Marco Salemi,

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, and Interim Director of UF Emerging Pathogens Institute. 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.

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).