Comparative Genomics

Group leader: Toni Gabaldón

Our research interests are focused around the use of comparative genomics and phylogenomics to study the origin, evolution and function of complex biological systems. This includes understanding how specific biochemical pathways, protein complexes or cellular organelles emerged and evolved as well as using this evolutionary information to gain insight into their function.

Through collaborations with experimental groups we apply comparative genomics to discover new mechanisms and genes involved in interesting processes, especially those of clinical relevance (see lines of research). On the technical side, our work often involves the development of new bioinformatics tools and algorithms that we make available to the community.

Analysis and manipulation of phylogenomic data using ETE

Posted Tue, 2010-05-04 12:00 by Toni Gabaldón

Organized by the Gabaldon's lab at CRG and The Gulbenkian Training Programme in Bioinformatics (GTPB)

Location: Oerias, Portugal

Dates:from 23rd June to 25th June, 2010

More Information and application

Date

Wed, 2010-06-23 09:00 - Fri, 2010-06-25 19:53

Bibliography

Huerta-Cepas, J, Dopazo J, Gabaldón T. 2010. ETE: a python Environment for Tree Exploration.. BMC bioinformatics. 11:24. Abstract
Huerta_cepas_et_al_2010_ETE.pdf
Pubmed

Huerta-Cepas, J, Bueno A, Dopazo J, Gabaldón T. 2008. PhylomeDB: a database for genome-wide collections of gene phylogenies.. Nucleic Acids Res.. 36:D491–D496. Abstract
Pubmed

DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.

Posted Thu, 2010-04-22 15:27 by Toni Gabaldón

Deathbase, a database of proteins involved in cell death has been officialy launched. This database compiles relevant data on the function, structure and evolution of proteins involved in apoptosis and other forms of cell death in several organisms. DeathBase is a joint effort betwen Gabaldon's group at CRG and the lab of Muñoz-Pinedo at IDIBELL.

Bibliography

Díez, J, Walter D, Muñoz-Pinedo C, Gabaldón T. 2010. DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.. Cell Death Differ.. 17:735–736.
Diez_DeathBase_CDD_2010.pdf
Pubmed

Toni Gabaldón's blog
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The pea aphid genome fully-sequenced.

Posted Thu, 2010-02-25 18:03 by Toni Gabaldón

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

Consortium, T I A G. 2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
Pubmed

Gerardo, NM., Altincicek B, Anselme C, Atamian H, Barribeau SM., de Vos M, Duncan E, Evans JD., Gabaldón T, Ghanim M et al.. 2010. Immunity and other defenses in pea aphids, Acyrthosiphon pisum.. Genome biology. 11:R21. Abstract
Pubmed

PhD candidate in Comparative Genomics

Posted Fri, 2010-01-15 15:59 by Toni Gabaldón

We are actively seeking for a PhD candidate to work in the Mitochondria and peroxisomes and their role in disease" funded by the Spanish ministryof Science. The project involves evolutionary analyses of mitochondrial and peroxisomal proteins to elucidate the role of disease-relevant proteins.

ETE: A python Environment for Tree Exploration, published

Posted Fri, 2010-01-15 12:35 by Toni Gabaldón

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

Huerta-Cepas, J, Dopazo J, Gabaldón T. 2010. ETE: a python Environment for Tree Exploration.. BMC bioinformatics. 11:24. Abstract
Huerta_cepas_et_al_2010_ETE.pdf
Pubmed

trimAl 1.2 has been released

Posted Tue, 2009-09-15 17:35 by Toni Gabaldón

Multiple sequence alignments (MSA) are central to many areas of bioinformatics and evolutionary biology. They are not only used in the phylogenetic analyses of biological sequences but also in many other bioinformatics applications such as homology modeling, database searchers and motif finding. Recently, such multiple sequence alignment based techniques have been incorporated in high-throughput pipelines such as genome annotation and large-scale phylogenetics.