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]
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]
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]
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]
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]
Jain, Shantanu; Trinidad, Marena; Nguyen, Thanh Binh; Jones, Kaiya; Neto, Santiago Diaz; Ge, Fang; Glagovsky, Ailin; Jones, Cameron; Moran, Giankaleb; Wang, Boqi; Rahimi, Kobra; Çalıcı, Sümeyra Zeynep; Cedillo, Luis R.; Berardelli, Silvia; Özden, Buse; Chen, Ken; Katsonis, Panagiotis; Williams, Amanda; Lichtarge, Olivier; Rana, Sadhna; Pradhan, Swatantra; Srinivasan, Rajgopal; Sajeed, Rakshanda; Joshi, Dinesh; Faraggi, Eshel; Jernigan, Robert; Kloczkowski, Andrzej; Xu, Jierui; Song, Zigang; Özkan, Selen; Padilla, Natàlia; de la Cruz, Xavier; Acuna-Hidalgo, Rocio; Grafmüller, Andrea; Barrón, Laura T. Jiménez; Manfredi, Matteo; Savojardo, Castrense; Babbi, Giulia; Martelli, Pier Luigi; Casadio, Rita; Sun, Yuanfei; Zhu, Shaowen; Shen, Yang; Pucci, Fabrizio; Rooman, Marianne; Cia, Gabriel; Raimondi, Daniele; Hermans, Pauline; Kwee, Sofia; Chen, Ella; Astore, Courtney; Kamandula, Akash; Pejaver, Vikas; Ramola, Rashika; Velyunskiy, Michelle; Zeiberg, Daniel; Mishra, Reet; Sterling, Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A, «HUMAN GENETICS», 2025, 144, pp. 295 - 308 [articolo]
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 [articolo]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 [articolo]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 [articolo]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 [articolo]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 [articolo]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 [articolo]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 [articolo]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 [articolo]
