Monzon, Alexander Miguel
Monzon, Alexander Miguel
Dipartimento di Scienze Biomediche - DSB
CAFA-evaluator: a Python tool for benchmarking ontological classification methods
2024 Piovesan, Damiano; Zago, Davide; Joshi, Parnal; De Paolis Kaluza, M Clara; Mehdiabadi, Mahta; Ramola, Rashika; Monzon, Alexander Miguel; Reade, Walter; Friedberg, Iddo; Radivojac, Predrag; Tosatto, Silvio C E
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
2024 Jain, Shantanu; Bakolitsa, Constantina; E Brenner, Steven; Radivojac, Predrag; Moult, John; Repo, Susanna; A Hoskins, Roger; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; K Kollipara, Naveen; Ly, Melissa; J Neumann, Andrew; R Pal, Lipika; Odell, Eric; Pandey, Gaurav; C Peters-Petrulewicz, Robin; Srinivasan, Rajgopal; F Yee, Stephen; Jyothsna Yeleswarapu, Sri; Zuhl, Maya; Adebali, Ogun; Patra, Ayoti; A Beer, Michael; Hosur, Raghavendra; Peng, Jian; M Bernard, Brady; Berry, Michael; Dong, Shengcheng; P Boyle, Alan; Adhikari, Aashish; Chen, Jingqi; Hu, Zhiqiang; Wang, Robert; Wang, Yaqiong; Miller, Maximilian; Wang, Yanran; Bromberg, Yana; Turina, Paola; Capriotti, Emidio; J Han, James; Ozturk, Kivilcim; Carter, Hannah; Babbi, Giulia; Bovo, Samuele; Di Lena, Pietro; Luigi Martelli, Pier; Savojardo, Castrense; Casadio, Rita; S Cline, Melissa; 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; J Huwe, Peter; Wei, Qiong; Xu, Qifang; L Dunbrack, Roland; Gotea, Valer; Elnitski, Laura; Margolin, Gennady; Fariselli, Piero; V Kulakovskiy, Ivan; J Makeev, Vsevolod; D Penzar, Dmitry; E Vorontsov, Ilya; V Favorov, Alexander; R Forman, Julia; Hasenahuer, Marcia; S Fornasari, Maria; Parisi, Gustavo; Avsec, Ziga; H Çelik, Muhammed; Yen Duong Nguyen, Thi; Gagneur, Julien; Shi, Fang-Yuan; D Edwards, Matthew; Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; K Gifford, David; Göke, Jonathan; Zaucha, Jan; Gough, Julian; S Ritchie, Graham R; Frankish, Adam; M Mudge, Jonathan; Harrow, Jennifer; L Young, Erin; Yu, Yao; D Huff, Chad; Murakami, Katsuhiko; Nagai, Yoko; Imanishi, Tadashi; J Mungall, Christopher; B Jacobsen, Julius O; Kim, Dongsup; Jeong, Chan-Seok; T Jones, David; Jun Li, Mulin; Beleva Guthrie, Violeta; Bhattacharya, Rohit; Chen, Yun-Ching; Douville, Christopher; Fan, Jean; Kim, Dewey; Masica, David; Niknafs, Noushin; Sengupta, Sohini; Tokheim, Collin; N Turner, Tychele; Ting Grace Yeo, Hui; Karchin, Rachel; Shin, Sunyoung; Welch, Rene; Keles, Sunduz; Li, Yue; Kellis, Manolis; Corbi-Verge, Carles; V Strokach, Alexey; M Kim, Philip; E Klein, Teri; Mohan, Rahul; A Sinnott-Armstrong, Nicholas; Wainberg, Michael; Kundaje, Anshul; Gonzaludo, Nina; Y Mak, Angel C; Chhibber, Aparna; K Lam, Hugo Y; Dahary, Dvir; Fishilevich, Simon; Lancet, Doron; Lee, Insuk; Bachman, Benjamin; Katsonis, Panagiotis; C Lua, Rhonald; J Wilson, Stephen; Lichtarge, Olivier; R Bhat, Rajendra; Sundaram, Laksshman; Viswanath, Vivek; Bellazzi, Riccardo; Nicora, Giovanna; Rizzo, Ettore; Limongelli, Ivan; M Mezlini, Aziz; Chang, Ray; Kim, Serra; Lai, Carmen; O'Connor, Robert; Topper, Scott; van den Akker, Jeroen; Y Zhou, Alicia; D Zimmer, Anjali; Mishne, Gilad; R Bergquist, Timothy; R Breese, Marcus; F Guerrero, Rafael; Jiang, Yuxiang; Kiga, Nikki; Li, Biao; Mort, Matthew; A Pagel, Kymberleigh; Pejaver, Vikas; H Stamboulian, Moses; Thusberg, Janita; D Mooney, Sean; Teerakulkittipong, Nuttinee; Cao, Chen; Kundu, Kunal; Yin, Yizhou; Yu, Chen-Hsin; Kleyman, Michael; Lin, Chiao-Feng; Stackpole, Mary; M Mount, Stephen; Eraslan, Gökcen; S Mueller, Nikola; Naito, Tatsuhiko; R Rao, Aliz; R Azaria, Johnathan; Brodie, Aharon; Ofran, Yanay; Garg, Aditi; Pal, Debnath; Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John; J Mucaki, Eliseos; K Rogan, Peter; M Schwarz, Jana; B Searls, David; Rie Lee, Gyu; Seok, Chaok; Krämer, Andreas; Shah, Sohela; V Huang, Chenglai; F Kirsch, Jack; Shatsky, Maxim; Cao, Yue; Chen, Haoran; Karimi, Mostafa; Moronfoye, Oluwaseyi; Sun, Yuanfei; Shen, Yang; Shigeta, Ron; T Ford, Colby; Nodzak, Conor; Uppal, Aneeta; Shi, Xinghua; Joseph, Thomas; Kotte, Sujatha; Rana, Sadhna; Rao, Aditya; G Saipradeep, V; Sivadasan, Naveen; Sunderam, Uma; Stanke, Mario; Su, Andrew; Adzhubey, Ivan; M Jordan, Daniel; Sunyaev, Shamil; Rousseau, Frederic; Schymkowitz, Joost; Van Durme, Joost; V Tavtigian, Sean; Carraro, Marco; Giollo, Manuel; Tosatto, Silvio; Adato, Orit; Carmel, Liran; E Cohen, Noa; Fenesh, Tzila; Holtzer, Tamar; Juven-Gershon, Tamar; Unger, Ron; Niroula, Abhishek; Olatubosun, Ayodeji; Väliaho, Jouni; Yang, Yang; Vihinen, Mauno; E Wahl, Mary; Chang, Billy; Chun Chong, Ka; Hu, Inchi; Sun, Rui; Ka Kei Wu, William; Xia, Xiaoxuan; C Zee, Benny; H Wang, Maggie; Wang, Meng; Wu, Chunlei; Lu, Yutong; Chen, Ken; Yang, Yuedong; M Yates, Christopher; Kreimer, Anat; Yan, Zhongxia; Yosef, Nir; Zhao, Huying; Wei, Zhipeng; Yao, Zhaomin; Zhou, Fengfeng; Folkman, Lukas; Zhou, Yaoqi; Daneshjou, Roxana; B Altman, Russ; Inoue, Fumitaka; Ahituv, Nadav; P Arkin, Adam; 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; P Ball, Mad; R Bobe, Jason; M Church, George; Consalvi, Valerio; N Cooper, David; A Buckley, Bethany; B Sheridan, Molly; R Cutting, Garry; Chiara Scaini, Maria; J Cygan, Kamil; M Fredericks, Alger; T Glidden, David; Neil, Christopher; L Rhine, Christy; G Fairbrother, William; Y Alontaga, Aileen; W Fenton, Aron; A Matreyek, Kenneth; M Starita, Lea; M Fowler, Douglas; Löscher, Britt-Sabina; Franke, Andre; I Adamson, Scott; R Graveley, Brenton; W Gray, Joe; J Malloy, Mary; P Kane, John; Kousi, Maria; Katsanis, Nicholas; Schubach, Max; Kircher, Martin; Y Mak, Angel C; F Tang, Paul L; Kwok, Pui-Yan; H Lathrop, Richard; T Clark, Wyatt; K Yu, Guoying; H LeBowitz, Jonathan; 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; C Aspromonte, Maria; Bellini, Mariagrazia; Leonardi, Emanuela; Liu, Xiaoming; Marshall, Christian; Richard McCombie, W; Elefanti, Lisa; Menin, Chiara; Stephen Meyn, M; Murgia, Alessandra; Y Nadeau, Kari C; L Neuhausen, Susan; L Nussbaum, Robert; Pirooznia, Mehdi; B Potash, James; F Dimster-Denk, Dago; D Rine, Jasper; R Sanford, Jeremy; Snyder, Michael; G Cote, Atina; Sun, Song; W Verby, Marta; Weile, Jochen; P Roth, Frederick; Tewhey, Ryan; C Sabeti, Pardis; Campagna, Joan; M Refaat, Marwan; Wojciak, Julianne; Grubb, Soren; Schmitt, Nicole; Shendure, Jay; B Spurdle, Amanda; J Stavropoulos, Dimitri; A Walton, Nephi; P Zandi, Peter; Ziv, Elad; Burke, Wylie; Chen, Flavia; R Carr, Lawrence; Martinez, Selena; Paik, Jodi; Harris-Wai, Julie; Yarborough, Mark; M Fullerton, Stephanie; A Koenig, Barbara; Mcinnes, Gregory; Shigaki, Dustin; Chandonia, John-Marc; Furutsuki, Mabel; Kasak, Laura; Yu, Changhua; Chen, Rui; Friedberg, Iddo; A Getz, Gad; Cong, Qian; N Kinch, Lisa; Zhang, Jing; V Grishin, Nick; Voskanian, Alin; G Kann, Maricel; Tran, Elizabeth; M Ioannidis, Nilah; M Hunter, Jesse; Udani, Rupa; Cai, Binghuang; A Morgan, Alexander; Sokolov, Artem; M Stuart, Joshua; Minervini, Giovanni; Monzon, Alexander Miguel; Batzoglou, Serafim; J Butte, Atul; S Greenblatt, Marc; K Hart, Reece; Hernandez, Ryan; P Hubbard, Tim J; Kahn, Scott; O'Donnell-Luria, Anne; C Ng, Pauline; Shon, John; Veltman, Joris; M Zook, Justin
Diversity and structural‐functional insights of alpha‐solenoid proteins
2024 Arrías, Paula Nazarena; Osmanli, Zarifa; Peralta, Estefanía; Chinestrad, Patricio Manuel; Monzon, Alexander Miguel; Tosatto, Silvio C. E.
DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology
2024 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
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB
2024 Clementel, Damiano; Arrías, Paula Nazarena; Mozaffari, Soroush; Osmanli, Zarifa; Castro, Ximena Aixa; Ferrari, Carlo; Kajava, Andrey V; Tosatto, Silvio C E; Monzon, Alexander Miguel
RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures
2024 Del , ; DEL CONTE, Alessio; Camagni, GIORGIA FRANCESCA; Clementel, Damiano; Minervini, Giovanni; Monzon, Alexander Miguel; Ferrari, Carlo; Piovesan, Damiano; Tosatto, Silvio
Searching and Using MobiDB Resource 6 to Explore Predictions and Annotations for Intrinsically Disordered Proteins
2024 Aspromonte, M. C.; Quaglia, F.; Monzon, A. M.; Clementel, D.; Del Conte, A.; Piovesan, D.; Tosatto, S. C. E.
STRPsearch: fast detection of structured tandem repeat proteins
2024 Mozaffari, S.; Arrias, P. N.; Clementel, D.; Piovesan, D.; Ferrari, C.; Tosatto, S. C. E.; Monzon, A. M.
Structured Tandem Repeats in Protein Interactions
2024 Mac Donagh, Juan; Marchesini, Abril; Spiga, Agostina; Fallico, Maximiliano José; Arrías, Paula Nazarena; Monzon, Alexander Miguel; Vagiona, Aimilia-Christina; Gonçalves-Kulik, Mariane; Mier, Pablo; Andrade-Navarro, Miguel A.
A STRP-ed definition of Structured Tandem Repeats in Proteins
2023 Monzon, Alexander Miguel; Arrías, Paula Nazarena; Elofsson, Arne; Mier, Pablo; Andrade-Navarro, Miguel A; Bevilacqua, Martina; Clementel, Damiano; Bateman, Alex; Hirsh, Layla; Fornasari, Maria Silvina; Parisi, Gustavo; Piovesan, Damiano; Kajava, Andrey V; Tosatto, Silvio C E
CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins
2023 Del Conte, A.; Bouhraoua, A.; Mehdiabadi, M.; Clementel, D.; Monzon, A. M.; Tosatto, S. C. E.; Piovesan, D.
Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q
2023 Escobedo, N.; Monzon, A. M.; Fornasari, M. S.; Palopoli, N.; Parisi, G.
Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2
2023 Del Conte, A.; Mehdiabadi, M.; Bouhraoua, A.; Monzon, A. M.; Tosatto, S. C. E.; Piovesan, D.
MobiDB: 10 years of intrinsically disordered proteins
2023 Piovesan, Damiano; Del Conte, Alessio; Clementel, Damiano; Monzon, Alexander Miguel; Bevilacqua, Martina; Aspromonte, Maria Cristina; Iserte, Javier A; Orti, Fernando E; Marino-Buslje, Cristina; Tosatto, Silvio C E
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins
2023 Ghafouri, Hamidreza; Lazar, Tamas; Del Conte, Alessio; Tenorio Ku, Luiggi G; Aspromonte, Maria Cristina; Leonardi, Emanuela; Tompa, Peter; Tosatto, Silvio C E; Monzon, Alexander Miguel
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
2023 Del Conte, A.; Monzon, A. M.; Clementel, D.; Camagni, G. F.; Minervini, G.; Tosatto, S. C. E.; Piovesan, D.
The repetitive structure of DNA clamps: An overlooked protein tandem repeat
2023 Arrias, P. N.; Monzon, A. M.; Clementel, D.; Mozaffari, S.; Piovesan, D.; Kajava, A. V.; Tosatto, S. C. E.
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure
2022 Escobedo, Nahuel; Tunque Cahui, Ronaldo Romario; Caruso, Gastón; García Ríos, Emilio; Hirsh, Layla; Monzon, Alexander Miguel; Parisi, Gustavo; Palopoli, Nicolas
Databases for intrinsically disordered proteins
2022 Piovesan, Damiano; Monzon, Alexander Miguel; Quaglia, Federica; Tosatto, Silvio C. E.
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
2022 Quaglia, Federica; Mészáros, Bálint; Salladini, Edoardo; Hatos, András; Pancsa, Rita; Chemes, Lucía B; Pajkos, Mátyás; Lazar, Tamas; Peña-Díaz, Samuel; Santos, Jaime; Ács, Veronika; Farahi, Nazanin; Fichó, Erzsébet; Aspromonte, Maria Cristina; Bassot, Claudio; Chasapi, Anastasia; Davey, Norman E; Davidović, Radoslav; Dobson, Laszlo; Elofsson, Arne; Erdős, Gábor; Gaudet, Pascale; Giglio, Michelle; Glavina, Juliana; Iserte, Javier; Iglesias, Valentín; Kálmán, Zsófia; Lambrughi, Matteo; Leonardi, Emanuela; Longhi, Sonia; Macedo-Ribeiro, Sandra; Maiani, Emiliano; Marchetti, Julia; Marino-Buslje, Cristina; Mészáros, Attila; Monzon, Alexander Miguel; Minervini, Giovanni; Nadendla, Suvarna; Nilsson, Juliet F; Novotný, Marian; Ouzounis, Christos A; Palopoli, Nicolás; Papaleo, Elena; Pereira, Pedro José Barbosa; Pozzati, Gabriele; Promponas, Vasilis J; Pujols, Jordi; Rocha, Alma Carolina Sanchez; Salas, Martin; Sawicki, Luciana Rodriguez; Schad, Eva; Shenoy, Aditi; Szaniszló, Tamás; Tsirigos, Konstantinos D; Veljkovic, Nevena; Parisi, Gustavo; Ventura, Salvador; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C E; Piovesan, Damiano