• Istituto di Biologia e Patologia Molecolari

Tel :+39 06 49910556
Fax :+39 06 4440062

Istitute of Molecular Biology and Pathology - National Research Council
Department of Biochemical Sciences - A. Rossi Fanelli.
My fields of expertise include cancer genomics, epigenomics and non-coding RNAs. In my 15 years of research in bioinformatics I gained great experience in data analysis produced by high-throughput sequencing (HTS) technologies. In particular, I specialized in the use of data deriving from HTS technologies for the study of non-coding RNA molecules, such as micro- and long non-coding RNAs, and their functional interactions within gene co-expression networks in cancer. From here I gained expertise in the integration of complex sets of genomic data produced by various declinations of HTS methodologies (such as RNA-Seq, PAR-CLIP, RIP-Seq). Most recently I became interested in the study of enigmatic ultra-conserved regions residing in the human genome. Specifically, I’m investigating their potential role in diseases of great social impact, such as tumors, based on the analysis of large collections of genomic data made available from The Cancer Genome Atlas consortium.
1) Guzzi R, Colombo T, Paci P. Inverse Problems in Systems Biology: A Critical Review. Methods in molecular biology (Clifton, N.J.). 2018; 1702:69-94. PMID: 29119503.
2) Verduci L, Ferraiuolo M, Sacconi A, Ganci F, Vitale J, Colombo T, Paci P, Strano S, Macino G, Rajewsky N, Blandino G. The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex. Genome biology. 2017; 18(1):237. PMID: 29262850.
3) Paci P, Colombo T, Fiscon G, Gurtner A, Pavesi G, Farina L. SWIM: a computational tool to unveiling crucial nodes in complex biological networks. Scientific reports. 2017; 7:44797. PMID:28317894.
4) Conte F, Fiscon G, Chiara M, Colombo T, Farina L, Paci P. Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PloS one. 2017; 12(2):e0171661. PMID: 28187158.
5) Krell J, Stebbing J, Carissimi C, Dabrowska AF, de Giorgio A, Frampton AE, Harding V, Fulci V, Macino G, Colombo T. and Castellano L. TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network. Genome Res. 2016 Mar;26(3):331-41. doi: 10.1101/gr.191759.115. Epub 2015 Dec 23. PubMed PMID: 26701625; PubMed Central PMCID: PMC4772015. 
6) Tavolaro S, Colombo T, Chiaretti S, Peragine N, Fulci V, Ricciardi MR, Messina M, Bonina S, Brugnoletti F, Marinelli M, Di Maio V, Mauro FR, Del Giudice I, Macino G, Foà R, Guarini A. Increased chronic lymphocytic leukemia proliferation upon IgM stimulation is sustained by the upregulation of miR-132 and miR-212. Genes Chromosomes Cancer. 2015 Apr;54(4):222-34. doi: 10.1002/gcc.22236. Epub 2015 Feb 2. PubMed PMID: 25645730.
7) Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, Laneve P, Caffarelli E. Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells. RNA biology. 2015; 12(12):1323-37. PMID: 26480000.
8) Paci P, Colombo T, Farina L. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC Syst Biol. 2014 Jul 17;8:83. doi: 10.1186/1752-0509-8-83. PubMed PMID: 25033876; PubMed Central PMCID: PMC4113672.
9) Frampton AE, Castellano L, Colombo T, Giovannetti E, Krell J, Jacob J, Pellegrino L, Roca-Alonso L, Funel N, Gall TM, De Giorgio A, Pinho FG, Fulci V, Britton DJ, Ahmad R, Habib NA, Coombes RC, Harding V, Knösel T, Stebbing J, Jiao LR. MicroRNAs cooperatively inhibit a network of tumor suppressor genes to promote pancreatic tumor growth and progression. Gastroenterology. 2014 Jan;146(1):268-77.e18. doi: 10.1053/j.gastro.2013.10.010. Epub 2013 Oct 9. PubMed PMID: 24120476. 
10) Fulci V, Colombo T, Chiaretti S, Messina M, Citarella F, Tavolaro S, Guarini A, Foà R, Macino G. Characterization of B- and T-lineage acute lymphoblastic leukemia by integrated analysis of MicroRNA and mRNA expression profiles. Genes Chromosomes Cancer. 2009 Dec;48(12):1069-82. doi: 10.1002/gcc.20709. PubMed PMID: 19760605.
Collaborations at IBPM:
• Veronica Morea
• Rodolfo Negri
• Allegra Via
External Collaborations:
• Annalisa Polverari, Verona University, Verona, IT
• Elodie Vandelle, Verona University, Verona, IT 
• Mauro Biffoni, Istituto Superiore di Sanità (ISS), Rome, IT
• Luca Pasquini, Istituto Superiore di Sanità (ISS), Rome, IT
• Rodolfo Guzzi, Sapienza University, Rome, IT
• Leandro Castellano, University of Sussex, Brighton, UK 

Full and updated list of publications: link
Author page on Publons - Web of Science: link
Author page on ORCID: link

I’m a biologist who turned to Bioinformatics right after graduation, that occurred at the Sapienza University of Rome back in 2002. At the end of the same year, freshly graduaded, I first met the "dry"-approach to molecular biology enrolling in the Master course "Bionformatics: Biomedical and Pharmaceutical Applications" just established by Prof. Anna Tramontano in the Department of Biochemical Sciences "A. Rossi Fanelli" of the same Sapienza University. And it was love at first glance.
After that, I have been gaining skills in the field of bioinformatics though a fortunate series of professional experiences and years of passionate work conducted in laboratories and centers of excellence both in Italy and abroad (such as the Center for Comparative and Functional Genomics of New York University, the unit of Systems Biology of Gene Regulatory Elements of the Max-Delbruck Center for Molecular Medicine in Berlin, the Department of Cellular Biotechnology and Hematology at Sapienza University of Rome, as well as the Institute for applied mathematics "Mauro Picone" and Institute for system analysis and computer science "Antonio Ruberti" at the National Research Council), with the chance to work with outstanding scientists like Prof Nikolaus Rajewsky and the Prof Giuseppe Macino.
Since 2009, I have been steadily teaching bioinformatics in several academic and advanced courses.
A full and updated list of publications that I co-authored is available here
A more detailed professional CV is available on ORCID at this link