Francesco Napolitano – Curriculum Vitae
University of Sannio – Department of Science and Technology
Via dei Mulini 74, 82100 Benevento, Italy
📧 francesco.napolitano@unisannio.it · ☎ +39 0824 305131
Last update: October 28, 2026

Short Bio
Francesco Napolitano is Associate Professor of Bioinformatics at the University of Sannio, Benevento. He also chairs the Degree Program Councils in Biotechnology and in Biotechnology for Health. His background is in Computer Science, specializing in Data Analysis and Machine Learning. His research applies Artificial Intelligence and Machine Learning to omics data, including transcriptomics at bulk, single-cell and spatial resolution. The main applications are drug discovery, drug repositioning and disease modeling. Before joining the University of Sannio, he worked at the Telethon Institute of Genetics and Medicine (TIGEM) in Naples and at King Abdullah University of Science and Technology (KAUST). He has developed and published software tools for data analysis and reproducible research. He has authored 66 scientific publications (H-index 17 on Scopus, 19 on Google Scholar).

Institutional Roles
Since 2025: Chair of the Bachelor’s Degree Program Council in Biotechnology and of the Master’s Degree Program Council in Biotechnology for Health, University of Sannio.
Since 2022: Member of the Faculty Board of the Ph.D. Program in Science and Technology for Environment and Health.
2022 – 2025: Elected member of the Research Committee, Department of Science and Technology.
Since 2021: Co-director of the Bioinformatics Laboratory, University of Sannio.

Current Position
Dec 2024 – present: Associate Professor of Bioinformatics, University of Sannio, Department of Science and Technology.

Previous Positions
Dec 2021 – Dec 2024: Tenure-track Assistant Professor (RTD-b), University of Sannio, Department of Science and Technology.
Jul – Dec 2022: Research Collaborator, BIOGEM S.c.a r.l., Ariano Irpino (AV), Italy. PON project “MEDIA – High-efficiency diagnostic methods for osteo-articular patients”.
Mar 2019 – Dec 2021: Research Scientist, King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Saudi Arabia.
Nov 2012 – Mar 2019: Senior Postdoctoral Researcher, Telethon Institute of Genetics and Medicine (TIGEM), Systems and Synthetic Biology Lab, Naples.
Apr – Oct 2012: Research Fellow, University of Salerno, Department of Computer Science.
May 2010 – Mar 2012: Postdoctoral Researcher, “G. d’Annunzio” University of Chieti-Pescara, Department of Medical and Biological Sciences.
Nov 2006 – Mar 2007: Research Collaborator, University of Salerno, in collaboration with Alenia Aeronautica S.p.A.

Education and Qualifications
2023: National Scientific Qualification (ASN) as Associate Professor, field 09/H1 (Information Processing Systems).
2021: National Scientific Qualification (ASN) as Associate Professor, field 01/B1 (Computer Science).
2017: Eligibility for a Researcher position (first runner-up), National Research Council (CNR) – Institute for Applied Mathematics (IAC), Naples.
Ph.D. in Computer Science (2009), University of Salerno. Thesis: Fast Search in Chemical Databases using Tanimoto Similarity Bounds and Clustering Techniques. Advisors: Prof. R. Tagliaferri, Prof. P. Baldi.
M.Sc. in Computer Science (2006), University of Salerno, Modeling curriculum. Thesis: An Interactive Approach to Hierarchical Clustering.
Summer Schools: 2008, Universidad San Pablo – CEU, Madrid, Spain (Advanced Statistics and Data Mining); 2007, University of Catania (Lipari International Summer School on Bioinformatics and Computational Biology).
Research Visits: Mar – Jun 2012, Visiting Postdoctoral Researcher, Institute of Biotechnology, University of Helsinki, Finland (HPC-Europa program); Mar – Sep 2009, Visiting Ph.D. Student, Institute for Genomics and Bioinformatics, University of California, Irvine, USA.

Projects, Fellowships and Funding
2023 – 2026: Research Unit Leader, PRIN 2022 (Italian Ministry of University and Research, MUR), “RegenAI”: Drug repositioning for Retinitis Pigmentosa by an artificial intelligence application to single-cell transcriptomics. €97,715 to the Research Unit, out of €240,000 total.
2024 – 2025: Collaborator, PNRR (MUR), MNESYS Extended Partnership, “ZINERgY” project: ZInc signal modulation in cell models of NEuRoinflammation and brain injurY. Coordinator: Prof. L. M. T. Canzoniero.
2021 – 2022: Co-PI, KAUST: A deconfounding adversarial classifier to encode gene expression profiles for drug repurposing ($50,000).
2019 – 2020: Co-PI, KAUST: Deep learning methods for the identification of drugs that inhibit breast cancer stem cell proliferation by inducing differentiation ($100,000).
2019: Postdoctoral Fellowship, Fondazione Umberto Veronesi: Computational identification of drugs that inhibit breast cancer stem cell proliferation by inducing differentiation.
2012: HPC-Europa Fellowship (European Union) for the research visit to the University of Helsinki.
2012: Research Fellowship, University of Salerno: Integration of bioinformatic data by means of Machine Learning and Computational Intelligence techniques.

Awards and Honors
2013: Travel Award, Broad Institute of MIT and Harvard, for participation in the LINCS Data Forum, Boston.

Teaching
2021 – present: University of Sannio
– Computer Skills and Principles of Bioinformatics (B.Sc. in Biotechnology)
– Principles of Bioinformatics with Laboratory (B.Sc. in Biological Sciences for Clinical Diagnostics)
– Molecular and Computational Biology, module B: Computational Biology; Computational Medicine and Advanced Biotechnology Laboratory, module A: Bioinformatics (M.Sc. in Biotechnology for Health)
– Bioinformatics (M.Sc. in Biology)
– Human Genetics, module C: Applications of Bioinformatics (inter-university M.D. program in High-Technology Medicine and Surgery, with the University of Naples Federico II)
– Foundations of Artificial Intelligence for Biomedical and Geophysical Image Analysis (Ph.D. in Science and Technology for Environment and Health)
2020: University of Naples Federico II, Ph.D. course lectures.
2017 – 2018: TIGEM, lecturer of Systems Biology and Functional Genomics for the SEMM Ph.D. program.
2014: University of Bologna, lecturer at the Summer School Chemical and genomics-based strategies in the discovery of novel drug targets.
2007 – 2011: University of Salerno, assistant lecturer for Computational Biology, Computer Architectures and Neural Networks. Tutor and lecturer at the Erasmus IP School Microarray Data Analysis (2010, 2011).

Thesis Supervision
2025: University of Sannio: M.Sc. in Biotechnology for Health (1 thesis); B.Sc. in Biotechnology (1 thesis); B.Sc. in Biological Sciences (1 thesis).
2023: University of Sannio, B.Sc. theses in Bioinformatics (2 theses).
2022: University of Sannio, B.Sc. thesis in Bioinformatics; KAUST, M.Sc. in Computer Science.
2017: SEMM – European School of Molecular Medicine, Ph.D. in Systems Medicine (co-supervisor).
2013: University of Naples Federico II, M.Sc. in Computer Science; University of Salerno, M.Sc. in Computer Science (co-supervisor).
2012: University of Salerno, M.Sc. in Computer Science (2 theses); B.Sc. in Computer Science.
2011: University of Salerno, B.Sc. in Computer Science (2 theses).

Editorial and Review Activities
Associate Editor: Journal of Translational Medicine – Medical Bioinformatics Section (since 2019); Frontiers in Neurogenomics (since 2021); Frontiers in Artificial Intelligence (since 2022); Frontiers in Big Data (since 2022).
Reviewer for scientific journals (since 2011): Bioinformatics, Cell Systems, Journal of Cheminformatics, npj Systems Biology and Applications, Scientific Reports, PLOS One, BMC Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Drug Discovery Today, Hepatology, Molecular Biosystems, IEEE Transactions on Cybernetics, Neural Computing and Applications, and others.
Grant review: Netherlands Organisation for Scientific Research (2017–2018); Innovation and Technology Commission, Hong Kong (2017–2018).

Invited Talks
2018: King Abdullah University of Science and Technology (KAUST), Saudi Arabia. Black- and white-box approaches to omics data analysis in Drug Discovery.
2017: International School for Advanced Studies (SISSA), Trieste, Italy. Comparative Transcriptomics – pushing Data Analysis towards explaining rather than predicting cellular mechanisms.
2016: Microsoft Research & University of Trento – COSBI, Rovereto, Italy. Transcriptomic Tools for Drug Repositioning and Biological Investigation.
2015: Senate of the Italian Republic, Rome, Italy. New technologies in rare disease research (public conference on orphan diseases).
2014: Italian Association of Neuroimmunology, Bergamo, Italy. Drug repositioning strategies: candidate selection through Machine Learning.

Conference Organization
2024: General Chair of the 19th edition of Computational Intelligence methods for Bioinformatics and Biostatistics(CIBB), University of Sannio.
2008, 2011: CIBB, Local Organizing Committee (University of Salerno).
2010, 2011: Erasmus IP School Microarray Data Analysis, Local Organizing Committee (University of Salerno).

Publications
66 publications: 41 journal articles, 22 conference papers, 1 book chapter, 2 preprints.
H-index: 17 (Scopus), 19 (Google Scholar). Citations: 1,258 (Scopus), 1,774 (Google Scholar). Data as of August 2026.

Scientific Software
gep2pep: R package (Bioconductor) that converts gene expression profiles into pathway-based expression profiles and supports Drug Set Enrichment Analysis.
gene2drug / DSEA: tools for pathway-based drug repositioning and for studying drug mode of action.
repo: R package (CRAN) for data-centered management of bioinformatic pipelines.
pyLeaf: Python package (PyPI) for defining data analysis pipelines as ASCII-art graphs.
MIDA: Matlab GUI toolbox for interactive dendrogram analysis (hierarchical clustering).