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Michael Martin

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Martin MA, Blenkinsop A, Moffa M, Reynolds SJ, Nalugoda F, Quinn TC, Kigozi G, Ssekubugu R, Gupta RK, Grayson NE, MacIntyre-Cockett G, Kagaayi J, Nakigozi G, Abeler-Dörner L, Fraser C, Ratmann O, Tobian AAR, Laeyendecker O, Moyo S, Kennedy CE, Bonsall D, Galiwango RM, Grabowski MK. (2026). Patterns of HIV-1 viral load suppression and drug resistance during the dolutegravir transition: a population-based longitudinal study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Shi YT, Martin MA, Weissman DB, Koelle K. (2026). Genetic drift acts strongly on influenza virus populations within acute human infections but is obscured by other factors within acutely infected swine. Virus evolution, 12(1)

Shi YT, Martin MA, Weissman DB, Koelle K. (2025). Genetic drift acts strongly on within-host influenza virus populations during acute infection but does not act alone. bioRxiv : the preprint server for biology

Martin MA, Reynolds SJ, Foley BT, Nalugoda F, Quinn TC, Kemp SA, Nakalanzi M, Kankaka EN, Kigozi G, Ssekubugu R, Gupta RK, Abeler-Dörner L, Kagaayi J, Ratmann O, Fraser C, Galiwango RM, Bonsall D, Grabowski MK, , . (2025). HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012-19: a population-based, longitudinal study. The Lancet. Microbe

Martin MA, Brizzi A, Xi X, Galiwango RM, Moyo S, Ssemwanga D, Blenkinsop A, Redd AD, Abeler-Dörner L, Fraser C, Reynolds SJ, Quinn TC, Kagaayi J, Bonsall D, Serwadda D, Nakigozi G, Kigozi G, Grabowski MK, Ratmann O, . (2025). Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data. PLoS pathogens, 21(4)

Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. (2024). Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study. Virus evolution, 10(1)

Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. (2024). Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda. medRxiv : the preprint server for health sciences

Martin MA, Reynolds SJ, Foley BT, Nalugoda F, Quinn TC, Kemp SA, Nakalanzi M, Kankaka EN, Kigozi G, Ssekubugu R, Gupta RK, Abeler-Dörner L, Kagaayi J, Ratmann O, Fraser C, Galiwango RM, Bonsall D, Grabowski MK. (2024). Population dynamics of HIV drug resistance during treatment scale-up in Uganda: a population-based longitudinal study. medRxiv : the preprint server for health sciences

Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. (2024). Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. Journal of virology

Martin MA, 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(1)

Shi YT, Harris JD, Martin MA, Koelle K. (2023). Transmission bottleneck size estimation from de novo viral genetic variation. Molecular biology and evolution

Park Y, Martin MA, Koelle K. (2023). Epidemiological inference for emerging viruses using segregating sites. Nature communications, 14(1)

Bianco CM, Moustafa AM, O'Brien K, Martin MA, Read TD, Kreiswirth BN, Planet PJ. (2023). Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Frontiers in cellular and infection microbiology, (13)

Babiker A, Martin MA, Marvil C, Bellman S, Petit Iii RA, Bradley HL, Stittleburg VD, Ingersoll J, Kraft CS, Li Y, Zhang J, Paden CR, Read TD, Waggoner JJ, Koelle K, Piantadosi A. (2022). Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic. Virus evolution, 8(1)

Koelle K, Martin MA, Antia R, Lopman B, Dean NE. (2022). The changing epidemiology of SARS-CoV-2. Science (New York, N.Y.), 375(6585)

Martin MA, VanInsberghe D, Koelle K. (2021). Insights from SARS-CoV-2 sequences. Science (New York, N.Y.), 371(6528)

Martin MA, 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, 13(617)

Smith PJ, Potter G, Manson M, Martin M, Cendales LC. (2021). Psychosocial Considerations in the Assessment of Hand Transplant Candidates: A Single-Center Experience and Brief Literature Review. Clinical transplantation

Parker I, Khalil G, Martin A, Martin MT, Vanichseni S, Leelawiwat W, McNicholl JM, Hickey A, Garcia-Lerma JG, Choopanya K, Curtis K. (2020). Altered Antibody Responses in Persons Infected with HIV-1 While Using PrEP. AIDS research and human retroviruses

Schotthoefer A, Stinebaugh K, Martin M, Munoz-Zanzi C. (2020). Tickborne disease awareness and protective practices among U.S. Forest Service employees from the upper Midwest, USA. BMC public health, 20(1)

Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. (2020). Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA. medRxiv : the preprint server for health sciences

Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. (2020). Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nature communications, 11(1)

Miller D, Martin MA, 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 NM, 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(1)

Bajema Kristina L., Oster Alexandra M., McGovern Olivia L., Lindstrom Stephen, Stenger Mark R., Anderson Tara C., Isenhour , Clarke Kevin R., Evans Mary E., Chu Victoria T., Biggs Holly M., Kirking Hannah L., Gerber Susan I., Hall Aron J., Fry Alicia M., Oliver Sara E., Abedi Glen, Bower William, Chatham-Stephens Kevin, Conklin Laura, Cooley Laura, Cortese Margaret, Curns Aaron, Dooling Kathleen, Gokhale Runa, Gold Jeremy, Grant Gavin, Gutman Julie, Hesse Elisabeth, Kamili Shifaq, Kim Lindsay, Kirkcaldy Robert, Koumans Emily, Kujawski Stephanie, Langley Gayle, Lively Joana, Lu Xiaoyan, Lynch Brian, Lyss Sheryl, Malapati Lakshmi, Martin Michael, Mbaeyi Sarah, McClung Paul, Midgley Claire, Miller Maureen, Morales Michelle, Murray Janna', Parker Fiebelkorn Amy, Patel Manisha, Peacock Georgina, Pierce Taran, Rha Brian, Sakthivel Senthilkumar, Schneider Eileen, Siegel David A., Sunshine Brittany, Wallace Megan, Wang Lijuan, Watson John, Whitaker Brett, Yousaf Anna. (2019). Persons Evaluated for 2019 Novel Coronavirus — United States, January 2020.69(6)

Lackey ACR, Martin MD, Tinghitella RM. (2018). Male competition and speciation: expanding our framework for speciation by sexual selection. Current zoology, 64(1)

Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. (2018). Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microbial genomics, 4(10)

Huyvaert KP, Russell RE, Patyk KA, Craft ME, Cross PC, Garner MG, Martin MK, Nol P, Walsh DP. (2018). Challenges and Opportunities Developing Mathematical Models of Shared Pathogens of Domestic and Wild Animals. Veterinary sciences, 5(4)

Mendelson TC, Gumm JM, Martin MD, Ciccotto PJ. (2018). Preference for conspecifics evolves earlier in males than females in a sexually dimorphic radiation of fishes. Evolution; international journal of organic evolution, 72(2)

Martin M, Weld LH, Tsai TF, Mootrey GT, Chen RT, Niu M, Cetron MS, . Advanced age a risk factor for illness temporally associated with yellow fever vaccination. Emerging infectious diseases, 7(6)

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