Affiliation: Center for Genomic Regulation
- ETE: a python Environment for Tree ExplorationJaime Huerta-Cepas
Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
BMC Bioinformatics 11:24. 2010..Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale...
- MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence scoreLeszek P Pryszcz
Bioinformatics and Genomics Programme, Centre de Regulacio Genomica CRG, Universitat Pompeu Fabra, Dr Aiguader, 88 08003, Barcelona, Spain
Nucleic Acids Res 39:e32. 2011..A webserver has been developed to easily access these data (http://orthology.phylomedb.org), which provides users with a global repository of phylogeny-based orthology and paralogy predictions...
- Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplicationJaime Huerta-Cepas
Centre for Genomic Regulation, Barcelona, Spain
Brief Bioinform 12:442-8. 2011..Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event...
- Assigning duplication events to relative temporal scales in genome-wide studiesJaime Huerta-Cepas
Centre for Genomic Regulation CRG, Barcelona, Spain
Bioinformatics 27:38-45. 2011..However, both measures have never been compared in a common framework...
- PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictionsJaime Huerta-Cepas
Bioinformatics and Genomics Programme, Centre de Regulacio Genomica, 08003 Barcelona, Spain
Nucleic Acids Res 39:D556-60. 2011..Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights...
- Comparative transcriptomics of early dipteran developmentEva Jimenez-Guri
EMBL CRG Research Unit in Systems Biology, Centre de Regulacio Genomica CRG, and Universitat Pompeu Fabra UPF, Barcelona, Spain
BMC Genomics 14:123. 2013..In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo)...
- PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and diseaseAgatha Schluter
Centre de Genètica Mèdica i Molecular, Institut d Investigació Biomèdica de Bellvitge Institut de Recerca Oncològica IDIBELL IRO Hospital Duran i Reynals, Granvia km 2, 7 08907 Hospitalet de Llobregat, Barcelona, Spain
Nucleic Acids Res 35:D815-22. 2007..PeroxisomeDB should contribute to the systematic characterization of the peroxisomal proteome and facilitate system biology approaches on the organelle...
- Evidence for systems-level molecular mechanisms of tumorigenesisPilar Hernandez
Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L Hospitalet, Barcelona, Spain
BMC Genomics 8:185. 2007..Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth...