Rife Magalis Lab

About 

Our research projects revolve around pathogen within-host dynamics and global molecular epidemiology. We apply and develop advanced "omic" techniques and evolutionary models, using biological samples from both human and animal model systems, to characterize the dynamic behavior of viruses and bacteria within the host and population. Our ultimate aim is to continue to improve these methods to better our understanding of the role of pathogen evolution in clinical and public health outcomes.

Key Research Areas

• Sociovirology: Developing and applying evolutionary models to identify potential mechanisms of viral cooperation that increase the survival of viral quasispecies and risk of pathogenicity (focus on HIV).
• HIV reservoir dynamics: Developing and applying phyloanatomic models for inferring origins of HIV infection and quantification of viral replication during suppressive antiretroviral therapy.
• HIV neuroadaptation: Combining viral and immunological data to determine viral and host factors that contribute to HIV infection of the brain.
• DNA synthesis screening: Developing and applying DNA and protein evolution models to improve the resilience of DNA synthesis screening against AI-driven evasion strategies aimed at synthesizing toxins and other sequences of concern.
• Infectious disease molecular epidemiology: Developing and applying deep learning phylogenetic models to forecast pathogen transmission dynamics in heterogeneous outbreak scenarios (e.g., COVID-19).

Current Projects

• R21 AI183992 – PI: Rife Magalis, Description of HIV social behavior using a phylogenetic model of structured co-evolution

Recent Publications

• Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics | LE Droske, AS Ramirez-Mata, MN Cash, J Estrada, SD Shank, ... | BIORXIV, 2025.10. 03.680205
• Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods | BR Magalis, A Riva, S Marini, M Salemi, M Prosperi | Infection, Genetics and Evolution 124, 105661
• Progress and prospects for a nucleic acid screening test set | NE Wheeler, C Bartling, SR Carter, A Clore, J Diggans, K Flyangolts, ... | Applied Biosafety 29 (3), 133-141 — 3 — 2024
• DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction | C Sun, R Fang, M Salemi, M Prosperi, B Rife Magalis | PLOS Computational Biology 20 (4), e1011351
• Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics | C Sun, Y Li, S Marini, A Riva, DO Wu, R Fang, M Salemi, B Rife Magalis | Bioinformatics Advances 4 (1), vbae158
• Application of phylodynamic tools to inform the public health response to COVID-19: qualitative analysis of expert opinions | SN Rich, V Richards, C Mavian, BR Magalis, N Grubaugh, ... | JMIR Formative Research 7 (1), e39409
• Machine learning prediction and phyloanatomic modeling of viral neuroadaptive signatures in the macaque model of HIV-mediated neuropathology | AS Ramirez-Mata, D Ostrov, M Salemi, S Marini, BR Magalis | Microbiology Spectrum 11 (2), e03086-22
• Severe acute respiratory syndrome coronavirus 2 Delta vaccine breakthrough transmissibility in Alachua County, Florida | B Rife Magalis, S Rich, MS Tagliamonte, C Mavian, MN Cash, A Riva, ... | Clinical infectious diseases 75 (9), 1618-1627
• Lessons learned and yet-to-be learned on the importance of RNA structure in SARS-CoV-2 replication | M Bassett, M Salemi, B Rife Magalis | Microbiology and Molecular Biology Reviews 86 (3), e00057-21
• Low‐frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled‐edged sword | BR Magalis, C Mavian, M Tagliamonte, SN Rich, M Cash, A Riva, ... | Journal of medical virology 94 (7), 3192-3202
• Rapid emergence and spread of severe acute respiratory syndrome coronavirus 2 gamma (P. 1) variant in Haiti | MS Tagliamonte, C Mavian, K Zainabadi, MN Cash, JA Lednicky, ... | Clinical Infectious Diseases 74 (11), 2057-2060
• Early emergence phase of SARS-CoV-2 Delta variant in Florida, US | E Cella, S Ali, SE Schmedes, B Rife Magalis, S Marini, M Salemi, ... | Viruses 14 (4), 766
• Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics | RMB Marini Simone , Mavian Carla , Riva Alberto , Prosperi Mattia , Salemi Marco | Bioinformatics 38 (3), 856-860
• Predator-prey dynamics of intra-host Simian immunodeficiency virus evolution within the untreated host | B Rife Magalis, P Autissier, KC Williams, X Chen, C Browne, M Salemi | Frontiers in Immunology 12, 709962
• SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy | M Giovanetti, E Cella, F Benedetti, B Rife Magalis, V Fonseca, S Fabris, ... | Communications biology 4 (1), 489

Team 

• Brittany Rife Magalis, PI, Asst. Prof. brittany.magalis@louisville.edu
• Gayathri Vanga, Lab Tech, gayathripriya.vanga@louisville.edu
• Faezeh Rafiei, PhD student, Faezeh.rafiei@louisville.edu
• Zoey Wexler, PhD student, zoey.wexler@louisville.edu