Education
January 2014 - December 2017: PhD in Computational Biology at European School of Molecular Medicine (SEMM), Milan, Italy.
Project title: “Genomic landscape and transcriptional regulation by Yap and Myc in the liver”
October 2010 - March 2013: Master's Degree in Medical, Molecular and Cellular Biotechnology, S. Raffaele University in Milan, Italy. Final mark: 110/110 cum laude.
Thesis title: “Functional and structural studies on the murine Sphingosine Kinase 2”
October 2007 - November 2010: Bachelor's Degree in Medical and Pharmaceutical Biotechnology, S. Raffaele University in Milan, Italy. Final mark: 110/110 cum laude.
Thesis title: “Computational analysis and structural interpretation of a missense mutation of the serum Transferrin associated with Human Congenital Hypotransferrinemia”
September 2002 - July 2007: High school leaving qualification in Chemistry, Cannizzaro Institute, Rho, Milan. Final mark: 100/100.
Working experience
April 2018 - Present: Postdoctoral researcher at Italian Institute of technology (IIT), Milan, Italy.
January 2018 - March 2018: Fellowship at Italian Institute of technology (IIT), Milan, Italy.
ChroKit: a web-based framework to interactively analyze and visualize genomic data
The advent of Next-generation sequencing (NGS) technologies strongly increased our capacity to investigate the mechanisms of gene regulation at genome-wide level. However, the biological interpretation of the high amount of data produced by NGS experiments requires deep knowledge of biological systems and computational skills. Therefore, there is a growing need within the scientific community for the development of computational tools which will enable biologists to directly analyse this kind of data in a fast and intuitive way. To this end, I developed ChroKit (The Chromatin ToolKit), a web-based framework that performs comprehensive genomic analyses with an interactive and user-friendly GUI.
The program accepts, as input, a list of genomic regions of interest or a list of genes and the aligned reads from the NGS experiments (bam/wig files). These data are then elaborated to help the biologists to understand the biological system under investigation. It allows the user to perform logical operations (i.e. union, intersection and others) on genomic regions defined by selected signals (i.e. TF binding, chromatin modifications, chromatin accessible regions, nucleosome positions and others), to resize genomic regions to a user-defined width, randomly subsample regions or center them at the point of maximum enrichment (summit detection) and to perform quantitative determination of signals within the defined regions (for example, calculate the intensity of selected chromatin marks in a subset of promoters). The results of these analyses can be displayed within ChroKit using a set of visualization tools commonly used in Genomics, such as boxplots and heatmaps. Some of these plots can be easily manipulated by point and click operations, thus allowing “on the fly” re-analysis and subsetting of the regions of interests.
This application is multiplatform and can be deployed on a server to take advantage of computational resources and share data and working sessions.
ChroKit source code can be found on GitHub at https://github.com/ocroci/ChroKit
Genome-wide transcriptional regulation by YAP in the liver
YAP, a transcriptional co-factor, is the downstream regulator of the Hippo pathway. When this pathway is switched off, YAP translocates into the nucleus and promotes the expression of genes involved in cell cycle, cell growth and de-differentiation together with its transcription factor binding partner, TEAD. Aberrant activity of YAP leads to hepatomegaly and oncogenic growth of hepatocytes. Our research activity is focused on the dissection of the mechanisms of the transcriptional regulation mediated by YAP in the liver.
As a model, we used transgenic mice in which an activated form of YAP is conditionally expressed in the liver. ChIP-Seq analyses reveals that YAP chromatin binding is dependent on TEAD and its activation leads to further chromatin binding, especially in distal regulatory elements. YAP induction is associated with the expression of genes involved in inflammation, cell cycle and liver cancer by promoting RNAPol2 pause release from their promoters. YAP also represses HNF4a target genes by reducing RNAPol2 elongation and chromatin accessibility on the promoters of these genes.
Bianchi, V., Ceol, A., Ogier, A., de Pretis, S., Galeota, E., Kishore, K., Bora, P., Croci, O., Campaner, S., Amati, B., Morelli, M.J., Pelizzola, M. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions. Front. Genet. 2016 May 6.
Donato, E., Croci, O., Sabò, A., Muller, H., Morelli, M.J., Pelizzola, M., Campaner, S. Compensatory RNA Polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc driven tumors. Leukemia. 2016 June 24.
Croci, O., De Fazio, S., Biagioni, F., Donato, E., Caganova, M., Curti, L., Doni, M., Sberna, S., Aldeghi, D., Biancotto, C., Verrecchia, A., Olivero, D., Amati, B., Campaner, S. Transcriptional integration of mitogenic and mechanical signals by Myc and YAP. Genes Dev. 2017 November 15.
Donato, E., Croci, O., Campaner, S. Elongation vs stalling: place your BET. Oncotarget. 2017 December 6.
Blaževitš, O., Bolshette, N., Vecchio, D., Guijarro, A., Croci, O., Campaner, S., Grimaldi, B. MYC-Associated Factor MAX is a Regulator of the Circadian Clock. Int J Mol Sci. 2020 March 26.
Wei, Q., Holle, A., Li, J., Posa, F., Biagioni, F., Croci, O., Benk, AS., Young, J., Noureddine, F., Deng, J., Zhang, M., Inman, GJ., Spatz, JP., Campaner, S., Cavalcanti-Adam, EA. BMP-2 Signaling and Mechanotransduction Synergize to Drive Osteogenic Differentiation via YAP/TAZ. Adv Sci (Weinh). 2020 June 16.
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.
