MrViniciusFranceschi

Faculty of Medicine, School of Public Health

Research Assistant

Contact

Location

School of Public HealthWhite City Campus

Summary

After completing a BSc in Biomedical Informatics and an MSc in Cell and Molecular Biology in Brazil, I have joined Erik Volz's group to work with phylogenetic and statistical analysis of virus genomic data to identify transmission fitness variants and quantify their impact.

My current research is primarily focused on supporting R package development, developing tree-based clustering algorithms to identify transmission fitness mutations, and applying scalable phylodynamic tools such as treedater, mlesky, and treestructure to different genomic datasets (especially for SARS-CoV-2 and HIV viruses) to determine changes in effective population size and growth rates through time, and to pinpoint hidden population structure in time-scaled phylogenetic trees. The main aim of this work is to improve the surveillance of infectious diseases using genomic data.

Selected Publications

Journal Articles

Drake K, Boyd O, Franceschi V, et al.Drake K, Boyd O, Franceschi V, Volz E, Colquhoun R, Ellaby N close, 2024, Phylogenomic early warning signals for SARS-CoV-2 epidemic waves, Ebiomedicine, Vol:100, ISSN:2352-3964

Bonetti Franceschi V, Volz E, 2024, Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2, Wellcome Open Research, Vol:9, ISSN:2398-502X

Gröhs Ferrareze PA, Zimerman RA, Franceschi VB, et al.Gröhs Ferrareze PA, Zimerman RA, Franceschi VB, Caldana GD, Netz PA, Thompson CE close, 2023, Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations, Journal of Biomolecular Structure & Dynamics, Vol:41, ISSN:0739-1102, Pages:3110-3128

Didelot X, Franceschi V, Frost SDW, et al.Didelot X, Franceschi V, Frost SDW, Dennis A, Volz EM close, 2023, Model design for nonparametric phylodynamic inference and applications to pathogen surveillance, Virus Evolution, Vol:9, ISSN:2057-1577

Franceschi VB, Caldana GD, de Menezes Mayer A, et al.Franceschi VB, Caldana GD, de Menezes Mayer A, Cybis GB, Neves CAM, Ferrareze PAG, Demoliner M, de Almeida PR, Gularte JS, Hansen AW, Weber MN, Fleck JD, Zimerman RA, Kmetzsch L, Spilki FR, Thompson CE close, 2021, Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil, Bmc Genomics, Vol:22

Franceschi VB, Ferrareze PAG, Zimerman RA, et al.Franceschi VB, Ferrareze PAG, Zimerman RA, Cybis GB, Thompson CE close, 2021, Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021, Virus Research, Vol:304, ISSN:0168-1702, Pages:198532-198532

Ferrareze PAG, Franceschi VB, Mayer ADM, et al.Ferrareze PAG, Franceschi VB, Mayer ADM, Caldana GD, Zimerman RA, Thompson CE close, 2021, E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil, Infection Genetics and Evolution, Vol:93, ISSN:1567-1348, Pages:104941-104941

Franceschi VB, Caldana GD, Perin C, et al.Franceschi VB, Caldana GD, Perin C, Horn A, Peter C, Cybis GB, Ferrareze PAG, Rotta LN, Cadegiani FA, Zimerman RA, Thompson CE close, 2021, Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021, Pathogens, Vol:10, Pages:988-988

Franceschi VB, Santos AS, Glaeser AB, et al.Franceschi VB, Santos AS, Glaeser AB, Paiz JC, Caldana GD, Machado Lessa CL, de Menezes Mayer A, Küchle JG, Gazzola Zen PR, Vigo A, Winck AT, Rotta LN, Thompson CE close, 2021, Population‐based prevalence surveys during the Covid‐19 pandemic: A systematic review, Reviews in Medical Virology, Vol:31, ISSN:1052-9276

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