Pubblicazioni

Exploring neural networks to uncover information-richer features for protein interaction prediction

2025 - EUROPEAN BIOPHYSICS JOURNAL

Grassmann, Greta; Di Rienzo, Lorenzo; Ruocco, Giancarlo; Milanetti, Edoardo; Miotto, Mattia

Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction

2024 - ELIFE

Latini, Sara; Venafra, Veronica; Massacci, Giorgia; Bica, Valeria; Graziosi, Simone; Pugliese, Giusj Monia; Iannuccelli, Marta; Frioni, Filippo; Minnella, Gessica; Marra, John Donald; Chiusolo, Patrizia; Pepe, Gerardo; Helmer Citterich, Manuela; Mougiakakos, Dimitros; BÃ¶ttcher, Martin; Fischer, Thomas; Perfetto, Livia; Sacco, Francesca

Merging multi-OMICs with proteome integral solubility alteration unveils antibiotic mode of action

2024 - ELIFE

Maity, Ritwik; Zhang, Xuepei; Liberati, Francesca Romana; Rossi, Chiara Scribani; Cutruzzola', Francesca; Rinaldo, Serena; Gaetani, Massimiliano; AÃnsa, JosÃ© Antonio; Sancho, Javier

Dynamical changes of SARS-CoV-2 spike variants in the highly immunogenic regions impact the viral antibodies escaping

2023 - PROTEINS

Di Rienzo, L.; Miotto, M.; Desantis, F.; Grassmann, G.; Ruocco, G.; Milanetti, E.

Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment

2023 - PLOS COMPUTATIONAL BIOLOGY

Chicco, D.; Ferraro Petrillo, U.; Cattaneo, G.

Deep Learning Methods for Network Biology

2022 - Deep Learning In Biology and Medicine

Madeddu, Lorenzo; Stilo, Giovanni

Deconvolution of malignant pleural effusions immune landscape unravels a novel macrophage signature associated with worse clinical outcome in lung adenocarcinoma patients

2022 - JOURNAL FOR IMMUNOTHERAPY OF CANCER

Bruschini, Sara; Pallocca, Matteo; Sperandio, Eleonora; D'Ambrosio, Lorenzo; Ascenzi, Francesca; De Vitis, Claudia; Salvati, Valentina; Esposito, Antonella; Di Martino, Simona; De Nicola, Francesca; Paolini, Francesca; Fattore, Luigi; Alessandrini, Gabriele; Facciolo, Francesco; Foddai, Maria Laura; Bassi, Massimiliano; Venuta, Federico; D'Ascanio, Michela; Ricci, Alberto; D' Andrilli, Antonio; Napoli, Christian; Aurisicchio, Luigi; Fanciulli, Maurizio; Rendina, Erino Angelo; Ciliberto, Gennaro; Mancini, Rita

Dominating lengthscales of zebrafish collective behaviour

2022 - PLOS COMPUTATIONAL BIOLOGY

Yang, Yushi; Turci, Francesco; Kague, Erika; Hammond, Chrissy L.; Russo, John; Royall, C. Patrick.

Deconvolution of malignant pleural effusions immune landscape unravels a novel macrophage signature associated with worse clinical outcome in lung adenocarcinoma patients

2022 - JOURNAL FOR IMMUNOTHERAPY OF CANCER

Bruschini, Sara; Pallocca, Matteo; Sperandio, Eleonora; D'Ambrosio, Lorenzo; Ascenzi, Francesca; DE VITIS, Claudia; Salvati, Valentina; Esposito, Antonella; Di Martino, Simona; De Nicola, Francesca; Paolini, Francesca; Fattore, Luigi; Alessandrini, Gabriele; Facciolo, Francesco; Laura Foddai, Maria; Bassi, Massimiliano; Venuta, Federico; D'Ascanio, Michela; Ricci, Alberto; D'Andrilli, ANTONIO LUCIO; Napoli, Christian; Aurisicchio, Luigi; Fanciulli, Maurizio; Rendina, Erino Angelo; Ciliberto, Gennaro; Mancini, Rita

AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning

2022 - SCIENTIFIC REPORTS

Charoenkwan, P.; Ahmed, S.; Nantasenamat, C.; Quinn, J. M. W.; Moni, M. A.; Lio, P.; Shoombuatong, W.

StackPR is a new computational approach for large-scale identification of progesterone receptor antagonists using the stacking strategy

2022 - SCIENTIFIC REPORTS

Schaduangrat, N.; Anuwongcharoen, N.; Moni, M. A.; Lio, P.; Charoenkwan, P.; Shoombuatong, W.

Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery

2021 - NPJ SYSTEMS BIOLOGY AND APPLICATIONS

Paci, P.; Fiscon, G.; Conte, F.; Wang, R. -S.; Farina, L.; Loscalzo, J.

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

2021 - PLOS COMPUTATIONAL BIOLOGY

Fiscon, G.; Conte, F.; Farina, L.; Paci, P.

An Overview of the computational models dealing with the regulatory ceRNA mechanism and ceRNA deregulation in cancer

2021 - Methods in Molecular Biology

Conte, F.; Fiscon, G.; Sibilio, P.; Licursi, V.; Paci, P.

Moses: A new approach to integrate interactome topology and functional features for disease gene prediction

2021 - GENES

Petti, M.; Farina, L.; Francone, F.; Lucidi, S.; Macali, Amalia; Palagi, L.; De Santis, M.

catRAPID omics v2.0: going deeper and wider in the prediction of proteinâRNA interactions

2021 - NUCLEIC ACIDS RESEARCH

Armaos, Alexandros; Colantoni, Alessio; Proietti, Gabriele; Rupert, Jakob; Tartaglia, Gian Gaetano

Chemical and bioinformatics analyses of the anti-leishmanial and anti-oxidant activities of hemp essential oil

2021 - BIOMOLECULES

Menghini, L.; Ferrante, C.; Carradori, S.; D'antonio, M.; Orlando, G.; Cairone, F.; Cesa, S.; Filippi, A.; Fraschetti, C.; Zengin, G.; Ak, G.; Tacchini, M.; Iqbal, K.

Target highlights in CASP14: Analysis of models by structure providers

2021 - PROTEINS

Alexander, L. T.; Lepore, R.; Kryshtafovych, A.; Adamopoulos, A.; Alahuhta, M.; Arvin, A. M.; Bomble, Y. J.; Bottcher, B.; Breyton, C.; Chiarini, V.; Chinnam, N. B.; Chiu, W.; Fidelis, K.; Grinter, R.; Gupta, G. D.; Hartmann, M. D.; Hayes, C. S.; Heidebrecht, T.; Ilari, A.; Joachimiak, A.; Kim, Y.; Linares, R.; Lovering, A. L.; Lunin, V. V.; Lupas, A. N.; Makbul, C.; Michalska, K.; Moult, J.; Mukherjee, P. K.; Nutt, W.; Oliver, S. L.; Perrakis, A.; Stols, L.; Tainer, J. A.; Topf, M.; Tsutakawa, S. E.; Valdivia-Delgado, M.; Schwede, T.

Tetrahydroquinazole-based secondary sulphonamides as carbonic anhydrase inhibitors: synthesis, biological evaluation against isoforms I, II, IV, and IX, and computational studies

2021 - JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Baglini, E; Ravichandran, R; Berrino, E; Salerno, S; Barresi, E; Marini, Am; Viviano, M; Castellano, S; Da Settimo, F; Supuran, Ct; Cosconati, S; Taliani, S.

Genome-wide expression of the residual lung reacting to experimental Pneumonectomy

2021 - BMC GENOMICS

Napolioni, Valerio; Bianconi, Fortunato; Potenza, Rossella; Carpi, Francesco M; Ludovini, Vienna; Picciolini, Matteo; Tofanetti, Francesca R; Bufalari, Antonello; Pallotti, Stefano; Poggi, Camilla; Anile, Marco; Daddi, NiccolÃ²; Venuta, Federico; Puma, Francesco; Vannucci, Jacopo

Metabolic networks classification and knowledge discovery by information granulation

2020 - COMPUTATIONAL BIOLOGY AND CHEMISTRY

Martino, Alessio; Giulian, Alessandro; Todde, Virginia; Bizzarri, Mariano; Rizzi, Antonello

Modelling and recognition of protein contact networks by multiple kernel learning and dissimilarity representations

2020 - ENTROPY

Martino, Alessio; De Santis, Enrico; Giuliani, Alessandro; Rizzi, Antonello

Ricerc@Sapienza

Pubblicazioni

Exploring neural networks to uncover information-richer features for protein interaction prediction

Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction

Merging multi-OMICs with proteome integral solubility alteration unveils antibiotic mode of action

Dynamical changes of SARS-CoV-2 spike variants in the highly immunogenic regions impact the viral antibodies escaping

Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment

Deep Learning Methods for Network Biology

Deconvolution of malignant pleural effusions immune landscape unravels a novel macrophage signature associated with worse clinical outcome in lung adenocarcinoma patients

Dominating lengthscales of zebrafish collective behaviour

Deconvolution of malignant pleural effusions immune landscape unravels a novel macrophage signature associated with worse clinical outcome in lung adenocarcinoma patients

AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning

StackPR is a new computational approach for large-scale identification of progesterone receptor antagonists using the stacking strategy

Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

An Overview of the computational models dealing with the regulatory ceRNA mechanism and ceRNA deregulation in cancer

Moses: A new approach to integrate interactome topology and functional features for disease gene prediction

catRAPID omics v2.0: going deeper and wider in the prediction of proteinâRNA interactions

Chemical and bioinformatics analyses of the anti-leishmanial and anti-oxidant activities of hemp essential oil

Target highlights in CASP14: Analysis of models by structure providers

Genome-wide expression of the residual lung reacting to experimental Pneumonectomy

The importance of urgency in decision making based on dynamic information

Co-evolution between codon usage and protein-protein interaction in bacteria

Tetrahydroquinazole-based secondary sulphonamides as carbonic anhydrase inhibitors: synthesis, biological evaluation against isoforms I, II, IV, and IX, and computational studies

Genome-wide expression of the residual lung reacting to experimental Pneumonectomy

Metabolic networks classification and knowledge discovery by information granulation

Modelling and recognition of protein contact networks by multiple kernel learning and dissimilarity representations