Publications - Joung
Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo".
Gene therapy comes of age.
Nodal patterning without Lefty inhibitory feedback is functional but fragile.
Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.
Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.
Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway.
CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.
Nucleic acid detection with CRISPR-Cas13a/C2c2.
Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway.
Oncotarget. 2017;8(27):43733-43751 - PMID: 28415827 - PMCID: PMC5546437 - DOI: 10.18632/oncotarget.16376
DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.
Genome Editing Technologies: Defining a Path to Clinic: Genomic Editing: Establishing Preclinical Toxicology Standards, Bethesda, Maryland 10 June 2014.
Mol Ther. 2016;23(5):796-806 - PMID: 28142000
Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.
Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.
Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737 - DOI: 10.1158/2159-8290.CD-15-1442
Open-source guideseq software for analysis of GUIDE-seq data.
Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.
Accelerating research through reagent repositories: the genome editing example.
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition.
Genome Editing in Human Cells Using CRISPR/Cas Nucleases.
Curr Protoc Mol Biol. 2015;112:31.3.1-31.3.18 - PMID: 26423589 - PMCID: PMC4852847 - DOI: 10.1002/0471142727.mb3103s112
CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.
Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.
Unwanted mutations: Standards needed for gene-editing errors.
Engineered CRISPR-Cas9 nucleases with altered PAM specificities.
Dimeric CRISPR RNA-guided FokI-dCas9 nucleases (RFNs) directed by truncated gRNAs for highly specific genome editing.
Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model.
PLoS Genet. 2015;11(5):e1005239 - PMID: 26000857 - PMCID: PMC4441453 - DOI: 10.1371/journal.pgen.1005239
Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided Nucleases.
Genome editing technologies: defining a path to clinic.
Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.
Chromatin regulation at the frontier of synthetic biology.
Fanconi Anemia Gene Editing by the CRISPR/Cas9 System.
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.
A Zebrafish Model of Myelodysplastic Syndrome Produced Through tet2 Genomic Editing.
Targeted genome editing in human cells using CRISPR/Cas nucleases and truncated guide RNAs.
Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo.
Genome editing: a tool for research and therapy: towards a functional understanding of variants for molecular diagnostics using genome editing.
Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage.
I?B kinase ? (IKBKB) mutations in lymphomas that constitutively activate canonical nuclear factor ?B (NF?B) signaling.
J Biol Chem. 2014;289(39):26960-72 - PMID: 25107905 - PMCID: PMC4175336 - DOI: 10.1074/jbc.M114.598763
What's changed with genome editing?
Targeted mutagenesis of zebrafish antithrombin III triggers disseminated intravascular coagulation and thrombosis, revealing insight into function.
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.
Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.
Cell Stem Cell. 2014;14(6):781-95 - PMID: 24704492 - PMCID: PMC4653065 - DOI: 10.1016/j.stem.2014.03.004
CRISPR-Cas systems for editing, regulating and targeting genomes.
Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.
Nucleic Acids Res. 2014;42(8):4800-12 - PMID: 24523353 - PMCID: PMC4005693 - DOI: 10.1093/nar/gku132
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.
Toddler: an embryonic signal that promotes cell movement via Apelin receptors.
Correction of Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair.
Invest Ophthalmol Vis Sci. 2013;55(1):387-395 - PMID: 24346171 - PMCID: PMC3921157 - DOI: 10.1167/iovs.13-13278
Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.
Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.
Locus-specific editing of histone modifications at endogenous enhancers.
Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases.
G3 (Bethesda). 2013;3(10):1707-1715 - PMID: 23979943 - PMCID: PMC3789795 - DOI: 10.1534/g3.113.006270
In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.
CRISPR RNA-guided activation of endogenous human genes.
Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System.
Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) Assembly.
Curr Protoc Mol Biol. 2013;Chapter 12:Unit12.16 - PMID: 23821439 - PMCID: PMC3767754 - DOI: 10.1002/0471142727.mb1216s103
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.
piggyBac transposase tools for genome engineering.
Proc Natl Acad Sci U S A. 2013;110(25):E2279-87 - PMID: 23723351 - PMCID: PMC3690869 - DOI: 10.1073/pnas.1305987110
TALEN-based Gene Correction for Epidermolysis Bullosa.
Robust, synergistic regulation of human gene expression using TALE activators.
Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic Diseases.
Efficient genome editing in zebrafish using a CRISPR-Cas system.
TALENs: a widely applicable technology for targeted genome editing.
Engineering Designer Transcription Activator--Like Effector Nucleases (TALENs) by REAL or REAL-Fast Assembly.
Curr Protoc Mol Biol. 2012;Chapter 12:Unit12.15 - PMID: 23026907 - PMCID: PMC3753116 - DOI: 10.1002/0471142727.mb1215s100
Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse Embryos.
A synthetic biology framework for programming eukaryotic transcription functions.
Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs.
Nucleic Acids Res. 2012;40(16):8001-10 - PMID: 22684503 - PMCID: PMC3439908 - DOI: 10.1093/nar/gks518
Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs).
FLASH assembly of TALENs for high-throughput genome editing.
Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects.
Nucleic Acids Res. 2012;40(12):5560-8 - PMID: 22373919 - PMCID: PMC3384306 - DOI: 10.1093/nar/gks179
In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases.
Engineering designer nucleases with customized cleavage specificities.
Curr Protoc Mol Biol. 2011;Chapter 12:Unit12.13 - PMID: 21987054 - PMCID: PMC3379964 - DOI: 10.1002/0471142727.mb1213s96
Engineering zinc finger nucleases for targeted mutagenesis of zebrafish.
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection.
Targeted gene disruption in somatic zebrafish cells using engineered TALENs.
Zinc-finger nucleases for somatic gene therapy: the next frontier.
Induction of stable drug resistance in human breast cancer cells using a combinatorial zinc finger transcription factor library.
Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases.
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences.
BMC Bioinformatics. 2010;11:543 - PMID: 21044337 - PMCID: PMC3098093 - DOI: 10.1186/1471-2105-11-543
Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion.
Nucleic Acids Res. 2010;38(22):8269-76 - PMID: 20716517 - PMCID: PMC3001086 - DOI: 10.1093/nar/gkq720
Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.
High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.
Proc Natl Acad Sci U S A. 2010;107(26):12028-33 - PMID: 20508152 - PMCID: PMC2900673 - DOI: 10.1073/pnas.0914991107
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.
Nucleic Acids Res. 2010;38(Web Server issue):W462-8 - PMID: 20435679 - PMCID: PMC2896148 - DOI: 10.1093/nar/gkq319
Targeted mutagenesis in zebrafish using customized zinc-finger nucleases.
Plant science. DNA binding made easy.
Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays.
Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells.
Cell Stem Cell. 2009;5(1):97-110 - PMID: 19540188 - PMCID: PMC2720132 - DOI: 10.1016/j.stem.2009.05.023
High-frequency modification of plant genes using engineered zinc-finger nucleases.
Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN).
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.
Nucleic Acids Res. 2008;37(Database issue):D279-83 - PMID: 18812396 - PMCID: PMC2686427 - DOI: 10.1093/nar/gkn606
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.
Mol Cell. 2008;31(2):294-301 - PMID: 18657511 - PMCID: PMC2535758 - DOI: 10.1016/j.molcel.2008.06.016
Zinc-finger nucleases: the next generation emerges.
Unexpected failure rates for modular assembly of engineered zinc fingers.
Comparison of zinc finger nucleases for use in gene targeting in mammalian cells.
Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.
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.
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method.
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
Nucleic Acids Res. 2007;35(Web Server issue):W599-605 - PMID: 17526515 - PMCID: PMC1933188 - DOI: 10.1093/nar/gkm349
Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.
The bacterial two-hybrid system as a reporter system for analyzing protein-protein interactions.
CSH Protoc. 2007;2007:pdb.prot4672 - PMID: 21357036
Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers.
Counter-selectable marker for bacterial-based interaction trap systems.
Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa.
Proc Natl Acad Sci U S A. 2005;102(31):11082-7 - PMID: 16043713 - PMCID: PMC1182424 - DOI: 10.1073/pnas.0502663102
A combined yeast/bacteria two-hybrid system: development and evaluation.
Mol Cell Proteomics. 2005;4(6):819-26 - PMID: 15781424 - PMCID: PMC2670611 - DOI: 10.1074/mcp.T500005-MCP200
Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands.
High-throughput beta-galactosidase assay for bacterial cell-based reporter systems.
An improved strategy for constructing "designer" Cys2His2 zinc finger proteins.
Discov Med. 2003;3(19):32-5 - PMID: 20705034
Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection.
Proc Natl Acad Sci U S A. 2003;100(21):12271-6 - PMID: 14527993 - PMCID: PMC218748 - DOI: 10.1073/pnas.2135381100
Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system.
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.
Proc Natl Acad Sci U S A. 2000;97(13):7382-7 - PMID: 10852947 - PMCID: PMC16554 - DOI: 10.1073/pnas.110149297
Activation of prokaryotic transcription through arbitrary protein-protein contacts.
Genetic strategy for analyzing specificity of dimer formation: Escherichia coli cyclic AMP receptor protein mutant altered in its dimerization specificity.
Genes Dev. 1995;9(23):2986-96 - PMID: 7498794
Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein.
Science. 1994;265(5180):1863-6 - PMID: 8091212