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]
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
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 [articolo]
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
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]
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 [articolo]Open Access
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 [articolo]
Mazwi, K. D.; Lekota, K. E.; Glover, B. A.; Kolo, F. B.; Hassim, A.; Rossouw, J.; Jonker, A.; Wojno, J. M.; Profiti, G.; Martelli, P. L.; Casadio, R.; Zilli, K.; Janowicz, A.; Marotta, F.; Garofolo, G.; van Heerden, H., Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa, «JOURNAL OF MICROBIOLOGY», 2024, 62, pp. 759 - 773 [articolo]
Madeo G.; Savojardo C.; Manfredi M.; Martelli P.L.; Casadio R., CoCoNat: a novel method based on deep learning for coiled-coil prediction, «BIOINFORMATICS», 2023, 39, Article number: btad495, pp. 1 - 8 [articolo]Open Access
S. Bovo,
G. Schiavo,
F. Fanelli,
A. Ribani,
F. Bertolini,
M. Gallo,
G. Galimberti,
Stefania Dall’Olio,
PL. Martelli,
R. Casadio,
U. Pagotto,
L. Fontanesi, Combined targeted and untargeted metabolomics in pigs coupled with genomic information: Towards a comprehensive genetic characterization of the pig metabolome, in: Proceedings of the 39th International Conference on Animal Genetics, Cape Town, South Africa (2023), 2023, pp. 15 - 16 (atti di: 39th International Conference on Animal Genetics, Cape Town, South Africa, 2-7 July 2023) [Contributo in Atti di convegno]
Schweke, H.; Xu, Q.; Tauriello, G.; Pantolini, L.; Schwede, T.; Cazals, F.; Lheritier, A.; Fernandez-Recio, J.; Rodriguez-Lumbreras, L. A.; Schueler-Furman, O.; Varga, J. K.; Jimenez-Garcia, B.; Reau, M. F.; Bonvin, A. M. J. J.; Savojardo, C.; Martelli, P. L.; Casadio, R.; Tubiana, J.; Wolfson, H. J.; Oliva, R.; Barradas-Bautista, D.; Ricciardelli, T.; Cavallo, L.; Venclovas, C.; Olechnovic, K.; Guerois, R.; Andreani, J.; Martin, J.; Wang, X.; Terashi, G.; Sarkar, D.; Christoffer, C.; Aderinwale, T.; Verburgt, J.; Kihara, D.; Marchand, A.; Correia, B. E.; Duan, R.; Qiu, L.; Xu, X.; Zhang, S.; Zou, X.; Dey, S.; Dunbrack, R. L.; Levy, E. D.; Wodak, S. J., Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study, «PROTEOMICS», 2023, 23, Article number: e2200323, pp. 1 - 21 [articolo]
