Gennaro Gambardella
Ricercatore in tenure track
- GSD 09/IBIO-01; SSD IBIO-01/A
- g.gambardella@ssmeridionale.it
- Via Mezzocannone, n.4-80134 (NA)
- Area Interdisciplinare Scientifico-Tecnologica
- ORCID: 0000-0001-7517-1347
- GithHub page URL
Bio
Gennaro Gambardella received his M.Sc. degree in Computer Science in November 2009 from the University of Naples “Federico II”.
In 2013, he completed his Ph.D. in Bioinformatics and Computational Biology at the University of Naples “Federico II”, working in the laboratory of Prof. Diego di Bernardo at the Telethon Institute of Genetics and Medicine (TIGEM).
He then joined King’s College London (UK) as a postdoctoral researcher in the laboratory of Dr. Francesca Ciccarelli, where he worked until August 2015. From September 2015 to April 2018, he returned to TIGEM as a postdoctoral researcher in the laboratory of Prof. Diego di Bernardo.
In May 2018, he was awarded a 2-year STAR (Sostegno Territoriale alle Attività di Ricerca) grant, followed by the prestigious My First AIRC Grant (MFAG) in 2020.
Since September 2020, he has been an independent researcher at TIGEM in Naples, where he leads his own laboratory. His research is highly interdisciplinary, bringing together a multidisciplinary team of biologists, mathematicians, oncologists, engineers, and computer scientists. Together, they integrate molecular genetics, data analysis, and theoretical modeling to study cancer biology and rare genetic diseases.
Research
Our group is actively engaged in multiple projects that leverage second- and third-generation sequencing platforms, along with the development of novel AI tools to analyze these data in the context of genetic diseases.
We are pioneering AI-driven approaches that utilize protein language models to enhance the diagnosis of genetic disorders and improve the prediction of germline mutation effects.
Additionally, we are implementing a Nanopore long-read sequencing strategy to reconstruct and characterize gene-editing techniques used in AAV and CRISPR-Cas9 genome therapy. Our goal is to assess their safety for clinical applications.
Our team is also developing an innovative bioinformatics approach to facilitate the identification and design of antisense oligonucleotide (ASO) therapies for patients with ultra-rare genetic diseases.
Selected Publications
1) Gambardella G. (2024). Deep-learning and shallow hybrid Nanopore-Illumina sequencing for affordable and accurate detection of germline variants. Preprint [link]
2) Pellecchia, S., Franchini, M., Viscido, G., Arnese, R., & Gambardella, G. (2024). Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer. Genome Medicine, 16(1). [ link]
3) Pellecchia, S., Viscido, G., Franchini, M., & Gambardella, G. (2023). Predicting drug response from single-cell expression profiles of tumours. BMC Medicine, 21(1). [ link]
4) Franchini, M., Pellecchia, S., Viscido, G., & Gambardella, G. (2023). Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data. NAR Genomics and Bioinformatics, 5(1). [ link]
5) Slovin, S., Carissimo, A., Panariello, F., Grimaldi, A., Bouche, V., Gambardella, G.*, & Cacchiarelli, D.* (2021). Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview. In RNA Bioinformatics (Vol. 2284, pp. 343–365). [ link]
6) Gambardella G. et al. (2020). GADD34 is a modulator of autophagy during starvation. Science Advances, 6(39). [link]
7) Gambardella G. et al. (2019). A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining. Frontiers in Genetics, 10. [link]
8) Gambardella G. et al. (2016). Patients with genetically heterogeneous synchronous colorectal cancer carry rare damaging germline mutations in immune-related genes. Nature Communications, 7(1). [ link]
9) Gambardella G. et al. (2017). The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. Nature Communications, 8(1). [ link]
10) Gambardella G. et al. (2016). MEGA-V: detection of variant gene sets in patient cohorts. Bioinformatics, 33(8), 1248–1249. [ link]
11) Gambardella G. et al. (2013). Differential Equation Based Reverse-Engineering Algorithms: Pros and Cons. In Gene Network Inference (pp. 49–61). Springer Science. [ link]
12) Gambardella G. et al. (2015). A reverse-engineering approach to dissect post-translational modulators of transcription factor’s activity from transcriptional data. BMC Bioinformatics, 16(1). [ link]
The full list of publications can be found on ORCID or Scholar profiles.
Corsi
A.a. 2023/2024 Complementi di Chimica e Biologia I modulo B ( Scuola Superiore Meridionale , primo anno, secondo semestre, 4 CFU, 32 ore)
A.a. 2022/2023 Bioinformatica e Biostatistica ( Scuola Superiore Meridionale , terzo anno, secondo semestre, 4 CFU, 32 ore)
News
Coming soon…
