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
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 [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
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]
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 [Scientific article]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 [Scientific article]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 [Scientific article]
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 [Scientific article]Open Access
Manfredi M.; Savojardo C.; Martelli P.L.; Casadio R., ISPRED-SEQ: Deep Neural Networks and Embeddings for Predicting Interaction Sites in Protein Sequences, «JOURNAL OF MOLECULAR BIOLOGY», 2023, 435, Article number: 167963 , pp. 167963 - 167971 [Scientific article]Open Access
Licata L.; Via A.; Turina P.; Babbi G.; Benevenuta S.; Carta C.; Casadio R.; Cicconardi A.; Facchiano A.; Fariselli P.; Giordano D.; Isidori F.; Marabotti A.; Martelli P.L.; Pascarella S.; Pinelli M.; Pippucci T.; Russo R.; Savojardo C.; Scafuri B.; Valeriani L.; Capriotti E., Resources and tools for rare disease variant interpretation, «FRONTIERS IN MOLECULAR BIOSCIENCES», 2023, 10, Article number: 1169109 , pp. 1 - 18 [Scientific article]Open Access
Martelossi J.; Forni G.; Iannello M.; Savojardo C.; Martelli P.L.; Casadio R.; Mantovani B.; Luchetti A.; Rota-Stabelli O., Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae), «INSECT MOLECULAR BIOLOGY», 2023, 23, pp. 118 - 131 [Scientific article]
Savojardo C.; Babbi G.; Baldazzi D.; Martelli P.L.; Casadio R., A glance into mthfr deficiency at a molecular level, «INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES», 2022, 23, Article number: 167 , pp. 1 - 9 [Scientific article]Open Access
