RE', MATTEO
RE', MATTEO
Dipartimento di Informatica Giovanni Degli Antoni
A Graphical Tool for the Exploration and Visual Analysis of Biomolecular Networks
2020 C.T. Ba, E. Casiraghi, M. Frasca, J. Gliozzo, G. Grossi, M. Mesiti, M. Notaro, P. Perlasca, A. Petrini, M. Re', G. Valentini
parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants
2020 A. Petrini, M. Mesiti, M. Schubach, M. Frasca, D. Danis, M. Re, G. Grossi, L. Cappelletti, T. Castrignano, P.N. Robinson, G. Valentini
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
2020 J. Gliozzo, P. Perlasca, M. Mesiti, E. Casiraghi, V. Vallacchi, E. Vergani, M. Frasca, G. Grossi, A. Petrini, M. Re, A. Paccanaro, G. Valentini
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
2019 N. Zhou, Y. Jiang, T.R. Bergquist, A.J. Lee, B.Z. Kacsoh, A.W. Crocker, K.A. Lewis, G. Georghiou, H.N. Nguyen, M.N. Hamid, L. Davis, T. Dogan, V. Atalay, A.S. Rifaioglu, A. Dalklran, R. Cetin Atalay, C. Zhang, R.L. Hurto, P.L. Freddolino, Y. Zhang, P. Bhat, F. Supek, J.M. Fernandez, B. Gemovic, V.R. Perovic, R.S. Davidovic, N. Sumonja, N. Veljkovic, E. Asgari, M.R.K. Mofrad, G. Profiti, C. Savojardo, P.L. Martelli, R. Casadio, F. Boecker, H. Schoof, I. Kahanda, N. Thurlby, A.C. Mchardy, A. Renaux, R. Saidi, J. Gough, A.A. Freitas, M. Antczak, F. Fabris, M.N. Wass, J. Hou, J. Cheng, Z. Wang, A.E. Romero, A. Paccanaro, H. Yang, T. Goldberg, C. Zhao, L. Holm, P. Toronen, A.J. Medlar, E. Zosa, I. Borukhov, I. Novikov, A. Wilkins, O. Lichtarge, P.-. Chi, W.-. Tseng, M. Linial, P.W. Rose, C. Dessimoz, V. Vidulin, S. Dzeroski, I. Sillitoe, S. Das, J.G. Lees, D.T. Jones, C. Wan, D. Cozzetto, R. Fa, M. Torres, A. Warwick Vesztrocy, J.M. Rodriguez, M.L. Tress, M. Frasca, M. Notaro, G. Grossi, A. Petrini, M. Re, G. Valentini, M. Mesiti, D.B. Roche, J. Reeb, D.W. Ritchie, S. Aridhi, S.Z. Alborzi, M.-. Devignes, D.C.E. Koo, R. Bonneau, V. Gligorijevic, M. Barot, H. Fang, S. Toppo, E. Lavezzo, M. Falda, M. Berselli, S.C.E. Tosatto, M. Carraro, D. Piovesan, H. Ur Rehman, Q. Mao, S. Zhang, S. Vucetic, G.S. Black, D. Jo, E. Suh, J.B. Dayton, D.J. Larsen, A.R. Omdahl, L.J. Mcguffin, D.A. Brackenridge, P.C. Babbitt, J.M. Yunes, P. Fontana, F. Zhang, S. Zhu, R. You, Z. Zhang, S. Dai, S. Yao, W. Tian, R. Cao, C. Chandler, M. Amezola, D. Johnson, J.-. Chang, W.-. Liao, Y.-. Liu, S. Pascarelli, Y. Frank, R. Hoehndorf, M. Kulmanov, I. Boudellioua, G. Politano, S. Di Carlo, A. Benso, K. Hakala, F. Ginter, F. Mehryary, S. Kaewphan, J. Bjorne, H. Moen, M.E.E. Tolvanen, T. Salakoski, D. Kihara, A. Jain, T. Smuc, A. Altenhoff, A. Ben-Hur, B. Rost, S.E. Brenner, C.A. Orengo, C.J. Jeffery, G. Bosco, D.A. Hogan, M.J. Martin, C. O'Donovan, S.D. Mooney, C.S. Greene, P. Radivojac, I. Friedberg
Patients’ networks for clinical phenotype/outcome prediction
2018 J. Gliozzo, P. Perlasca, M. Mesiti, J. Caceres Silva, A. Petrini, E. Casiraghi, M. Frasca, G. Grossi, M. Re', A. Paccanaro, G. Valentini
Modeling biomolecular profiles in a graph-structured sample space for clinical outcome prediction with melanoma and ovarian cancer patients
2017 J. Gliozzo, M. Notaro, A. Petrini, P. Perlasca, M. Mesiti, E. Casiraghi, M. Frasca, G. Grossi, M. Re, A. Paccanaro, G. Valentini
Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants
2017 M. Schubach, M. Re, P.N. Robinson, G. Valentini
Within network learning on big graphs using secondary memory-based random walk kernels
2017 J. Lin, M. Mesiti, M. Re, G. Valentini
RANKS : a flexible tool for node label ranking and classification in biological networks
2016 G. Valentini, G. Armano, M. Frasca, J. Lin, M. Mesiti, M. Re
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
2016 Y. Jiang, T.R. Oron, W.T. Clark, A.R. Bankapur, D. D’Andrea, R. Lepore, C.S. Funk, I. Kahanda, K.M. Verspoor, A. Ben-Hur, D.C.E. Koo, D. Penfold-Brown, D. Shasha, N. Youngs, R. Bonneau, A. Lin, S.M..E. Sahraeian, P.L. Martelli, G. Profiti, R. Casadio, R. Cao, Z. Zhong, J. Cheng, A. Altenhoff, N. Skunca, C. Dessimoz, T. Dogan, K. Hakala, S. Kaewphan, F. Mehryary, T. Salakoski, F. Ginter, H. Fang, B. Smithers, M. Oates, J. Gough, P. Törönen, P. Koskinen, L. Holm, C. Chen, W. Hsu, K. Bryson, D. Cozzetto, F. Minneci, D.T. Jones, S. Chapman, D. Bkc, I.K. Khan, D. Kihara, D. Ofer, N. Rappoport, A. Stern, E. Cibrian-Uhalte, P. Denny, R.E. Foulger, R. Hieta, D. Legge, R.C. Lovering, M. Magrane, A.N. Melidoni, P. Mutowo-Meullenet, K. Pichler, A. Shypitsyna, B. Li, P. Zakeri, S. Elshal, L. Tranchevent, S. Das, N.L. Dawson, D. Lee, J.G. Lees, I. Sillitoe, P. Bhat, T. Nepusz, A.E. Romero, R. Sasidharan, H. Yang, A. Paccanaro, J. Gillis, A.E. Sedeño-Cortés, P. Pavlidis, S. Feng, J.M. Cejuela, T. Goldberg, T. Hamp, L. Richter, A. Salamov, T. Gabaldon, M. Marcet-Houben, F. Supek, Q. Gong, W. Ning, Y. Zhou, W. Tian, M. Falda, P. Fontana, E. Lavezzo, S. Toppo, C. Ferrari, M. Giollo, D. Piovesan, S.C.E. Tosatto, A. del Pozo, J.M. Fernández, P. Maietta, A. Valencia, M.L. Tress, A. Benso, S. Di Carlo, G. Politano, A. Savino, H.U. Rehman, M. Re, M. Mesiti, G. Valentini, J.W. Bargsten, A.D..J. van Dijk, B. Gemovic, S. Glisic, V. Perovic, V. Veljkovic, N. Veljkovic, D.C. Almeida-e-Silva, R.Z..N. Vencio, M. Sharan, J. Vogel, L. Kansakar, S. Zhang, S. Vucetic, Z. Wang, M.J..E. Sternberg, M.N. Wass, R.P. Huntley, M.J. Martin, C. O’Donovan, P.N. Robinson, Y. Moreau, A. Tramontano, P.C. Babbitt, S.E. Brenner, M. Linial, C.A. Orengo, B. Rost, C.S. Greene, S.D. Mooney, I. Friedberg, P. Radivojac
Prediction of human gene - phenotype associations by exploiting the hierarchical structure of the human phenotype ontology
2015 G. Valentini, S. Köhler, M. Re, M. Notaro, P.N. Robinson
A Hierarchical Ensemble Method for DAG-Structured Taxonomies
2015 P.N. Robinson, M. Frasca, S. Köhler, M. Notaro, M. Re, G. Valentini
Analysis of bio-molecular networks through semi-supervised graph-based learning methods
2014 M. Re, M. Mesiti, M. Frasca, J. Lin, G. Valentini
Think globally and solve locally : secondary memory-based network learning for automated multi-species function prediction
2014 M. Mesiti, M. Re, G. Valentini
An automated pipeline for multi-species protein function prediction from the UniProt Knowledgebase
2014 M. Re, M. Mesiti, G. Valentini
On the automated function prediction of big multi-species networks
2014 M. Re, M. Mesiti, G. Valentini
An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods
2014 G. Valentini, A. Paccanaro, H. Caniza, A.E. Romero, M. Re
Scalable Network-based Learning Methods for Automated Function Prediction based on the Neo4j Graph-database
2013 M. Mesiti, M. Re, G. Valentini
A neural network algorithm for semi-supervised node label learning from unbalanced data
2013 M. Frasca, A. Bertoni, M. Re, G. Valentini
Network integration boosts disease gene prioritization
2013 G. Valentini, A. Paccanaro, H. Vierci, A. Romero, M. Re