Bioinformatics
The Bioinformatics team, established in 2023, is a dedicated group focused on enhancing the analytical capabilities of FPS. The members of the unit are Aldo Pastore and Paolo Aretini. This team plays a pivotal role in supporting FPS researchers across various domains by providing expertise in data analysis, statistical methodologies, machine learning models, and the management of the technological platform. Specifically, the Bioinformatics team is actively involved in most of the FPS research projects that require robust data analysis methodologies. The team collaborates both internally with most FPS members and externally with other researchers.
Beyond providing support services, the team leads bioinformatics research projects in the field of “Biomarkers identification”. In 2024, the Bioinformatics team successfully published the work “NADPH-Fluorescence Lifetime Imaging informed machine learning modelling reliably predicts Temozolomide responsiveness in Glioblastoma”. The project focuses on obtaining novel Glioblastoma biomarkers and implementing a NADPH-FLIM informed machine learning model to predict TMZ responsiveness. Additionally, the team led another bioinformatics research project, delving into the topic of Tumor Educated Platelets for early-diagnosis in Pancreatic Ductal Adenocarcinoma. This project is actually in its final stage and will produce a manuscript that will be submitted in 2025.
As regards external collaborations, the Bioinformatics Unit in 2024 joined the COST Action CA 21116 TRANSPAN for the European project “Identification of biological markers for prevention and translational medicine in pancreatic cancer”.
Selected Pubblications
Porto Cruz MF, Zucchini E, Vomero M, Pastore A, Vasilaș IG, Delfino E, Di Lauro M, Asplund M, Fadiga L, Stieglitz T. Bridging circuit modeling and signal analysis to understand the risk of crosstalk contamination in brain recordings. Nat Commun. 2025 May 22;16(1):4744. doi: 10.1038/s41467-025-59391-0. PMID: 40399305
Farinella R, Felici A, Peduzzi G, Testoni SGG, Costello E, Aretini P, Blazquez-Encinas R, Oz E, Pastore A, Tacelli M, Otlu B, Campa D, Gentiluomo M. From classical approaches to artificial intelligence, old and new tools for PDAC risk stratification and prediction. Semin Cancer Biol. 2025 Mar 26;112:71-92. doi: 10.1016/j.semcancer.2025.03.004. Epub ahead of print. PMID: 40147701.
Murray K, Oldfield L, Stefanova I, Gentiluomo M, Aretini P, O’Sullivan R, Greenhalf W, Paiella S, Aoki MN, Pastore A, Birch-Ford J, Rao BH, Uysal-Onganer P, Walsh CM, Hanna GB, Narang J, Sharma P, Campa D, Rizzato C, Turtoi A, Sever EA, Felici A, Sucularli C, Peduzzi G, Öz E, Sezerman OU, Van der Meer R, Thompson N, Costello E. Biomarkers, omics and artificial intelligence for early detection of pancreatic cancer. Semin Cancer Biol. 2025 Jun;111:76-88. doi: 10.1016/j.semcancer.2025.02.009. Epub 2025 Feb 20. PMID: 39986585.
Carli F, Di Chiaro P, Morelli M, Arora C, Bisceglia L, De Oliveira Rosa N, Cortesi A, Franceschi S, Lessi F, Di Stefano AL, Santonocito OS, Pasqualetti F, Aretini P, Miglionico P, Diaferia GR, Giannotti F, Liò P, Duran-Frigola M, Mazzanti CM, Natoli G, Raimondi F. Learning and actioning general principles of cancer cell drug sensitivity. Nat Commun. 2025 Feb 15;16(1):1654. doi:10.1038/s41467-025-56827-5. PMID: 39952993; PMCID: PMC11828915.
E. Degl’Innocenti, T.E. Poloni, V. Medici, F. Olimpico, F. Finamore, X. Profka, K. Bascarane, C. Morrone, A. Pastore, C. Escartin, LA McDonnell, MT Dell’Anno. Astrocytic centrin-2 expression in the entorhinal cortex correlates with Alzheimer’s disease severity. Glia. 2024 Dec;72(12):2158-2177. IF: 5.4
A Pastore, E Corradi, M Morelli, CM Mazzanti, P Aretini. NAD(P)H-Fluorescence Lifetime Imaging Informed Machine Learning Modelling Reliably Predicts Temozolomide Responsiveness in Glioblastoma. Journal of Biotech and Biomedicine, July 2024, Volume 7 Issue 3 359 IF: 5.3
Aretini P, Presciuttini S, Pastore A, Galli A, Panepinto S, Tancredi M, Ghilli M, Guglielmi C, Sidoti D, Congregati C, Caligo MA. The BRCA1 c.4096+1G>A Is a Founder Variant Which Originated in Ancient Times. Int J Mol Sci. 2023 Oct 24;24(21):15507. doi: 10.3390/ijms242115507. PMID: 37958491; PMCID: PMC10648645.
Pastore A, Tomassini A, Delis I, Dolfini E, Fadiga L, D’Ausilio A. Speech listening entails neural encoding of invisible articulatory features. Neuroimage. 2022 Dec 1; 264:119724. doi: 10.1016/j.neuroimage.2022.119724. Epub 2022 Oct 31. PMID: 36328272 Free article.