Iorio Group
Iorio group’s Apps, Tools and Computable Manuscripts
Lo Iorio Group lavora tra biologia, machine learning, statistica e teoria dell’informazione con l’obiettivo di comprendere e prevedere il ruolo delle alterazioni genomiche e dei tratti molecolari derivanti da altre -omiche nei processi patologici, nel ri-cablaggio dei circuiti biologici e il loro impatto sulla risposta terapeutica nei tumori umani e in altre malattie.
La nostra ricerca mira a migliorare la salute umana sviluppando algoritmi, strumenti di calcolo e nuovi metodi analitici per l’integrazione e l’analisi di set di dati di farmacogenomica e genomica funzionale, con l’obiettivo di identificare nuovi target terapeutici, biomarcatori e opportunità per il riposizionamento dei farmaci.
Con i nostri collaboratori, stiamo contribuendo alla creazione di una mappa completa di tutte le dipendenze genetiche e le vulnerabilità dei tumori umani e allo sviluppo di un’infrastruttura computazionale per tradurre questa mappa in linee guida per le fasi iniziali dello sviluppo di farmaci e per la medicina di precisione.
Sviluppiamo, implementiamo e gestiamo metodi bioinformatici e nuovi strumenti per la valutazione di modelli preclinici, la pre-elaborazione, l’analisi e la visualizzazione di dati provenienti da screening di genome-editing, per la correzione in silico di bias specifici in tali dati e per l’ottimizzazione di librerie di RNA a guida singola per screenings CRISPR-Cas9 aggregati e altri setting sperimentali.
Il nostro interesse è anche rivolto all’analisi di big-data, allo sviluppo di modelli predittivi biomedici basati su dati non biomedici, e a strategie informatiche efficienti per la randomizzazione vincolata utile a testare proprietà combinatorie in reti biologiche e dati genomici su larga scala.
Membri del gruppo
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Francesco Iorio
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Lorenzo Mathieu Brochier
PhD Student -
Ottavio Croci
Senior Data Scientist -
Letizia De Pietri
Postgraduate Intern -
Irene Fernández Rebollo
PhD Student -
Athanasios Oikonomou
Postdoc -
Flavio Passante
PhD Student -
Ludovica Proietti
Postdoc -
Nevenka Radic
Postdoc -
Vanessa Spagnolo
Senior Technician -
Gianluca Vozza
Postdoc
Pubblicazioni
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02/2026 - FEBS Letters
Genetic interactions, synthetic lethality and complexity in cancer vulnerability mapping—Insights and perspectives from the 2nd EuroDepMap symposium
Large-scale perturbational approaches have transformed cancer research, enabling systematic identification of tumour-specific dependencies and therapeutic vulnerabilities. However, many clinically relevant vulnerabilities arise from genetic interactions, including synthetic lethal and buffering relationships, and are shaped by cellular state, lineage and treatment history. Interpreting complex dependency landscapes increasingly relies on advanced computational and AI-based approaches integrating molecular, […]
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08/2025 - The EMBO Journal
Tau uptake by human neurons depends on receptor LRP1 and kinase LRRK2
Extracellular release and uptake of pathogenic forms of the microtubule-associated protein tau contribute to the pathogenesis of several neurodegenerative diseases, including Alzheimer’s disease. Defining the cellular mechanisms and pathways for tau entry to human neurons is essential to understanding tauopathy pathogenesis and enabling the rational design of disease-modifying therapeutics. Here, whole-genome, loss-of-function CRISPR screens in […]
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07/2025 - Nature Genetics
The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types
Metastatic uveal melanoma is an aggressive disease with limited effective therapeutic options. To comprehensively map monogenic and digenic dependencies, we performed CRISPR–Cas9 screening in ten extensively profiled human uveal melanoma cell line models. Analysis involved genome-wide single-gene and combinatorial paired-gene CRISPR libraries. Among our 76 uveal melanoma-specific essential genes and 105 synthetic lethal gene pairs, […]
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07/2025 - BMC Genomics
Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA
Background Understanding the molecular interactions between cells, tissues or organs is key to understanding the functioning of a biological system as a whole. Results Here, we propose crossWGCNA: a co-expression-based method that identifies highly interacting genes unbiasedly and that we employ to study stroma-epithelium communication in breast cancer. CrossWGCNA can be applied to bulk, single […]
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06/2025 - Molecular Therapy Methods and Clinical Development.
Impact of Culture Platform Transition on Adipose-derived Mesenchymal Stromal Cells Molecular Signatures: A Multi-Omics Analysis of Small-Scale versus Large-Scale Production
Mesenchymal stromal cells (MSCs) are being tested in numerous clinical trials, yet the limited progression of these trials to advanced stages indicates unresolved translational challenges. Expanding MSCs is a critical step in most therapeutic applications and bioreactor-based culture offers large-scale production compared to monolayer cultures. Nevertheless, since MSCs sense their microenvironment, it is crucial to […]
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