Stefano Ceri, Professor at Politecnico di Milano, will give a talk on Thursday, September 29th, 2016, 14:30, in Amphi Jade, Télécom ParisTech, 46 rue Barrault (Paris 13).
Data-Driven Genomic Computing
Abstract
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 or how environment influences cancer development.The GeCo Project (Data-Driven Genomic Computing, ERC Advanced Grant currently undergoing the contract preparation) has the objective or revisiting genomic computing through the lens of basic data management, through models, languages, and instruments; the research group of DEIB is among the few which are centering their focus on genomic data integration. Starting from an abstract model, we already developed a system that can be used to query processed data produced by several large Genomic Consortia, including Encode and TCGA; the system employs internally the Spark, Flink, and SciDB data engines, and prototypes can already be accessed from Cineca servers or be downloaded from PoliMi 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.
Most diseases have a genetic component, hence a system which is capable of integrating “big data” of genomics is of paramount importance. Among the objectives of the project, the creation of an “open source” system available to biological and clinical research; while the GeCo project will provide public services which only use public data (anonymized and made available for secondary use, i.e., knowledge discovery), the use of the GeCo system within protected clinical contexts will enable personalized medicine, i.e. the adaptation of therapies to specific genetic features of patients. The most ambitious objective is the development, during the 5-years ERC project, of an “Internet for Genomics”, i.e. a protocol for collecting data from Consortia and individual researchers, and a “Google for Genomics”, supporting indexing and search over huge collections of genomic datasets.
Bio
Stefano Ceri about himself:I am professor of Database Systems at the Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB) of Politecnico di Milano. I was visiting professor at the Computer Science Department of Stanford University (1983-1990). I was the chairman of the Computer Science Section of DEI (1992-2004), and the chairman of LaureaOnLIne, a fully online curriculum in Computer Engineering (2004-2008).
I was the director of Alta Scuola Politecnica, the school of excellence for top-level master students selected from Engineering, Architecture, and Design Faculties of Politecnico di Milano and Politecnico di Torino (October 2010 - September 2013).
I was associate editor of ACM-Transactions on Database Systems and IEEE-Transactions on Software Engineering, and I am currently an associated editor of several international journals. I am co-editor in chief (with Mike Carey) of the book series "Data Centric Systems and Applications"(Springer-Verlag).
I am a member of the Executive Committee of ALFC - Associazione Lombarda Fibrosi Cistica (April 2013 - April 2016).
I am the recipient of the ACM-SIGMOD "Edward T. Codd Innovation Award" (New York, June 26, 2013). I am an ACM Fellow and a member of Academia Europaea.
