Brittany Rife Magalis,
Assistant Professor
Department:
MD-PATHOLOGY-GENERAL
Business Phone:
(352) 273-5759
Business Email:
brittany.rife@ufl.edu
Accomplishments
Co-organizer
2018-Current
·
International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology
Research Fellow
2016
·
South African Medical Research Council Flagship Program
Teaching Profile
Courses Taught
2023
GMS6140 Principles of Immunology
Research Profile
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)
0000-0001-6088-4651
Publications
2024
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction
PLOS Computational Biology.
20(4)
[DOI] 10.1371/journal.pcbi.1011351.
2023
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.
2023
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.
2022
Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US.
Viruses.
14(4)
[DOI] 10.3390/v14040766.
[PMID] 35458495.
2022
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.
2022
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.
2022
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.
2022
Rapid Emergence and Spread of Severe Acute Respiratory Syndrome Coronavirus 2 Gamma (P.1) Variant in Haiti
Clinical Infectious Diseases.
74(11):2057-2060
[DOI] 10.1093/cid/ciab736.
[PMID] 34471930.
2022
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.
2021
Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets
Journal of NeuroVirology.
27(1):101-115
[DOI] 10.1007/s13365-020-00927-z.
[PMID] 33405206.
2021
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.
2021
Molecular epidemiology of foodborne pathogens
Foodborne Infections and Intoxications.
47-62
[DOI] 10.1016/b978-0-12-819519-2.00007-4.
2021
Molecular Evolution of Human Norovirus GII.2 Clusters
Frontiers in Microbiology.
12
[DOI] 10.3389/fmicb.2021.655567.
[PMID] 33828543.
2021
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.
2021
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.
2020
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.
2020
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.
2020
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.
2020
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.
2019
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Methods in Molecular Biology.
427-468
[DOI] 10.1007/978-1-4939-9074-0_14.
2019
National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort
Open Forum Infectious Diseases.
6(4)
[DOI] 10.1093/ofid/ofz135.
[PMID] 31041344.
2019
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.
2018
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.
2018
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.
2018
Neutral Theory and Rapidly Evolving Viral Pathogens
Molecular Biology and Evolution.
35(6):1348-1354
[DOI] 10.1093/molbev/msy088.
[PMID] 29688481.
2017
Emergence of recombinant Mayaro virus strains from the Amazon basin.
Scientific reports.
7(1)
[DOI] 10.1038/s41598-017-07152-5.
[PMID] 28821712.
2017
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.
2017
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.
2016
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.
2016
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.
2016
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.
2015
Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves.
Scientific reports.
5
[DOI] 10.1038/srep10170.
[PMID] 25973685.
2015
Intra-host Bayesian Phylogeography linking viral evolution and pathogenesis comes to an age
British Journal of Virology.
2(4)
[DOI] 10.17582/journal.bjv/2015/2.4.58.61.
2015
On the early dynamics and spread of HIV-1
Trends in microbiology.
23(1)
[DOI] 10.1016/j.tim.2014.11.004.
2015
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.
2014
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.
2013
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.
DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
.
[DOI] 10.1101/2021.01.21.427647.
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces v1
.
[DOI] 10.17504/protocols.io.brcwm2xe.
High-throughput single-cell sequencing for retroviral reservoir characterization
.
[DOI] 10.1101/2022.05.04.490630.
Grants
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
Role: Co-Investigator
Funding: UNIV OF MIAMI
via AIDS HEALTHCARE FOUNDATION
Apr 2021
– Mar 2022
Identification of SARS-CoV-2 genomic epidemiology in Miami
Role: Co-Investigator
Funding: UNIV OF MIAMI
via AIDS HEALTHCARE FOUNDATION
Education
PhD
2012-2017
·
University of Florida
BS
2009-2012
·
James Madison University
Contact Details
Phones:
- Business:
- (352) 273-5759
Emails:
- Business:
- brittany.rife@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100275
GAINESVILLE FL 32610 - Business Street:
-
2055 MOWRY RD
EMERGING PATHOGENS INSTITUTE
GAINESVILLE FL 32610-3010