Publications

62. S. Choi, Y. S. Park, K. W. Lee, Y. J. Park, H. J. Jang, D.-M. Kim, T. H. Yoo, “Sensitive methods to detect single-stranded nucleic acids of food pathogens based on cell-free protein synthesis and retroflection signal detection,” Journal of Agricultural and Food Chemistry, 2024, 72, 3783-3792, online

61. Y. Y. Xu, S. Choi, T. H. Yoo,* J. K. Lee,* “Enhancement of sensitivity for retroflection-based-biosensor by controlling polymer brush of Janus particles,” Macromolecular Chemistry and Physics, 2024, *Co-corresponding authors, accepted.

60. Y. S. Park, S. Choi, H. J. Jang, T. H. Yoo,* “Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules,” Frontiers in Bioengineering and Biotechnology, 2023, 10, 3389, online

59. H. J. Park, Y. Kim, K. W. Lee, M. Won, H. C. Yoon,* T. H. Yoo,* “Coupling hCG-based protease sensors with a commercial pregnancy test strip for simple analyses of protease activities,” Biosensors and Bioelectronics, 2023, 235, 115364. online

58. A. D. Pagar, H. Jeon, T. P. Khobragade, S. Sarak, P. Giri, S. Lim, T. H. Yoo, H. Yun, “Non-canonial amino acid-based engineering of  (R)-amine transaminase,” Frontiers in Chemistry, 2022, 10, 839636. online

57. Y. S. Park, A. Nasir, T. P. Nguyen-Vo, H. Ryu, J. Y. Seok, G. Y. Jung,* S. Park,* T. H. Yoo,* “Engineering of the substrate pocket of alpha-ketoglutaric semialdehyde dehydrogenase for improving the activity toward 3-hydroxypropanal,” Biotechnology and Bioprocess Engineering, 2022, https://doi.org/10.1007/s12257-021-0335-3. online

56. H. J. Park, C. Jung, T. H. Yoo, “Development of one-step isothermal methods to detect RNAs using hairpin-loop signal converters and proximity proteolysis reaction,” Biosensors and Bioelectronics, 2022, 197, 113769. online

55. B. S. Lee, W. J. Choi, S. W. Lee, B. J. Ko, T. H. Yoo, “Towards engineering an orthogonal protein translation initiation system,” Frontiers in Chemistry, 2021, 9, 772648. online

54. H. J. Park, Y. Kim, T. H. Yoo, “One-pot colorimetric detection of molecules based on proximity proteolysis reaction,” 2021, Biosensors and Bioelectronics, 2021, 188, 113349. online

53. A. D. Pagar, M. D. Patil, D. T. Flood, T. H. Yoo, P. E. Dawson, H. Yun, “Recent advances in biocatalysis with chemical modification and expanded amino acid alphabet,” Chemical Review, 2021, 121, 6173-6245. online

52. B. Kim, S. S. Lee, T. H. Yoo, J. M. Kim, “Viscoelastic particle focusing in human biofluids,” Electrophoresis, 2021, 42, 2238-2245. online

51. J. Park, S. Lee, Y. Kim, T. H. Yoo, "Methods to generate site-specific conjugates of antibody and protein,” Bioorganic & Medicinal Chemistry, 2021, 39, 115946. online

50. A. Nasir, S. Ashok, J. Y. Shim, S. Park, T. H. Yoo, "Recent Progress in the Understanding and Engineering of Coenzyme B12-Dependent Glycerol Dehydratase,” Frontiers in Bioengineering and Biotechnology, 2020, 8, 500867. online

49. W.-W. Park, K. M. Lee, B. S. Lee, Y. J. Kim, S. H. Joo, S. K. Kwak,* T. H. Yoo,* O.-H. Kwon,* “Hydrogen-bon free energy of local biological water,” Angewandte Chemie, 2020, 59, 7089-7096. *Co-corresponding authors. online

48. B. S. Lee, Y. Lee, J. Park, B. S. Jeong, M. Jo, S. T. Jung, T. H. Yoo, “Construction of an immunotoxin via site-specific conjugation of anti-Her2 IgG and engineered Pseudomonas exotoxin A,” Journal of Biological Engineering, 2019, 13, 56. online

47. M. W. Min, C.-E. Kim, S. Chauhan, H. J. Park, C.-S. Park, T. H. Yoo, T. J. Kang, “Identification of peptide inhibitors of matrix metalloproteinase 1 using an in-house assay system for the enzyme,” Enzyme Microb. Technol., 2019, 127, 65-69. online

46. A. Achek, M. Shah, J. Y. Seo, H.-K. Kwon, X. Gui, H.-J. Shin, E.-Y. Cho, B. S. Lee, D.-J. Kim, S. H. Lee, T. H. Yoo, M. S. Kim, S. Choi, “Linear and rationally designed stapled peptides abrogate TLR4 pathway and relieve inflammatory symptoms in RA rat model,” J. Med. Chem. 2019, 62, 6495-6511. online

45. B. Lim, S. S. Lee, T. H. Yoo, S. Kim, S. Y. Kim, S.-h. Choi, J. M. Kim, “Normal stress difference-driven particle focusing in nanoparticle colloidal dispersion,” Science Advances, 2019, 5, eaav4819. online

44. Y.-J. Jang, K.-H. Lee, T. H. Yoo, D.-M. Kim, “Interfacing a personal glucose meter with cell-free protein synthesis for rapid analysis of amino acids,” Analytical Chemistry, 2019, 91, 2531-2535. online

43. J. Y. Park, S. H. Park, M. G. Kim, S. H. Park, T. H. Yoo, M. S. Kim, “Biomimetic scaffolds for bone tissue engineering,” Adv. Exp. Med. Biol. 2018, 1064, 109-121. online

42. H. J. Park, T. H. Yoo, “Nucleic Acid Detection by a Target-Assisted Proximity Proteolysis Reaction,” ACS Sensors, 2018, 10, 2066-2070. online

41. J. Park, Y. Lee, B. J. Ko, T. H. Yoo, “Peptide-Directed Photo-Cross-Linking for Site-Specific Conjugation of IgG,” Bioconjugate Chemistry, 2018, 29, 3240-3244. online

40. J. Y. Seok, J Yang, S. J. Choi, H. G. Lim, U. J. Choi, K. J. Kim, S. Park, T. H. Yoo,* G. Y. Jung,* “Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device” Metabolic Engineering, 2018, 47, 113-120. *Co-corresponding authors. online

39. Y. S. Park, U. J. Choi, N. H. Nam, S. J. Choi, A. Nasir, S.-G. Lee, K. J. Kim, G. Y. Jung, S. Choi, J. Y. Shim, S. Park,* T. H. Yoo,* “Engineering an aldehyde dehydrogenase toward its substrate, 3-hydroxypropanal and NAD+, for enhancing the production of 3-hydroxypropionic acid” Scientific Reports, 2017, 7:17155. *Co-corresponding authors. online

38. Y.-J. Jang, K.-H. Lee, T. H. Yoo,* D.-M. Kim,* “Complementary cell-free translational assay for quantification of amino acids,” Analytical Chemistry, 2017, 89, 9638-9642. *Co-corresponding authors. online

37. S. H. Park, J. S. Kwon, B. S. Lee, J. H. Park, B. K. Lee, J.-H. Yun, B. Y. Lee, J.-H. Kim, B. H. Min, T. H. Yoo,* M. S. Kim,* “BMP2-immobilized injectable hydrogel for osteogenic differentiation of human periodontal ligament stem cells” Scientific Reports, 2017, 7:6603. *Co-corresponding authors. online

36. T. H. Shin, S. Lee, K. R. Choi, D. Y. Lee, Y. Kim, M. J. Paik, C. Seo, S. Kang, M. S. Jin, T. H. Yoo, S. H. Kang, G. Lee, “Decreased quality freshness of human bone marrow-derived mesenchymal stem cells over time” Scientific Reports, 2017, 7:1106. online

35. H. F. Son, S. Park, T. H. Yoo, G. Y. Jung, K.-J. Kim, “Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense” Scientific Reports, 2017, 7:46005. online

34. S. Park, H. J. Shin, M. Shah, H. Y. Cho, M. A. Anwar, A. Achek, H. K. Kwon, B. Lee, T. H. Yoo, S. Choi, “TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation” Biomaterials, 2017, 126, 49-60. online

33. B. S. Lee. S. Kim, B. J. Ko, T. H. Yoo, “An efficient system for incorporation of unnatural amino acids in response to the four-base codon AGGA in Escherichi coli” Biochim Biophys. Acta, 2017, 1861, 3016-3023. online

32. J. Kim, S. H. Seok, E. Hong, T. H. Yoo, M. D. Seo, Y. Ryu, “Crystal structure and characterization of esterase Est25 mutants reveal improved enantioselectivity toward (S)-ketoprofen ethylester” Appl Microbiol Biotechnol, 2017, 101, 2333-2343. online

31. C. H. Heo, M. K. Cho, S. Shin, T. H. Yoo*, H. M. Kim*, “Real-time monitoring of vesicle pH in an endocytic pathway using an EGF-conjugated two-photon probe” Chem Comm, 2016, 52, 14007-14010. *Co-corresponding authors. online

30. D. Yang, H. J. Park, T. H. Yoo, “A colorimetric protease activity assay method using engineered procaspase-3 enzymes” Analytical Methods, 2016, 8, 6270-6276. online

29. S. E. Kim, K.-H. Lee, S.-W. Park, T. H. Yoo, C. H. Oh, J.-H. Park, S. Y. Yang, Y.-S. Kim, D.-M. Kim, “Cell-free production and streamlined assay of cytosol-penetrating antibodies” Biotechnology and Bioengineering, 2016, 113, 2107-2112. online

28. C. Q. Zhang, Y. M. Park, D. Yang, T. H. Yoo*, H. C. Yoon*, “Development of a matrix metalloproteinase-2 biosensing system by integrating an enzyme-mediated color development reaction into a common electronics components setup” BioChip Journal, 2016, 10, 198-207. *Co-corresponding authors. online

27. K.-H. Seo, H.-S. Chu, T. H. Yoo, S.-G. Lee, J.-I. Won, “Separation efficiency of free-solution conjugated electrophoresis with drag-tags incorporating a synthetic amino acid” Electrophoresis, 2016, 37, 818-825. online

26. Y. Ravikumar, S. P. Nadarajan, T. H. Yoo, C.-S. Lee, H. Yun, “Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications,” Biotechnol. J. 2015, 10, 1862-1876. online

25. J. S. Kim, D. K. Choi, S. W. Park, S. M. Shin, J. Bae, D. M. Kim, T. H. Yoo, Y. S. Kim, “Quantitative assessment of cellular uptake and cytosolic access of antibody in living cells by an enhanced split GFP complementation assay,” Biochem. Biophys. Res. Commun. 2015, 467, 771-777. online

24. Y. Ravikumar, S. P. Nadarajan, T. H. Yoo, C.-S. Lee, H. Yun, “Unnatural amino acid mutagenesis-based enzyme engineering,” Trends in Biotechnology, 2015, 33, 462-470. online

23. B. S. Lee, S. Shin, J. Y. Jeon, K.-S. Jang, B. Y. Lee, S. Choi, T. H. Yoo, “Incorporation of unnatural amino acids in response to the AGG codon” ACS Chemical Biology, 2015, 10, 1648-1653. online

22. K. Deepankumar, S. P. Nadarajan, S. Mathew, S.-G. Lee, T. H. Yoo, E. Y. Hong, B.-G. Kim, H. Yun, “Engineering Transaminase for Stability Enhancement and Site-Specific Immobilization through Multiple Noncanonical Amino Acids Incorporation” ChemCatChem, 2015, 7, 417-421. online

21. J. A. Van Deventer, K. P. Yuet, T. H. Yoo, D. A. Tirrell, “Cell surface display yields evolvable, clickable antibody fragments” ChemBioChem, 2014, 15, 1777-1781. online

20. H. Kim, H. K. Yoon, T. H. Yoo, “Engineering β-lactamase zymogens for use in protease activity assays” Chem Comm, 2014, 50, 10155-10157. online

19. M. Kim, H.-J. Lee, S. Oh, Y. Kim, H. Jung, M.-K. Oh, Y. J. Yoon, T. H. Yoo, T.-S. Yoon, H. H. Lee, “Robust ZnO nanoparticle embedded memory device using vancomycin conjugate and its biorecognition for electrical charging node” Biosensors and Bioelectronics, 2014, 56, 33-38. online

18. S. Yoon, S. Kim, S. Park, E. Hong, J. Kim, S. Kim, T. H. Yoo, Y. Ryu, “Improving the enantioselectivity of an esterase toward (S)-ketoprofen ethyl ester through protein engineering” Journal of Molecular Catalysis B: Enzymatic, 2014, 100, 25-31. online

17. H. K. Yoon and T. H. Yoo, “A novel protease activity assay based on an engineered autoinhibited protein using an enzyme-linked immunoassay” Analyst, 2013, 138, 7164-7168. online

16. O. Paley, G. Agnello, J. Cantor, T. H. Yoo, G. Georgiou, E. Stone, “GFP reporter screens fro the engineering amino acid degrading enzymes from libraries expressed in bacteria” Enzyme Engineering: Methods and Protocols, Methods in Molecular Biology, 2013, 978, 31-44.

15. J. Mittal*, T. H. Yoo*, G. Georgiou, T. M. Truskett, “Structural ensemble of an intrinsically disordered polypeptide” J Phys Chem B, 2013, 117, 118-124. *Equally contributed.

14. H. K. Yoon, S. T. Jung, J.-H. Kim, T. H. Yoo**, “Recent Development of Highly Sensitive Protease Assay Methods: Signal Amplification through Enzyme Cascades” Biotechnology and Bioprocess Engineering, 2012, 17, 1113-1119.

13. N. Soundrarajan, S. Sokalingam, G. Raghunathan, N. Budisa, H.-J. Park, Y. H. Yoo, S.-G. Lee, “Conjugation of Proteins by Installing BIO-Orthogonally Reactive Groups at Their N-Termini” PLOS One, 7, e46741.

12. S. Basith, B. Manavalan, T. H. Yoo, S. G. Kim, S. Choi, “Roles of toll-like receptors in Cancer: A double-edged sword for defense and offense” Archives of Pharmacal Research, 2012, 35, 1297-1316.

11. F. Truong, T. H. Yoo, T. J. Lampo, D. A. Tirrell, “Two-strain, cell-selective protein labeling in mixed bacterial cultures” JACS, 2012, 134, 8551-8556.

10. T. H. Yoo*, M. Pogson*, B. L. Iverson, G. Georgiou, “Directed evolution of highly selective proteases using a novel FACS based screen that capitalizes on the p53 regulator MDM2” ChemBioChem, 2012, 13, 649-653. *Equally contributed

9. J. R. Cantor*, T. H. Yoo*, A. Dixit, B. Iverson, T. G. Forsthuber, G. Georgiou, “Therapeutic enzyme deimmunization by combinatorial T-cell epitope removal using neutral drift,” PNAS, 2011, 108, 1272-1277. *Equally contributed

8. O. H. Kwon*, T. H. Yoo*, C. M. Othon, J. A. Van Deventer, D. A. Tirrell, and A. H. Zewail, “Hydration dynamics at fluorinated protein surfaces,” PNAS, 2010, 107, 17101-17106. *Equally contributed

7. E. Schmitt, I. C. Tanrikulu, T. H. Yoo, M. Panvert, D. A. Tirrell, and Y. Mechulam, “Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity,” Journal of Molecular Biology, 2009, 394, 843-851.

6. J. T. Ngo, J. A. Champion , A. Mahdavi , I. C. Tanrikulu , K. E. Beatty , R. E. Connor, T. H. Yoo, D. Dieterich , E. Schuman , and D. A. Tirrell, "Cell-selective metabolic labeling of proteins," Nature Chemical Biology, 2009, 5, 715-717. (Commentary in Nature, 2009, 460, 805)

5. N. Ayyadurai, R. Neelamegam, S. Nagasundarapandian, S. Edwardraja, H. S. Park, S. J. Lee, T. H. Yoo, H. Yoon, and S.-G. Lee, “Importance of expression system in the production of unnatural recombinant proteins in Escherichia coli,” Biotechnology and Bioprocess Engineering, 2009, 14, 257-265.

4. T. H. Yoo, A. J. Link, and D. A. Tirrell, “Evolution of a fluorinated green fluorescent protein,” PNAS, 2007, 104, 13887-13890.

3. T. H. Yoo, and D. A. Tirrell, “High-throughput screening for methionyl-tRNA synthetases that enable residue-specific incorporation of noncanonical amino acids into recombinant proteins in bacterial cells,” Angewandte Chemie International Edition, 2007, 46, 5340-5343. (Listed as Very Important Paper (VIP))

2. H.S. Kim, T. H. Yoo, H. Kim, J. Y. Park, B. K. Hur, Y. W. Ryu, and J. S. Kim, “An animal model to evaluate the protective efficacy of Haemophilus influenzae type b conjugate vaccine”, Biotechnology and Bioprocess Engineering, 2004, 9, 490-494.

1. T. H. Yoo, S. S. Park, E. Y. Bang, H. S. Kim, Y. K. Oh, L. S. Kim, and J. S. Kim, “A method for measuring free polyribosylribitol phosphate (PRP) in PRP-tetanus toxoid conjugate vaccine using antibody/ammonium sulfate precipitation”, Journal of Microbiology and Biotechnology, 2003, 13, 469-472.