Brittany Rife Magalis,
Research Assistant Scientist
Business Phone: (352) 273-5759
Business Email: firstname.lastname@example.org
Co-organizer2018-Current · International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology
Research Fellow2016 · South African Medical Research Council Flagship Program
GMS6140 Principles of Immunology
My research interests revolve around molecular evolution and epidemiology of infectious diseases both within and among hosts, with a focus in phyloanatomy, sociovirology, and transmission cluster dynamics. The goal of my research is to identify relationships among genetic sequence data that can inform us as to the driving factors of pathogen evolution, interaction, and spread.
Open Researcher and Contributor ID (ORCID)
Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions
JMIR Formative Research. 7 [DOI] 10.2196/39409. [PMID] 36848460.
Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology
Microbiology Spectrum. 11(2) [DOI] 10.1128/spectrum.03086-22. [PMID] 36847516.
Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US.
Viruses. 14(4) [DOI] 10.3390/v14040766. [PMID] 35458495.
Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication
Microbiology and Molecular Biology Reviews. 86(3) [DOI] 10.1128/mmbr.00057-21. [PMID] 35862724.
Low‐frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled‐edged sword
Journal of Medical Virology. 94(7):3192-3202 [DOI] 10.1002/jmv.27726. [PMID] 35307848.
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics
Bioinformatics. 38(3):856-860 [DOI] 10.1093/bioinformatics/btab725. [PMID] 34672334.
Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida
Clinical Infectious Diseases. 75(9):1618-1627 [DOI] 10.1093/cid/ciac197. [PMID] 35271704.
Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches
Molecular Biology and Evolution. 38(3):1184-1198 [DOI] 10.1093/molbev/msaa263. [PMID] 33064823.
Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host.
Frontiers in immunology. 12 [DOI] 10.3389/fimmu.2021.709962. [PMID] 34691023.
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
Communications biology. 4(1) [DOI] 10.1038/s42003-021-02025-0. [PMID] 33883675.
Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study.
Viruses. 12(9) [DOI] 10.3390/v12090921. [PMID] 32842636.
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Molecular Biology and Evolution. 37(1):295-299 [DOI] 10.1093/molbev/msz197. [PMID] 31504749.
Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host
Virus Evolution. 6(1) [DOI] 10.1093/ve/veaa005. [PMID] 32355568.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Proceedings of the National Academy of Sciences. 117(23):12522-12523 [DOI] 10.1073/pnas.2007295117. [PMID] 32381734.
Origin and dissemination of hepatitis B virus genotype C in East Asia revealed by phylodynamic analysis and historical correlates.
Journal of viral hepatitis. 26(1):145-154 [DOI] 10.1111/jvh.13006. [PMID] 30199591.
Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts
Virus Evolution. 4(1) [DOI] 10.1093/ve/vey018. [PMID] 29951250.
Identification of conserved, primary sequence motifs that direct retrovirus RNA fate.
Nucleic acids research. 46(14):7366-7378 [DOI] 10.1093/nar/gky369. [PMID] 29846681.
Neutral Theory and Rapidly Evolving Viral Pathogens
Molecular Biology and Evolution. 35(6):1348-1354 [DOI] 10.1093/molbev/msy088. [PMID] 29688481.
Emergence of recombinant Mayaro virus strains from the Amazon basin.
Scientific reports. 7(1) [DOI] 10.1038/s41598-017-07152-5. [PMID] 28821712.
Insights into the Impact of CD8+ Immune Modulation on Human Immunodeficiency Virus Evolutionary Dynamics in Distinct Anatomical Compartments by Using Simian Immunodeficiency Virus-Infected Macaque Models of AIDS Progression.
Journal of virology. 91(23) [DOI] 10.1128/JVI.01162-17. [PMID] 28931681.
Phylodynamic applications in 21st century global infectious disease research
Global Health Research and Policy. 2(1) [DOI] 10.1186/s41256-017-0034-y. [PMID] 29202081.
Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis.
Journal of virology. 90(13):6112-6126 [DOI] 10.1128/JVI.00137-16. [PMID] 27122578.
Phylogenetics and phyloanatomy of HIV/SIV intra-host compartments and reservoirs: the key role of the central nervous system
Current HIV research. 14(2) [DOI] 10.2174/1570162×13666151029102413.
Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.
The Journal of biological chemistry. 291(5):2331-44 [DOI] 10.1074/jbc.M115.674564. [PMID] 26607354.
Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves.
Scientific reports. 5 [DOI] 10.1038/srep10170. [PMID] 25973685.
Intra-host Bayesian Phylogeography linking viral evolution and pathogenesis comes to an age
British Journal of Virology. 2(4) [DOI] 10.17582/journal.bjv/2015/18.104.22.168.
On the early dynamics and spread of HIV-1
Trends in microbiology. 23(1) [DOI] 10.1016/j.tim.2014.11.004.
Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques.
Journal of virology. 89(16):8484-96 [DOI] 10.1128/JVI.01010-15. [PMID] 26041280.
Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element.
Biochemistry. 53(13):2172-84 [DOI] 10.1021/bi500180p. [PMID] 24628426.
Structural study of interaction between brinzolamide and dorzolamide inhibition of human carbonic anhydrases
Bioorganic \& medicinal chemistry. 21(22) [DOI] 10.1016/j.bmc.2013.08.033.
Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions (Preprint)
. [DOI] 10.2196/preprints.39409.
Contrast-FEL – a test for differences in selective pressures at individual sites among clades and sets of branches
. [DOI] 10.1101/2020.05.13.091363.
DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
. [DOI] 10.1101/2021.01.21.427647.
Machine learning prediction and phyloanatomic modeling of viral neuroadaptive signatures in the macaque model of HIV-mediated neuropathology
. [DOI] 10.1101/2022.06.17.496109.
Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood
. [DOI] 10.1101/494856.
Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics
. [DOI] 10.1101/2022.04.10.487587.
SARS-CoV-2 infection of BNT162b2(mRNA)-vaccinated individuals is not restricted to variants of concern or high-risk exposure environments
. [DOI] 10.1101/2021.05.19.21257237.
Mar 2022 – Mar 2022
The role of defective HIV proviral DNA in promoting viral escape
Role: Principal Investigator
Funding: TULANE UNIV via NATL INST OF HLTH OD
Jan 2022 – Dec 2022
Identification of SARS-CoV-2 genomic epidemiology
Funding: UNIV OF MIAMI via AIDS HEALTHCARE FOUNDATION
Apr 2021 – Mar 2022
Identification of SARS-CoV-2 genomic epidemiology in Miami
Funding: UNIV OF MIAMI via AIDS HEALTHCARE FOUNDATION
Aug 2016 – Jul 2017
Intra-Host Phylogeography and population dynamics of SIV in the Rhesus Macaque Model of NeuroAIDS
Role: Principal Investigator
Funding: NATL INST OF HLTH
PhD2012-2017 · University of Florida
BS2009-2012 · James Madison University
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