Director Prof. Michele Ceccarelli

The Computational Biology Laboratory, coordinated by Prof. Michele Ceccarelli, is a multidisciplinary research group dealing with computational biology and precision oncology. The main research areas of the laboratory are:

• Cancer genomics and drug resistance. This research area focuses on the in-depth analysis of the molecular mechanisms that drive cancer progression and the development of resistance to oncological treatments. Specific attention is paid to gliomas, a particularly aggressive and complex form of brain tumor. Cancer genomics investigates the genetic and genomic alterations that contribute to the malignancy of tumors, identifying mutations, amplifications and deletions in genes that regulate cell growth and response to drugs. The main goal is to understand how these molecular alterations influence the behavior of tumors and their resistance to treatments. Through the analysis of the genetic and transcriptional profiles of tumor cells, researchers can identify predictive biomarkers of drug response and resistance.

• Immunological characterization of tumors. Using advanced technologies such as Next-Generation Sequencing (NGS), the laboratory develops computational approaches to analyze the tumor microenvironment. The study of the mechanisms of interaction between the immune system and cancer cells mainly aims at the identification of biomarkers that can predict the response to immunotherapies. The laboratory is actively involved in a research project funded by AIRC (Italian Association for Cancer Research) to study the role of methylation in tumor progression in patients affected by metastatic melanoma and pleural mesothelioma.

• Development of bioinformatics tools. The laboratory is specialized in the development of open-source bioinformatics software for the analysis and integration of omics data, improving the identification of genetic mutations and the immune characterization of tumors, including: SCEVAN for the identification of the clonal structure of tumors; MOViDA, a deep learning-based approach, used for the prediction of drug sensitivity; scTHI that analyzes ligand-receptor interactions to identify the mechanisms of communication between the tumor and the host cells. The laboratory also developed the CPTACBiolinks and TCGABiolinks software, widely used by the scientific community for downloading and analyzing CPTAC and TCGA data.

• Early diagnosis of tumors. The laboratory research focuses on the development of advanced tests for the early diagnosis of tumors, based on the DNA methylation analysis from liquid biopsies. DNA methylation techniques are crucial for identifying epigenetic modifications associated with the tumor onset and progression. Through the analysis of specific biomarkers in circulating DNA, it is possible to develop non-invasive tests that make possible to detect early signals of tumor lesions and to constantly monitor the patients and to adapt the treatments according to changes in the epigenetic profile.

Furthermore, the computational biology laboratory actively collaborates with top-level international research institutions, combining expertise in oncology, immunology and bioinformatics, and contributing to the advancement of knowledge in the field of personalized cancer therapy.