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01/16/14 5:38 PM

A joint effort: More than thirty scientists

The team after the Seville's meeting.
The team after the Seville's meeting.

A total of six research Spanish centers and more than thirty researchers are involved in Lynxgenomics, which aims is the generation of a first map of the Iberian lynx genome (an annotated draft) and of a comprehensive set of markers for genomic analyses in the species. Specialists in genomic and biology have joined forces and knowledge to reach these two aims under EBD's coordination in this project, framed in the Project Zero program FGCSIC 2010 in Endangered Species, and financed by Banco Santander and Fundación General CSIC

This research is funded by the Proyectos Cero in Endangered Species, a granted supported by Banco Santander, the Spanish National Research Council (CSIC), supplemented with the Fundación General CSIC's own resources. The Centre Nacional d'Anàlisis Genòmica (CNAG), the Centre for Genomic Regulation (CRG), the Centro de Investigaciones Biológicas CSIC (CIB), the Estación Biológica de Doñana CSIC (EBD), Primates Genomics Lab (IBE, CSIC-UPF), and the Evolutionary Genomics Group (UPF-IMIM).

 

Centre Nacional d'Anàlisis Genòmica (CNAG)

  • Tasks: Data generation, Genome assembly
  • Team Leader: Ivo Gut
  • Team: Tyler Alioto, André Corvelo, Leonor Frías, Paolo Ribeca, Simon JHeath, Mònica Bayés and Marta Gut
  • The National Center for Genome Analysis (CNAG) was created in September 2009 with support from the Spanish Ministry of Science and Innovation and the Catalan Government with the mission to carry out large‐scale projects in DNA sequencing and analysis in collaboration with researchers from Catalonia, Spain and from the international research community in order to ensure the competitiveness of our country in the strategic area of genomics.

    The Center –led by Ivo Gut– has a staff of 40 highly qualified individuals (50% of the staff holds a PhD degree), and is equipped with 12 last-generation sequencing systems, which has enabled the center to obtain a sequencing capacity of up to 600 Gbases/day, the equivalent of sequencing six human genomes at 30x coverage per day. This capacity positions the CNAG as the second leading European center in terms of sequencing capacity. The sequencing operation is supported by an extensive informatics infrastructure that has been designed, implemented and is being administrated by the Barcelona Supercomputing Center

 

Bioinformatics and Genomics-Centre for Genomic Regulation (CRG)

  • Tasks: Genome annotation, transcriptome analyses
  • Team Leader: Roderic Guigó
  • Team: Francisco Cámara, Anna Viasova, Ernesto Lowly, Luca CozzutoFrancisco Cámara, Anna Vlasova, Ernesto Lowly, Luca Cozzuto
  • The Bionformatics and Genomics group at CRG, led by Roderic Guigó, focuses in the development of methods for the identification of functional domains in genomic sequences and the investigation of their underlying sequence motifs.

    They have developed tools that have become standards for the finding of new genes and the annotation of whole genomes. Roderic Guigó participates in the ENCODE project, a public research consortium whose goal is to find all functional elements in genomes, where he leads the RNA analysis group. The group has contributed to the annotation of many genome projects (mosquito, rat, chicken, cow, Tetraodon, Dyctiostelium, pea aphid, tomato, melon, the twelve drosophilas, many fungal genomes, etc) and Roderic Guigó had a leadership role on the mouse genome project.

 

CRG-Comparative Genomics

  • Tasks: Comparative genomics
  • Team Leader: Toni Gabaldón
  • Team: Marina Maret-Houben, José Luis Rodríguez Ales and Salvador Capella Gutierre
  • The main research interest of his group is to understand the complex relationships between genome sequences and phenotypes and how these two features evolve across species. They generally use large-scale phylogenetics approaches that allow looking at the evolution of genomes from the perspective of all of their genes, and they apply these analyses to a variety of biological questions related the evolution and function of organelles, pathways, and protein families. They have developed a number of bioinformatic tools and databases for the analyses of these issues that have found wide use in the research community.
  • Link to the group

 

CRG-Comparative Bioinformatics

  • Tasks: Annotate and study long non-coding RNAs (lncRNA)
  • Team Leader: Cedric Notredame
  • Team: Ionas Erb, Miquel Orobitg, Pablo Prieto
  • The main focus of the group is the development of novel algorithms for the comparison of multiple biological sequences that incorporate 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

 

Centro de Investigaciones Biológicas

  • Tasks: Cell culture, library construction
  • Team Leader: José Luis García
  • Team: Beatriz Galán
  • The Environmental Biotechnology group at the Centre for Biological Research, led by José Luis García, has a large experience in the field of Biochemistry and Molecular Microbiology, focused on the catabolism of aromatic compounds by microorganism. Their research has included the sequencing of the genomes of bacterias and bacteriophages. Most relevant to this project is his experience with DNA sequencing technologies, a field he led with the implantation of the first automatic DNA sequencing system in our country. He has founded two spin-off companies at CSIC devoted to genome analysis (Lifesequencing) and genetic diagnosis (Secugen).

 

Estación Biológica Doñana, CSIC (EBD)

  • Tasks: SNP validation, population and conservation genetics, communication and outreach coordination
  • Team Leader and General Coordinator: José A. Godoy
  • Team: Mireia Casas-Marce, Fernando Cruz, Juan Miguel González-Aranda, Elena Marmesat and Laura Soriano
  • The Conservation Genetics group at EBD led by José A. Godoy has extensively collaborated with field scientist at EBD in the incorporation of molecular markers to ecological and evolutionary studies. Their research covers a wide suite of questions and species centered around the inference of demographic and evolutionary processes from the patterns of genetic variation in natural populations.

    The group has studied some of the most emblematic species of the endangered Iberian fauna, including the bearded vulture, the imperial eagle, the Dupont's lark and the Iberian lynx.Ongoing research includes the analysis of contemporary, historical and ancient genetic variation in the Iberian lynx to understand the genetic consequences of species decline.

    Genetic analyses are also guiding the species conservation and management through contracted research with conservation agencies and through José A. Godoy's role as Coordinator of the Advisory Group in Genetic Aspects for the Ex-situ Conservation Program of the Iberian lynx. He acts as coordinator to the lynx genome project.

 

Evolutionary Genomics Group, UPF-IMIM

  • Tasks: Footprints of natural selection and evolutionary innovation
  • Team Leader: M. Mar Albà
  • Team: José Luis Villanueva-Cañas
  • The Evolutionary Genomics group at Universitat Pompeu Fabra (UPF) and Institut Municipal d'Investigació Mèdica (IMIM) uses computational methods to learn about the evolution and function of mammalian genes and genomes. The group, led by ICREA researcher Mar Albà, studies the role of positive selection in shaping the evolution of protein-coding genes and its relationship to physiological adaptations. They also investigate the emergence of novel protein sequences and complete genes in mammalian genomes using transcriptome sequencing and comparative genomics.

 

Primates Genomics Lab, IBE, CSIC-UPF

  • Tasks: Structural and copy number variation
  • Team Leader: Tomàs Marques-Bonet
  • Team: Belen Lorente and Javier Prado
  • The research of the Primate Genomics group at IBE, led by Tomás Marqués, is centered in the discovery of the extent of genome structural polymorphism within the great ape species. The goal is to create an integrated view of structural variation evolution by studying changes in the composition, frequency, size and location at every major branchpoint of human divergence from other primates.

     

    The results of these analyses will 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. The group has contributed its expertise to the analyses of these aspects for the human, chimpanzee, gorilla, orang-utan, neanderthal and Denisova genomes.

 

Structural Computational Biology - CNIO

  • Tasks: Annotation and analysis of transposable elements and splicing isoforms
  • Team Leader: Alfonso Valencia
  • Team: Federico Abascal, Michael Tress, José Manuel Rodríguez, Vicor de la Torre
  • The National Center for Genome Analysis (CNAG) was created in September 2009 with support from the Spanish Ministry of Science and Innovation and the Catalan Government with the mission to carry out large‐scale projects in DNA sequencing and analysis in collaboration with researchers from Catalonia, Spain and from the international research community in order to ensure the competitiveness of our country in the strategic area of genomics.

    The main interest of our Group lies in the mechanistic understanding of cancer progression by combining molecular and evolutionary approaches. Our research focuses on the problem of functional specificity and selective molecular interactions in the context of cancer genome research.

    The strategic goals of the Structural Computational Biology Group are: i) to analyse the function, structure and specific interactions of proteins related to cancer; ii) to develop novel methods and software platforms for the extraction, integration and representation of cancer genomic data, including the statistical analysis of molecular, genomic, epigenomic and phenotypic information in collaboration with cancer genome projects; and iii), to design the next generation of computational methods for the interpretation of personalised cancer genome information.

 

Molecular Biology of Cancer – IUOPA-UO

  • Tasks: Annotation and analysis of whole set of proteases (the degradome)
  • Team Leader: Carlos López-Otín
  • Team: Víctor Quesada
  • The work carried out by the group has enabled the identification of more than sixty new human genes and the analysis of their functions in tumour progression and other normal and pathological processes. It has also contributed to the annotation of the human genome and various model organisms. These studies led to the introduction of new concepts such as the degradome, enabling a general definition and analysis of the structures and functions of protease-coding genes.

    His laboratory has produced studies which have opened the doors to important means of research for pathologies such as cancer, arthritis and a number of hereditary diseases. It is also responsible for the sequencing of the chimpanzee genome.

Available languages: Spanish
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