Manfredi, M.; Vazzana, G.; Savojardo, C.; Martelli, P. L.; Casadio, R., Alpha&ESMhFolds: An Updated Web Server for the Comparison, Evaluation, and Annotation of Human AlphaFold2 and ESMFold Models, «JOURNAL OF MOLECULAR BIOLOGY», in corso di stampa, in press, Article number: 169663, pp. 1 - 9 [articolo]
Vazzana, Gabriele; Martelli, Pier Luigi; Casadio, Rita, Can Human Canonical Glutathione S-Transferases Act as RNA-Binding Proteins?, «JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY», 2026, 25, pp. 627 - 640 [articolo]
Vazzana, G.; Manfredi, M.; Savojardo, C.; Martelli, P. L.; Casadio, R., Embedding-Based Alignments Capture Structural and Sequence Domains of Distantly Related Multifunctional Human Proteins, «COMPUTATION», 2026, 14, Article number: 25, pp. 1 - 13 [articolo]Open Access
Luise, D.; Palladino, G.; Correa, F.; Palumbo, F.; Graziosi, M. V.; Calvo, E. Perez; Litta, G.; Scicchitano, D.; Babbi, G.; Castagnetti, A.; Rampelli, S.; Candela, M.; Martelli, P. L.; Trevisi, P., 133. Farming conditions and dietary interventions can affect the health and performance of pigs from weaning to growing via modulation of the microbial profile and its metabolism, in: Proceedings of the 16th International Symposium on Digestive Physiology of Pigs (DPP2025), «ANIMAL. SCIENCE PROCEEDINGS», 2025, 16, pp. 370 - 370 (atti di: 16th International Symposium on Digestive Physiology of Pigs (DPP2025), Lake Geneva, WI, USA, 20/05/2025 - 23/05/2025) [atti di convegno-abstract]
Trevisi, P.; Luise, D.; Palladino, G.; Scicchitano, D.; Babbi, G.; Castagnetti, A.; Rampelli, S.; Candela, M.; Martelli, P. L.; Correa, F., 151. EU Circles project: Multi-kingdom microbiota analysis identified distinct microbial networks associated with the supplementation of a blend of chestnut and quebracho extracts, impacting the metabolism of nursery pigs reared under different farming conditions, in: Proceedings of the 16th International Symposium on Digestive Physiology of Pigs (DPP2025), «ANIMAL. SCIENCE PROCEEDINGS», 2025, 16, pp. 378 - 378 (atti di: 16th International Symposium on Digestive Physiology of Pigs (DPP2025), Lake Geneva, WI, USA, 20/05/2025 - 23/05/2025) [atti di convegno-abstract]
Correa, F.; Luise, D.; Palladino, G.; Palumbo, F.; Scicchitano, D.; Babbi, G.; Castagnetti, A.; Soverini, M.; Rampelli, S.; Candela, M.; Martelli, P. L.; Trevisi, P., 4. EU circles project: machine learning approaches to multi-kingdom gut microbiota reveal key predictors of piglet growth during the nursery phase, in: Proceedings of the 16th International Symposium on Digestive Physiology of Pigs (DPP2025), «ANIMAL. SCIENCE PROCEEDINGS», 2025, 16, pp. 308 - 309 (atti di: 16th International Symposium on Digestive Physiology of Pigs (DPP2025), Lake Geneva, WI, USA, 20/05/2025 - 23/05/2025) [atti di convegno-abstract]
Podda, Marco; Savojardo, Castrense; Luigi Martelli, Pier; Casadio, Rita; Sîrbu, Alina; Priami, Corrado; Brozzi, Alessandro, A descriptor-free machine learning framework to improve antigen discovery for bacterial pathogens, «PLOS ONE», 2025, 20, Article number: e0323895, pp. 1 - 22 [articolo]Open Access
Manfredi, Matteo; Vazzana, Gabriele; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation, «COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL», 2025, 27, pp. 461 - 466 [articolo]Open Access
Turina, P.; Petrosino, M.; Enriquez Sandoval, C. A.; Novak, L.; Pasquo, A.; Alexov, E.; Alladin, M. A.; Ascher, D. B.; Babbi, G.; Bakolitsa, C.; Casadio, R.; Cheng, J.; Fariselli, P.; Folkman, L.; Kamandula, A.; Katsonis, P.; Li, M.; Li, D.; Lichtarge, O.; Mahmud, S.; Martelli, P. L.; Pal, D.; Panday, S. K.; Pires, D. E. V.; Portelli, S.; Pucci, F.; Rodrigues, C. H. M.; Rooman, M.; Savojardo, C.; Schwersensky, M.; Shen, Y.; Strokach, A. V.; Sun, Y.; Woo, J.; Radivojac, P.; Brenner, S. E.; Chiaraluce, R.; Consalvi, V.; Capriotti, E., Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges, «HUMAN GENETICS», 2025, Hum Gen (2025), Article number: 245403, pp. 1 - 16 [articolo]
Turina, P.; Dal Cortivo, G.; Enriquez Sandoval, C. A.; Alexov, E.; Ascher, D. B.; Babbi, G.; Bakolitsa, C.; Casadio, R.; Fariselli, P.; Folkman, L.; Kamandula, A.; Katsonis, P.; Li, D.; Lichtarge, O.; Martelli, P. L.; Panday, S. K.; Pires, D. E. V.; Portelli, S.; Pucci, F.; Rodrigues, C. H. M.; Rooman, M.; Savojardo, C.; Schwersensky, M.; Shen, Y.; Strokach, A. V.; Sun, Y.; Woo, J.; Radivojac, P.; Brenner, S. E.; Dell'Orco, D.; Capriotti, E., Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges, «HUMAN GENETICS», 2025, Hum Gen (2024), Article number: 620793, pp. 113 - 125 [articolo]
Aspromonte, M. C.; Del Conte, A.; Zhu, S.; Tan, W.; Shen, Y.; Zhang, Y.; Li, Q.; Wang, M. H.; Babbi, G.; Bovo, S.; Martelli, P. L.; Casadio, R.; Althagafi, A.; Toonsi, S.; Kulmanov, M.; Hoehndorf, R.; Katsonis, P.; Williams, A.; Lichtarge, O.; Xian, S.; Surento, W.; Pejaver, V.; Mooney, S. D.; Sunderam, U.; Srinivasan, R.; Murgia, A.; Piovesan, D.; Tosatto, S. C. E.; Leonardi, E., CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs), «HUMAN GENETICS», 2025, 144, pp. 227 - 242 [articolo]Open Access
Rastogi, Ruchir; Chung, Ryan; Li, Sindy; Li, Chang; Lee, Kyoungyeul; Woo, Junwoo; Kim, Dong-Wook; Keum, Changwon; Babbi, Giulia; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Chennen, Kirsley; Weber, Thomas; Poch, Olivier; Ancien, François; Cia, Gabriel; Pucci, Fabrizio; Raimondi, Daniele; Vranken, Wim; Rooman, Marianne; Marquet, Céline; Olenyi, Tobias; Rost, Burkhard; Andreoletti, Gaia; Kamandula, Akash; Peng, Yisu; Bakolitsa, Constantina; Mort, Matthew; Cooper, David N.; Bergquist, Timothy; Pejaver, Vikas; Liu, Xiaoming; Radivojac, Predrag; Brenner, Steven E.; Ioannidis, Nilah M., Critical assessment of missense variant effect predictors on disease-relevant variant data, «HUMAN GENETICS», 2025, 144, Article number: 101213, pp. 281 - 293 [articolo]
Savojardo, Castrense; Manfredi, Matteo; Martelli, Pier Luigi; Casadio, Rita, DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning, «BIOINFORMATICS», 2025, 41, Article number: btaf019, pp. 1 - 7 [articolo]Open Access
Correa, F.; Luise, D.; Palladino, G.; Estelle, J.; Turroni, S.; Scicchitano, D.; Babbi, G.; Rampelli, S.; Candela, M.; Martelli, P. L.; Stefanelli, C.; Perez-Calvo, E.; Trevisi, P., Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing, «ANIMAL MICROBIOME», 2025, 7, Article number: 110, pp. 1 - 23 [articolo]Open Access
Chen, Yile; Lee, Kyoungyeul; Woo, Junwoo; Kim, Dong-wook; Keum, Changwon; Babbi, Giulia; Casadio, Rita; Martelli, Pier Luigi; Savojardo, Castrense; Manfredi, Matteo; Shen, Yang; Sun, Yuanfei; Katsonis, Panagiotis; Lichtarge, Olivier; Pejaver, Vikas; Seward, David J.; Kamandula, Akash; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; O'Donnell-Luria, Anne; Mooney, Sean D.; Jain, Shantanu, Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers, «HUMAN GENETICS», 2025, 1, pp. 1 - 16 [articolo]Open Access
