Papers

Here are all of the papers generated by the MIDGE Center along with PDF copies of the papers and links to preprint versions of the papers, the papers' Google Scholar page, GitHub repositories, and underlying data. If you click on the "Science" tab above, you will find a listing of the papers that have been published for each project within the Center.

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PDF version of published paper
Preprint version of manuscript
GitHub repository for paper
Raw data used in manuscript
Google Scholar page

Shankar C, Narayanan DB, Miihlbach A, McNamara S, Brennan B, Miles-Jay A, Blankenship HM, Bahr A, Snitkin ES. 2025. Preprint: Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade.
Rapala JR, Siddiq M, Wittkopp P, O’Meara MJ, O’Meara TR. 2025. Preprint: Deep homology and design of proteasome chaperone proteins in Candida auris.
McFadden MJ, Anku JAE, Davis FA, Luke C, Obi A, O'Meara TR. 2025. Preprint: Growth phase influences virulence in Candidozyma auris systemic infection models.
Gontjes KJ, Pirani A, Narayanan DB, Lojek LJ, Han J, Tolomeo P, Goldstein EJ, Lautenbach E, Snitkin E. 2025. Preprint: Identifying drivers of β-lactam/β-lactamase inhibitor resistance emergence and spread before their clinical deployment.
Farjo M and Brooke CB. 2025. Preprint: The fitness consequences of coinfection and reassortment for segmented viruses depend upon viral genetic structure.
Doorley LA, La Bella AA, Jones SJ, Zhao G, Asadzadeh M, Choudhury QJ, Ahmad S, Mokaddas E, Al-Obaid I, Alfouzan W, Al-Banwan K, O’Meara TR, Santiago Tirado FH, Flores Mireles AL, Rybak JM. 2025. Preprint: Convergent evolution on RBA1 regulates Candidozyma auris host adaptation.
Campbell AJ, Shephard M, Paulos AP, Pauly M, Vu M, Stenkamp-Strahm C, Bushfield K, Hunter-Binns B, Sablon O, Bendall EE, Fitzimmons WJ, Brizuela K, Quirk G, Kumar N, McCluskey B, Shetty N, Marr LC, Guthmiller JJ, Abernathy K, Lauring AS, Melody BT, Wolfe M, Lombard J, Lakdawala SS. 2025. Preprint: Surveillance on California dairy farms reveals multiple sources of H5N1 transmission. DOI: 10.1101/2025.07.31.666798.
Boyko JD, Gontjes KJ, Snitkin ES, Smith SA. 2025. Preprint: Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction.
Thiede SN, Steinberg H, Benedict E, Sansom S, Aroutcheva A, Gontjes KJ, Winner K, Royzenblat S, Pirani A, Weinstein RA, Zawitz C, Moore NM, Popovich KJ, Snitkin ES. 2025. Antibiotic-resistance plasmid amplified among MRSA cases in an urban jail and its connected communities. Nat Commun. 17: 420. DOI: 10.1038/s41467-025-67113-9.
Gontjes KJ, Singh A, Sansom SE, Boyko JD, Smith SA, Lautenbach E, Snitkin E. 2025. Phylogenetic context of antibiotic resistance provides insights into the dynamics of resistance emergence and spread. J Infect Dis. 232: e992-e1002. DOI: 10.1093/infdis/jiaf478.
Zhao G, Lyu J, Veniaminova NA, Zarnowski R, Mattos E, Johnson CJ, Quintanilla D, Hautau H, Hold LA, Xu B, Anku JAE, Steltzer S, Dasgupta K, Santana DJ, Ibrahim A, Andes D, Nett JE, Singh S, Abraham AC, Killian ML, Kahlenberg JM, Wong SY, O'Meara TR. 2025. Candida auris skin colonization is mediated by Als4112 and interactions with host extracellular matrix proteins. Nature Communications. 16: 5673. DOI: 10.1038/s41467-025-60876-1.
Simonich CAL, McMahon TE, Ju X, Yu TC, Brunette N, Stevens-Ayers T, Boeckh MJ, King NP, Greninger AL, Bloom JD. 2025. RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera. J. Virology. 99: e0053125. DOI: 10.1128/jvi.00531-25.
Bendall EE and Lauring AS. 2025. In depth sequencing of a serially sampled household cohort reveals the within host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants. Microbiol Resour Announc. 14: e00901-25. DOI: 10.1128/mra.00901-25.
Bendall EE, Dimcheff D, Papalambros L, Fitzsimmons WJ, Zhu Y, Schmitz J, Halasa N, Chappell JD, Martin ET, Biddle JE, Smith-Jeffcoat SE, Rolfes MA, Mellis A, Talbot HK, Grijalva C, Lauring AS. 2025. In depth sequencing of a serially sampled household cohort reveals the within host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants. PLoS Pathogens. 21: e1013434. DOI: 10.1371/journal.ppat.1013134.
Lauring AS, Edson C, Surie D, Dawood F, Self W, Lucero-Obusan C, Holodniy M. 2025. Genomic surveillance of RSV in the United States by vaccination status, 2023-2024. JAMA. DOI: 10.1001/jama.2025.1225.