2023
Mulroney L., Birney E., Leonardi T., Nicassio F.
Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data
Current Protocols, vol. 3, (no. 2)
2022
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Williamson M.K., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frige G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Correa I.R., Ettwiller L., Clementi N., Clementi M., Mancini N., Birney E., Akeson M., Nicassio F., Matthews D.A., Leonardi T.
Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Nucleic Acids Research, vol. 50, (no. 6), pp. 3475-3489
2021
Furlan M., Delgado-Tejedor A., Mulroney L., Pelizzola M., Novoa E.M., Leonardi T.
Computational methods for RNA modification detection from nanopore direct RNA sequencing data
RNA Biology, vol. 18, (no. S1), pp. 31-40
2021
Mazzarella L., Santoro F., Ravasio R., Massa P.E., Rodighiero S., Gavilán E., Romanenghi M., Achutti Duso B., Bonetti E., Pallavi R., Trastulli D., Pallavicini I., Gentile C., Leonardi T., Pasqualato S., Buttinelli G., Di Martino A., Fedele G., Schiavoni I., Stefanelli P., Meroni g., Steinkuhler C., Fossati G., Minucci S., Pelicci P.G.
Inhibiting LSD1 suppresses coronavirus-induced inflammation but spares innate antiviral activity
bioRxiv
Article
Journal
2021
Santos-Rosa H., Millan-Zambrano G., Han N., Leonardi T., Klimontova M., Nasiscionyte S., Pandolfini L., Tzelepis K., Bartke T., Kouzarides T.
Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication
Molecular Cell, vol. 81, (no. 13), pp. 2793-2807.e8
2021
Leonardi T., Leger A.
Nanopore RNA Sequencing Analysis
Methods in molecular biology (Clifton, N.J.), vol. 2284, pp. 569-578
2021
Peruzzotti-Jametti L., Bernstock J.D., Willis C.M., Manferrari G., Rogall R., Fernandez-Vizarra E., Williamson J.C., Braga A., van den Bosch A., Leonardi T., Krzak G., Kittel A., Beninca C., Vicario N., Tan S., Bastos C., Bicci I., Iraci N., Smith J.A., Peacock B., Muller K.H., Lehner P.J., Buzas E.I., Faria N., Zeviani M., Frezza C., Brisson A., Matheson N.J., Viscomi C., Pluchino S.
Neural stem cells traffic functional mitochondria via extracellular vesicles
PLoS Biology, vol. 19, (no. 4)
2021
Leger A., Amaral P.P., Pandolfini L., Capitanchik C., Capraro F., Miano V., Migliori V., Toolan-Kerr P., Sideri T., Enright A.J., Tzelepis K., van Werven F.J., Luscombe N.M., Barbieri I., Ule J., Fitzgerald T., Birney E., Leonardi T., Kouzarides T.
RNA modifications detection by comparative Nanopore direct RNA sequencing
Nature Communications, vol. 12, (no. 1)
2020
Furlan M., Tanaka I., Leonardi T., de Pretis S., Pelizzola M.
Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts
Frontiers in Genetics, vol. 11
2019
Leonardi T.
Bedparse: feature extraction from BED files
The journal of open source software, vol. 4, (no. 34), pp. 1228
2019
Leger A., Leonardi T.
pycoQC, interactive quality control for Oxford Nanopore Sequencing
The journal of open source software, vol. 4, (no. 34), pp. 1236
2019
Leger A., Amaral P.P., Pandolfini L., Capitanchik C., Capraro F., Barbieri I., Migliori V., Luscombe N.M., Enright A.J., Tzelepis K., Ule J., Fitzgerald T., Birney E., Leonardi T., Kouzarides T.
RNA Modifications Detection by Comparative Nanopore Direct RNA Sequencing
bioRxiv
2019
Leonardi T., Leger A., Amaral P., Che H., Pandolfini L., Santo Rosa H., Enright A.J., Fitzgerlad T., Birney E., Kouzarides T.
Signal level RNA modifications detection in eukaryotic ncRNAs
Oxford Nanopore Technologies London Calling Conference
2019
Bernstock J.D., Peruzzotti-Jametti L., Leonardi T., Vicario N., Ye D., Lee Y.-J., Maric D., Johnson K.R., Mou Y., Van Den Bosch A., Winterbone M., Friedman G.K., Franklin R.J.M., Hallenbeck J.M., Pluchino S.
SUMOylation promotes survival and integration of neural stem cell grafts in ischemic stroke
EBioMedicine, vol. 42, pp. 214-224
2018
Amaral P.P., Leonardi T., Han N., Vire E., Gascoigne D.K., Arias-Carrasco R., Buscher M., Pandolfini L., Zhang A., Pluchino S., Maracaja-Coutinho V., Nakaya H.I., Hemberg M., Shiekhattar R., Enright A.J., Kouzarides T.
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci
Genome Biology, vol. 19, (no. 1)