Publications
†Denotes equal contribution
Manuscripts in revision
Mathis, S.M.†, A.E. Webber†, A. Basu, J.M. Drake, L.A. White, E.L. Murray, M. Sun, T.M. Leon, A.J. Hu, D. Shemetov, L.C. Brooks, R.J. Tibshirani, A. Green, D.J. McDonald, R. Rosenfeld, S. Kandula, T.K. Yamana, S. Pei, R. Yaari, J. Shaman, A. Meiyappan, S. Omar, … A.C. Perofsky, … M. Biggerstaff, R.K. Borchering. Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. 2023. medRxiv 2023.12.08.23299726. Preprint
Manuscripts in press
Perofsky, A.C., C.L. Hansen, R. Burstein, S. Boyle, R. Prentice, C. Marshall, D. Reinhart, B. Capodanno, M. Truong, K. Schwabe-Fry, K. Kuchta, B. Pfau, Z. Acker, J. Lee, T.R. Sibley, E. McDermot, L. Rodriguez-Salas, J. Stone, L. Gamboa, P.D. Han, A. Adler, A. Waghmare, M.L. Jackson, M. Famulare, J. Shendure, T. Bedford, H.Y. Chu, J.A. Englund, L.M. Starita, C. Viboud. Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. 2024. medRxiv Preprint, Code Accepted at Nature Communications
Publications
Paredes, M.I., A.C. Perofsky, L. Frisbie, L.H. Moncla, P. Roychoudhury, H. Xie, S.A. Mohamed Bakhash, K. Kong, I. Arnould, T.V. Nguyen, S.T. Wendm, P. Hajian, S. Ellis, P.C. Mathias, A.L. Greninger, L.M. Starita, C.D. Frazar, E. Ryke, W. Zhong, L. Gamboa, M. Threlkeld, J. Lee, J. Stone, E. McDermot, M. Truong, J. Shendure, H.N. Oltean, C. Viboud, H. Chu, N.F. Müller†, T. Bedford†. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. 2024. PLOS Pathogens, 20(3), e1012117. Article
Perofsky, A.C., J. Huddleston, C. Hansen, J.R. Barnes, T. Rowe, X. Xu, R. Kondor, D.E. Wentworth, N. Lewis, L. Whittaker, B. Ermetal, R. Harvey, M. Galiano, R. Stuart Daniels, J.W. McCauley, S. Fujisaki, K. Nakamura, N. Kishida, S. Watanabe, H. Hasegawa, S.G. Sullivan, I.G. Barr, K. Subbarao, F. Krammer, T. Bedford, C. Viboud. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. 2024. eLife 13:RP91849 Article, Code, Phylogenetics Workflow, eLife Press Release
Hansen, C.L., A.C. Perofsky, R. Burstein, M. Famulare, S. Boyle, R. Prentice, C. Marshall, B.J.J. McCormick, D. Reinhart, B. Capodanno, M. Truong, K. Schwabe-Fry, K. Kuchta, B. Pfau, Z. Acker, J. Lee, T.R. Sibley, E. McDermot, L. Rodriguez-Salas, J. Stone, … C. Viboud. Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network. 2022. JAMA Network Open 5(12):e2245861. Article
Perofsky, A.C., S. Tempia, J. Bingham, C. Maslo, M. Toubkin, A. Laubscher, S. Walaza, J.R.C. Pulliam, C. Viboud, C. Cohen. The direct and indirect effects of the COVID-19 pandemic on private healthcare utilization in South Africa. 2022. Clinical Infectious Diseases ciac055. Article, Code
Perofsky, A.C., L. Ancel Meyers, L.A. Abondano, A. Di Fiore, R.J. Lewis. Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes. 2021. Molecular Ecology 30: 6759–6775. Article, Code, Press: UT News
McBride, D.S.†, A.C. Perofsky†, J.M. Nolting, M.I. Nelson, A.S. Bowman. Tracing the source of influenza A virus zoonoses in interconnected circuits of swine exhibitions. 2021. The Journal of Infectious Diseases jiab122. Article †Co-first authors
Perofsky, A.C. and M.I. Nelson. Seasonal influenza: The challenges of vaccine strain selection. 2020. eLife 9:e62955. Article
Nelson, M.I., A. Perofsky, D.S. McBride, B.L. Rambo-Martin, M.M. Wilson, J.R. Barnes, H. van Bakel, J.M. Nolting, A.S. Bowman. A heterogenous swine show circuit drives zoonotic transmission of influenza A viruses in the United States. 2020. Journal of Virology 94(24):e01453-20. Article
Viboud, C., K. Gostic, M.I. Nelson, G.E. Price, A. Perofsky, K. Sun, N. Sequeira Trovão, B. Cowling, S. Epstein, D.J. Spiro. Beyond Clinical Trials: Evolutionary and Epidemiological Considerations for Development of a Universal Flu Vaccine. 2020. PLOS Pathogens 16:e1008583. Article
Perofsky, A.C., R.J. Lewis, L. Ancel Meyers. Terrestriality and bacterial transfer: A comparative study of gut microbiomes in sympatric Malagasy mammals. 2018. The ISME Journal 13:50–63. Article
Perofsky, A.C., R.J. Lewis, L. Abondano, A. Di Fiore, L. Ancel Meyers. Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka. 2017. Proceedings of the Royal Society B: Biological Sciences 284:20172274. Article, Code, Press: UT News, Daily Texan
Rakotomalala,E.J., F. Rakotondraparany, A.C. Perofsky, R.J. Lewis. Characterization of the tree holes used by Lepilemur ruficaudatus in the dry, deciduous forest of Kirindy Mitea National Park. 2017. Folia Primatologica 88:28-41. Article.
Berry, B.S.†, K. Magori†, A.C. Perofsky, D.E. Stallknecht, A.W. Park. Wetland cover dynamics drive hemorrhagic disease patterns in white-tailed deer in the United States. 2013. Journal of Wildlife Diseases 49(3):501-509. Article. Press: UGA Odum School of Ecology