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SAVOJARDO, CASTRENSE

SAVOJARDO, CASTRENSE  

DIPARTIMENTO DI FARMACIA E BIOTECNOLOGIE  

Ricercatori a tempo determinato  

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Titolo Autore(i) Anno Periodico Editore Tipo File
CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences Manfredi, Matteo; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita 9999-01-01 BIO-PROTOCOL - 1.01 Articolo in rivista -
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study Schweke H.; Xu Q.; Tauriello G.; Pantolini L.; Schwede T.; Cazals F.; Lheritier A.; Fernandez-Rec...io 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. 9999-01-01 PROTEOMICS - 1.01 Articolo in rivista -
A multidisciplinary approach to describe population structure of Solea solea in the Mediterranean Sea Rachele Corti, Elisabetta Piazza, Enrico Nicola Armelloni, Alice Ferrari, Audrey J. Geffen, Grego...ry E. Maes, Francesco Masnadi, Castrense Savojardo, Giuseppe Scarcella, Marco Stagioni, Fausto Tinti, Alex Zemella, Alessia Cariani 2024-01-01 FRONTIERS IN MARINE SCIENCE - 1.01 Articolo in rivista fmars-11-1372743.pdf
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods 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, Mario; Su, Andrew; Adzhubey, Ivan; Jordan, Daniel M.; Sunyaev, Shamil; Rousseau, Frederic; Schymkowitz, Joost; Van Durme, Joost; Tavtigian, Sean V.; Carraro, Marco; Giollo, Manuel; Tosatto, Silvio C. E.; Adato, Orit; Carmel, Liran; Cohen, Noa E.; Fenesh, Tzila; Holtzer, Tamar; Juven-Gershon, Tamar; Unger, Ron; Niroula, Abhishek; Olatubosun, Ayodeji; Väliaho, Jouni; Yang, Yang; Vihinen, Mauno; Wahl, Mary E.; Chang, Billy; Chong, Ka Chun; Hu, Inchi; Sun, Rui; Wu, William Ka Kei; Xia, Xiaoxuan; Zee, Benny C.; Wang, Maggie H.; Wang, Meng; Wu, Chunlei; Lu, Yutong; Chen, Ken; Yang, Yuedong; Yates, Christopher M.; Kreimer, Anat; Yan, Zhongxia; Yosef, Nir; Zhao, Huying; Wei, Zhipeng; Yao, Zhaomin; Zhou, Fengfeng; Folkman, Lukas; Zhou, Yaoqi; Daneshjou, Roxana; Altman, Russ B.; Inoue, Fumitaka; Ahituv, Nadav; Arkin, Adam P.; Lovisa, Federica; Bonvini, Paolo; Bowdin, Sarah; Gianni, Stefano; Mantuano, Elide; Minicozzi, Velia; Novak, Leonore; Pasquo, Alessandra; Pastore, Annalisa; Petrosino, Maria; Puglisi, Rita; Toto, Angelo; Veneziano, Liana; Chiaraluce, Roberta; Ball, Mad P.; Bobe, Jason R.; Church, George M.; Consalvi, Valerio; Cooper, David N.; Buckley, Bethany A.; Sheridan, Molly B.; Cutting, Garry R.; Scaini, Maria Chiara; Cygan, Kamil J.; Fredericks, Alger M.; Glidden, David T.; Neil, Christopher; Rhine, Christy L.; Fairbrother, William G.; Alontaga, Aileen Y.; Fenton, Aron W.; Matreyek, Kenneth A.; Starita, Lea M.; Fowler, Douglas M.; Löscher, Britt-Sabina; Franke, Andre; Adamson, Scott I.; Graveley, Brenton R.; Gray, Joe W.; Malloy, Mary J.; Kane, John P.; Kousi, Maria; Katsanis, Nicholas; Schubach, Max; Kircher, Martin; Mak, Angel C. Y.; Tang, Paul L. F.; Kwok, Pui-Yan; Lathrop, Richard H.; Clark, Wyatt T.; Yu, Guoying K.; LeBowitz, Jonathan H.; Benedicenti, Francesco; Bettella, Elisa; Bigoni, Stefania; Cesca, Federica; Mammi, Isabella; Marino-Buslje, Cristina; Milani, Donatella; Peron, Angela; Polli, Roberta; Sartori, Stefano; Stanzial, Franco; Toldo, Irene; Turolla, Licia; Aspromonte, Maria C.; Bellini, Mariagrazia; Leonardi, Emanuela; Liu, Xiaoming; Marshall, Christian; McCombie, W. Richard; Elefanti, Lisa; Menin, Chiara; Meyn, M. Stephen; Murgia, Alessandra; Nadeau, Kari C. Y.; Neuhausen, Susan L.; Nussbaum, Robert L.; Pirooznia, Mehdi; Potash, James B.; Dimster-Denk, Dago F.; Rine, Jasper D.; Sanford, Jeremy R.; Snyder, Michael; Cote, Atina G.; Sun, Song; Verby, Marta W.; Weile, Jochen; Roth, Frederick P.; Tewhey, Ryan; Sabeti, Pardis C.; Campagna, Joan; Refaat, Marwan M.; Wojciak, Julianne; Grubb, Soren; Schmitt, Nicole; Shendure, Jay; Spurdle, Amanda B.; Stavropoulos, Dimitri J.; Walton, Nephi A.; Zandi, Peter P.; Ziv, Elad; Burke, Wylie; Chen, Flavia; Carr, Lawrence R.; Martinez, Selena; Paik, Jodi; Harris-Wai, Julie; Yarborough, Mark; Fullerton, Stephanie M.; Koenig, Barbara A.; McInnes, Gregory; Shigaki, Dustin; Chandonia, John-Marc; Furutsuki, Mabel; Kasak, Laura; Yu, Changhua; Chen, Rui; Friedberg, Iddo; Getz, Gad A.; Cong, Qian; Kinch, Lisa N.; Zhang, Jing; Grishin, Nick V.; Voskanian, Alin; Kann, Maricel G.; Tran, Elizabeth; Ioannidis, Nilah M.; Hunter, Jesse M.; Udani, Rupa; Cai, Binghuang; Morgan, Alexander A.; Sokolov, Artem; Stuart, Joshua M.; Minervini, Giovanni; Monzon, Alexander M.; Batzoglou, Serafim; Butte, Atul J.; Greenblatt, Marc S.; Hart, Reece K.; Hernandez, Ryan; Hubbard, Tim J. P.; Kahn, Scott; O’Donnell-Luria, Anne; Ng, Pauline C.; Shon, John; Veltman, Joris; Zook, Justin M. 2024-01-01 GENOME BIOLOGY - 1.01 Articolo in rivista CAGI flag 2024.pdf; 13059_2023_3113_MOESM1_ESM.docx; 13059_2023_3113_MOESM2_ESM.xls; 13059_2023_3113_MOESM3_ESM.xlsx; 13059_2023_3113_MOESM4_ESM.xls; 13059_2023_3113_MOESM5_ESM.xls; 13059_2023_3113_MOESM6_ESM.xls; 13059_2023_3113_MOESM8_ESM.docx; 13059_2023_3113_MOESM7_ESM.xls
Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment 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 2024-01-01 ANIMAL MICROBIOME - 1.01 Articolo in rivista s42523-024-00305-8.pdf
MultifacetedProtDB: a database of human proteins with multiple functions Bertolini, Elisa; Babbi, Giulia; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita 2024-01-01 NUCLEIC ACIDS RESEARCH - 1.01 Articolo in rivista gkad783.pdf
Routes of dispersion of antibiotic resistance genes from the poultry farm system Daniel Scicchitano, Giulia Babbi, Giorgia Palladino, Silvia Turroni, Yitagele Terefe Mekonnen, Cé...dric 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 2024-01-01 SCIENCE OF THE TOTAL ENVIRONMENT - 1.01 Articolo in rivista 1-s2.0-S0048969723077161-main-min.pdf
CoCoNat: a novel method based on deep learning for coiled-coil prediction Madeo G.; Savojardo C.; Manfredi M.; Martelli P.L.; Casadio R. 2023-01-01 BIOINFORMATICS - 1.01 Articolo in rivista btad495.pdf; btad495_supplementary_data.pdf
Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps Nicolini F.; Martelossi J.; Forni G.; Savojardo C.; Mantovani B.; Luchetti A. 2023-01-01 FRONTIERS IN ECOLOGY AND EVOLUTION - 1.01 Articolo in rivista 23_Nicolinietal_FEE.pdf
Finding functional motifs in protein sequences with deep learning and natural language models Savojardo C.; Martelli P.L.; Casadio R. 2023-01-01 CURRENT OPINION IN STRUCTURAL BIOLOGY - 1.01 Articolo in rivista 1-s2.0-S0959440X2300115X-main.pdf
ISPRED-SEQ: Deep Neural Networks and Embeddings for Predicting Interaction Sites in Protein Sequences Manfredi M.; Savojardo C.; Martelli P.L.; Casadio R. 2023-01-01 JOURNAL OF MOLECULAR BIOLOGY - 1.01 Articolo in rivista 1-s2.0-S0022283623000190-main.pdf; 1-s2.0-S0022283623000190-mmc1(2).docx
Resources and tools for rare disease variant interpretation Licata L.; Via A.; Turina P.; Babbi G.; Benevenuta S.; Carta C.; Casadio R.; Cicconardi A.; Facch...iano 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. 2023-01-01 FRONTIERS IN MOLECULAR BIOSCIENCES - 1.01 Articolo in rivista fmolb-10-1169109.pdf; 1169.zip
Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae) Martelossi J.; Forni G.; Iannello M.; Savojardo C.; Martelli P.L.; Casadio R.; Mantovani B.; Luch...etti A.; Rota-Stabelli O. 2023-01-01 INSECT MOLECULAR BIOLOGY - 1.01 Articolo in rivista -
A glance into mthfr deficiency at a molecular level Savojardo C.; Babbi G.; Baldazzi D.; Martelli P.L.; Casadio R. 2022-01-01 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES - 1.01 Articolo in rivista ijms-23-00167-v2.pdf
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing Rosignoli, Serena; Cosenza, Francesco; Moscou, Matthew J; Civolani, Laura; Musiani, Francesco; Fo...restan, Cristian; Milner, Sara Giulia; Savojardo, Castrense; Tuberosa, Roberto; Salvi, Silvio 2022-01-01 THE PLANT GENOME - 1.01 Articolo in rivista 78_2022_Rosignoli_PlantGenome.pdf
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants Manfredi, Matteo; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita 2022-01-01 BIOINFORMATICS - 1.01 Articolo in rivista btac678.pdf
Machine learning solutions for predicting protein–protein interactions Casadio R.; Martelli P.L.; Savojardo C. 2022-01-01 WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE - 1.01 Articolo in rivista WIREs Comput Mol Sci - 2022 - Casadio - Machine learning solutions for predicting protein protein interactions.pdf
Mapping human disease-associated enzymes into Reactome allows characterization of disease groups and their interactions Castrense Savojardo, Davide Baldazzi, Giulia Babbi, Pier Luigi Martelli, Rita Casadio 2022-01-01 SCIENTIFIC REPORTS - 1.01 Articolo in rivista s41598-022-22818-5.pdf
Molecular Effects of Mutations in Human Genetic Diseases Leonardi, Emanuela; Savojardo, Castrense; Minervini, Giovanni 2022-01-01 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES - 1.03 Recensione in rivista ijms-23-06408.pdf
Pathogenic variation types in human genes relate to diseases through Pfam and InterPro mapping Babbi, Giulia; Savojardo, Castrense; Baldazzi, Davide; Martelli, Pier Luigi; Casadio, Rita 2022-01-01 FRONTIERS IN MOLECULAR BIOSCIENCES - 1.01 Articolo in rivista fmolb-09-966927-1.pdf