Simone Marini

Department of Epidemiology
University of Florida
2004 Mowry raod
Gainesville, FL 32603
simone _DOT marini AT_ ufl _DOT_ edu

Simone Marini, PhD is a biomedical engineer by training. He designs AI applications for medicine, molecular biology, and public health. These applications are aimed at (a) enhancing the understanding the molecular machinery of the studied phenomena, e.g., providing a biological insight, hypothesis generation; (b) assisting clinical and public health decision making, e.g., diagnosis, prognosis, causal inference; and (c) facilitating research and data analysis (bioinformatics tools). Dr. Marini is currently focused on HIV, SARS-CoV-2, antimicrobial resistance, and the molecular aspects of the inflammatory process. Dr. Marini teaches two graduate courses: Topics in Precision Medicine and Public Health Informatics, and Computational Data Science for Epidemiology.

Education
2008-2012 PhD, Bioengineering. Thesis: “Qualitative and quantitative protein interaction prediction with machine learning”. Division of Bioengineering, Hong Kong University of Science and Technology, Hong Kong
2004-2007 MSc, Biomedical Engineering. Thesis: “Design of a classifier by coevolution of genetic algorithms and genetic programming”. Electrical, Computer and Biomedical Engineering department, University of Pavia, Italy
2000-2004 BSc, Biomedical Engineering. Thesis: “Bone tissue engineering, effects of mechanical shear stress on human osteoblast SAOS2”. Electrical, Computer and Biomedical Engineering department, University of Pavia, Italy

Professional Appointments
Assistant Professor 
08/2022-present Department of Epidemiology, University of Florida, Gainesville, FL, USA

Research Assistant Scientist 
01/2020-05/2020 Department of Epidemiology, University of Florida, Gainesville, FL, USA

Research Investigator 
08/2017-12/2019 Department of Computational Medicine and Bioinformatics and Department of Surgery, University of Michigan, Ann Arbor, MI, USA

Postdoctoral Fellow
12/2016-07/2017 Department of Elecrtical, Computer, and Biomedical Engineering, University of Pavia, Italy
11/2015-11/2016 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan
01/2013-10/2015 Department of Elecrtical, Computer, and Biomedical Engineering, University of Pavia, Italy

Scientific publications
50+ peer-reviewed journal papers, including Nature Bone Research, Bioinformatics, Briefings in Bioinformatics, The Journal of Clinical Investigation, and Developmental Cell;
5+ peer-reviewed conference papers; 20+ peer-reviewed conference abstracts; 1 book chapter; for a detailed list, see my CV (pdf) or my Google Scholar Profile.

Awards and Fellowships
02/2018 Elsevier Outstanding contribution in reviewing
11/2015 Japanese Society for the Promotion of Science Postdoctoral Fellowship
06/2015 Elsevier Outstanding contribution in reviewing
10/2011 Bioengineering Division Graduate Student Research Award, 1st ranked
03/2010 HKUST Overseas Research Award for PhD Students

Invited Talks and Lectures (extramural)
12/2021 The role of AI in the battle against antimicrobial resistance. Center for Health Technologies, University of Pavia
08/2021 When and how should I down-sample large viral datasets? A demo of TARDIS. Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology, virtual meeting
07/2020 Single-cell transcriptomics: General principles, databases and bioinformatic tools. Transversal Course on Big Data (postgraduate), University of Pavia
07/2020 Multi-sample, multi-condition analysis in scRNAseq data sets. ISMB 2020, BioinfoCore Workshop
06/2019 Enhancing data analysis by leveraging prior biomedical knowledge. Department of Epidemiology, University of Florida
06/2018 Data exploration of single-cell landscapes. Center for Health Technologies, University of Pavia
10/2017 Joint data integration for precision oncology. UFHCC Topics in Cancer seminar series, University of Florida
07/2017 miRNA Bioinformatics, sequence analysis and statistical processes. Training school "Omics technologies and bioinformatics application in ME/CFS research”, University of Pavia
01/2017 Investigating epileptogenesis with data fusion. University of Michigan
09/2016 Mining heterogeneous data sources to enhance association studies. University of Arizona
06/2016 Leveraging public databases for novel peptidase target discovery, University of Pavia
05/2011 Motif search, sequence alignment and Support Vector Regression for Dscam protein self- and hetero-binding affinity prediction. Institute of Biophysics, The Chinese Academy of Science, Beijing

Miscellanea
I am from Voghera, Italy, hometown of the Maserati brothers, and Valentino. I live in Gainesville.

Regarding my Italian name, I understand it does not sound familiar to non-native Italian speakers. That's fine, you can call me with the English "Simon", or properly pronounce my Italian name.
Just please please please do not call me with the Spanish "Simón".