Research Summary
My research focuses on the Design and development of efficient algorithms and data structures for sequence analysis with application to Bioinformatics. I am interested in both methodological and theoretical aspects related to the efficiency of the proposed algorithms and data structures, and software development for the application to real data analysis.
During my carrier I have been working on different computational problems in bioinformatics, starting with motif discovery during my PhD, and then moving to alignment-free techniques applied to phylogeny and metagenomics to solve clustering and classification problems.
Recently I have been working on phenotype prediction and variant calling, exploting machine and deep learning techniques with a focus on explainable AI, within a collaboration with the Comparative Biomedicine and Food Science department (BCA) on a PNNR Project first, and now on the European project EUAqua.
Moreover, results on general aspects of pattern matching can be applied also in contexts other than bioinformatics. This led in the past to collaborations with collegues working on different fields, for example text processing and temporal data analysis for smart cities.
Research Projects
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EUAqua.Org is a research project funded by Horizon Europe that is advancing innovative breeding for sustainable and organic European aquaculture
Role: I collaborate with the department of Comparative Biomedicine and Food Science (BCA) of Unipd in the desing and development of bioinformatics pipeline for the analysis of SNP data from several fish species. -
The CONVECS project (COmuNità VEneta per il Calcolo Scientifico) provides a high-performance computing infrastructure to support outstanding scientific research and promote the development of innovative technological applications.
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The National Biodiversity Centre conducts research and promotes the development of solutions to monitor, preserve, and restore functional biodiversity, with the aim of mitigating anthropogenic impacts and the effects of climate change, and supporting ecosystem services.
Role: Participant in Spoke n. 2 - Solutions to reverse marine biodiversity loss and manage marine resources sustainably. I have supervised two young researchers exploring machine learning techniques for phenotype prediction, and proposed new schemes for encoding biological information. -
Financed by the Department of Information Engineering, University of Padova
Role: participant. Collaborating in the development of novel approaches for kmer sampling with application to metagenomics (SAKEIMA). -
PRIN Project 20122F87B2
co-financed by the Italian Ministry of Education, University and Research
Role: Principal Investigator. Coordination at the national level of three units, and at a local level of the University of Padova Unit, including the supervision of two young researchers. This research project proposed a synergetic design of models for data characterization and algorithms for data mining in order to infer hidden information from omics data that, on a selected number of specific contexts, allowed us to: (obj1) obtain a more meaningful and essential data description, including functional or structural information carried by omics data; (obj2) devise the best possible strategy to analyze the data, through the development of specialized algorithms. As a further contribution (obj3) of the project, the proposed techniques have been implemented as prototypes for bioinformatics analysis, in order to both validate the results and disseminate them to the interested communities. -
Financed by the University of Padova
Role: Co-writing of the project proposal and contribution to the design and devlopment of whole genome comparison algorithms. -
Financed by the European Union, MTKD-CT-2006-042794 under FP6.
Role: participant. Visiting the Renyi Institute of Mathematics of the Hungarian Academy of Science within the "transfer of knowledge" framework. Development of efficient algorithms for maximal subgraph extaction with application to animal monitoring. -
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Financed by Fondazione CARIPARO
Role:Participant -
Financed by the Italian Ministry of Education and Research
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Role: participant. During my post-doc in Helsinki I designed and developed several algorithms for weighted pattern matching, most notably MOODS, that is still currently used in bioinformatics pipelines. -
Funded by the Italian Ministry of Education and Research
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Financed by the University of Padova
Role: Participant with a research contract. I designed and implemented MOST a multistep approach for motif discovery. The paper was published as COVER PAPER on Nucleic Acid Research international journal.