mehra R, Olson ST, Joung JK, Shavit JA
Blood. 2014;124(1):142-50 - PMID: 24782510 - PMCID: PMC4125349

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.

Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK
Nat Biotechnol. 2014;32(6):569-76 - PMID: 24770325 - PMCID: PMC4090141

Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.

Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K
Cell Stem Cell. 2014;14(6):781-95 - PMID: 24704492 - PMCID: PMC4653065

CRISPR-Cas systems for editing, regulating and targeting genomes.

Sander JD, Joung JK
Nat Biotechnol. 2014;32(4):347-55 - PMID: 24584096 - PMCID: PMC4022601

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.

Guilinger JP, Pattanayak V, Reyon D, Tsai SQ, Sander JD, Joung JK, Liu DR
Nat Methods. 2014;11(4):429-35 - PMID: 24531420 - PMCID: PMC4010127

An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.

Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD
Nucleic Acids Res. 2014;42(8):4800-12 - PMID: 24523353 - PMCID: PMC4005693

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.

Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK
Nat Biotechnol. 2014;32(3):279-84 - PMID: 24463574 - PMCID: PMC3988262

Toddler: an embryonic signal that promotes cell movement via Apelin receptors.

Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF
Science. 2014;343(6172):1248636 - PMID: 24407481 - PMCID: PMC4107353

Correction of Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair.

Low BE, Krebs MP, Joung JK, Tsai SQ, Nishina PM, Wiles MV
Invest Ophthalmol Vis Sci. 2013;55(1):387-395 - PMID: 24346171 - PMCID: PMC3921157

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.

Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R
Cell. 2013;155(7):1507-20 - PMID: 24360274 - PMCID: PMC3905448

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

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
Nat Biotechnol. 2013;31(12):1137-42 - PMID: 24108092 - PMCID: PMC3858462

Locus-specific editing of histone modifications at endogenous enhancers.

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE
Nat Biotechnol. 2013;31(12):1133-6 - PMID: 24013198 - PMCID: PMC3858395

Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases.

Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF
G3 (Bethesda). 2013;3(10):1707-1715 - PMID: 23979943 - PMCID: PMC3789795

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK
Nucleic Acids Res. 2013;41(19):e181 - PMID: 23945932 - PMCID: PMC3799455

CRISPR RNA-guided activation of endogenous human genes.

Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK
Nat Methods. 2013;10(10):977-9 - PMID: 23892898 - PMCID: PMC3794058

Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System.

Hwang WY, Fu Y, Reyon D, Maeder ML, Kaini P, Sander JD, Joung JK, Peterson RT, Yeh JR
PLoS One. 2013;8(7):e68708 - PMID: 23874735 - PMCID: PMC3706373

Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) Assembly.

Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK
Curr Protoc Mol Biol. 2013;Chapter 12:Unit12.16 - PMID: 23821439 - PMCID: PMC3767754

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.

Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD
Nat Biotechnol. 2013;31(9):822-6 - PMID: 23792628 - PMCID: PMC3773023

piggyBac transposase tools for genome engineering.

Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB, Bushman FD, Sinn PL, Craig NL
Proc Natl Acad Sci U S A. 2013;110(25):E2279-87 - PMID: 23723351 - PMCID: PMC3690869

TALEN-based Gene Correction for Epidermolysis Bullosa.

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
Mol Ther. 2013;21(6):1151-1159 - PMID: 23546300 - PMCID: PMC3677309

Robust, synergistic regulation of human gene expression using TALE activators.

Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK
Nat Methods. 2013;10(3):243-5 - PMID: 23396285 - PMCID: PMC3584229

Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic Diseases.

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 ...
Mol Ther. 2013;21(2):266-268 - PMID: 23369965 - PMCID: PMC3594019

Efficient genome editing in zebrafish using a CRISPR-Cas system.

Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK
Nat Biotechnol. 2013;31(3):227-9 - PMID: 23360964 - PMCID: PMC3686313

TALENs: a widely applicable technology for targeted genome editing.

Joung JK, Sander JD
Nat Rev Mol Cell Biol. 2012;14(1):49-55 - PMID: 23169466 - PMCID: PMC3547402

Engineering Designer Transcription Activator--Like Effector Nucleases (TALENs) by REAL or REAL-Fast Assembly.

Reyon D, Khayter C, Regan MR, Joung JK, Sander JD
Curr Protoc Mol Biol. 2012;Chapter 12:Unit12.15 - PMID: 23026907 - PMCID: PMC3753116

Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse Embryos.

Hermann M, Maeder ML, Rector K, Ruiz J, Becher B, Bürki K, Khayter C, Aguzzi A, Joung JK, Buch T, Pelczar P
PLoS One. 2012;7(9):e41796 - PMID: 22970113 - PMCID: PMC3435328

A synthetic biology framework for programming eukaryotic transcription functions.

Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ
Cell. 2012;150(3):647-58 - PMID: 22863014 - PMCID: PMC3653585

Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs.

Cade L, Reyon D, Hwang WY, Tsai SQ, Patel S, Khayter C, Joung JK, Sander JD, Peterson RT, Yeh JR
Nucleic Acids Res. 2012;40(16):8001-10 - PMID: 22684503 - PMCID: PMC3439908

Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs).

Moore FE, Reyon D, Sander JD, Martinez SA, Blackburn JS, Khayter C, Ramirez CL, Joung JK, Langenau DM
PLoS One. 2012;7(5):e37877 - PMID: 22655075 - PMCID: PMC3360007

FLASH assembly of TALENs for high-throughput genome editing.

Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK
Nat Biotechnol. 2012;30(5):460-5 - PMID: 22484455 - PMCID: PMC3558947

Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects.

Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, Scharenberg AM, Joung JK
Nucleic Acids Res. 2012;40(12):5560-8 - PMID: 22373919 - PMCID: PMC3384306

In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases.

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
Stem Cells. 2011;29(11):1717-26 - PMID: 21898685 - PMCID: PMC3285772

Engineering designer nucleases with customized cleavage specificities.

Sander JD, Maeder ML, Joung JK
Curr Protoc Mol Biol. 2011;Chapter 12:Unit12.13 - PMID: 21987054 - PMCID: PMC3379964

Engineering zinc finger nucleases for targeted mutagenesis of zebrafish.

Sander JD, Yeh JR, Peterson RT, Joung JK
Methods Cell Biol. 2011;104:51-8 - PMID: 21924156

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection.

Pattanayak V, Ramirez CL, Joung JK, Liu DR
Nat Methods. 2011;8(9):765-70 - PMID: 21822273 - PMCID: PMC3164905

Targeted gene disruption in somatic zebrafish cells using engineered TALENs.

Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR
Nat Biotechnol. 2011;29(8):697-8 - PMID: 21822241 - PMCID: PMC3154023

Zinc-finger nucleases for somatic gene therapy: the next frontier.

Rahman SH, Maeder ML, Joung JK, Cathomen T
Hum Gene Ther. 2011;22(8):925-33 - PMID: 21631241 - PMCID: PMC3159524

Induction of stable drug resistance in human breast cancer cells using a combinatorial zinc finger transcription factor library.

Lee J, Hirsh AS, Wittner BS, Maeder ML, Singavarapu R, Lang M, Janarthanan S, McDermott U, Yajnik V, Ramaswamy S, Joung JK, Sgroi DC
PLoS One. 2011;6(7):e21112 - PMID: 21818254 - PMCID: PMC3139592

Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases.

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
Plant Physiol. 2011;156(2):466-73 - PMID: 21464476 - PMCID: PMC3177250

ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.

Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR
BMC Genomics. 2011;12:83 - PMID: 21276248 - PMCID: PMC3042413

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).

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
Nat Methods. 2010;8(1):67-9 - PMID: 21151135 - PMCID: PMC3018472

Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences.

Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D
BMC Bioinformatics. 2010;11:543 - PMID: 21044337 - PMCID: PMC3098093

Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion.

Söllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T
Nucleic Acids Res. 2010;38(22):8269-76 - PMID: 20716517 - PMCID: PMC3001086

Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.

Thibodeau-Beganny S, Maeder ML, Joung JK
Methods Mol Biol. 2010;649:31-50 - PMID: 20680826

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.

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
Proc Natl Acad Sci U S A. 2010;107(26):12028-33 - PMID: 20508152 - PMCID: PMC2900673

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.

Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D
Nucleic Acids Res. 2010;38(Web Server issue):W462-8 - PMID: 20435679 - PMCID: PMC2896148

Targeted mutagenesis in zebrafish using customized zinc-finger nucleases.

Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR
Nat Protoc. 2009;4(12):1855-67 - PMID: 20010934 - PMCID: PMC2814337

Plant science. DNA binding made easy.

Voytas DF, Joung JK
Science. 2009;326(5959):1491-2 - PMID: 20007890

Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays.

Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK
Nat Protoc. 2009;4(10):1471-501 - PMID: 19798082 - PMCID: PMC2858690

Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells.

Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L
Cell Stem Cell. 2009;5(1):97-110 - PMID: 19540188 - PMCID: PMC2720132

High-frequency modification of plant genes using engineered zinc-finger nucleases.

Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF
Nature. 2009;459(7245):442-5 - PMID: 19404258 - PMCID: PMC2743854

Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN).

Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK
PLoS One. 2009;4(2):e4348 - PMID: 19198653 - PMCID: PMC2634973

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.

Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D
Nucleic Acids Res. 2008;37(2):506-15 - PMID: 19056825 - PMCID: PMC2632909

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.

Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF
Nucleic Acids Res. 2008;37(Database issue):D279-83 - PMID: 18812396 - PMCID: PMC2686427

Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.

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, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T, Voytas DF, Joung JK
Mol Cell. 2008;31(2):294-301 - PMID: 18657511 - PMCID: PMC2535758

Zinc-finger nucleases: the next generation emerges.

Cathomen T, Joung JK
Mol Ther. 2008;16(7):1200-7 - PMID: 18545224

Unexpected failure rates for modular assembly of engineered zinc fingers.

Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK
Nat Methods. 2008;5(5):374-5 - PMID: 18446154

Comparison of zinc finger nucleases for use in gene targeting in mammalian cells.

Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH
Mol Ther. 2008;16(4):707-17 - PMID: 18334988

Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.

Thibodeau-Beganny S, Joung JK
Methods Mol Biol. 2008;408:317-34 - PMID: 18314590

DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases.

Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Joung JK, Cathomen T
Mol Ther. 2007;16(2):352-8 - PMID: 18026168

Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method.

Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA
Nucleic Acids Res. 2007;35(11):e81 - PMID: 17537811 - PMCID: PMC1920264

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.

Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D
Nucleic Acids Res. 2007;35(Web Server issue):W599-605 - PMID: 17526515 - PMCID: PMC1933188

Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.

Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF, Joung JK
Nat Protoc. 2007;1(3):1637-52 - PMID: 17406455

The bacterial two-hybrid system as a reporter system for analyzing protein-protein interactions.

Giesecke AV, Joung JK
CSH Protoc. 2007;2007:pdb.prot4672 - PMID: 21357036

Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers.

Giesecke AV, Fang R, Joung JK
Mol Syst Biol. 2006;2:2006.2011 - PMID: 16732192 - PMCID: PMC1681485

Counter-selectable marker for bacterial-based interaction trap systems.

Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA
Biotechniques. 2006;40(2):179-84 - PMID: 16526407

Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa.

Vallet-Gely I, Donovan KE, Fang R, Joung JK, Dove SL
Proc Natl Acad Sci U S A. 2005;102(31):11082-7 - PMID: 16043713 - PMCID: PMC1182424

A combined yeast/bacteria two-hybrid system: development and evaluation.

Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA
Mol Cell Proteomics. 2005;4(6):819-26 - PMID: 15781424 - PMCID: PMC2670611

Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands.

Nguyen-Hackley DH, Ramm E, Taylor CM, Joung JK, Dervan PB, Pabo CO
Biochemistry. 2004;43(13):3880-90 - PMID: 15049695

High-throughput beta-galactosidase assay for bacterial cell-based reporter systems.

Thibodeau SA, Fang R, Joung JK
Biotechniques. 2004;36(3):410-5 - PMID: 15038156

An improved strategy for constructing "designer" Cys2His2 zinc finger proteins.

Thibodeau SA, Joung JK
Discov Med. 2003;3(19):32-5 - PMID: 20705034

Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection.

Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK
Proc Natl Acad Sci U S A. 2003;100(21):12271-6 - PMID: 14527993 - PMCID: PMC218748

Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system.

Joung JK
J Cell Biochem Suppl. 2002;Suppl 37:53-7 - PMID: 11842428

A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions.

Joung JK, Ramm EI, Pabo CO
Proc Natl Acad Sci U S A. 2000;97(13):7382-7 - PMID: 10852947 - PMCID: PMC16554

Activation of prokaryotic transcription through arbitrary protein-protein contacts.

Dove SL, Joung JK, Hochschild A
Nature. 1997;386(6625):627-30 - PMID: 9121589

Genetic strategy for analyzing specificity of dimer formation: Escherichia coli cyclic AMP receptor protein mutant altered in its dimerization specificity.

Joung JK, Chung EH, King G, Yu C, Hirsh AS, Hochschild A
Genes Dev. 1995;9(23):2986-96 - PMID: 7498794

Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein.

Joung JK, Koepp DM, Hochschild A
Science. 1994;265(5180):1863-6 - PMID: 8091212

Synergistic activation of transcription by Escherichia coli cAMP receptor protein.

Joung JK, Le LU, Hochschild A
Proc Natl Acad Sci U S A. 1993;90(7):3083-7 - PMID: 7681995 - PMCID: PMC46241