Publications

Articles in peer-reviewed journals

* contributed equally

2025

Martin, M.A., Brizzi, A., Xiaoyue, Xi, Galiwango, R.M., Moyo, Sikhulile, Ssemwanga, D., Blenkinsop, A., Redd, A.D., Abeler-Drner, L., Fraser, C., Reynolds, S.J., Quinn, T.C., Kagaayi, J., Bonsall, D., Serwadda, D., Nakigozi, G., Kigozi, G., Grabowski, M.K., Ratmann, O., with the PANGEA-HIV Consortium and the Rakai Health Sciences Program. (2024). Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data. PLOS Pathogens. 10.1371/journal.ppat.1013065. [PDF]

2024

Kim, S., Kigozi, G., Martin, M.A., Galiwango, R.M., Quicc, T.C., Redd, A.D., Ssekubugu, R., Bonsall, D., Ssemwanga, D., Rambaut, A., Herbeck, J.T., Reynolds, S.J., Foley, B., Abeler-Dörner, L., Fraser, C., Ratmann, O., Kagaayi, J., Laeyendecker, O., Grabowski, M.K. (2024). Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study. Virus Evolution. 10.1093/ve/veae065.

Martin, M.A., Berg, N., Koelle, K. (2024). Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks. Virus Evolution. 10.1093/ve/veae042. [PDF]

Farjo, M., Koelle, K., Martin, M.A., Gibson, L.L., Walden, K.K.O., Rendon, G., Fields, C.J., Alnaji, F.G., Gallagher, N., Luo, C.H., Mostafa, H.H., Manabe, Y.C., Pekosz, A., Smith, R.L., McManus, D.D., Brooke, C.B. (2024). Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. Journal of Virology. 10.1128/jvi.01618-23. [PDF]

Shi, T., Harris, J.D., Martin, M.A., Koelle, K. (2024). Transmission bottleneck size estimation from de novo viral genetic variation. Molecular Biology and Evolution. 10.1093/molbev/msad286. [PDF]

2023

Park, Y., Martin, M.A., Koelle, K. (2023). Epidemiological inference for emerging viruses using segregating sites. Nature Communications. 10.1038/s41467-023-38809-7. [PDF]

Bianco, C.M., Moustafa, A.M., O’Brien, K., Martin, M.A., Read, T.D., Kreiswirth, B.N., Planet, P.J. (2023). Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Frontiers in Cellular and Infection Microbiology. 10.3389/fcimb.2023.1081070. [PDF]

2022

Koelle, K., Martin, M.A., Antia, R., Lopman, B., Dean, N.E. (2022). The changing epidemiology of SARS-CoV-2. Science. 10.1126/science.abm4915. [PDF]

Babiker, A.*, Martin, M.A.*, Marvil, C., Bellman, S., Pettit III, R.A., Bradler, H.L., Sittleburg, V.D., Kunkes, A., Ingersoll, J., Kraft, C.S., Read, T.D., Waggoner, J., Koelle, K., Piantadosi, A. (2022). Unrecognized introductions of SARS-CoV-2 into the state of Georgia shaped the early epidemic. Virus Evolution. 10.1093/ve/veac011. [PDF]

2021

Martin, M.A., Koelle, K. (2021). Comment on “Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.” Science Translational Medicine. 10.1126/scitranslmed.abh1803. [PDF]

Martin, M.A., VanInsberghe, D., Koelle, K. (2021). Insights from SARS-CoV-2 sequences. Science, 371(6528). 10.1126/science.abf3995. [PDF]

2020

Moreno, G.K.*, Braun, K.M.*, Riemersma, K.K.*, Martin, M.A., Halfmann, P.J., Crooks, C.M., Prall, T., Baker, D., Baczenas, J.J., Heffron, A.S., Ramuta, M., Khubbar, M., Weiler, A.M., Accola, M.A., Rehrauer, W.M., O’Connor, S.L., Safdar, N., Pepperell, C.S., Dasu, T., Bhattacharyya, S., Kawaoka, Y., Koelle, K., O’Connor, D.H., Friedrich, T.C. (2020). Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introductions and spread. Nature Communications, 11(5558). 10.1038/s41467-020-19346-z. [PDF]

Miller, D.*, Martin, M.A.*, Harel, N.*, Tirosh O.*, Kustin, T.*, Meir, M., Sorek, N., Gefen-Halevi, S., Amit, S., Vorontsov, O., Shaag, A., Wolf, D., Peretz, A., Shemer-Avni, Y., Roif-Kaminsky, D., Kopelman, N.M., Huppert, A., Koelle, K., Stern, A. (2020). Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nature Communications, 11(5518). 10.1038/s41467-020-19248-0. [PDF]

2018

Martin, M.A., Lee, R.S., Cowley, L.A., Gardy, J.L., & Hanage, W.P. (2018). Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microbial genomics, 4(10). 10.1099/mgen.0.000217. [PDF]