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Tommaso Leonardi

Genomic Science
Research center

My main scientific interest is in the field of computational RNA biology. My team at the Center for Genomic Science (CGS@SEMM) develops algorithms, software and data-analysis strategies to study the function, evolution and regulation of RNA molecules. We have a particular focus on the application and development of methods based on Nanopore direct RNA-Sequencing, a new technology that for the first time allows to sequence full-length, native RNA molecules without the need for retrotranscription or amplification.

By designing and creating dedicated tools we  leverage the potential of this technology to dissect the transcriptional output of complex loci, quantify isoform expression and determine non genomically encoded transcript features, such as epitranscriptional modifications or polyA tail length.


Title: PhD
Institute: EMBL-European Bioinformatics Institute, University of Cambridge,
Location: Cambridge
Country: United Kingdom
From: 2012 To: 2016

Title: Masters
Institute: Vita Salute San Raffaele
Location: Milan
Country: Italy
From: 2009 To: 2011

Title: Bachelor
Institute: Vita Salute San Raffaele
Location: Milan
Country: Italy
From: 2006 To: 2011

Top Publications
Leger A., Leonardi T.
pycoQC, interactive quality control for Oxford Nanopore Sequencing
The journal of open source software, vol. 4, (no. 34), pp. 1236
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
Article Journal
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)
Davis M.P., Carrieri C., Saini H.K., van Dongen S., Leonardi T., Bussotti G., Monahan J.M., Auchynnikava T., Bitetti A., Rappsilber J., Allshire R.C., Shkumatava A., O'Carroll D., Enright A.J.
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution
EMBO Reports, vol. 18, (no. 7), pp. 1231-1247
Clark M.B., Mercer T.R., Bussotti G., Leonardi T., Haynes K.R., Crawford J., Brunck M.E., Cao K.-A.L., Thomas G.P., Chen W.Y., Taft R.J., Nielsen L.K., Enright A.J., Mattick J.S., Dinger M.E.
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing
Nature Methods, vol. 12, (no. 4), pp. 339-342
Article Journal
All Publications
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
Review Journal
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
Article Journal
Santos-Rosa H., Millán-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
Article Journal
Leonardi T., Leger A.
Nanopore RNA Sequencing Analysis
Methods in molecular biology (Clifton, N.J.), vol. 2284, pp. 569-578
Book Chapter Book Series
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)
Article Journal