2019 - Present: Post Doc, Epigenomics and Transcriptional Regulation Group (IIT)
2016 - 2019: Ph.D. student, Epigenomics and Transcriptional Regulation Group (IIT), Computational Biology Group (INFN)
2014: Three months internship, Institute of Atmospheric Sciences and Climate (ISAC-CNR)
The main focus of my research activity is the study of the RNA life cycle, I address this topic with computational methods based on the mathematical modelling of RNA sequencing data.
Motivation
RNA is one of the fundamental actors in the context of cellular biology and it is involved, directly or indirectly, in any cellular process. Therefore, the composition of the transcriptome is kept under strict regulation by the cell and adapted in response to external and internal stimuli. This control is mediated by many regulatory mechanisms involving any step of the RNA life cycle and their characterisation is mandatory to acquire a full comprehension of cellular biology.
The most common approach to investigate the RNA life cycle is to collect information about gene expression through RNA sequencing experiments, however, this datum reflects the choral effect of this complex plethora of modulations, for this reason, it must be carefully analysed to deconvolve all these contributes and avoid incorrect conclusions. For instance, the increase of a gene expression level between two conditions is usually assumed to be a proxy of its transcriptional induction, nonetheless, the same observation could be due to a modulation of transcripts stability.
To sum up, the investigation of RNA metabolism is indispensable and requires the development and application of dedicated computational approaches which combine mathematical modelling and inference; this is the scope of my research.
INSPEcT
INSPEcT is R/bioconductor package (INSPEcT) for the genome-wide inference and study of RNA life cycle dynamics. It first release (de Pretis et al. 2015) allowed the estimation of synthesis, processing and degradation rates from the joint analysis of Total and Nascent RNA sequencing data; both at steady state and in time-course.
The quantification of Nascent RNA requires sophisticated techniques which significantly increase costs and complexity of the experiments. For this reason, I spent my PhD contributing to the extension of the package with novel routines for the study of transcriptional and post-transcriptional dynamics from Total RNA-seq data only (Furlan et al. 2019).
INSPEcT is now suitable to estimate the full set of kinetic rates from standard time-course RNA-seq experiments. At steady state, the tool provides the quantification of the processing over degradation rate ratio which is not informative about any specific layer of the RNA life cycle but allows the identification of post-transcriptional regulations between conditions.
Projects
I am currently collaborating with colleagues from the Polytechnic of Turin on the development of a bayesian framework for the study of RNA dynamics based on Gaussian Mixture Models. This approach, which includes genes clustering in the inference procedure, allows to exploit all the information available in the dataset with a consequent improvement of the quality of the models. Moreover, it provides a method for the automatic clustering of the kinetic rates according to non-trivial features.
I am also working on the study of RNA dynamics in the context of m6A metabolism. Specifically, I am developing a computational approach based on Nanopore sequencing data to investigate, at the single molecule and isoform resolution, the effect of RNA methylation on transcriptional and post-transcriptional dynamics (Furlan et al. 2020).
First authorship
I received my Ph.D. Cum Laude
I received my Master's degree Cum Laude and Honourable Mention
L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.
IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.
Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.
Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei, 17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali
La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.
Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance). The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.
IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators, 110 researchers and technologists, 350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion is 41% female against 59% male.
In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.
So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications, 12 up start-ups and as many which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.
