Computational Genomics @ PRBB

Groups

Mar Albà

Mar Alba

Evolutionary Genomics, IMIM

Research in our group focuses on the use of comparative genomics and large-scale data analysis to gain an understanding on the evolution of genes and genomes and to predict functional elements. We have a strong computational focus but collaborate with experimental groups in some of our projects.

Robert Castelo

Robert Castelo

Functional Genomics, UPF

Research in our group aims at contributing to narrow the gap between sequence and function by developing computational tools to build network models of molecular regulatory mechanisms from high-throughput genetics and genomics data.

Eduardo Eyras

Eduardo Eyras

Regulatory Genomics, UPF

Our group focuses on the development of computational predictive models for the study of RNA biology. In particular, we are interested in the role of chromatin and non-coding RNAs in the regulation of splicing, and the relevance of these mechanisms in cancer.

Guillaume Filion

Guillaume Filion

Genome Architecture, CRG

The 20th century has been the triumph of genetics. However, we fully understand a mere 3% of the human genome - that is, the coding genome. More challenging is to understand how this tiny fraction is orchestrated by the much larger regulatory genome. What does the regulatory genome consist of? How does it encode information? How is it organized and how does it evolve? Contrary to the coding genome, the information of the regulatory genome is context-dependent. For example, the same promoter can have different levels of activity, the same enhancers can activate one gene or another, depending on available transcription factors and on the local chromatin marks. So the DNA sequence is not enough to understand the function of regulatory sequences. Our research lines focus on the influence of the chromatin context on transcription; and on the co-evolution between the genome and its chromatin context.

Toni Gabaldón

Toni Gabaldón

Comparative Genomics, CRG

The main research interest of our group is to understand the complex relationships between genome sequences and phenotypes and how these two features evolve across species. We generally use large-scale phylogenetics approaches that allow looking at the evolution of genomes from the perspective of all of their genes, and we apply these analyses to a variety of biological questions related the evolution and function of organelles, pathways, and protein and lncRNA families.

Roderic Guigó

Roderic Guigó

Bioinformatics and Genomics, CRG

The overarching theme of the research in our group is the understanding of the information encoded in genomic sequences, and how this information is processed in the pathway leading from DNA to protein sequences. We are specficially interestes in RNA processsing and its genetic and epigenetic regulation.

Heinz Himmelbauer

Heinz Himmelbauer

Genomics unit, CRG

The scope of the Genomics Unit is to provide excellent, state-of-the-art services in the fields of microarray technology and next-generation sequencing. Furthermore, the Unit is dedicated to test, implement, and to develop new protocols (wet lab and bioinformatics) to advance the analysis of genes and genomes. Such work includes, for instance, the identification of biases in high-throughput sequencing data, and the development of robust procedures for the assembly of complex genomes as prerequisite to their annotation.

Fyodor Kondrashov

Fyodor Kondrashov

Evolutionary Genomics, CRG

We are currently a small laboratory mostly utilizing computational tools to invertigate questions of evolution on the molecular, cellular and organismal levels. At the same time we are actively developing an experimental venue of research, where we hope to be able to apply massive DNA sequencing technologies to ask simple questions on adaptation and selection in the field. We hope that our experimental efforts will supplement our theoretical and computational venues.

Nuria Lopez-Bigas

Nuria Lopez-Bigas

Biomedical Genomics, UPF

The Biomedical Genomics Group is focussed on the computational study of human genetic diseases, including hereditary diseases and cancer, at genomic level. The lab is at the frontier between medical genomics and bioinformatics, which requires a multidisciplinary formation of the team members.

Ernesto Lowy

Ernesto Lowy

Bioinformatics core unit, CRG

The Bioinformatics core facility aims to provide expertise and infrastructure to all researchers at the Center of Genomic Regulation (CRG), PRBB, and other external entities on different aspects of the Bioinformatics field. More specifically, the unit is operated as a full service facility focused on providing services of consultation, data analysis and management, software development, and access to computing resources. Furthermore, the unit is involved in different dissemination activities such as courses, workshops and symposiums designed to train researchers on the use of the different bioinformatics tools available for conducting their research projects.

Thomas Marques

Thomas Marques

Primate Genomics Lab, UPF

Our main line of research is centered in the discovery of the extent of genomic polymorphism within the great ape species. The goal is to create an integrated view of genome evolution by studying changes in the composition, frequency, size and location at every major branch-point of human divergence from other primates. The results our lines of research are aimed to assess the rate of genome variation in primate evolution, characterize regional deletions and copy-number expansions as well as determine the patterns of selection acting upon them and whether the diversity of these segments is consistent with other forms of genetic variation among humans and great apes.

Marc Martí-Renom

Marc Martí-Renom

Structural Genomics, CRG

We are interested in the molecular mechanisms that regulate cell fate. To study such mechanisms, we employ the laws of physics and the rules of evolution to develop and apply computational methods for predicting the 3D structures of macromolecules and their complexes.

Arcadi Navarro

Arcadi Navarro

Evolutionary Genomics Lab, UPF

Currently, the main research goals of the group focus on to elucidating how evolution, and particularly natural selection, has shaped genome and phenotype diversity in our lineage. To this end, we combine experiments, models and data analysis.

Cedric Notredame

Cedric Notredame

Comparative Bioinformatics, CRG

The main focus of the group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. Our goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences. Using such heterogeneous signals serves two complementary purposes: (i) producing better models that take advantage of the signal evolutionary resilience, (ii) improving our understanding of the evolutionary processes that lead to the diversification of biological functions. All the applications related to our work are provided to the community through an international network of web servers that can be accessed from http://www.tcoffee.org

Stephan Ossowski

Stephan Ossowski

Genomic and Epigenomic Variation in Disease, CRG

The focus of our group is the analysis of Next Generation Sequencing (NGS) data in order to detect genomic, genic and epigenomic variation related to disease or intolerance to specific treatments. We seek to develop analysis tools for related sequencing applications including genome re-sequencing and assembly, DNA methylation detection, transcriptome analysis and structural variant prediction. We further aim to incorporate all algorithms into a general analysis framework, allowing for quick adaptation to the challenges of coming sequencing technologies and approaches, e.g. single molecule sequencing, longer read length and further increased throughput. The direct and easy applicability of our framework to sequencing data produced at the CRG or freely available via sequencing read archives is of particular importance for us and we make use of our experience with NGS analysis in several collaborations with experimental groups working on both prokaryotes and eukaryotes.

Gian Gaetano Tartaglia

Gian Gaetano Tartaglia

Gene Function and Evolution, CRG

Our research focuses on gene and proteins, since these are the molecules that enable, regulate and control all the chemical processes on which life depends. In order to function the large majority of RNAs and proteins need to fold into a specific three-dimensional structure. The wide variety of highly specific structures that results from protein folding, and which serves to bring functional groups into close proximity, has enabled living systems to develop astonishing diversity and selectivity in their underlying chemical processes by using a common set of just twenty building blocks, the amino acids. Most of our research activity focuses on the understanding of regulation of gene expression and on the prediction of the mechanisms of protein folding and aggregation through a combination of in vivo, in vitro and in silico studies. We are currently investigating the conditions under which specific cellular pathways become aberrant and give rise to pathologies. This project, that we call pathosome, involves the in silico prediction of changes in protein-protein and protein-gene interactions that impair cell viability and will have an experimental validation in vivo.