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Peer-reviewed journal papers

  1. Mills E., Truong K. Analysis and regulation of amoeboid-like cell motility using synthetic  Ca2+-sensitive proteinsCell Calcium. in press
  2. Nagaraj S., Mills E., Wong S.S  and Truong K.  Programming membrane fusion and subsequent apoptosis into mammalian cellsACS Synthetic Biology. in press 
  3. Wong SS., Mills E., Truong K. Simultaneous assembly of two target proteins using split inteinsProtein Engineering, Design and Selection. 26(3):207-13. (2013)
  4. Mills E, Pham E., Nagaraj S. and Truong K.  Engineered networks of synthetic and natural proteins to control cell migration. ACS Synthetic Biology. 6(1):211–220. (2012) 
  5. Pham E. and Truong K. Engineered regulation of lysozyme by the SH3-CB1 binding interaction. Protein Engineering, Design and Selection. 25(6):307-11. (2012). Read article [.pdf, 196 kb].
  6. Nagaraj S., Wong S.S. and Truong K. Parts-based assembly of synthetic transmembrane proteins in mammalian cells. ACS Synthetic Biology.  4(1):111-117. (2012).
  7. Pham E., Wong S.S., Nagaraj S. and Truong K. Effects of rapamycin-induced oligomerization of Parvalbumin, Stim1 and Orai1 in puncta formation.  Cell Calcium. 51:418-425. (2012). Read article [.pdf, 1952 kb].
  8. Mills E., Chen X., Pham E., Wong S.S, and Truong K. Engineering a photoactivated caspase-7 for rapid induction of apoptosis.  ACS Synthetic Biology. 3(1):75-82. (2012).
  9. Wong S.S., Kotera I., Mills E., Suzuki H. and Truong K. Split-intein mediated re-assembly of genetically encoded  Ca2+ indicators.  Cell Calcium. 51:57-64. (2012). Read article [.pdf, 1006 kb].
  10. Shahravan S.H., Li I.T., Truong K. and Shin J.A.  FRep: a fluorescent protein-based bioprobe for in vivo detection of protein-DNA interactions. Analytical Chemistry. 83:9643-50. (2011). Read article [.pdf, 2384 kb].
  11. Mills E. and Truong K. Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity and pathway rewiring.  Chemistry and Biology. 18: 1611-1619. (2011). Read article [.pdf, 1026 kb].
  12. Pham E., Mills E. and Truong K. A synthetic photoactivated protein to generate local or global Ca2+  signals.  Chemistry and Biology. 18:880-90. (2011). Read article [.pdf, 1365 kb].  Previewed by Romanin C.
  13. Wong S.S. and Truong K. Fluorescent protein-based methods for on-plate screening of gene insertionPLoS ONE. 5(12):e14274. (2010). Read article [.pdf, 1119 kb]
  14. Chen X., Pham E. and Truong K. TEV protease-facilitated stoichiometric delivery of multiple genes using a single expression vector. Protein Science. 19:2379-88. (2010). Read article [.pdf, 2988 kb]
  15. Mills E., Pham E. and Truong K. Structure based design of a Ca2+-sensitive RhoA protein that controls cell morphologyCell Calcium. 48:195–201. (2010). Read article [.pdf, 880 kb]
  16. Li I.T., Mills E and Truong K. A computational tool for Monte Carlo simulations of biomolecular reaction networks modeled on physical principlesIEEE Transactions in Nanobioscience 9(1), 24-30. (2010). Read article [.pdf, 562 kb].  Supplemental materials [.pdf, 48 kb].
  17. Mills E and Truong K. Engineering Ca2+/calmodulin-mediated modulation of protein translocation by overlapping binding and signaling peptide sequencesCell Calcium. 47:369–377. (2010). Read article [.pdf, 1370 kb]
  18. Mills E. and Truong K. Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch. BMC Syst Biol. 3(1):72. (2009). Read article [.pdf, 432 kb]
  19. Mills E. and Truong K. Rate and extent of protein localization is controlled by peptide-binding domain association kinetics and morphology. Protein Sci. 18(6):1252-60. (2009). Read article [.pdf, 398 kb]
  20. Li I.T., Pham E., Chiang J.J. and Truong K. FRET evidence that an isoform of caspase-7 binds but does not cleave its substrate. Biochem Biophys Res Commun. 373(4):325-9. (2008). Read article [.pdf, 665 kb]
  21. Li I.T., Shum W. and Truong K. 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA). BMC Bioinformatics. 8(1):185. (2007). Read article [.pdf, 286 kb]
  22. Pham E., Chiang J.J., Li I.T., Shum W. and Truong K. A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space. Structure. 15(5), 515-23. (2007). Read article [.pdf, 752 kb]
  23. Li I.T., Ranjith K.R. and Truong K. Sequence reversed peptide from CaMKK binds to calmodulin in reversible Ca2+-dependent manner. Biochem Biophys Res Commun. 352(4):932-5. (2007).  Read article [.pdf, 437 kb]
  24. Chiang J.J., Li I.T. and Truong K. Creation of circularly permutated yellow fluorescent proteins using fluorescence screening and a tandem fusion template. Biotechnology Letters 28(7), 471-5. (2006). Read article [.pdf, 256 kb]
  25. Chiang J.J. and Truong K. Computational modeling of a new fluorescent biosensor for caspase proteolytic activity improves dynamic range. IEEE Transactions in Nanobioscience 5(1), 41-5. (2006). Read article [.pdf, 597 kb]
  26. Chiang J.J. and Truong K. Using co-cultures expressing fluorescence resonance energy transfer based protein biosensors to simultaneously image caspase-3 and Ca2+ signaling. Biotechnology Letters 27(16), 1219 - 1227. (2005). Read article [.pdf, 452 kb]
  27. Truong K., Khorchid A. and Ikura M. Fluorescent cassette-based strategy for engineering of multiple domain fusion proteins. BMC Biotechnology 3(1): 8. (2003). Read article [.pdf, 682 kb]
  28. Truong K. and Ikura M. Domain fusion analysis by applying relational algebra to protein sequence and domain databases. BMC Bioinformatics 4(1): 16. (2003). Read article [.pdf, 446 kb]
  29. Stavropoulos D.J., Bradshaw P.S., Li X. Pasic I., Truong K., Ikura M., Ungrin M. and Meyn M. The Bloom syndrome helicase BLM interacts with TRF2 in ALT cells and promotes telomeric DNA synthesis. Human Molecular Genetics 11, 3135-44. (2002). Read article [.pdf, 1495 kb]
  30. Truong K. and Ikura M. The cadherin superfamily database. Journal of Structural and Functional Genomics 2, 135-43. (2002). Read article [.pdf, 309 kb]
  31. Truong K. and Ikura M. Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach. BMC Bioinformatics 3(1): 1. (2002). Read article [.pdf, 846 kb]
  32. Truong K., Sawano A., Mizuno H., Hama H., Tong K.I., Mal T.K., Miyawaki A. and Ikura M. FRET-based in vivo Ca2+ imaging by a new calmodulin-GFP fusion molecule. Nature Structural Biology 8,1069-73. (2001). Read article [.pdf, 2029 kb]
  33. Yap K.L., Kim J., Truong K., Sherman M., Yuan T and Ikura M. Calmodulin target database. Journal of Structural and Functional Genomics 1,8-14. (2000). Read article [.pdf, 796 kb]

Peer-reviewed conference papers

  1. Truong K, Pham E. Exploring the conformational space of FRET biosensors for improved designs. Proceedings of SPIE Photonics West Conference. (2008).
  2. Li, I.T., Chiang J.J., and Truong K. FRET evidence that an isoform of caspase-7 binds but does not cleave its substrate. 28th Annual International IEEE Engineering Conference in Medicine and Biology. (2006). Read article[.pdf, 720 kb]
  3. Chiang J.J., Li, I.T., Pham E. and Truong K. The FPMOD: a modeling tool for sampling the conformational space of fusion proteins. 28th Annual International IEEE Engineering Conference in Medicine and Biology. (2006). Read article [.pdf, 394 kb]
  4. Chiang J.J., Studniberg M., Shaw J., Seto S. and Truong K. Hardware accelerator for genomic sequence alignment. 28th Annual International IEEE Engineering Conference in Medicine and Biology. (2006). Read article [.pdf, 303 kb]

Reviews

  1. Pham E., Li I.T. and Truong K. Computational modeling approaches for studying of synthetic biological networks. Current Bioinformatics. May. 3 (2): 130-141. (2008). Read review [.pdf, 335 kb]
  2. Li I.T., Pham E. and Truong K. Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics. Biotechnology Letters. Dec. 28 (24):1971-82. (2006). Read review [.pdf, 284 kb]
  3. Truong K. and Ikura M. The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Current Opinions in Structural Biology 11,573-8. (2001). Read review [.pdf, 504 kb]
  4. Tepass U., Truong K., Godt D., Ikura M. and Peifer M. Cadherins in embryonic and neural morphogenesis. Nature Reviews Molecular Cell Biology 1,91-100. (2000). Read review [.pdf, 1614 kb]

Book Chapters

  1. Pham E. and Truong K. Design of fluorescent fusion protein probes. Methods Mol Biol. 591:69-91 (2010). Read book chapter [.pdf, 866kb]
  2. Li I.T., Pham E. and Truong K. Current approaches for engineering proteins with diverse biological properties. Adv Exp Med Biol. 620 : 18-33 . (2007). Read book chapter [.pdf, 294 kb]
  3. Truong K., Sawano A., Miyawaki A. and Ikura M. Ca2+ indicators based on calmodulin-fluorescent protein fusions. Methods in Molecular Biology. Protein Engineering Protocols. 71-82. (2007). Read book chapter [.pdf, 1320 kb]
  4. Hoeflich K.P., Truong K., Ikura M. Ca2+ as a second messenger. new reporters for Ca2+ (cameleons and camgaroos). Cell Biology: A Laboratory Handbook. (2003). Book chapter (proofs unavailable)

 

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