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», in corso di stampa, 14, pp. 1 - 10 [Scientific article]
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», in corso di stampa, 23, Article number: 2200323 , pp. 1 - 21 [Scientific article]
Rachele Corti, Elisabetta Piazza, Enrico Nicola Armelloni, Alice Ferrari, Audrey J. Geffen, Gregory E. Maes, Francesco Masnadi, Castrense Savojardo, Giuseppe Scarcella, Marco Stagioni, Fausto Tinti, Alex Zemella, Alessia Cariani, A multidisciplinary approach to describe population structure of Solea solea in the Mediterranean Sea, «FRONTIERS IN MARINE SCIENCE», 2024, 11, pp. 1 - 21 [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; Fernández, Alejandro; Montalban, Gemma; Ootes, Lars; Özkan, Selen; Padilla, Natàlia; Riera, Casandra; De la Cruz, Xavier; Diekhans, Mark; Huwe, Peter J.; Wei, Qiong; Xu, Qifang; Dunbrack, Roland L.; Gotea, Valer; Elnitski, Laura; Margolin, Gennady; Fariselli, Piero; Kulakovskiy, Ivan V.; Makeev, Vsevolod J.; Penzar, Dmitry D.; Vorontsov, Ilya E.; Favorov, Alexander V.; Forman, Julia R.; Hasenahuer, Marcia; Fornasari, Maria S.; Parisi, Gustavo; Avsec, Ziga; Çelik, Muhammed H.; Nguyen, Thi Yen Duong; Gagneur, Julien; Shi, Fang-Yuan; Edwards, Matthew D.; Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Gifford, David K.; Göke, Jonathan; Zaucha, Jan; Gough, Julian; Ritchie, Graham R. S.; Frankish, Adam; Mudge, Jonathan M.; Harrow, Jennifer; Young, Erin L.; Yu, Yao; Huff, Chad D.; Murakami, Katsuhiko; Nagai, Yoko; Imanishi, Tadashi; Mungall, Christopher J.; Jacobsen, Julius O. B.; Kim, Dongsup; Jeong, Chan-Seok; Jones, David T.; Li, Mulin Jun; Guthrie, Violeta Beleva; Bhattacharya, Rohit; Chen, Yun-Ching; Douville, Christopher; Fan, Jean; Kim, Dewey; Masica, David; Niknafs, Noushin; Sengupta, Sohini; Tokheim, Collin; Turner, Tychele N.; Yeo, Hui Ting Grace; Karchin, Rachel; Shin, Sunyoung; Welch, Rene; Keles, Sunduz; Li, Yue; Kellis, Manolis; Corbi-Verge, Carles; Strokach, Alexey V.; Kim, Philip M.; Klein, Teri E.; Mohan, Rahul; Sinnott-Armstrong, Nicholas A.; Wainberg, Michael; Kundaje, Anshul; Gonzaludo, Nina; Mak, Angel C. Y.; Chhibber, Aparna; Lam, Hugo Y. K.; Dahary, Dvir; Fishilevich, Simon; Lancet, Doron; Lee, Insuk; Bachman, Benjamin; Katsonis, Panagiotis; Lua, Rhonald C.; Wilson, Stephen J.; Lichtarge, Olivier; Bhat, Rajendra R.; Sundaram, Laksshman; Viswanath, Vivek; Bellazzi, Riccardo; Nicora, Giovanna; Rizzo, Ettore; Limongelli, Ivan; Mezlini, Aziz M.; Chang, Ray; Kim, Serra; Lai, Carmen; O’Connor, Robert; Topper, Scott; van den Akker, Jeroen; Zhou, Alicia Y.; Zimmer, Anjali D.; Mishne, Gilad; Bergquist, Timothy R.; Breese, Marcus R.; Guerrero, Rafael F.; Jiang, Yuxiang; Kiga, Nikki; Li, Biao; Mort, Matthew; Pagel, Kymberleigh A.; Pejaver, Vikas; Stamboulian, Moses H.; Thusberg, Janita; Mooney, Sean D.; Teerakulkittipong, Nuttinee; Cao, Chen; Kundu, Kunal; Yin, Yizhou; Yu, Chen-Hsin; Kleyman, Michael; Lin, Chiao-Feng; Stackpole, Mary; Mount, Stephen M.; Eraslan, Gökcen; Mueller, Nikola S.; Naito, Tatsuhiko; Rao, Aliz R.; Azaria, Johnathan R.; Brodie, Aharon; Ofran, Yanay; Garg, Aditi; Pal, Debnath; Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John; Mucaki, Eliseos J.; Rogan, Peter K.; Schwarz, Jana M.; Searls, David B.; Lee, Gyu Rie; Seok, Chaok; Krämer, Andreas; Shah, Sohela; Huang, ChengLai V.; Kirsch, Jack F.; Shatsky, Maxim; Cao, Yue; Chen, Haoran; Karimi, Mostafa; Moronfoye, Oluwaseyi; Sun, Yuanfei; Shen, Yang; Shigeta, Ron; Ford, Colby T.; Nodzak, Conor; Uppal, Aneeta; Shi, Xinghua; Joseph, Thomas; Kotte, Sujatha; Rana, Sadhna; Rao, Aditya; Saipradeep, V. G.; Sivadasan, Naveen; Sunderam, Uma; Stanke, Mar, 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
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
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
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
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
Rosignoli, Serena; Cosenza, Francesco; Moscou, Matthew J; Civolani, Laura; Musiani, Francesco; Forestan, Cristian; Milner, Sara Giulia; Savojardo, Castrense; Tuberosa, Roberto; Salvi, Silvio, Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing, «THE PLANT GENOME», 2022, 15, Article number: e20187 , pp. 1 - 15 [Scientific article]Open Access
