NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

Por Giollo, Manuel, Martin, Alberto JM, Walsh, Ian, Ferrari, Carlo, Tosatto, Silvio CE
Publicado em 2014

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity

Por Piovesan, Damiano, Giollo, Manuel, Leonardi, Emanuela, Ferrari, Carlo, Tosatto, Silvio C.E.
Publicado no Nucleic Acids Res (2015)

Design and Analysis of a Petri Net Model of the Von Hippel-Lindau (VHL) Tumor Suppressor Interaction Network

Por Minervini, Giovanni, Panizzoni, Elisabetta, Giollo, Manuel, Masiero, Alessandro, Ferrari, Carlo, Tosatto, Silvio C. E.
Publicado em 2014

BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data

Por Giollo, Manuel, Minervini, Giovanni, Scalzotto, Marta, Leonardi, Emanuela, Ferrari, Carlo, Tosatto, Silvio C. E.
Publicado no PLoS One (2015)

Crohn disease risk prediction – best practices and pitfalls with exome data

Por Giollo, Manuel, Jones, David T., Carraro, Marco, Leonardi, Emanuela, Ferrari, Carlo, Tosatto, Silvio C.E.
Publicado no Hum Mutat (2017)

RepeatsDB: a database of tandem repeat protein structures

Por Di Domenico, Tomás, Potenza, Emilio, Walsh, Ian, Gonzalo Parra, R., Giollo, Manuel, Minervini, Giovanni, Piovesan, Damiano, Ihsan, Awais, Ferrari, Carlo, Kajava, Andrey V., Tosatto, Silvio C.E.
Publicado em 2014

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

Por Carraro, Marco, Minervini, Giovanni, Giollo, Manuel, Bromberg, Yana, Capriotti, Emidio, Casadio, Rita, Dunbrack, Roland, Elefanti, Lisa, Fariselli, Pietro, Ferrari, Carlo, Gough, Julian, Katsonis, Panagiotis, Leonardi, Emanuela, Lichtarge, Olivier, Menin, Chiara, Martelli, Pier Luigi, Niroula, Abhishek, Pal, Lipika R., Repo, Susanna, Scaini, Maria Chiara, Vihinen, Mauno, Wei, Qiong, Xu, Qifang, Yang, Yuedong, Yin, Yizhou, Zaucha, Jan, Zhao, Huiying, Zhou, Yaoqi, Brenner, Steven E., Moult, John, Tosatto, Silvio C.E.
Publicado no Hum Mutat (2017)

Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants

Por Kasak, Laura, Bakolitsa, Constantina, Hu, Zhiqiang, Yu, Changhua, Rine, Jasper, Dimster-Denk, Dago F., Pandey, Gaurav, Baets, Greet De, Bromberg, Yana, Cao, Chen, Capriotti, Emidio, Casadio, Rita, Durme, Joost Van, Giollo, Manuel, Karchin, Rachel, Katsonis, Panagiotis, Leonardi, Emanuela, Lichtarge, Olivier, Martelli, Pier Luigi, Masica, David, Mooney, Sean D., Olatubosun, Ayodeji, Pal, Lipika R., Radivojac, Predrag, Rousseau, Frederic, Savojardo, Castrense, Schymkowitz, Joost, Thusberg, Janita, Tosatto, Silvio C.E., Vihinen, Mauno, Väliaho, Jouni, Repo, Susanna, Moult, John, Brenner, Steven E., Friedberg, Iddo
Publicado no Hum Mutat (2019)

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

Por Cai, Binghuang, Li, Biao, Kiga, Nikki, Thusberg, Janita, Bergquist, Timothy, Chen, Yun-Ching, Niknafs, Noushin, Carter, Hannah, Tokheim, Collin, Beleva-Guthrie, Violeta, Douville, Christopher, Bhattacharya, Rohit, Yeo, Hui Ting Grace, Fan, Jean, Sengupta, Sohini, Kim, Dewey, Cline, Melissa, Turner, Tychele, Diekhans, Mark, Zaucha, Jan, Pal, Lipika R., Cao, Chen, Yu, Chen-Hsin, Yin, Yizhou, Carraro, Marco, Giollo, Manuel, Ferrari, Carlo, Leonardi, Emanuela, Tosatto, Silvio C.E., Bobe, Jason, Ball, Madeleine, Hoskins, Roger A., Repo, Susanna, Church, George, Brenner, Steven E., Moult, John, Gough, Julian, Stanke, Mario, Karchin, Rachel, Mooney, Sean D.
Publicado no Hum Mutat (2017)

Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Por Daneshjou, Roxana, Wang, Yanran, Bromberg, Yana, Bovo, Samuele, Martelli, Pier L, Babbi, Giulia, Di Lena, Pietro, Casadio, Rita, Edwards, Matthew, Gifford, David, Jones, David T, Sundaram, Laksshman, Bhat, Rajendra, Li, Xiaolin, Pal, Lipika R., Kundu, Kunal, Yin, Yizhou, Moult, John, Jiang, Yuxiang, Pejaver, Vikas, Pagel, Kymberleigh A., Li, Biao, Mooney, Sean D., Radivojac, Predrag, Shah, Sohela, Carraro, Marco, Gasparini, Alessandra, Leonardi, Emanuela, Giollo, Manuel, Ferrari, Carlo, Tosatto, Silvio C E, Bachar, Eran, Azaria, Johnathan R., Ofran, Yanay, Unger, Ron, Niroula, Abhishek, Vihinen, Mauno, Chang, Billy, Wang, Maggie H, Franke, Andre, Petersen, Britt-Sabina, Pirooznia, Mehdi, Zandi, Peter, McCombie, Richard, Potash, James B, Altman, Russ, Klein, Teri E., Hoskins, Roger, Repo, Susanna, Brenner, Steve E, Morgan, Alexander A
Publicado no Hum Mutat (2017)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Por Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T., Bankapur, Asma R., D’Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S., Kahanda, Indika, Verspoor, Karin M., Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M. E., Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T., Chapman, Samuel, BKC, Dukka, Khan, Ishita K., Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E., Hieta, Reija, Legge, Duncan, Lovering, Ruth C., Magrane, Michele, Melidoni, Anna N., Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L., Lee, David, Lees, Jonathan G., Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E., Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E., Pavlidis, Paul, Feng, Shou, Cejuela, Juan M., Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio C.E., del Pozo, Angela, Fernández, José M., Maietta, Paolo, Valencia, Alfonso, Tress, Michael L., Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W., van Dijk, Aalt D. J., Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C., Vencio, Ricardo Z. N., Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael J. E., Wass, Mark N., Huntley, Rachael P., Martin, Maria J., O’Donovan, Claire, Robinson, Peter N., Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C., Brenner, Steven E., Linial, Michal, Orengo, Christine A., Rost, Burkhard, Greene, Casey S., Mooney, Sean D., Friedberg, Iddo, Radivojac, Predrag
Publicado no Genome Biol (2016)