2006: PhD “Complexity in post-genomic biology”. University of Torino, Advisor M. Caselle.
2003: MS “Bioinformatics”. University of Milano-Bicocca, Advisor P. Ricciardi-Castagnoli.
2001: MSc “Industrial Biotechnologies”. University of Milano-Bicocca.
2011 Researcher. Team leader of the Epigenomics and Transcriptional Regulation unit at the Center for Genomic Science, c/o IFOM-IEO Campus, Milano.
2009 Postdoctoral Research Associate. Genomic Analysis Lab, Salk Institute, Advisor J.R. Ecker.
2007 Postdoctoral Research Associate. Biostatistic Division, Yale University, Advisor A. Molinaro.
2001 Computational biologist. Genopolis Consortium (University of Milano-Bicocca), Italy.
1999 Molecular biologist. University of Milano-Bicocca, Italy.
Current research activities
Myc-dependent dynamics of transcriptional and epigenetic regulation
Genomic and epigenomic determinants of RNA methylation (EPITRAN COST Action - European Epitranscriptomics Network)
Development of tools for the integrative analysis of public epigenomic HTS datasets
Past Research activities
Epigenomics
· Development of methods for the integrative analysis of heterogeneous HTS epigenomics datasets (Galeota E et al. Briefings in Bioinformatics 2016).
· Development of methods for the analysis of DNA methylation and epigenomics data: the methylPipe and compEpiTools R packages were developed for the integrative analysis of DNA methylation data and other epigenomics data; both packages are available in the Bioconductor project (Kishore K et al. BMC Bioinformatics 2015).
· Integrative analysis of transcriptional and epigenetic patterns associated with the modulation of Myc binding on the genome of mouse B-cells supports the notion that Myc acts primarily by regulating specific groups of genes, only indirectly leading to transcriptional amplification (Sabo A*, Kress TR*, Pelizzola M* et al. Nature 2014).
· Integrative analysis of the DNA methylomes of induced pluripotent stem cells (iPSC), stem cells, and somatic cells, reveal the presence of hotspots of aberrant epigenomic reprogramming in iPSC (Lister R*, Pelizzola M* et al, Nature 2010).
· The first single-base resolution maps of methylated cytosines in human embryonic stem cells and fetal fibroblasts (along with integrative analysis of mRNA, smallRNA, histone modifications, TFBS). Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes (Lister R*, Pelizzola M* et al, Nature 2009).
· Identification of DNA methylation markers in human melanoma samples (Koga Y*, Pelizzola M* et al. Genome Research 2009).
· Dissecting the relationship between promoter methylation and transcriptional activity: the role of the methyl-cytosines density, their distance from the TSS, and the promoter CpG content (Koga Y*, Pelizzola M* et al, Genome Res 2009).
· Modeling the relationship between MeDIP enrichment and the DNA methylation level: a model implemented in a Bioconductor library (MEDME) allows predicting absolute and relative methylation levels from MeDIP-chip enrichment values (Pelizzola M*, Koga Y* et al, Genome Res 2008).
Transcriptional Regulation
· Integrative analysis of the dynamics of transcriptional regulation following the MYC activation (de Pretis S et al. Genome Research 2017).
· Modeling the dynamics of transcriptional regulation: we developed INSPEcT, a computational tool for the genome-wide inference of the rates of RNA synthesis, degradation and pre-mRNA processing (de Pretis S et al. Bioinformatics 2015).
· AMDA: a pipeline for the automatic analysis of Affymetrix microarray data, providing a PDF report inclusive of results and documentation with one click software (Pelizzola M et al, BMC Bioinformatics 2006).
· PLGEM: a Bioconductor library including a global error model and its application for the identification of differentially expressed features in transcriptomics and proteomics datasets (Pavelka N*, Pelizzola M* et al, BMC Bioinformatics 2004; Pavelka N et al, Mol Cell Proteomics 2006).
Software Development
· OnASSIs: Ontology Annotation and Semantic SImilarity software
· INSPEcT: an R/Bioconductor package to study the dynamics of transcriptional regulation (de Pretis S et al. Bioinformatics 2015).
· compEpiTools: an R/Bioconductor package for the integrative analysis of epigenomics data (Kishore K et al. BMC Bioinformatics 2015).
· methylPipe: an R/Bioconductor package for the analysis of DNA methylation data (Kishore K et al. BMC Bioinformatics 2015).
· MEDME: an R/Bioconductor package for the analysis of MeDIP-chip data (Pelizzola M*, Koga Y* et al. Genome Research 2009).
· AMDA: an R package for the automatic microarray data analysis (Pelizzola M et al. BMC Bioinformatics 2006).
· PLGEM: an R/Bioconductor package for the identification of differentially epressed genes and proteins (Pavelka N*, Pelizzola M* et al. BMC Bioinformatics 2004).
Publications, last authorship:
Selected publications, first (co)authorship:
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.
