Simone Marini

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

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Simone Marini

My research focuses on artificial intelligence applied to biology and medicine. I am particularly interested in data integration, i.e. in developing models by harvesting heterogeneous data from genomics, proteomics, medical literature, ontologies, and knowledgebases. I coordinated multi-disciplinary, international research teams comprising medical doctors, biologists, and engineers, across 8 institutions in Europe, Asia, and North America.

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
Research Assistant Professor 
06/2020-present Department of Epidemiology, Emergent Pathogens Intitute, University of Florida, Gainesville, FL, USA

Research Assistant Scientist 
01/2020-05/2020 Department of Epidemiology and Emergent Pathogens Intitute,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, 01/2013-11/2016 Department of Elecrtical, Computer, and Biomedical Engineering, University of Pavia, Italy
11/2015-11/2016 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan

Scientific publications
34 peer-reviewed journal papers, including Nature Bone Research, Bioinformatics, Briefings in Bioinformatics, The Journal of Clinical Investigation, and Developmental Cell;
4 peer-reviewed conference papers; 14 peer-reviewed conference abstracts; 1 book chapter; for a detailed list, see my CV (pdf)

Awards and Fellowships
02/2018 Elsevier Outstanding contribution in reviewing
11/2015-11/2016 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)
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, Gainesville, FL, USA
06/2018 Data exploration of single-cell landscapes. Center for Health Technologies, Pavia, Italy
10/2017 Joint data integration for precision oncology. UFHCC Topics in Cancer seminar series, University of Florida, Gainsville, FL, USA
07/2017 miRNA Bioinformatics, sequence analysis and statistical processes. Training school "Omics technologies and bioinformatics application in ME/CFS research”, University of Pavia, Pavia, Italy
01/2017 Investigating epileptogenesis with data fusion. University of Michigan, Ann Arbor, USA
09/2016 Mining heterogeneous data sources to enhance association studies. University of Arizona, Tucson, USA
06/2016 Leveraging on public databases for novel peptidase target discovery, University of Pavia, Pavia, Italy
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, China

Teaching and Mentoring Experiences
University of Florida, USA
01/2020-present Supervising 1 postdoc, 1 PhD student, 1 OSP
06/2020-present Instructor of record: Computational Epidmiology (postgraduate)

University of Michigan, USA
08/2017-12/2019 Supervised 1 postdoc, 2 postgraduates and 1 undergraduate students

Kyoto University, Japan
06/2016-09/2016 Supervised 1 undergraduate student

University of Pavia, Italy
12/2018 Lecturer: Introduction to Single cell RNA-seq data analysis (postgraduate)
09/2013-09/2015 Instructor of record: Medical Informatics (undergraduate)
09/2013-09/2015 Instructor of record: Automatic Learning in Medicine (graduate)
01/2013-11/2015, 12/2016-07/2017 Supervised 7 postgraduate and 5 undergraduate students

The Hong Kong University of Technology, China
01/2010-06/2010 Teaching assistant: Introduction to Bioengineering (postgraduate)

Service to Profession
Artificial Intelligence Advisor
12/2016-present enGenome srl, Pavia, Italy

Journal Reviewer
Bioinformatics, Molecules, Plos One, Journal of Biomedical Informatics, Computers in Biology and Medicine, Briefings in Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Journal of Biomedical and Health Informatics, Complex and intelligent Systems, Algorithms, Nature Scientific Reports, Molecules

Conference Reviewer
Artificial Intelligence in Medicine (AIME), AMIA joint Summits on TranslationalScience, IEEE International Conference on Healthcare Informatics (ICHC)

Conference Program Committee Member
IEEE International Symposium on Computer-Based Medical Systems (CBMS), IEEE ICTS4eHealth, ACM International Conference on Information and Knowledge Management (ACM-CIKM), ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

Non-Academic Work
09/2013-06/2014 High school math teacher, EU program to fight against school dropout. Centro Servizi Formazione, Pavia, Italy)
11/2007-06/2008 University tutor. Private one-to-one tutoring of undergraduate and graduate students. CESD, Pavia, Italy

Volunteering and community outreach
Introducing machine learning in high school
04/2017,11/2015, 05/2014, 03/2013 Introduction to data science and artificial intelligence. G. Galilei high school, Voghera, Italy.
01/2013-03/2013 Introduction to data science and artificial intelligence. Settore Istruzione e Politiche Giovanili, Pavia. Italy.

06/2020 Revised the Italian translation of the N95decon documents. N95decon is a scientific consortium for data-driven study of N95 filtering facepiece respirator decontamination.

Software developer
06/2014 VSO Poverty Alleviation, remote services. Development of a software to help managing dairy cooperatives. DCPUK, Bangladesh.

06/2007-12/2013 OMP, non-profit publishing house, the first copyleft (Creative Commons) publishing house in Italy.

Editor in Chief
08/2007-08/2008 Kronstadt, student-based local news magazine, Pavia, Italy. Monthly issued, city audience (2000 copies).

Front desk volunteer
01/2006-08/2008 City social services of Pavia, Italy. Helping immigrants to deal with local bureaucracy and job search.

I am from Voghera, Italy, hometown of the Maserati brothers, and Valentino. I lived in Pavia, Madrid, Hong Kong, Beijing, Kyoto, and Ann Arbor. I live in Gainesville.

Regarding my Italian name, I understand it does not sound familiar to non-Italian speakers. That's fine, you can call me "Simon" in the English way, or properly pronounce my Italian name. Just please please please do not call me "Simòn" :)