Publications

camlhmp: a simple framework for building reproducible microbial genome-based typing tools. 20 April 2026; Microbiol Resour Announc 0:e00201-26. https://doi.org/10.1128/mra.00201-26

Robert A. Pettit III, Chayse M. Rowley, Taylor R. Fearing, Stefaan Verwimp, Rob G. Christensen, Jim A. Mildenberger, JosephM. Reed, Timothy D. Read

Physics-informed deep learning for infectious disease forecasting. J R Soc Interface. 1 November 2025; 22 (232): 20250379. https://doi.org/10.1098/rsif.2025.0379

Ying Qian, Kui Zhang, Eric Marty, Avranil Basu, Eamon B. O'Dea, Xianqiao Wang, Spencer J. Fox, Pejman Rohani, John M. Drake, He Li

N-glycosylation at the receptor binding site drives differences in receptor binding specificity between influenza B

virus lineages. J Virol 0:e01039-25. https://doi.org/10.1128/jvi.01039-25

Page CK, Mubassir MHM, Chopra P, Gay LC, Geiger G, Ray SD, Shepard JD, Miller RJ, Perez D, Bahl J, Boons GJ, Tompkins SM

Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation. Molecular Biology and

Evolution, Volume 42, Issue 8, August 2025, msaf199, https://doi.org/10.1093/molbev/msaf199.

Mandev S Gill, Guy Baele, Marc A Suchard, Philippe Lemey

Multilayer modular fusion graph attention network (MMF-GAT) for epidemic prediction. PLOS Complex Systems

2(10): e0000070. https://doi.org/10.1371/journal.pcsy.0000070

Fujimoto K, Liu L, Kuo J, Gao B, Chan HK, et al. (2025)

Characterizing potential interaction between respiratory syncytial virus and seasonal influenza in the U.S., Epidemics. Volume 52,2025,100850, ISSN 1755-4365, https://doi.org/10.1016/j.epidem.2025.100850.

Jiani Chen, Deven V. Gokhale, Ludy Registre Carmola, Liang Liu, Pejman Rohani, Justin Bahl.

Three things we can do now to reduce the risk of avian influenza spillovers. PNAS. 122 (31) e2503565122. https://doi.org/10.1073/pnas.2503565122

Kenneth B. Yeh, William P. Bahnfleth, Elaine Bradforda, Carol Cardona, Kristen K. Coleman, Peter J. Hudson Bernadeta Dadonaite, Rebecca J. Hutchins, Anthony Maresso, C. Raina MacIntyre, and Matthew Scotch.

Tracing SARS-CoV-2 Clusters Across Local-scales Using Genomic Data. PNAS. U.S.A. 122 (32) e2501435122 https://doi.org/10.1073/pnas.2501435122

Leke Lyu, Guppy Stott, Cody Dailey, Sachin Subedi, Kayo Fujimoto, Ryker Penn, Pamela Brown, Roger Sealy, Justin Bahl.

Methicillin-Resistant Staphylococcus aureus Bacteremia Relapses Show Diverse Genomic Profiles but Convergence in Bacteremia-Associated Genes. J Infect Dis. 2025 Jul 25:jiaf352. doi: 10.1093/infdis/jiaf352. Epub ahead of print. PMID: 40709822.

Talbot BM, Jacko NF, Hofstetter KS, Alahakoon T, Bouiller K, Read TD, David MZ.

Balancing Accuracy and Actionability: An Assessment of Minimal- Input Wastewater Models for COVID-19 Prediction. medRxiv. 2025.07.03.25330828; doi: https://doi.org/10.1101/2025.07.03.25330828

L. M. Lariscy, M. E. Lott, A. Handel, A. M. Foley, C. Melendez-Declet, L. Metsker, E. K. Lipp.

Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic. Commun Med 5, 165 (2025). https://doi.org/10.1038/s43856-025-00888-6

Lyu L, Veytsel G, Stott G, Fox S, Dailey C, Damodaran L, et. al.

Iquitos Virus in Traveler Returning to the United States from Ecuador. Emerging Infectious Diseases. 30(11), 2447-2451. https://doi.org/10.3201/eid3011.240708.

Baer, K., Arora, I., Kimbro, J., Haider, A., Mott, M., Marshall, K., Waggoner, J. J. 2024.

Sequence-based detection of emerging antigenically novel influenza A viruses. Proceedings of the Royal Society B: Biological Sciences. 2024;291(2028):20240790

Forna A, Weedop KB, Damodaran L, Hassell N, Kondor R, Bahl J, et al.

Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests. medRxiv. 2024.08.19.24311993

Emmanuela Jules, Charlie Decker, Brianna Jeanne Bixler, Alaa Ahmed, Zijing (Carol) Zhou, Itika Arora, Henok Tafesse, Hannah Dakanay, Andrei Bombin, Ethan Wang, Jessica Ingersoll, Kathy Bifulco, Jennifer K. Frediani, Richard Parsons, Julie Sullivan, Morgan Greenleaf, Jesse J. Waggoner, Greg S. Martin, Wilbur A. Lam, Anne Piantadosi

Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar. PeerJ. 12, p.e17805

Talbot, B.M., Clennon, J.A., Rakotoarison, M.F.N., Rautman, L., Durry, S., Ragazzo, L.J., Wright, P.C., Gillespie, T.R. and Read, T.D., 2024

Preparation of SARS-CoV-2 Particles in Raw Wastewater Samples for Sequencing on Illumina Platforms Using an ARTIC V4.1 Tiled Amplicon Approach . protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzj6zrlx1/v1

Leah Lariscy, Amanda Sullivan, Katie Dillon, Megan Lott, Travis Glenn, Erin Lipp 2024.

Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. mSystems. 9:e00143-24.

Vishnu Raghuram, Robert A. Petit, III, Zach Karol, Rohan Mehta, Daniel B. Weissman, Timothy D. Read

Beyond scale-free networks: integrating multilayer social networks with molecular clusters in the local spread of COVID-19. Scientific Reports. 2023;13(1):21861

Fujimoto K, Kuo J, Stott G, Lewis R, Chan HK, Lyu L, et al.