About us

Groups at the CRG's Bioinformatics and Genomics program perform research in Biology using computation. Focus is on Genomics and Evolution.

We use computation as a means both to interrogate and to model biological phenomena. We use existing tools, but we also design and implement novel computational tools and databases, and we are also interested in basic research in algorithms.

The Groups at CRG's Bioinformatics and Genomics Program have strong collaborations with the CRG's Bioinformatics core and with other experimental groups at the CRG. We believe that it is at the intersection between Experimentation and Computation that the Biology of the XXIst century will be edificated, and at the program we have our own experimental laboratory.  

We have also strong collaborations with the Research Group of Biomedical Informatics (GRIB, from the UPF-IMIM, http://grib.imim.es), and with the computatational genomics groups at the GRIB, we form the computational genomics cluster at the PRBB (http://genome.prbb.cat).

Groups

Development of algorithms and software for the comparison of biological recordings such as sequences, genomes, phenotypes and structures

Using comparative genomics and evolutionary analyses to understand complex biological systems

Investigation of sequence patterns in the genome responsible for functionality

Computational and Theoretical investigation of the evolution of genes and genomes

Predictions of Interactomes and Evolution of Proteomes

Evaluation of how different types of genetic variants, epigenetic modifications and non-coding RNA pathways contribute to human disorders.

News

Research on bioinformatics and computational genomics

PhylomeDB V4 released

The new version of PhylomeDB has been released. Version 4  

MetaPhOrs: orthologs and paralogs accross 829 genomes, based on multiple phylogenetic evidence

We have launched MetaPhOrs, a meta-method to predict orthology and paralogy from multiple phylogenetic evidence. To maximize reliability and coverage, we retrieved gene trees from PhylomeDB, Ensembl, TreeFam and Orthogroups. In addition we built maximum likelihood trees for orthologous gene families in OrthoMCL, COG, and EggNOG.

Bibliography

PhylomeDB v3.0 released

A new version of PhylomeDB has been released. With over 400.000 phylogenetic trees, PhylomeDB is currently the major public phylogenetic repository. It contains phylomes from model (Human, Yeast, Drosophila, Arabidopsis), but also alternative models such as the fungal pathogen Candida albicans, or the insects T. castaneum, N. vitripenis  and A. pisum.  New features have been added to the user's front end, including fully interactive tree images and link outs to external information.

Bibliography

Nothing found

Gene Function and Evolution

Group leader:  Gian Gaetano Tartaglia
Predictions of Interactomes and Evolution of Proteomes

 

New trends in protein sequence divergence

In an article published online in Nature, we validated the hypothesis that compensatory interactions allow most protein sequences, even the most conservative ones, to maintain the same function while diverging in sequence almost without limit.

 

 

The pea aphid genome fully-sequenced.

Two of the groups in our programme (Gabaldón and Guigó) have participated in the analysis of the genomic sequence of the pea aphid Acyrtosiphon pisum, published this week in PLoS Biology. This first published genome of a basal hemimetabolous insect, provides an out-group for comparison with other sequenced insects, and pavesthe way to elucidate molecular mechanisms in

Bibliography

Compensatory evolution and fitness valleys

Negative selection prevents the fixation of deleterious alleles. Thus, although some deleterious alleles can segregate in the population, conventional wisdom holds that deleterious mutations are evolutionary dead ends. In an letter to Nature published today online we show that for mt-tRNAs this is not always the case.

ETE: A python Environment for Tree Exploration, published

ETE our python Environment for Tree Exploration has just been published:

Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24. [ link ]

Bibliography

Theories on gene duplication are classified

A review article detailing and contrasting different theories on the evolution of gene duplications has been published online in Nature Reviews Genetics. In this article we present the modern state of the theory of duplicated genes and provide concrete recommendations for future experiments that may do a better job at elucidating the selective mechanisms at work in the evolution of duplicated genes.

Exon Wrap

By comparing exon-intron position in higher eukaryotes to available large scale nucleosome positioning datasets, we have find that exons tend to have higher nucleosome occupancy than introns (Tilgner et al., NSMB 2009)

Bibliography

Syndicate content