22. E. Segelhurst, J. E. Bard, S. Gallo, D. A. Yergeau, V. Huang, A. Pohlman, J. A. Surtees, I. M. Bradley, Y. Ye*. Recovering wastewater RNA for virome sequencing by systematically optimized tangential-flow filtration and Nanotrap microbiome particles. (2025). Appl. Environ. Microbiol. e00777-25. doi/full/10.1128/aem.00777-25.
21. C. Zhu, Y. Ye*. Reactivity of viral proteins with free chlorine: Structural insights and implications for virus inactivation. (2025). Environ. Sci. Technol. Vol 59 (32), 17188-17197. doi.org/10.1021/acs.est.5c01689. (Featured on the supplementary cover)
20. S. Liu, Y. Ye, B. Guo, Y. Hu, K. Jiang, C. Liang, S. Xia, H. Wang*. (2025). ViOTUcluster: A high-speed, all-in-one pipeline for virome analysis from metagenomic data. iMetaOmics, Vol2 (2), e70023. doi/full/10.1002/imo2.70023.
19. D. T. Hill, M. Alazawi, J. Moran, L. J. Bennett, I. Bradley, M. B. Collins, C. Gobler, H. Green, T. Insaf, B. Kmush, D. Neigel, S. Raymond, M. Wang, Y. Ye, D. A. Larson*. (2023). Wastewater surveillance provides 10-days forecasting of COVID-19 hospitalizations superior to cases and test positivity: A prediction study. Infect. Dis. Model. Vol 8 (4), 1138-1150. doi.org/10.1016/j.idm.2023.10.004.
18. M. Neyra, D. T. Hill, L. J. Bennett, C. N. Dunham, D. A. Larson*, New York State Wastewater Surveillance Network Team (M. Alazawi, B. Bedard, I. M. Bradley, M. Collins, A. Fehrman, C. Gobler, A. Godinez, H. Green, B. Hanson, T. Insaf, H. Kappus-Kron, D. Lang, E. J. Moran, D. Neigel, S. J. Raymond, Y. Ye). (2023). Establishing a statewide wastewater surveillance system in response to the COVID-19 pandemic: A reliable model for continuous and emerging public health threats. J. Public Health Manag. Pract. Vol 29(6), 854-862. doi.org/ 10.1097/PHH.0000000000001797.
17. L. E. Quispe Cardenas, P. Deptula, C. Huerta, C. Zhu, Y. Ye, S. Wang, Y. Yang*. (2023). Electro-Fenton and induced electro-Fenton as versatile wastewater treatment processes for decontamination and nutrient removal without byproduct formation. ES&T Eng. Vol 3 (10), 1547-1556. doi.org/10.1021/acsestengg.3c00128.
16. E. Segelhurst, J. E. Bard, A. N. Pillsbury, M. M. Alam, N. A. Lamb, C. Zhu, A. Pohlman, A. Boccolucci, J. Emerson, B. J. Marzullo, D. A. Yergeau, N. J. Nowak, I. M. Bradley, J. A. Surtees, Y. Ye* (2023). Robust performance of SARS-CoV-2 whole-genome sequencing from wastewater with a nonselective virus concentration method. ACS ES&T Water. Vol 3 (4), 954-962. doi:10.1021/acsestwater.2c00456
15. L. M. Halwatura, I. S. Mclerran, D. L. Weglarski, Z. U. Ahmed, Y. Ye, I. M. Bradley, D. S. Aga*. (2022). Complementing RNA detection with pharmaceutical monitoring for early warning of viral outbreaks through wastewater-based epidemiology. Enviro. Sci. Technol. Lett. Vol 9 (6), 567-574. doi.org/10.1021/acs.estlett.2c00259
14. D. Mantilla-Calderon, K. K. Huang, A. Li, K. Chibwe, X, Yu, Y. Ye, L. Liu, F. Ling*. (2022). Emerging investigator series: meta-analyses on SARS-CoV-2 viral RNA levels in wastewater and their correlations to epidemiological indicators. Environ. Sci.: Water Res. Technol. Vol 8, 1391-1407. doi:10.1039/D2EW00084A
13. Z. Qiao, Y. Ye, A. Szczuka, K. Harrison, M. Dodd, K. R. Wigginton*. (2021). Reactivity of viral nucleic acids with chlorine and the impact of virus encapsidation. Environ. Sci. Technol. Vol 56 (1), 218-227. doi.org/10.1021/acs.est.1c04239
12. Y. Ye, A. C. Swensen, Y. Wang, M. Kaushal, D. Salamon, A. Knoten, C. Nicora, L. Marks, J. Gaut, A. Vijayan, D. Orton, P. Mudd, C. Parikh, W.-J. Qian, J. O’Halloran, P. Piehowski, S. Jain*. (2021). A pilot study of urine proteomics in COVID-19-associated acute kidney injury. Kidney Int. Rep. Vol 6 (12), 3064. doi.org/10.1016/j.ekir.2021.09.010
11. X. Zhang, S. Xia, Y. Ye, H. Wang*. (2021). Opportunistic pathogens exhibit distinct growth dynamics in rainwater and tap water storage systems. Water Res. Vol 204, 117581. doi.org/10.1016/j.watres.2021.117581
10. A. C. Swensen, J. He, A. C. Fang, Y. Ye, C. D. Nicora, T. Shi, A. Y. Liu, T. K. Sigdel, M. M. Sarwal, and W.-J. Qian*. (2021). A comprehensive urine proteome database generated from patients with various renal conditions and prostate cancer. Frontiers in Medicine, Vol 8. doi.org/10.3389/fmed.2021.548212
9. M. Rui, H. Chen, Y. Ye, H. Deng, H. Wang*. (2020). Effect of flow configuration on nitrifiers in biological activated carbon filters for potable water production. Environ. Sci. Technol., Vol 54, 14646-14655. doi.org/10.1021/acs.est.0c02479
8. N. M. Negretti, Y. Ye, L. M. Malavasi, S. M. Pokharel, S. Huynh, S. Noh, C. R. Gourley, C. A. Ragle, S. Bose, T. Looft, C. T. Parker, G. Clair, J. N. Adkins, M. E. Konkel*. (2020). A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni. Gut Microbes, Vol 12, 1-25. doi.org/10.1080/19490976.2020.1814121
7. Y. Ye, L. Zhao, M. J. Imperiale, K. R. Wigginton*. (2019). Integrated cell culture-mass spectrometry method for human infectious virus monitoring. Environ. Sci. Technol. Lett., Vol 6, 407-412. doi.org/10.1021/acs.estlett.9b00226 (Editors’ choice; Featured on the front cover)
6. Z. Qiao, Y. Ye, P. H. Chang, D. Thirunarayanan, K. R. Wigginton*. (2018). Nucleic acid photolysis by UV254 and the impact of virus encapsidation. Environ. Sci. Technol., Vol 52, 10408-10415. doi.org/10.1021/acs.est.8b02308
5. Y. Ye, P. H. Chang, J. Hartert, K. R. Wigginton*. (2018). Reactivity of enveloped virus genome, proteins, and lipids with free chlorine and UV254. Environ. Sci. Technol., Vol 52, 7698-7708. doi.org/10.1021/acs.est.8b00824
4. Y. Ye, R. M. Ellenberg, K. E. Graham, K. R. Wigginton*. (2016). Survivability, partitioning, and recovery of enveloped viruses in untreated municipal wastewater. Environ. Sci. Technol., Vol 50, 5077-5085.doi.org/10.1021/acs.est.6b00876
3. K. R. Wigginton*, Y. Ye, R. M. Ellenberg. (2015). Emerging investigators series: the source and fate of pandemic viruses in the urban water cycle. Environ. Sci.: Water Res. Technol., Vol 1, 735-746. (Featured on the front cover)doi.org/10.1039/C5EW00125K
2. H. Wang*, Y. Ye, J. Qi, F. Li, Y. Tang. (2013). Removal of titanium dioxide nanoparticles by coagulation: effects of coagulants, typical ions, alkalinity and natural organic matters. Water Sci. Technol., Vol 68, 1137-1142. doi.org/10.2166/wst.2013.356
1. J. Qi, Y. Ye, J. Wu, H. Wang*, F. Li. (2013). Dispersion and stability of titanium dioxide nanoparticles in aqueous suspension: effects of ultrasonication and concentration. Water Sci. Technol., Vol 67, 147-151. doi.org/10.2166/wst.2012.545