Marco Salemi

Marco Salemi

Professor

Department: MD-PATHOLOGY-GENERAL
Business Phone: (352) 273-9567
Business Email: salemi@pathology.ufl.edu

About Marco Salemi

I am a full professor of Experimental Pathology at the Department of Pathology, Inmunology and Laboratory Medicine of UF College of Medicine, and Holloway and McClamma 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).

Accomplishments

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 Profile

Through my research I have gained, over the past 20 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 170 peer-reviewed publications in scholarly journals including Nature, Science and PNAS. My published work has overall been cited 8,200 times, with an h-index of 44, and an i10-index of 133 (http://scholar.google.com). I am currently involved (as PI and co-Investigator) in two major NIH R01 projects focusing on HIV/SIV pathogenesis, and carried out (as PI) a five-year NIH funded project to study SIV intra-host evolution in the macaque model of neuroAIDS (R01 NS063897) that was renewed for other five years in 2017. I am also PI in an NIH R21 centering on the development of novel bioinformatic tools to monitor the HIV epidemic in Florida and design public health intervention strategies, a task particularly urgent in Florida, since the state has one of the highest HIV incidence in USA. Lately, my research has focused on the development of novel phylogenetic algorithms for the analysis of next generation sequence data, 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).

Publications

2020 Proceedings of the National Academy of Sciences of the United States of America. Biological Sciences
2020 Pathogens and global health (Online)
2018 Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
2015 Trends in Microbiology
2012 International Reviews of Immunology
2008 American Journal of Physical Anthropology

Grants

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 ACTIVE
RAPID: Dynamic Identification of SARS-COV-2 Transmission Epicenters in Presence of Spatial Heterogeneity (COV-DYNAMITE)
NATL SCIENCE FOU ·
Apr 2020 ACTIVE
COVID-19: RAPID: Epidemiological and Phylogenetic models for Contact-Based Control of COVID-19
UNIVERSITY OF LOUISIANA AT LAFAYETTE · Principal Investigator
Sep 2019 – May 2020
Mobile Prevention Services to Respond to Expanding HIV Clusters in South Florida
UNIV OF MIAMI · Principal Investigator
Jul 2019 ACTIVE
DRPD-ROF2019: Single-cell sequencing of the citrus Huanglongbing pathogen, Candidatus Liberibacter asiaticus to advance understanding of pathogen biology
UF RESEARCH ·
Apr 2019 ACTIVE
Cholera in Goma, DRC
NATL INST OF HLTH NIAID ·
Apr 2018 ACTIVE
Monocyte traffic and neuropathogenesis of AIDS
Boston College · Principal Investigator
Feb 2018 ACTIVE
HIV Dynamic Modelling for Identification of Transmission Epicenters (HIV-DYNAMITE)
NATL INST OF HLTH NIAID ·
Jan 2018 ACTIVE
Regression, Phylogenetics, and Study Design in Infectious Disease Epidemiology
OHIO STATE UNIV ·
Sep 2017 ACTIVE
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 FOU · Mentor
Dec 2016 ACTIVE
Cholera persistence, transmission, and clinical illness in Haiti
NATL INST OF HLTH NIAID ·
Aug 2016 – Jul 2017
Intra-Host Phylogeography and population dynamics of SIV in the Rhesus Macaque Model of NeuroAIDS
NATL INST OF HLTH · Mentor
Jul 2016 ACTIVE
Cholera transmission and evolution in Port-au-Prince, Haiti
NATL INST OF HLTH NIAID ·
Jul 2016 – Jul 2016
Whole Genome Sequencing of Neisseria Meningitidis Serogroup Isolates
FL DEPT OF HLTH · Principal Investigator
Jun 2016 – Oct 2017
Bacterial Population Genetics of select agent Pathogens
US DEPT OF HOMELAND SECURITY · Project Manager
Oct 2015 – Jun 2016
Whole Genome Sequencing of Neisseria meningitidis serogr
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
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 ACTIVE
GA: support reserach fellowship in Pediatrics Immune Disorders
UF FOU · Principal Investigator
Jul 2007 – Aug 2016
Clinical and Translational Science Institute
UF RESEARCH FOU · Project Manager

Education

Postdoctoral Associate
2002-2004 · University of California, Irvine, USA
Postdoctoral Scientist
1999-2002 · University of Leuven, Belgium
PhD
1999 · Catholic University of Leuven, Belgium
Specialty in Biotechnology
1995 · University of Milan, Italy
B.Sc/Master in Chemistry
1991 · University of Pavia, Italy

Contact Details

Phones:
Business:
(352) 273-9567
Emails: