• Battison, A.S., Balsbaugh, J.L.,Borniger, J.C., 2025. APEX2 and TurboID define unique subcellular proteomes. Sci Rep, 15, 43547.

  • Becker, J.T., Auerbach, A.A.,Harris, R.S., 2023. APEX3 - An Optimized Tool for Rapid and Unbiased Proximity Labeling. Journal of Molecular Biology, 435(13):168145.

  • Berlec, A., Skrlec, K., Kocjan, J., Olenic, M.,Strukelj, B., 2018. Single plasmid systems for inducible dual protein expression and for CRISPR-Cas9/CRISPRi gene regulation in lactic acid bacterium Lactococcus lactis. Sci Rep, 8, 1009.

  • Costanzo, L.F.D., 2025. Viral proteases: Structural basis of function, evolution, and drug design. Enzymes, 58, 19-57.

  • Dong, B., Chen, Y., Wang, X., Li, J., Zhang, S., Kang, X., Li, Y., Li, B., Liao, L., Zhang, Z., Xiong, J., Shao, L., Huang, S., Feng, Y.,Jiang, T., 2025. Development of a highly sensitive luciferase assay for intracellular evaluation of coronavirus Mpro activity. Frontiers in Microbiology, 16:1560251.

  • Eid, M., Barayeu, U., Sulkova, K., Aranda-Vallejo, C.,Dick, T.P., 2024. Using the heme peroxidase APEX2 to probe intracellular H(2)O(2) flux and diffusion. Nat Commun, 15, 1239.

  • Elmsaouri, S., Markmiller, S.,Yeo, G.W., 2022. APEX Proximity Labeling of Stress Granule Proteins. Methods Mol Biol, 2428, 381-399.

  • Geng, C.A., Chen, F.Y., Zheng, J.B., Liao, P., Li, T.Z., Zhang, X.M., Chen, X.,Chen, J.J., 2023. Rubiginosin B selectively inhibits Treg cell differentiation and enhances anti-tumor immune responses by targeting calcineurin-NFAT signaling pathway. Phytomedicine, 116, 154898.

  • Guo, Z., Zhong, X., Lin, L., Wu, S., Wang, T., Chen, Y., Zhai, X., Wang, Y., Wu, H., Tong, L., Han, Y., Pan, B., Peng, Y., Si, X., Zhang, F., Zhao, W.,Zhong, Z., 2014. A 3C(pro)-dependent bioluminescence imaging assay for in vivo evaluation of anti-enterovirus 71 agents. Antiviral Res, 101, 82-92.

  • Han, Y., Branon, T.C., Martell, J.D., Boassa, D., Shechner, D., Ellisman, M.H.,Ting, A., 2019. Directed Evolution of Split APEX2 Peroxidase. ACS Chemical Biology, 14, 619-635.

  • Hayashi, T., Hirano, J., Murakami, K., Fujii, Y., Kobayashi, S., Tanikawa, T., Kitamura, M.,Someya, Y., 2025. Identification of FDA-Approved Drugs That Inhibit SARS-CoV-2 and Human Norovirus Replication. Biol Pharm Bull, 48, 994-1000.

  • Hung, V., Udeshi, N.D., Lam, S.S., Loh, K.H., Cox, K.J., Pedram, K., Carr, S.A.,Ting, A.Y., 2016. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc, 11, 456-475.

  • Kaewsapsak, P., Shechner, D.M., Mallard, W., Rinn, J.L.,Ting, A.Y., 2017. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. Elife, 66:e29224.

  • Kalocsay, M., 2019. APEX Peroxidase-Catalyzed Proximity Labeling and Multiplexed Quantitative Proteomics. Methods Mol Biol, 2008, 41-55.

  • Kapust, R.B., Tozser, J., Copeland, T.D.,Waugh, D.S., 2002. The P1' specificity of tobacco etch virus protease. Biochem Biophys Res Commun, 294, 949-955.

  • Kim, Y., Lovell, S., Tiew, K.C., Mandadapu, S.R., Alliston, K.R., Battaile, K.P., Groutas, W.C.,Chang, K.O., 2012. Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses. J Virol, 86, 11754-11762.

  • Kleeman, B., Olsson, A., Newkold, T., Kofron, M., Delay, M., Hildeman, D.,Grimes, H.L., 2018. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry A, 93, 556-562.

  • Lee, I.G., Lee, J., Hong, S.H.,Seo, Y.J., 2023. Apigenin's Therapeutic Potential Against Viral Infection. Front Biosci (Landmark Ed), 28, 237.

  • Leonard, R.A., Rao, V.N., Bartlett, A., Froggatt, H.M., Luftig, M.A., Heaton, B.E.,Heaton, N.S., 2023. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol, 97, e0059723.

  • Liu, X., Zhang, Q., Li, M., Qin, S., Zhao, Z., Lin, B., Ding, Y., Xiang, Y.,Li, C., 2023. Horseradish peroxidase (HRP) and glucose oxidase (GOX) based dual-enzyme system: Sustainable release of H(2)O(2) and its effect on the desirable ping pong bibi degradation mechanism. Environ Res, 229, 115979.

  • Lobingier, B.T., Huttenhain, R., Eichel, K., Miller, K.B., Ting, A.Y., Von Zastrow, M.,Krogan, N.J., 2017. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell, 169, 350-360.e312.

  • Ma, C., Tan, H., Choza, J., Wang, Y.,Wang, J., 2022. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharmaceutica Sinica B, 12, 1636-1651.

  • Muramatsu, T., Takemoto, C., Kim, Y.-T., Wang, H., Nishii, W., Terada, T., Shirouzu, M.,Yokoyama, S., 2016. SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proceedings of the National Academy of Sciences, 113, 12997-13002.

  • Nicholls, S.B., Chu, J., Abbruzzese, G., Tremblay, K.D.,Hardy, J.A., 2011. Mechanism of a genetically encoded dark-to-bright reporter for caspase activity. J Biol Chem, 286, 24977-24986.

  • Ovechkina, V.S., Zakian, S.M., Medvedev, S.P.,Valetdinova, K.R., 2021. Genetically Encoded Fluorescent Biosensors for Biomedical Applications. Biomedicines, 9(11):1528.

  • Pena-Francesch, M., Vanoaica, L.D., Zhu, G.F., Stumpe, M., Sankar, D.S., Nowag, H., Valencia-Camargo, A.D., Hammerschmidt, W., Dengjel, J., Ligeon, L.A.,Munz, C., 2023. The autophagy machinery interacts with EBV capsids during viral envelope release. Proc Natl Acad Sci U S A, 120, e2211281120.

  • Ran, Y., Chen, Z., Sacramento, C.Q., Fan, L., Cui, Q., Rong, L.,Du, R., 2025. Scutellaria barbata D. Don extracts alleviate SARS-CoV-2 induced acute lung injury by inhibiting virus replication and bi-directional immune modulation. Virol Sin, 40, 430-438.

  • Scott, D., Dikici, E., Ensor, M.,Daunert, S., 2011. Bioluminescence and its impact on bioanalysis. Annu Rev Anal Chem (Palo Alto Calif), 4, 297-319.

  • Senapati, S., Kaushik, A., Rajan, Singh, A., Gupta, I., Virkar, R., Kulkarni, S.S., Arankalle, V.,Singh, J.P., 2025. Rapid, On-Site SARS-CoV-2 Variant Detection and Differentiation Using GLAD-Pristine Silver Nanorod Arrays and Machine Learning-Enhanced SERS. ACS Omega, 10, 44978-44988.

  • Shen, H., Liu, S., Shang, L., Liu, Y., Sha, Y., Lei, D., Zhang, Y., Jin, C., Wu, S., Zhang, M., Wen, H., Jia, C.,Wang, J., 2025. Discovery of Small-Molecule Inhibitors Against Norovirus 3CL(pro) Using Structure-Based Virtual Screening and FlipGFP Assay. Viruses, 17(11):1277.

  • Sun, L.Y., Chen, C., Su, J., Li, J.Q., Jiang, Z., Gao, H., Chigan, J.Z., Ding, H.H., Zhai, L.,Yang, K.W., 2021. Ebsulfur and Ebselen as highly potent scaffolds for the development of potential SARS-CoV-2 antivirals. Bioorg Chem, 112, 104889.

  • Takashima, J.A., Woroniecka, H.A.,Charest, P.G., 2024. APEX2-Mediated Proximity Protein Labeling in Dictyostelium. Methods Mol Biol, 2814, 119-131.

  • Trompet, D., Melis, S., Chagin, A.S.,Maes, C., 2024. Skeletal stem and progenitor cells in bone development and repair. J Bone Miner Res, 39, 633-654.

  • Vuong, W., Khan, M.B., Fischer, C., Arutyunova, E., Lamer, T., Shields, J., Saffran, H.A., Mckay, R.T., Van Belkum, M.J., Joyce, M.A., Young, H.S., Tyrrell, D.L., Vederas, J.C.,Lemieux, M.J., 2020. Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nature Communications, 11(1):4282.

  • Woo, J., Park, H., Na, Y., Kim, S., Choi, W.I., Lee, J.H., Seo, H.,Sung, D., 2020. Novel fluorescein polymer-based nanoparticles: facile and controllable one-pot synthesis, assembly, and immobilization of biomolecules for application in a highly sensitive biosensor. RSC Adv, 10, 2998-3004.

  • Ye, J., Zhang, R., Zhou, J., Xu, T., Liu, X.,Chen, Y., 2025. Systematic Reevaluation of Repurposed Drugs Against the Main Protease of SARS-CoV-2 via Combined Experiments. J Med Virol, 97, e70229.

  • Zhang, Q., Schepis, A., Huang, H., Yang, J., Ma, W., Torra, J., Zhang, S.-Q., Yang, L., Wu, H., Nonell, S., Dong, Z., Kornberg, T.B., Coughlin, S.R.,Shu, X., 2019. Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. Journal of the American Chemical Society, 141, 4526-4530.

  • Zhang, R., Yan, H., Zhou, J., Yan, G., Liu, X., Shang, C.,Chen, Y., 2024. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol, 96, e29498.

  • Zhou, G., Wan, W.W.,Wang, W., 2022. Modular Peroxidase-Based Reporters for Detecting Protease Activity and Protein Interactions with Temporal Gating. Journal of the American Chemical Society, 144, 22933-22940.

  • Zhou, J., Zhang, R., Yan, H., Liu, X., Shang, C.,Chen, Y., 2025. Evaluation of natural products from virtual screenings as SARS-CoV-2 main protease inhibitors using combinational experiments. Nat Prod Res, 39, 1493-1496.