Davide Prandi



Short Bio

I am a researcher in the Software Engineering Unit of the Digital Industry center in FBK. My research focusses on model-based design and automatic test generation.

During my PhD at the University of Trento, from 2003 to 2006, I studied programming languages semantics and concurrency theory with application in the domains of systems biology and web semantics. In particular, I worked on the stochastic semantics of process algebras and their quantitative model checking. In 2008, I joined the Microsoft Research - University of Trento Centre for Computational and Systems Biology(COSBI) developing methods for efficient simulation and formal verification of stochastic parallel programs. In 2010, I moved to the Department of Cellular, Computational and Integrative Biology (CIBIO) at the University of Trento. At CIBIO, I developed a method to infer the order in which genetic aberrations emerge in cancer based on a graph representation of tumor evolution.

Selected Publications

    • Ferdous, R., Kifetew, F., Prandi, D., Prasetya, I.S.W.B., Shirzadehhajimahmood, S. and Susi, A., 2021. Search-Based Automated Play Testing of Computer Games: A Model-Based Approach. In International Symposium on Search Based Software Engineering (pp. 56-71). Springer, Cham. DOI: 10.1007/978-3-030-88106-1_5

    • Locallo, A., Prandi, D., Fedrizzi, T. and Demichelis, F., 2019. TPES: tumor purity estimation from SNVs. Bioinformatics, 35(21), pp.4433-4435. DOI: 10.1093/bioinformatics/btz406

    • Persi, E., Prandi, D., Wolf, Y.I., Pozniak, Y., Barnabas, G.D., Levanon, K., Barshack, I., Barbieri, C., Gasperini, P., Beltran, H. and Faltas, B.M., 2019. Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Proceedings of the National Academy of Sciences, 116(34), pp.16987-16996. DOI: 10.1073/pnas.1908790116

    • Faltas, B.M., Prandi, D., Tagawa, S.T., Molina, A.M., Nanus, D.M., Sternberg, C., Rosenberg, J., Mosquera, J.M., Robinson, B., Elemento, O. and Sboner, A., 2016. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nature genetics, 48(12), pp.1490-1499. DOI: 10.1038/ng.3692

    • Beltran, H., Prandi, D., Mosquera, J.M., Benelli, M., Puca, L., Cyrta, J., Marotz, C., Giannopoulou, E., Chakravarthi, B.V., Varambally, S. and Tomlins, S.A., 2016. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nature medicine, 22(3), pp.298-305. DOI: 10.1038/nm.4045

    • Abeshouse, A., et al., 2015. The molecular taxonomy of primary prostate cancer. Cell, 163(4), pp.1011-1025. DOI: 10.1016/j.cell.2015.10.025

    • Prandi, D., Baca, S.C., Romanel, A., Barbieri, C.E., Mosquera, J.M., Fontugne, J., Beltran, H., Sboner, A., Garraway, L.A., Rubin, M.A. and Demichelis, F., 2014. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome biology, 15(8), pp.1-16. DOI: 10.1186/s13059-014-0439-6

    • Baca, S.C., Prandi, D., Lawrence, M.S., Mosquera, J.M., Romanel, A., Drier, Y., Park, K., Kitabayashi, N., MacDonald, T.Y., Ghandi, M. and Van Allen, E., 2013. Punctuated evolution of prostate cancer genomes. Cell, 153(3), pp.666-677. DOI: 10.1016/j.cell.2013.03.021

    • Dematté, L. and Prandi, D., 2010. GPU computing for systems biology. Briefings in bioinformatics, 11(3), pp.323-333. DOI: 10.1093/bib/bbq006

    • Forlin, M., Mazza, T. and Prandi, D., 2010. Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. In 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification (pp. 105-115). IEEE. DOI: 10.1109/PDMC-HiBi.2010.22

    • Ballarini, P., Forlin, M., Mazza, T. and Prandi, D., 2009. Efficient parallel statistical model checking of biochemical networks. In 8th Int. Conf. on Parallel and Distributed Methods in Verification (PDMC09), EPTCS 14, 2009, pp. 47-61. DOI: 10.4204/EPTCS.14.4

    • Mura, I., Prandi, D., Priami, C. and Romanel, A., 2009. Exploiting non-Markovian bio-processes. Electronic Notes in Theoretical Computer Science, 253(3), pp.83-98. DOI: 10.1016/j.entcs.2009.10.007