Research
Who I am
I work as Post Doctoral Researcher in the Genomic Computing (GeCo) project led by Professor Stefano Ceri at the Department of Electronics, Information and Bioengineering of Politecnico di Milano.
I received my PhD in February 2021, with a thesis on integration of genomic data and metadata. My advisors were Prof. Stefano Ceri and Prof. Alessandro Campi.
Projects
My main research area is data-driven Genomic Computing. I am interested in modeling genomic data and metadata with the aim to collecting heterogeneous sources in integrative repositories solving a number of problems, such as schema unification and value harmonization (possibly with biomedical ontologies). I also investigate effective methodologies for searching datasets for downstream analysis. Providing domain experts with successful search procedures means joining data integration efforts with usability and effectiveness of user interfaces.
If you are a master student, you may want to check my thesis proposals on genomic data integration.
In the last two years I worked mainly on viral sequences integration and search. We reapplied some of the paradigms observed for human genomics, but on a novel problem: making sequences characteristics explicit and comparable so to help mitigate the fight against COVID-19, which is involving the broad scientific community in the last months.
If you are a master student, you may want to check my thesis proposals on viral sequences processing.
Always on the problems related to COVID-19 I also investigated characteristics of COVID-19 communication, based on IT platforms, dashboards, and Geographical Information Systems. In the last months, there has been an emergence of data visualization tools that offer an interesting (yet very limited) perspective on the disease.
As a follow up of my master thesis, I continued a minor research path on Formal Methods applied to partial models (i.e., systems that may be incomplete in the specifications of some parts — either states or transitions).
Research collaborations
I collaborated with the Bioinformatics group of the Institute of Systems Analysis and Computer Science Antonio Ruberti of the Italian National Research Council (IASI – CNR) and Università degli Studi Roma Tre for a study on data integration from the biggest repository of open cancer genomics data (Genomic Data Commons). We realized a system that allows to import and transform such data, by enriching it with annotations and identifiers useful for integration with other sources. OpenGDC can be found at http://geco.deib.polimi.it/opengdc/.
I collaborated with the group of Prof. Mario Cannataro (University “Magna Græcia” di Catanzaro) for an application of the GenoMetric Query Language to computations that combine both public and private datasets.
I am organizing the 1st Workshop on Conceptual Modeling for Life Sciences (http://www.bioinformatics.deib.polimi.it/cmls/) in conjunction with the International Conference of Conceptual Modeling ER 2020. The organization is in collaboration with the PROS group of Prof. Oscar Pastor at Universidad Politècnica de València.
We are collaborating with the group of Ilaria Capua at One Health Center of Excellence, Gainesville, Florida to understand the requirements of virologists using software to search and analysis viral sequences.
I am collaborating with the group of Prof. Wolfgang Nejdl at Leibniz University of Hannover on a new project of genomic data protection.
I am working with Dr. Claudio Menghi on formalizing techniques for combining model checking and theorem proving for partially specified systems, particularly working on Linear Temporal Logic properties.