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Emerging Pathogens Institute University of Florida
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About Overview

Administration

Director

Marco Salemi

Marco Salemi

Emerging Pathogens Institute Interim Director; Holloway Professor In Experimental Pathology
Phone: (352) 273-9567
Email: salemi@pathology.ufl.edu
CV: View Curriculum Vitae:

I am full professor of Experimental Pathology at the Department of Pathology, Inmunology and Laboratory Medicine of UF College of Medicine, and Holloway Chair for research in Chronic and Infectious Diseases. As a Marie-Curie Fellow, at the Rega Institute (Leuven, Belgium), and post-doctoral scientist with Walter M. Fitch, at the University of California, Irvine (USA), I have been trained in the field of molecular evolution of viruses and phylogenetic analysis. During the last fifteen years, as UF faculty, my research interests have included molecular epidemiology, intra-host viral evolution, and the application of phylogenetic and population genetic methods to the study of human and simian pathogenic viruses (in particular HIV/SIV, HCV, HTLV and influenza). More recently, I have been applying the Bayesian coalescent framework to study molecular evolution and phylogeography of emergent and re-emergent bacterial pathogens, such as MRSA, Shigella, and Vibrio cholerae, using genome-wide SNPs. In addition, my laboratory has developed ad hoc protocols for the generation of high-throughput sequence data (including DNA sequencing, transcriptomics, and miRNA expression profiles) and droplet digital PCR quantitative analyses of viral and bacterial pathogens, as well as several automated bioinformatic and machine learning pipelines for the analysis of large sequence data sets (big data). Since the beginning of the COVID-19 pandemic, my group has been tracking the emergence and spread of SARS-CoV-2 variants in Florida, and we are currently running a coronavirus genomic surveillance program sequencing hundreds of samples per week from infected patients in Florida and the Caribbean area.

Accomplishments:
  • Exemplary Teacher Award
    2020 · University of Florida College of Medicine
  • Term Professorship Award
    2017 · University of Florida
  • Excellence Awards for Assistant Professors
    2012 · University of Florida
  • Honor Aedificanti Award for his efforts in AIDS research
    2008 · Kiwanis International Association
  • Distinguish International Educator Award
    2004 · University of Florida
  • Award for best PhD thesis in Science
    2002 · Katholieke Universiteit Leuven, Belgium
  • Best scientific paper originated in Ireland
    2001 · Science Foundation Ireland
Research Summary:

Through my research I have gained, over the past 25 years, broad knowledge of high-resolution phylogenetic and population genetic (phylodynamic) analysis applied to the study of viral and bacterial pathogens, with special emphasis on HIV/SIV. My contributions to the field of viral and bacterial evolution and molecular epidemiology have resulted so far in more than 200 peer-reviewed publications in scholarly journals including Nature, Science and PNAS. My published work has been cited over 10,000 times, with an h-index of 49, and an i10-index of 149 (http://scholar.google.com). I am currently involved (as PI and co-Investigator) in several NIH R01 projects focusing on HIV/SIV pathogenesis, neuroAIDS, molecular epidemiology pathogens (HIV, cholera, SARS-CoV-2), and development of artificial intelligence methods to forecast epidemic spread. My lab is particularly involved in the development of novel bioinformatic tools to monitor the HIV and SARS-CoV-2 epidemics in Florida, as well as design public health intervention strategies. In particular, we have been developing novel phylogenetic algorithms for the analysis of next generation sequence data of both viral and bacterial pathogens, including genome-wide single nucleotide polymorphisms (SNPs). I have extensive national and international teaching experience in the field of phylogenetics: I have been the teacher/co-organizer of the international workshop on viral evolution and molecular epidemiology since 1997, and I am editor of two of the main textbooks in applied phylogenetic inference (Salemi, Vandamme, The Phylogenetic Handbook – A Practical Approach to DNA and Protein Phylogeny, Cambridge University Press, New York, 2003; Lemey, Salemi, Vandamme, The Phylogenetic Handbook – A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, New York, 2009).

Research Interests:
  • Bioinformatics
  • HIV
  • Molecular Infectious Disease Epidemiology
  • Molecular epidemiology
Publications:
Grants:
  • Jan 2025 ACTIVE
    Utilizing phylodynamic and causal artificial intelligence methods for predicting and characterizing antibiotic resistant bacterial transmission within and beyond hospital settings
    NATL INST OF HLTH NIAID · Other
  • Jul 2024 ACTIVE
    Description of HIV social behavior using a phylogenetic model of structured co-evolution
    UNIVERSITY OF LOUISVILLE RES FOU · Principal Investigator
  • May 2024 ACTIVE
    Recurrence of Cholera in Haiti: Exploration of Contributing Factors and Intervention Strategies
    NATL INST OF HLTH NIAID · Co-Investigator
  • Jul 2023 ACTIVE
    Effects of CSF1R blockade on repopulation of SIV reservoirs from the CNS to the periphery after antiretroviral therapy interruption
    BOSTON COLLEGE · Principal Investigator
  • Jun 2023 ACTIVE
    Revealing HIV-1 persistence in myeloid cell reservoirs
    UNIV OF MIAMI · Principal Investigator
  • May 2023 ACTIVE
    Defining a Role for Liver Myeloid Cells in Viral Persistence under ART
    UNIV OF MIAMI · Principal Investigator
  • Jul 2022 ACTIVE
    A Phylodynamic Artificial Intelligence framework to predict evolution of SARS-CoV-2 variants of concern in Immunocompromised persons with HIV (PhAI-CoV)
    NATL INST OF HLTH NIAID · Principal Investigator
  • Jul 2022 ACTIVE
    Effects of CSF1R blockade on repopulation of SIV reservoirs from the CNS to the periphery after antiretroviral therapy interruption
    BOSTON COLLEGE · Principal Investigator
  • Jan 2022 – Dec 2022
    Identification of SARS-CoV-2 genomic epidemiology
    UNIV OF MIAMI · Principal Investigator
  • Jul 2021 – Jun 2022
    Effects of CSF1R blockade on repopulation of SIV reservoirs from the CNS to the periphery after antiretroviral therapy interruption
    BOSTON COLLEGE · Principal Investigator
  • Jul 2021 ACTIVE
    Linking within- and between-host dynamics in tracking recent Mycobacterium tuberculosis transmission
    NATL INST OF HLTH NIAID · Other
  • Jun 2021 – Aug 2022
    Expanding genomic surveillance and epidemiology capacity in Central Florida and Southeastern US
    THE ROCKEFELLER FOU · Principal Investigator
  • Apr 2021 – Mar 2022
    Identification of SARS-CoV-2 genomic epidemiology in Miami
    UNIV OF MIAMI · Principal Investigator
  • May 2020 ACTIVE
    Forecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning framework
    NATL INST OF HLTH NIAID · Principal Investigator
  • Apr 2020 – Mar 2021
    COVID-19: RAPID: Epidemiological and Phylogenetic models for Contact-Based Control of COVID-19
    UNIVERSITY OF LOUISIANA AT LAFAYETTE · Principal Investigator
  • Apr 2020 – Mar 2023
    RAPID: Dynamic Identification of SARS-COV-2 Transmission Epicenters in Presence of Spatial Heterogeneity (COV-DYNAMITE)
    NATL SCIENCE FOU · Co-Investigator
  • Sep 2019 – Feb 2021
    Mobile Prevention Services to Respond to Expanding HIV Clusters in South Florida
    UNIV OF MIAMI · Principal Investigator
  • Jul 2019 – Jun 2022
    DRPD-ROF2019: Single-cell sequencing of the citrus Huanglongbing pathogen, Candidatus Liberibacter asiaticus to advance understanding of pathogen biology
    UF RESEARCH · Co-Project Director/Principal Investigator
  • Jul 2019 – Jun 2024
    OoR Matching Support for CTSI
    UF DIV OF SPONSORED RES MATCHING FUNDS · Project Manager
  • Apr 2019 ACTIVE
    Cholera in Goma, DRC
    NATL INST OF HLTH NIAID · Co-Investigator
  • Apr 2018 – Dec 2020
    Monocyte traffic and neuropathogenesis of AIDS
    BOSTON COLLEGE · Principal Investigator
  • Feb 2018 – Jan 2022
    HIV Dynamic Modelling for Identification of Transmission Epicenters (HIV-DYNAMITE)
    NATL INST OF HLTH NIAID · Principal Investigator
  • Jan 2018 – Dec 2020
    Regression, Phylogenetics, and Study Design in Infectious Disease Epidemiology
    OHIO STATE UNIV · Co-Investigator
  • Sep 2017 – Jun 2024
    Viral evolution in peripheral macrophages and brain during progression to AIDS
    NATL INST OF HLTH NINDS · Principal Investigator
  • Apr 2017 – Mar 2019
    Salivary microRNA as novel biomarkers of HIV/AIDS disease progression in people living with HIV.
    UF FOUNDATION · Other
  • Dec 2016 – Nov 2023
    Cholera persistence, transmission, and clinical illness in Haiti
    NATL INST OF HLTH NIAID · Co-Investigator
  • Jul 2016 – Jul 2016
    Whole Genome Sequencing of Neisseria Meningitidis Serogroup Isolates
    FL DEPT OF HLTH · Principal Investigator
  • Jul 2016 – Jun 2022
    Cholera transmission and evolution in Port-au-Prince, Haiti
    NATL INST OF HLTH NIAID · Co-Investigator
  • Jun 2016 – Oct 2017
    Mapping and modeling Bacillus anthracis and Clostridiumbotulinum across North Africa and the Middle East with high resolutiongenetic sequencing and spatial analysis.
    US DEPT OF HOMELAND SECURITY · Project Manager
  • Oct 2015 – Jun 2016
    Whole Genome Sequencing of Neisseria meningitidis serogroup W135 Isolates
    FL DEPT OF HLTH · Principal Investigator
  • Oct 2015 – Mar 2018
    Monocyte Traffic and Neuropathogenesis of AIDS
    BOSTON COLLEGE · Principal Investigator
  • Sep 2013 – Jul 2017
    Molecular Features and Approach to the HIV CNS Reservoir Post cART
    UNIV OF CALIFORNIA SAN FRANCISCO · Principal Investigator
  • Sep 2012 – Aug 2017
    The Center for HIV RNA Studies (CRNA)
    UNIV OF MICHIGAN · Principal Investigator
  • Dec 2011 – Jun 2016
    Cholera Transmission in Gressier Region, Haiti
    NATL INST OF HLTH NIAID · Project Manager
  • Aug 2010 – Oct 2020
    GA: support reserach fellowship in Pediatrics Immune Disorders
    UF FOUNDATION · Principal Investigator
  • Jul 2007 – Aug 2016
    Clinical and Translational Science Institute
    UF RESEARCH FOU · Project Manager
Education:
  • 2002-2004
    Postdoctoral Associate
    University of California, Irvine, USA
  • 1999-2002
    Postdoctoral Scientist
    University of Leuven, Belgium
  • 1999
    PhD
    Catholic University of Leuven, Belgium
  • 1995
    Specialty in Biotechnology
    University of Milan, Italy
  • 1991
    B.Sc/Master in Chemistry
    University of Pavia, Italy
Full Profile

Assistant Director

Miriam Hill
Department: RE-EMERGING PATHOGENS

Miriam Hill

Assistant Director, Admin
Phone: (352) 273-7526

Administration Team

Department: RE-EMERGING PATHOGENS

Nicole M Darrow

Grant Administration Manager
Phone: (352) 273-8273
Department: RE-EMERGING PATHOGENS

Pam Anders

Administrative Specialist
Phone: (352) 273-7526
Department: RE-EMERGING PATHOGENS

Alexa Sauvagere

Communications Manager
Phone: (352) 294-5754
Department: RE-EMERGING PATHOGENS

Tasha S Graham MBA, C-TAGME

Project Manager III
Phone: (352) 294-5168
Department: RE-EMERGING PATHOGENS

Sydney M Burge

Writer
Phone: (352) 273-7526
Department: RE-EMERGING PATHOGENS

Lauren Williams

Communications Assistant
Phone: (407) 587-5711
Department: RE-EMERGING PATHOGENS

Kayla Q Nguyen

Social Media Assistant
Phone: (352) 294-3585

Operations Team

Department: RE-EMERGING PATHOGENS

Daniel W Bainbridge

Engineer III
Phone: (352) 824-3704
Department: RE-EMERGING PATHOGENS

Mark D Paschall

Facilities Operations Specialist
Phone: (352) 273-5905
Department: RE-EMERGING PATHOGENS

Tracey L Moquin

Scientific Laboratory Manager
Phone: (352) 273-9188

Information Technology Team

Department: RE-EMERGING PATHOGENS

Ronald M Scott

IT Manager
Phone: (352) 273-7941
Department: RE-EMERGING PATHOGENS

John C Powell

End User Computing Specialist III
Phone: (352) 273-9568
Department: RE-EMERGING PATHOGENS

Cyrus Saleem

Data Management Analyst III
Phone: (352) 273-7526