Talk by Stefano Ceri: Data-Driven Genomic Computing: Making Sense of the Signals from the Genome

20.07.2017 14:00
20.07.2017 15:00

CAB G 51 

Talk by Stefano Ceri (Politecnico di Milano, Italy): Data-Driven Genomic Computing: Making Sense of the Signals from the Genome


Genomic computing is a new science focused on understanding the functioning of the genome, as a premise to fundamental discoveries in biology and medicine. Next Generation Sequencing (NGS) allows the production of the entire human genome sequence at a cost of about 1000 US $; many algorithms exist for the extraction of genome features, or "signals", including peaks (enriched regions), mutations, or gene expression (intensity of transcription activity). The missing gap is a system supporting data integration and exploration, giving a “biological meaning” to all the available information; such a system can be used, e.g., for better understanding cancer development. The GeCo Project (Data-Driven Genomic Computing, ERC Advanced Grant, 2016-2021) has the objective or revisiting genomic computing through the lens of basic data management, through models, languages, and instruments, focusing on genomic data integration. Starting from an abstract model, we developed a query language and data management system that can be used to query processed genomic data; the system employs internally the Spark engine, and prototypes can already be downloaded or accessed from our servers. During the five-years of the ERC project, the system will be enriched with data analysis tools and environments and will be made increasingly efficient. Among the objectives of the project, the creation of an “open source” repository of public data, available to biological and clinical research through queries, web services and search interfaces. At the end of the seminar, Pietro Pinoli (GeCo post-doc) will explain how biological applications are systematically addressed using GMQL integrated with Python, and Anna Bernasconi (GeCo PhD student) will describe the first results in the development of the public repository (integration of TCGA, Encode and Geo).


Stefano Ceri is professor of Database Systems at the Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB) of Politecnico di Milano; he was visiting professor at the Computer Science Department of Stanford University (1983-1990). His research work covers four decades (1976-2016) and is generally concerned with extending data technologies in order to incorporate new features: distribution, object-orientation, rules, streaming data; with the advent of the Web, his research has been targeted towards the engineering of Web-based applications and to search systems. More recently he turned to crowd searching, to social media analytics, and to genomic computing. He is the recipient of two ERC Advanced Grants: "Search Computing (SeCo)" (2008-2013), focused upon the rank-aware integration of search engines in order to support multi-domain queries and “Data-Centered Genomic Computing (GeCo)” (2016-2021), focused upon new abstractions for querying and integrating genomic datasets. He is the recipient of the ACM-SIGMOD "Edward T. Codd Innovation Award" (New York, June 26, 2013), an ACM Fellow and a member of Academia Europaea.