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, Article number: 17, pp. 1 - 15 [articolo]Open Access
Attafi, Omar Abdelghani; Clementel, Damiano; Kyritsis, Konstantinos; Capriotti, Emidio; Farrell, Gavin; Fragkouli, Styliani-Christina; Castro, Leyla Jael; Hatos, András; Lenaerts, Tom; Mazurenko, Stanislav; Mozaffari, Soroush; Pradelli, Franco; Ruch, Patrick; Savojardo, Castrense; Turina, Paola; Zambelli, Federico; Piovesan, Damiano; Monzon, Alexander Miguel; Psomopoulos, Fotis; Tosatto, Silvio C E, DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology, «GIGASCIENCE», 2024, 13, Article number: giae094, pp. 1 - 8 [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]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 [articolo]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 [articolo]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) [atti di convegno-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 [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
Nicolini F.; Martelossi J.; Forni G.; Savojardo C.; Mantovani B.; Luchetti A., Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps, «FRONTIERS IN ECOLOGY AND EVOLUTION», 2023, 11, Article number: 1046960, pp. 1 - 10 [articolo]Open Access
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]
Savojardo C.; Martelli P.L.; Casadio R., Finding functional motifs in protein sequences with deep learning and natural language models, «CURRENT OPINION IN STRUCTURAL BIOLOGY», 2023, 81, Article number: 102641, pp. 1 - 12 [articolo]Open Access
