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...
- PhylomeDB v4: zooming into the plurality of evolutionary histories of a genomeJaime Huerta-Cepas
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader, 88 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats ICREA, Pg Lluis Companys 23, 08010 Barcelona, Spain
Nucleic Acids Res 42:D897-902. 2014....
- 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)...
- 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...
- eggNOG v4.0: nested orthology inference across 3686 organismsSean Powell
European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain, CUBE Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Atlanta
Nucleic Acids Res 42:D231-9. 2014..Users can access the complete database of orthologous groups via a web interface, as well as through bulk download. ..
- 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...
- 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...