Submitted manuscripts

  1. Kostandova, N., R. Corgel, S. Bansal, S. Bérubé, E. Cleary, C. Hansen, M.D.T. Hitchings, B. García-Carreras, L. Gardner, M.U.G. Kraemer, S. Lai, Y. Li, A.C. Perofsky, G. Pullano, J.M. Read, G. Ribeiro dos Santos, H. Salje, S. Takahashi, C. Viboud, J. Wang, D.A.T. Cummings, A. Wesolowski. Data and model needs for generalizable inferences linking human mobility and infectious disease transmission.

  2. Tran-Kiem, C., M.I. Paredes, A.C. Perofsky, L.A. Frisbie, H. Xie, K. Kong, A. Weixler, A.L. Greninger, P. Roychoudhury, J.M. Peterson, A. Delgado, H. Halstead, D. MacKellar, P. Dykema, L. Gamboa, C.D. Frazar, E. Ryke, J. Stone, D. Reinhart, L. Starita, A. Thibodeau, C. Yun, F. Aragona, A. Black, C. Viboud, T. Bedford. Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences. medRxiv, 2024.05.24.24307811. Preprint

  3. Mathis, S.M., A.E. Webber, … A.C. Perofsky, … R.K. Borchering (110 authors). 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


  1. 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. Nature Communications, 15, 4164. DOI, Code
  2. 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. DOI

  3. 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 DOI, Code, Phylogenetics Workflow
  4. 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. DOI

  5. 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 75(1), e1000-e1010. DOI, Code

  6. 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. DOI, Code
  7. 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. DOI †Co-first authors

  8. Perofsky, A.C. and M.I. Nelson. Seasonal influenza: The challenges of vaccine strain selection. 2020. eLife 9:e62955. DOI

  9. 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. DOI

  10. 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. DOI

  11. 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. DOI

  12. 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. DOI, Code
  13. 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. DOI.

  14. 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. DOI.