Joung Lab
Publications
   

Publications

Original Articles

  1. Ruben S, Perkins A, Purcell R, Joung K, Sia R, Burghoff R, Haseltine WA, Rosen CA. Structural and Functional Characterization of Human Immunodeficiency Virus tat Protein. Journal of Virology 1989; 63: 1-8.
  2. Joung JK, Le LU, Hochschild A. Synergistic activation of transcription by the E. coli cAMP receptor protein. Proc. Natl. Acad. Sci. USA, 1993; 90: 3083-7.
  3. Joung JK, Koepp DM, Hochschild A. Synergistic Activation of Transcription by Bacteriophage l cI Protein and E. coli cAMP Receptor Protein. Science 1994; 265: 1863-6.
  4. Joung JK, Chung EH, King G, Yu C, Hirsh AS, Hochschild A. Genetic strategy for analyzing specificity of dimer formation: Escherichia coli cyclic AMP receptor protein mutant altered in its dimerization specificity. Genes and Development 1995; 9: 2986-2996.
  5. Dove SL, Joung JK, Hochschild A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 1997; 386: 627-630.
  6. 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.
  7. 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.
  8. 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.
  9. Thibodeau SA, Fang R, Joung JK. An optimized high-throughput b-galactosidase assay for bacterial cell-based reporter systems, Biotechniques 2004, 36: 410-415.
  10. 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.
  11. 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.
  12. 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.
  13. Giesecke AV, Fang R, Joung JK. Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc fingers, Molecular Systems Biology, 2006, doi: 10.1038/msb4100053
  14. 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, Nature Protocols, 2006, 1: 1637-1652.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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, in press.

Reviews, Chapters, and Editorials

  1. Hochschild A, Joung JK Synergistic activation of transcription in Escherichia coli. Nucleic Acids and Molecular Biology 1997; 11: 101-114.
  2. Serebriiskii I, Joung JK Yeast and Bacterial Two-hybrid Selection Systems for Studying Protein-Protein Interactions. In:Protein-Protein Interactions: A Molecular Cloning Manual, E.A. Golemis, editor. Cold Spring Harbor Laboratory Press, 2001, pp. 93-142.
  3. Joung JK Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system. J Cell Biochem. 2001, Supp 37: 53-57.
  4. Joung JK, Lewandrowski KB Laboratory Safety: An Overview. In: Lewandrowski KB, editor. Clinical Chemistry – Laboratory Management and Clinical Correlations. Lippincott Williams & Wilkins, 2002, pp. 40-50.
  5. Thibodeau SA, Joung JK An improved strategy for constructing “designer” Cys2His2 zinc finger proteins. Discovery Medicine, 2003, 3: 32-35.
  6. Hirsh AS, Joung JK Designer zinc finger proteins for gene therapy: progress and challenges. Gene Therapy and Regulation, 2004, 2: 191-206
  7. Giesecke A, Joung JK A bacterial two-hybrid system for studying and modifying protein-protein interactions. In: Protein-Protein Interactions: A Molecular Cloning Manual, 2nd ed., E.A. Golemis, editor. Cold Spring Harbor Laboratory Press, 2005, pp. 195-216.
  8. Thibodeau-Beganny S, Joung JK. Engineering Cys2His2 Zinc Finger Domains using a Bacterial Cell-Based Two-Hybrid Selection System, Methods in Molecular Biology, 2007, in press.
  9. Giesecke AV, Joung JK.  The Bacterial Two-Hybrid System as a Reporter System for Analyzing Protein-Protein Interactions, CSH Protocols, 2007, doi:10.1101/pdb.prot4672
  10. Cathomen T, Joung JK.  Zinc-Finger Nucleases - The Next Generation Emerges, Mol Ther., 2008, 16: 1200-1207.
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