www.ibpm.cnr.it

RESEARCH INTERESTS

My fields of expertise include cancer genomics and epigenomics. Over the past 18 years of research in genomics, I have gained extensive experience in the analysis of data produced by high-throughput sequencing (HTS) technologies. In particular, I have specialized in leveraging HTS data 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.

Through this work, I have developed expertise in integrating complex genomic datasets generated by various HTS methodologies, including RNA-Seq, PAR-CLIP, and RIP-Seq. More recently, I have been exploring the integration of large-scale expression and annotation data for the functional investigation of moonlighting proteins and their potential role in different cancer types.

In addition, my lab has recently embarked on a new line of research focused on applying machine learning approaches in functional genomics. One such investigation is centered on studying phenotypic clusters predictive of susceptibility to SARS-CoV-2 infection and COVID-19 disease outcomes, utilizing large-scale serological, epidemiological, genetic, and clinical data from the SerGenCovid-19 study of the National Research Council (CNR).

SELECTED PUBLICATIONS

1) Pacelli C, Rossi A, Milella M, Colombo T, Le Pera L. RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping. Int J Mol Sci. 2023 Oct 3;24(19). doi: 10.3390/ijms241914862. PubMed PMID: 37834310.

2) Caudai C, Galizia A, Geraci F, Le Pera L, Morea V, Salerno E, Via A, Colombo T. AI applications in functional genomics. Comput Struct Biotechnol J. 2021;19:5762-5790. eCollection 2021. Review. doi: 10.1016/j.csbj.2021.10.009, PMID: 34765093.

3) Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci. 2020 Jun 30;21(13). doi: 10.3390/ijms21134684. Review. PubMed PMID: 32630140.

4) 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.

5) 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.

6) Krell J, Stebbing J, Carissimi C, Dabrowska AF, de Giorgio A, Frampton AE, Harding V, Fulci V, Macino G, Colombo T*, 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. (*) shared last authorship.

7) 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. (*) shared first authorship.

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. (*) shared first authorship.

COLLABORATIONS

Collaborations at IBPM:

• Giulia Guarguaglini
• Veronica Morea

• Angela Tramonti

Collaborations at CNR:

• Claudia Caudai, Ist. di Scienza e Tecnologie dell'Informazione "A. Faedo" (ISTI), Pisa
• Antonella Galizia, Ist. di Matematica Applicata e Tecnologie Informatiche "E. Magenes" (IMATI), Genova
• Filippo Geraci, Ist. di Informatica e Telematica (IIT), Pisa
• Armida Torreggiani, Ist. per la Sintesi Organica e la Fotoreattività (ISOF), Bologna
• Emanuele Salerno, Ist. di Scienza e Tecnologie dell'Informazione "A. Faedo" (ISTI), Pisa

External Collaborations:

• Anna Marabotti, Dip. di Chimica e Biologia, Università di Salerno
• Michele Milella, Dip. di Ingegneria per la medicina di innovazione, Università di Verona

• Loredana Le Pera, Grandi Strumentazioni e Core Facilities (FAST), Istituto Superiore di Sanità

• Stefania Millevoi, Cancer Research Center of Toulouse, INSERM
• Andreas Zanzoni, Aix-Marseille University

• Allegra Via, Dip. di Scienze Biochimiche "A. Rossi Fanelli", Università Sapienza di Roma

LINK

Author page on ORCID: link

CV

I am a biologist who transitioned into bioinformatics immediately after graduating from the Sapienza University of Rome in 2002. Later that year, freshly graduated, I encountered the "dry" approach to molecular biology when I enrolled in the newly-established Master’s course in "Bioinformatics: Biomedical and Pharmaceutical Applications," led by Prof. Anna Tramontano at the Department of Biochemical Sciences "A. Rossi Fanelli" at Sapienza. It was love at first sight.

Since then, I have honed my bioinformatics skills through a fortunate series of professional experiences and years of passionate work in laboratories and centers of excellence both in Italy and abroad. These include the Center for Comparative and Functional Genomics at New York University, the Unit of Systems Biology of Gene Regulatory Elements at the Max Delbrück 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 the Institute for System Analysis and Computer Science "Antonio Ruberti" at the National Research Council. Along the way, I had the privilege of working with outstanding scientists such as Prof. Nikolaus Rajewsky and Prof. Giuseppe Macino.

Since 2009, I have been consistently teaching bioinformatics in various academic and advanced courses, including both curricular and postgraduate programs. Since 2017, I have also been dedicated to introducing and promoting bioinformatics in high schools through targeted PCTO (Pathways for Transversal Competences and Orientation) programs. Additionally, I am actively involved in scientific dissemination and the promotion of STEM careers among young people, participating in various science festivals and outreach activities.

A full and updated list of my co-authored publications is available here

For a more detailed professional CV, please visit my ORCID profile at this link

User Login