CASIRAGHI, ELENA
CASIRAGHI, ELENA
Dipartimento di Informatica Giovanni Degli Antoni
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation
2025 M. Nicolini, E. Saitto, R.E. Jimenez Franco, E. Cavalleri, A.J. Galeano Alfonso, D. Malchiodi, A. Paccanaro, P.N. Robinson, E. Casiraghi, G. Valentini
Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing
2025 J. Gliozzo, M. Soto-Gomez, V. Guarino, A. Bonometti, A. Cabri, E. Cavalleri, J. Reese, P.N. Robinson, M. Mesiti, G. Valentini, E. Casiraghi
SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning
2024 E. Cavalleri, M. Soto Gomez, A. Pashaeibarough, D. Malchiodi, J.H. Caufield, J.T. Reese, C. Mungall, P.N. Robinson, E. Casiraghi, G. Valentini, M. Mesiti
Fine-Tuning of Conditional Transformers Improves the Generation of Functionally Characterized Proteins
2024 M. Nicolini, D. Malchiodi, A. Cabri, E. Cavalleri, M. Mesiti, A. Paccanaro, P.N. Robinson, J. Reese, E. Casiraghi, G. Valentini
Fine-tuning of Conditional Transformers Improves the Generalization of Functionally Characterized Proteins
2024 M. Nicolini, D. Malchiodi, A. Cabri, E. Cavalleri, M. Mesiti, A. Paccanaro, N. Robinson Peter, J. Reese, E. Casiraghi, G. Valentini
The Use of Artificial Intelligence in Head and Neck Cancers: A Multidisciplinary Survey
2024 C. Giannitto, G. Carnicelli, S. Lusi, A. Ammirabile, E. Casiraghi, A. De Virgilio, A. Esposito, D. Farina, F. Ferreli, C. Franzese, G.M. Frigerio, A. Lo Casto, L. Malvezzi, L. Lorini, A. Othman, L. Preda, M. Scorsetti, P. Bossi, G. Mercante, G. Spriano, L. Balzarini, M. Francone
Spatial distribution of tumour immune infiltrate predicts outcomes of patients with high-risk soft tissue sarcomas after neoadjuvant chemotherapy
2024 S. Pasquali, V. Vallacchi, L. Lalli, P. Collini, M. Barisella, C. Romagosa, S. Bague, J.M. Coindre, A.P. Dei Tos, E. Palmerini, V. Quagliuolo, J. Martin-Broto, A. Lopez-Pousa, G. Grignani, J.-. Blay, R.D. Beveridge, E. Casiraghi, S. Brich, S.L. Renne, L. Bergamaschi, B. Vergani, M. Sbaraglia, P.G. Casali, L. Rivoltini, S. Stacchiotti, A. Gronchi
Cancer-associated foam cells hamper protective T cell immunity and favor tumor progression in human colon carcinogenesis
2024 E. Daveri, B. Vergani, L. Lalli, G. Ferrero, E. Casiraghi, A. Cova, M. Zorza, V. Huber, M. Gariboldi, P. Pasanisi, S. Guarrera, D. Morelli, F. Arienti, M. Vitellaro, P.A. Corsetto, A.M. Rizzo, M. Stroscia, P. Frati, V. Lagano, L. Cattaneo, G. Sabella, B.E. Leone, M. Milione, L. Sorrentino, L. Rivoltini
An ontology-based knowledge graph for representing interactions involving RNA molecules
2024 E. Cavalleri, A. Cabri, M. Soto-Gomez, S. Bonfitto, P. Perlasca, J. Gliozzo, T.J. Callahan, J. Reese, P.N. Robinson, E. Casiraghi, G. Valentini, M. Mesiti
Chemical Reaction Enhanced Graph Learning for Molecule Representation
2024 A. Li, E. Casiraghi, J. Rousu
Unbiased clustering and molecular characterisation of novel metabolic phenotypes in a heart failure cohort
2024 E. Esenkova, T. Koeck, G. Valentini, P. Wild, E. Casiraghi, E. Araldi
RNA Knowledge Graph Analysis via Embedding Methods
2024 F. Torgano, E. Cavalleri, J. Gliozzo, F. Stacchietti, E. Saitto, M. Mesiti, E. Casiraghi, G. Valentini
Association of post-COVID phenotypic manifestations with new-onset psychiatric disease
2024 B. Coleman, E. Casiraghi, T.J. Callahan, H. Blau, L.E. Chan, B. Laraway, K.B. Clark, Y. Re’Em, K.R. Gersing, K.J. Wilkins, N.L. Harris, G. Valentini, M.A. Haendel, J.T. Reese, P.N. Robinson
Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning
2024 L. Cappelletti, L. Rekerle, T. Fontana, P. Hansen, E. Casiraghi, V. Ravanmehr, C.J. Mungall, J. Yang, L. Spranger, G. Karlebach, J.H. Caufield, L. Carmody, B. Coleman, T. Oprea, J. Reese, G. Valentini, P.N. Robinson
An open source knowledge graph ecosystem for the life sciences
2024 T.J. Callahan, I.J. Tripodi, A.L. Stefanski, L. Cappelletti, S.B. Taneja, J.M. Wyrwa, E. Casiraghi, N.A. Matentzoglu, J. Reese, J.C. Silverstein, C.T. Hoyt, R.D. Boyce, S.A. Malec, D.R. Unni, M.P. Joachimiak, P.N. Robinson, C.J. Mungall, E. Cavalleri, T. Fontana, G. Valentini, M. Mesiti, L.A. Gillenwater, B. Santangelo, N.A. Vasilevsky, R. Hoehndorf, T.D. Bennett, P.B. Ryan, G. Hripcsak, M.G. Kahn, M. Bada, W.A. Baumgartner, L.E. Hunter
An expectation-maximization framework for comprehensive prediction of isoform-specific functions
2023 G. Karlebach, L. Carmody, J.C. Sundaramurthi, E. Casiraghi, P. Hansen, J. Reese, C.J. Mungall, G. Valentini, P.N. Robinson
Towards the Construction of an RNA-based Knowledge Graph
2023 E. Cavalleri, S. Bonfitto, A. Cabri, J. Gliozzo, P. Perlasca, M. Soto-Gomez, G. Trucco, E. Casiraghi, G. Valentini, M. Mesiti
The promises of large language models for protein design and modeling
2023 G. Valentini, D. Malchiodi, J. Gliozzo, M. Mesiti, M. Soto Gomez, A. Cabri, J. Reese, E. Casiraghi, P.N. Robinson
A Semi-Automatic Approach for feeding Bio-Medical KGs
2023 S. Bonfitto, M. Dileo, E. Casiraghi, S.T. Gaito, G. Valentini, M. Mesiti
Predictive models of long COVID
2023 B. Antony, H. Blau, E. Casiraghi, J.J. Loomba, T.J. Callahan, B.J. Laraway, K.J. Wilkins, C.C. Antonescu, G. Valentini, A.E. Williams, P.N. Robinson, J.T. Reese, T.M. Murali