Manfredi, Matteo; Vazzana, Gabriele; Babbi, Giulia; Bertolini, Elisa; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, Predicting the Pathogenicity of Human Protein Variants: Not Only a Matter of Residue Labeling, in: Methods in Molecular Biology, London, Humana Press Inc., 2025, pp. 189 - 199 (METHODS IN MOLECULAR BIOLOGY) [Chapter or essay]
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) [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) [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) [Abstract]
Manfredi, Matteo; Savojardo, Castrense; Iardukhin, Georgii; Salomoni, Davide; Costantini, Alessandro; Martelli, Pier Luigi; Casadio, Rita, Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and ESMFold Models of the Human Reference Proteome, «JOURNAL OF MOLECULAR BIOLOGY», 2024, 436, Article number: 168593 , pp. 168593 - 168600 [Scientific article]Open Access
Zhang, J.; Kinch, L.; Katsonis, P.; Lichtarge, O.; Jagota, M.; Song, Y. S.; Sun, Y.; Shen, Y.; Kuru, N.; Dereli, O.; Adebali, O.; Alladin, M. A.; Pal, D.; Capriotti, E.; Turina, M. P.; Savojardo, C.; Martelli, P. L.; Babbi, G.; Casadio, R.; Pucci, F.; Rooman, M.; Cia, G.; Tsishyn, M.; Strokach, A.; Hu, Z.; van Loggerenberg, W.; Roth, F. P.; Radivojac, P.; Brenner, S. E.; Cong, Q.; Grishin, N. V., Assessing predictions on fitness effects of missense variants in HMBS in CAGI6, «HUMAN GENETICS», 2024, 1, pp. 1 - 17 [Scientific article]Open Access
Null, Null; Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; Repo, Susanna; Hoskins, Roger A.; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; Kollipara, Naveen K.; Ly, Melissa; Neumann, Andrew J.; Pal, Lipika R.; Odell, Eric; Pandey, Gaurav; Peters-Petrulewicz, Robin C.; Srinivasan, Rajgopal; Yee, Stephen F.; Yeleswarapu, Sri Jyothsna; Zuhl, Maya; Adebali, Ogun; Patra, Ayoti; Beer, Michael A.; Hosur, Raghavendra; Peng, Jian; Bernard, Brady M.; Berry, Michael; Dong, Shengcheng; Boyle, Alan P.; Adhikari, Aashish; Chen, Jingqi; Hu, Zhiqiang; Wang, Robert; Wang, Yaqiong; Miller, Maximilian; Wang, Yanran; Bromberg, Yana; Turina, Paola; Capriotti, Emidio; Han, James J.; Ozturk, Kivilcim; Carter, Hannah; Babbi, Giulia; Bovo, Samuele; Di Lena, Pietro; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Cline, Melissa S.; De Baets, Greet; Bonache, Sandra; Díez, Orland; Gutiérrez-Enríquez, Sara; Ferná, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods, «GENOME BIOLOGY», 2024, 25, pp. 1 - 46 [Scientific article]Open Access
Manfredi, Matteo; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences, «BIO-PROTOCOL», 2024, 14, pp. 1 - 10 [Scientific article]Open Access
Stenton, Sarah L.; O'Leary, Melanie C.; Lemire, Gabrielle; VanNoy, Grace E.; DiTroia, Stephanie; Ganesh, Vijay S.; Groopman, Emily; O'Heir, Emily; Mangilog, Brian; Osei-Owusu, Ikeoluwa; Pais, Lynn S.; Serrano, Jillian; Singer-Berk, Moriel; Weisburd, Ben; Wilson, Michael W.; Austin-Tse, Christina; Abdelhakim, Marwa; Althagafi, Azza; Babbi, Giulia; Bellazzi, Riccardo; Bovo, Samuele; Carta, Maria Giulia; Casadio, Rita; Coenen, Pieter-Jan; De Paoli, Federica; Floris, Matteo; Gajapathy, Manavalan; Hoehndorf, Robert; Jacobsen, Julius O. B.; Joseph, Thomas; Kamandula, Akash; Katsonis, Panagiotis; Kint, Cyrielle; Lichtarge, Olivier; Limongelli, Ivan; Lu, Yulan; Magni, Paolo; Mamidi, Tarun Karthik Kumar; Martelli, Pier Luigi; Mulargia, Marta; Nicora, Giovanna; Nykamp, Keith; Pejaver, Vikas; Peng, Yisu; Pham, Thi Hong Cam; Podda, Maurizio S.; Rao, Aditya; Rizzo, Ettore; Saipradeep, Vangala G.; Savojardo, Castrense; Schols, Peter; Shen, Yang; Sivadasan, Naveen; Smedley, Damian; Soru, Dorian; Sri, Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project, «HUMAN GENOMICS», 2024, 18, Article number: 44 , pp. 1 - 25 [Scientific article]Open Access
Scicchitano, Daniel; Leuzzi, Daniela; Babbi, Giulia; Palladino, Giorgia; Turroni, Silvia; Laczny, Cédric Christian; Wilmes, Paul; Correa, Federico; Leekitcharoenphon, Pimlapas; Savojardo, Castrense; Luise, Diana; Martelli, Pierluigi; Trevisi, Paolo; Aarestrup, Frank Møller; Candela, Marco; Rampelli, Simone, Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment, «ANIMAL MICROBIOME», 2024, 6, Article number: 17 , pp. 1 - 15 [Scientific article]Open Access
Manfredi, Matteo; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, E-pRSA: Embeddings Improve the Prediction of Residue Relative Solvent Accessibility in Protein Sequence, «JOURNAL OF MOLECULAR BIOLOGY», 2024, 436, Article number: 168494 , pp. 1 - 7 [Scientific article]Open Access
Bertolini, Elisa; Babbi, Giulia; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, MultifacetedProtDB: a database of human proteins with multiple functions, «NUCLEIC ACIDS RESEARCH», 2024, 52, pp. 494 - 501 [Scientific article]Open Access
Daniel Scicchitano, Giulia Babbi, Giorgia Palladino, Silvia Turroni, Yitagele Terefe Mekonnen, Cédric Laczny, Paul Wilmes, Pimlapas Leekitcharoenphon, Andrea Castagnetti, Federica D'Amico, Patrizia Brigidi, Castrense Savojardo, Gerardo Manfreda, Pierluigi Martelli, Alessandra De Cesare, Frank Møller Aarestrup, Marco Candela, Simone Rampelli, Routes of dispersion of antibiotic resistance genes from the poultry farm system, «SCIENCE OF THE TOTAL ENVIRONMENT», 2024, 912, Article number: 169086 , pp. 1 - 12 [Scientific article]Open Access
Vazzana, Gabriele; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, Testing the alignment-based capability of embeddings on the GST superfamily classification: the role of protein length, in: 23rd European Conference on Computational Biology (ECCB 2024), 2024(atti di: 23rd European Conference on Computational Biology (ECCB 2024), Turku, Finland, 16-20 September 2024) [Poster]
Vazzana, Gabriele; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita, Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length, «MOLECULES», 2024, 29, Article number: 4616 , pp. 1 - 12 [Scientific article]
