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 [Scientific article]
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 [Scientific article]
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 [Scientific article]
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 [Scientific article]
Bovo, S; Ribani, A; Fanelli, F; Galimberti, G; Martelli, Pl; Trevisi, P; Bertolini, F; Bolner, M; Casadio, R; Dall'Olio, S; Gallo, M; Luise, D; Mazzoni, G; Schiavo, G; Taurisano, V; Zambonelli, P; Bosi, P; Pagotto, U; Fontanesi, L, Merging metabolomics and genomics provides a catalog of genetic factors that influence molecular phenotypes in pigs linking relevant metabolic pathways, «GENETICS SELECTION EVOLUTION», 2025, 57, Article number: 11 , pp. 1 - 27 [Scientific article]Open Access
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
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», 2024, Hum Gen (2024), Article number: 620793 , pp. 1 - 13 [Scientific article]
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, 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]
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
