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Tommaso Leonardi

Visiting Scientist
Genomic Science
Address
Research center
Interests
About

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.

Education

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
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
2021
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Kavanagh Williamson M., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frige G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Corrêa I.R., Ettwiller L., Clementi N., Clementi M., Mancini N., Birney E., Akeson M., Nicassio N., Matthews D.A., Leonardi T.
Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
bioRxiv
Article Journal
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
Article Journal
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)
2017
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
All Publications
2022
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Williamson M.K., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frigè G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Corrêa 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
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
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
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Kavanagh Williamson M., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frige G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Corrêa I.R., Ettwiller L., Clementi N., Clementi M., Mancini N., Birney E., Akeson M., Nicassio N., Matthews D.A., Leonardi T.
Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
bioRxiv
Article Journal

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