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Peer-reviewed journal papers

  1. Qudrat A., Mosabbir A., Truong K. Engineered proteins program mammalian cells to target TNFα sources. Cell Chemical Biology. in press
  2. Mosabbir A., Truong K. Ca2+-mediated rewiring of cell homing and fusion to VEGF sources. Cell Calcium. in press.
  3. Qudrat A., Truong K. Engineering synthetic proteins to generate Ca2+  signals in mammalian cells. ACS Synthetic Biology. in press.
  4. Qudrat A., Truong K. Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells. BMC Biotechnology. 16(1):88 (2016)
  5. Mosabbir A., Truong K. Genomic integration occurs in the packaging cell via unexported lentiviral precursors. Biotechnology Letters. 38(10):1715-21 (2016). Read article [.pdf, 0.80 mb]
  6. Qudrat A., Kim JI, Truong K. The spatiotemporal relationship between local Ca2+  signaling and P2X2R-activated membrane blebbing. Cell Calcium. 59(4):164-71. (2016) Read article [.pdf, 1.84 mb]
  7. Wong S.S., Mosabbir A., Truong K. An Engineered Split Intein for Photoactivated Protein Trans-Splicing. PLoS One. 10(8):e0135965. (2015). Read article [.pdf, 4.19 mb]
  8. Mills E., Truong K. Analysis and regulation of amoeboid-like cell motility using synthetic  Ca2+-sensitive proteinsCell Calcium. 53(3):231-40. (2013). Read article [.pdf, 1.22 mb] 
  9. Nagaraj S., Mills E., Wong S.S, Truong K.  Programming membrane fusion and subsequent apoptosis into mammalian cellsACS Synthetic Biology2(4):173–179. (2013)
  10. Wong S.S., Mills E., Truong K. Simultaneous assembly of two target proteins using split inteinsProtein Engineering, Design and Selection. 26(3):207-13. (2013)
  11. Mills E, Pham E., Nagaraj S., Truong K.  Engineered networks of synthetic and natural proteins to control cell migration. ACS Synthetic Biology. 6(1):211–220. (2012). Read article [.pdf, 4338 kb].
  12. Pham E., 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].
  13. Nagaraj S., Wong S.S., Truong K. Parts-based assembly of synthetic transmembrane proteins in mammalian cells. ACS Synthetic Biology.  4(1):111-117. (2012).
  14. Pham E., Wong S.S., Nagaraj S., 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].
  15. Mills E., Chen X., Pham E., Wong S.S, Truong K. Engineering a photoactivated caspase-7 for rapid induction of apoptosis.  ACS Synthetic Biology. 3(1):75-82. (2012).
  16. Wong S.S., Kotera I., Mills E., Suzuki H., Truong K. Split-intein mediated re-assembly of genetically encoded  Ca2+ indicators.  Cell Calcium. 51:57-64. (2012). Read article [.pdf, 1006 kb].
  17. Shahravan S.H., Li I.T., Truong K., 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].
  18. Mills E., Truong K. Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity and pathway rewiringCell Chemical Biology. 18: 1611-1619. (2011). Read article [.pdf, 1026 kb].
  19. Pham E., Mills E., Truong K. A synthetic photoactivated protein to generate local or global Ca2+  signalsCell Chemical Biology. 18:880-90. (2011). Read article [.pdf, 1365 kb].  Previewed by Romanin C.
  20. Wong S.S.,Truong K. Fluorescent protein-based methods for on-plate screening of gene insertionPLoS ONE. 5(12):e14274. (2010). Read article [.pdf, 1119 kb]
  21. Chen X., Pham E., 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]
  22. Mills E., Pham E., 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]
  23. Li I.T., Mills E, 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].
  24. Mills E, 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]
  25. Mills E., 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]
  26. Mills E., 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]
  27. Li I.T., Pham E., Chiang J.J., 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]
  28. Li I.T., Shum W., 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]
  29. Pham E., Chiang J.J., Li I.T., Shum W., 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]
  30. Li I.T., Ranjith K.R., 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]
  31. Chiang J.J., Li I.T., 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]
  32. Chiang J.J., 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]
  33. Chiang J.J., 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]
  34. Truong K., Khorchid A., Ikura M. Fluorescent cassette-based strategy for engineering of multiple domain fusion proteins. BMC Biotechnology 3(1): 8. (2003). Read article [.pdf, 682 kb]
  35. Truong K., 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]
  36. Stavropoulos D.J., Bradshaw P.S., Li X. Pasic I., Truong K., Ikura M., Ungrin M., 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]
  37. Truong K., Ikura M. The cadherin superfamily database. Journal of Structural and Functional Genomics 2, 135-43. (2002). Read article [.pdf, 309 kb]
  38. Truong K., 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]
  39. Truong K., Sawano A., Mizuno H., Hama H., Tong K.I., Mal T.K., Miyawaki A., 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]
  40. Yap K.L., Kim J., Truong K., Sherman M., Yuan T, 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., 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., 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., Truong K. Hardware accelerator for genomic sequence alignment. 28th Annual International IEEE Engineering Conference in Medicine and Biology. (2006). Read article [.pdf, 303 kb]


  1. Mills E, Truong K. Photoswitchable protein degradation: a generalizable control module for cellular function? Cell Chemical Biology. 20(4):458-60. (2013)
  2. Pham E., Li I.T., Truong K. Computational modeling approaches for studying of synthetic biological networks. Current Bioinformatics. May. 3 (2): 130-141. (2008). Read review [.pdf, 335 kb]
  3. Li I.T., Pham E., 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]
  4. Truong K., 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]
  5. Tepass U., Truong K., Godt D., Ikura M., 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. Qudrat A, Mosabbir A, Truong K. LOV2-Controlled Photoactivation of Protein Trans-Splicing. Methods Mol Biol. 1495:227-237. (2017).
  2. Pham E., Truong K. Design of fluorescent fusion protein probes. Methods Mol Biol. 591:69-91 (2010). Read book chapter [.pdf, 866kb]
  3. Li I.T., Pham E., 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]
  4. Truong K., Sawano A., Miyawaki A., 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]
  5. 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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