Centro de Investigacion Principe Felipe

Description of Organizationpfcirgb72-4

The Prince Felipe Research Center (Centro de Investigacion Principe Felipe, CIPF) is a non-profit foundation. The center´s mission is to become the platform for Biomedical Research and Technological Health Innovation in the Valencia Region. The CIPF is currently composed of three main programs that cover different aspects of omics technologies and diseases. The Computational Genomics Institute (CGI) carries out outstanding bioinformatics research in different areas of genomics from the point of view of systems biology, which include the study of PPI, regulatory networks, pathways, etc. In particular, the CGI is interested in the study of complex phenotypes, including diseases and, specifically, personalized medicine. The CGI is leader in the development of concepts, algorithms and applications for genomic data analysis, which comprise genome resequencing, transcriptomics, methylomics, etc., based on different technologies that cover from microarrays to NGS. The Biomedicine Institute aims to study the molecular bases of pathologies that require new diagnostics and clinical procedures for their identification, such as rare diseases, hepatic encephalopathy, diabetes or foetal alcohol syndrome, among others. The Biomedical Biotechnology Institute is dedicated to understand the molecular mechanisms underlying biological processes and alterations leading to pathological conditions using biochemical or genetic methods.


Previous experience

The ICG has vast experience in genomic data analysis as well as development of software for massive genomic data analysis and integration, having developed large-scale projects such as the Babelomics (http://www.babelomics.org). The ICG has been involved in several consortia, such as the Rat genome annotation (Saar et al., 2008, Nat Genet) or the FDA’s MAQC initiative to establish best practices for developing disease predictors using microarrays (Shi et al., 2010, Nat Biotech). At present the ICG is involved in several genomic initiatives. Two of them are related to genomics in the clinics: The Medical Genome Project (http://www.medicalgenomeproject.com/en), a private-public partnership aiming to sequence 1000 patients with genetic diseases (and 300 healthy controls) and the FutureClinic project, an initiative of the Regional Government of Valencia coordinated by the CIPF (http://www.futureclinic.es/), to include personalized genome information in the electronic health record of the patient. The ICG is also coordinating the STATegra, a FP7 funded EU project in the topic of health. STATegra aims at developing statistical methods for integration of NGS functional -omics data (RNA-seq, miRNA-seq, ChiP-seq, Methyl-seq, DNAse-seq, etc.), proteomics and metabolomics. The ICG also leads a consortium on HPC for genomic data analysis (http://bioinfo.cipf.es/hpc4g) focusing on developing algorithms and analysis pipelines that make use of HPC for the fast processing of large volumes of sequencing data.


Profile of staff members

Joaquin Dopazo, the Scientific Director of the CIPF and the Head of the CGI is an international reference in the field of genomic data analysis and functional genomics. He has launched several genomic projects such as the Medical Genome Project or the FutureClinic project. Ana Conesa heads the Genomics of Gene Expression Unit of the CGI and is a recognized expert in RNA-seq and transcriptomics. She leads the STATegra EU project. Ignacio Medina heads the Computational Biology Unit as is responsible for the large-scale software projects of the ICG. David Montaner heads the Biostatiscial Unit of the ICG and is an expert in massive data analysis and development of biostatistical algorithms.







Five recent publications relevant to the project

1) Bleda M, Medina I, Alonso R, De Maria A, Salavert F, Dopazo J. (2012) Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res . 40(Web Server issue):W168-72.


2) Medina I, De Maria A, Bleda M, et al. (2012) VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res 40(Web Server issue):W54-8.


3) Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. (2011) Differential expression in RNA-seq: A matter of depth. Genome research. 21(12):2213-23


4) Shi et al. (2010). The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 28(8):827-38.


5) Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J. (2010) Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic acids research. 38:W210-3. (Featured in NAR)