Course on Bioinformatics for Integrative Genomics

Exploring and making sense of multidimensional data sets that result from merging heterogeneous genomic data resources

21-22 June 2011

Course Description

In the last few years, the study of the genetic basis of complex diseases has undergone a profound transformation. High-throughput techniques, such as microarrays and next generation sequencing technologies, allow scientists to identify alterations at genome-wide level in patient’s genomes and transcriptomes. The application of these technologies yields complex, multidimensional genomic data sets that describe in detail the myriad changes that occur within individual cells and how these changes differ between patients, cells or conditions. Usually we want to use this data to answer some specific questions. For instance, which of the long list of mutations detected are likely to affect the function of the protein and which are probably neutral? Which of the genes affected by those mutations are already known to be involved in cancer or other diseases? Which pathways or biological processes are affected by the transcriptomic alterations detected in my experiment? Etc.

We need to apply bioinformatic approaches to answer these questions. The course will provide the students with theoretical and practical expertise in the field of bioinformatics for integrative genomics. Attendees will be updated on the state of the art in the field and they will become capable of handling and analyzing genomics data. Upon completion, the attendees will be able to perform integrative analysis and interpret the results, in order to answer specific biological questions.

To achieve these objectives we will use three tools developed in our lab:

IntOGen: Integrative OncoGenomics (IntOGen:, a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.

Reference: Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney S and Lopez-Bigas N. IntOGen: Integration and data-mining of multidimensional oncogenomic data. Nature Methods, 7, 92-93 (2010)

Gitools ( is a framework for analysis and visualization of genomic data. Data and results are represented as interactive heatmaps. Gitools allows importing data directly from IntOGen, Biomart, KEGG and Gene Ontology. It performs several analyses like enrichment analysis, correlations, overlaps, identification of driver alterations and combination of experiments.

Reference: Christian Perez-Llamas and Lopez-Bigas N. Gitools: analysis and visualization of genomic data using interactive heat-maps. PLoS ONE 6, e19541 (2011)

Condel ( is a method to integrate the output of various methods to identify deleterious non-synonymous variants, which we have shown to perform significantly better that any of the methods alone. Condel outputs a score for each SNVs that can be used as an indicator of the impact of the mutation on the functionality of the mutant protein.

Reference: Abel Gonzalez-Perez and Lopez-Bigas N. Improving the assessment of the outcome of non-synonymous SNVs with a Consensus deleteriousness score (Condel). Am J Hum Genet, 88(4):440-9 (2011).


Nuria Lopez-Bigas is the head of the Biomedical Genomics group at the Universitat Pompeu Fabra in Barcelona. She completed her PhD degree on 2002 on the molecular basis of deafness at the Oncologic Research Institute in Barcelona. She then moved to the European Bioinformatics Institute in Hinxton (Cambridge, UK) to initiate a project on the computational study of disease and cancer genes. Since 2006 is a group leader at the UPF focusing on cancer genomics and bioinformatics.
Universitat Pompeu Fabra (UPF), Barcelona, Spain

Sophia Derdak obtained her PhD in immunology from the Medical University of Vienna, Austria, in 2003. After a postdoctoral project at the German Cancer Research Center (Heidelberg, Germany), she moved to Barcelona to work in cancer biomarker discovery at Oryzon Genomics before joining the Biomedical Genomics Group in 2010. She is interested in integrative Omics, personalized genomics and the analysis of Next Generation Sequencing data.

Alba Jené-Sanz is a Biologist from the Universitat Pompeu Fabra. She has a Master in Bioinformatics from the same university and she is currently pursuing a PhD at the Biomedical Genomics group of the University Pompeu Fabra. Her main interests are the study of regulatory pathways in cancer from an epigenomics point of view, and the use of sequencing technologies for large-scale cancer genomics studies.
Universitat Pompeu Fabra (UPF), Barcelona, Spain

Target Audience

The course is directed to researchers in biology and medicine. Background knowledge in bioinformatics is not necessary.

Course Pre-requisites

Basic Molecular Biology. Elementary computing skills.


Participation to the course is free of charge and open to all the scientific community, but you need to register.

In order to register please send a CV and a motivation letter to Melquíades Calzado (mcalzado at imim dot es)

The course will be held within the UPF (Universitat Pompeu Fabra) facilities in the Life and Health Sciences building, which is next to the Barcelona Biomedical Research Park (PRBB). Follow this link for the exact location in the map.

Universitat Pompeu Fabra
Dr. Aiguader building (Mar campus) - Doctor Aiguader, 80
08003 Barcelona, Spain

More detailed information will be provided soon.

Follow this link to the COURSE SITE.