|
Reyon
D, Tsai SQ, Khayter C, Foden JA, Sander JD*, Joung JK*. FLASH
Assembly of TALENs Enables High-Throughput
Genome Editing. Nat Biotechnol. 2012; in press.
*Co-corresponding authors
Ramirez
CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey
AP, Cathomen T, Scharenberg AM,
Joung JK. Engineered zinc finger nickases induce homology-directed
repair with reduced mutagenic effects.
Nucleic Acids Res. 2012 Feb 28. [Epub ahead of print].
Sander
JD, Maeder ML, Joung JK. Engineering designer nucleases
with customized cleavage specificities.
Curr 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 zebrafish. Methods 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 nucleases. Stem
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 selection. Nat 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 TALENs. Nat
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, Yajnik V,
Ramaswamy S, Joung JK*, Sgroi DC*. Induction of stable
drug resistance in human breast cancer
cells using a combinatorial zinc finger transcription factor
library. PLoS 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
frontier. Hum 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 technologies. Plant
Physiol. 2011 Jun;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 organisms.
BMC Genomics. 2011 Jan 28;12:83.
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 sequences. BMC 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 deletion.
Nucleic 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 tool. Nucleic 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 nucleases. Proc Natl Acad Sci U S A. 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 system. Methods Mol Biol.
2010;649:31-50.
Joung
JK, Voytas DF, Cathomen T. Reply to Genome editing with
modularly assembled
zinc-finger nucleases, Nat
Methods, 2010, 7: 91-92.
Voytas
DF, Joung JK. Plant science. DNA binding made easy,
Science, 2009, 326: 1491-1492.
Foley
JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR.
Targeted mutagenesis in
zebrafish using customized zinc-finger
nucleases, Nat 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 Arrays, Nat
Protocols, 2009, 4: 1471-1501.
Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny
S, Chou, B-K, Chen G, Ye Z, Park
I-H, Daley GQ,
Porteus MH, Joung JK, Cheng L. Gene targeting of a disease-related
gene in human induced pluripotent
stem and embryonic stem cells, Cell 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 Nucleases,
Nature, 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
proteins, Nucleic 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
arrays, Nucleic Acids Res., 2009, 35: D279-D283.
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 modification, Mol 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 fingers, Nat 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 Cells, Mol 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
nucleases, Mol Ther.,
2008, 16: 352-8.
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 Tool, Nucleic Acids Res.,
2007, 35: W599-W605.
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 assembly, Nat Protocols, 2006,
1: 1637-1652.
Giesecke AV, Fang R, Joung JK. Synthetic protein-protein
interaction domains created by shuffling
Cys2His2 zinc fingers, Mol 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 systems, Biotechniques, 2006, 40: 179-184.
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 aeruginosa, Proc.
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 evaluation, Mol
Cell Proteomics 2005, 4:
819-826.
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 systems, Biotechniques 2004;
36: 410-415.
Hurt, JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK. Highly
specific zinc finger proteins obtained
by directed domain shuffling and cell-based selection,
Proc. Natl. Acad. Sci. USA 2003;
100: 12271-12276.
Joung JK, Ramm EI, Pabo CO. A bacterial two-hybrid selection
system for studying protein-DNA and
protein-protein interactions, Proc. Natl. Acad. Sci.
USA 2000; 97: 7382-7387.
Dove SL, Joung JK, Hochschild A. Activation of prokaryotic
transcription through arbitrary protein-protein contacts,
Nature 1997; 386: 627-630.
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