Cross-cutting computational approaches for the multi-omics scene
Staff - Faculty of Informatics
Date: / -
USI Lugano Campus, room SI-004, Informatics building (Via G. Buffi 13)
Vincenzo Bonnici, University of Verona, Italy
In the last decades, advantages in data gathering technologies in the biotechnological field have allowed previously uncovered investigation perspectives for analysing the internal system of biological cells, their interaction with external agents and even their evolutionary history. In this, a biological system can be seen as a scene in which different omic domains give specific points of view, and the research, like a director, has to cut and merge them in order to obtain the perspective that best describes the studied phenomenon.
Recent methodologies try to face multi-omic scenes by developing holistic models in which all such an heterogeneity is merged together in an highly abstractive representation. A disadvantage in such approaches is the flattening of the informational diversity in the biological scene. Alternative approaches integrate evidences extracted from specific omic data into heterogeneous models for the investigation of different but related biological cuts.
In this seminar, approaches that exploit theoretical results or empirical observations obtained in one or more omic domain for the investigation of other domains are presented. The omic knowledge is often represented via networks for which the search for specific substructures is a fundamental but hard to solve problem, thus efficient solutions are researched. Such methods often require big computational resources, thus the engineering of suitable data structures and the development of solutions based on parallel computation play a key role in their application to real-life cases. Parallel architectures, such as SMPs and GP-GPUs, are exploited by adapting the needs of theoretical solutions to the constraints of the specific hardware.
Vincenzo Bonnici is currently a research fellow at the Department of Computer Science of the University of Verona. His research interests are bioinformatics, computational biology, algorithms and data structures, graph theory and parallel computing. He received the Master degree in Computer Science from the University of Catania (Italy) in 2011, and the PhD degree in Computer Science from the University of Verona (Italy) in 2015. His master thesis was focused on solving the subgraph isomorphism problem for biological networks. For the PhD thesis, he extended his interest to other bioinformatic fields such as genome sequence analysis and omic data integration. He has been abroad for his scientific studies and training at the Institute for Genomics and Bioinformatics of the University of California, Irvine (USA), and at the Fondazione per la Ricerca e la Cura dei Linfomi nel Ticino, Istituto Oncologico della Svizzera Italiana, Bellinzona (CH). He has been a temporary professor for the Bachelor degree in Computer Science, and he is temporary professor for the Bachelor degree in Bioinformatics and student mentor for the Master degree in Medical Bioinformatics. He his reviewer for several scientific journal published by IEEE, Elsevier, Frontiers, Oxford University Press and Springer. He has been editor for the MDPI journals Future Internet and Energies, and he is review editor for the Applied Mathematics and Statistics Journal of Frontiers.
Hosts: Prof. Rolf Krause (ICS) and Dr. Luciano Cascione (IOR)