Affiliation: Center for Genomic Regulation
- Functional and evolutionary implications of gene orthologyToni Gabaldón
Bioinformatics and Genomics Programme, Centre for Genomic Regulation and Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
Nat Rev Genet 14:360-6. 2013..Here we discuss the complexity of the evolution of gene-phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles...
- Immunity and other defenses in pea aphids, Acyrthosiphon pisumNicole M Gerardo
Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E, Clifton Road NE, Atlanta, GA 30322, USA
Genome Biol 11:R21. 2010....
- Evolution of spliceosomal introns following endosymbiotic gene transferNahal Ahmadinejad
Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Dusseldorf, Germany
BMC Evol Biol 10:57. 2010..We circumvent this problem by using genes originated by endosymbiotic gene transfer, in which an intron-less structure at the time of the transfer can be assumed...
- Large-scale assignment of orthology: back to phylogenetics?Toni Gabaldón
Bioinformatics and Genomics Program, Center for Genomic Regulation, Doctor Aiguader 88, Barcelona, Spain
Genome Biol 9:235. 2008..Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies...
- Peroxisome diversity and evolutionToni Gabaldón
Centre for Genomic Regulation CRG, Dr Aiguader, 88 08003 Barcelona, Spain
Philos Trans R Soc Lond B Biol Sci 365:765-73. 2010..Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes...
- PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolomeAgatha Schluter
Neurometabolic Disease Lab, Institut de Neuropatologia de Bellvitge, Gran Via n 199, 08907 L Hospitalet de Llobregat, Barcelona, Spain
Nucleic Acids Res 38:D800-5. 2010..0 is a freely available, highly interactive functional genomics platform that offers an extensive view on the peroxisomal metabolome across lineages, thus facilitating comparative genomics and systems analysis of the organelle...
- 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 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...
- 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...
- 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...
- TreeKO: a duplication-aware algorithm for the comparison of phylogenetic treesMarina Marcet-Houben
Centre for Genomic Regulation, UPF, Doctor Aiguader 88, 08003 Barcelona, Spain
Nucleic Acids Res 39:e66. 2011..In addition treeKO, implements the possibility of computing phylome support values, and reconciliation-based measures such as the number of inferred duplication and loss events...
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analysesSalvador Capella-Gutierrez
Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain
Bioinformatics 25:1972-3. 2009..Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized...
- 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...
- Measuring guide-tree dependency of inferred gaps in progressive alignersSalvador Capella-Gutierrez
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Doctor Aiguader 88 and Universitat Pompeu Fabra, Barcelona, Spain
Bioinformatics 29:1011-7. 2013..It has been found that patterns of inferred gaps in alignments contain information towards the true phylogeny, but it is as yet unknown whether gaps are simply reflecting information that was already present in the guide-tree...
- Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungiSalvador Capella-Gutierrez
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG and UPF, Doctor Aiguader, 88, 08003 Barcelona, Spain
BMC Biol 10:47. 2012..Due to the presence of accelerated evolutionary rates, phylogenetic analyses involving microsporidia are prone to methodological artifacts, such as long-branch attraction, especially when taxon sampling is limited...
- Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergenceMarina Marcet-Houben
Comparative Genomics, Centre for Genomics Regulation, 08003 Barcelona, Spain
BMC Evol Biol 9:295. 2009..To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species...
- The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)Juliane C Dohm
1 Max Planck Institute for Molecular Genetics, Ihnestraße 63 73, 14195 Berlin, Germany 2 Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain 3 Universitat Pompeu Fabra UPF, C Dr Aiguader 88, 08003 Barcelona, Spain 4
Nature 505:546-9. 2014..The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology...
- Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrusMarina Marcet-Houben
Centre for Genomic Regulation, Barcelona, Spain
BMC Genomics 13:646. 2012..digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina...
- A midzone-based ruler adjusts chromosome compaction to anaphase spindle lengthGabriel Neurohr
Centre for Genomic Regulation CRG, Barcelona, Spain
Science 332:465-8. 2011..Thus, the anaphase spindle may function as a ruler to adapt the condensation of chromatids, promoting their segregation regardless of chromosome or spindle length...
- 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...
- TACC3-TSC2 maintains nuclear envelope structure and controls cell divisionLaia Gómez-Baldó
Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Barcelona, Spain
Cell Cycle 9:1143-55. 2010....
- Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosisLeszek P Pryszcz
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Barcelona, Spain
Genome Biol Evol 5:2382-92. 2013..Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis...
- Acquisition of prokaryotic genes by fungal genomesMarina Marcet-Houben
Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Doctor Aiguader, 88 08003 Barcelona, Spain
Trends Genet 26:5-8. 2010..Transferred genes included bacterial arsenite reductase, catalase, different racemases and peptidoglycan metabolism enzymes. Our results suggest an important role for HGT in fungal evolution...
- 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. ..
- Comparative genomics of emerging pathogens in the Candida glabrata cladeToni Gabaldón
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
BMC Genomics 14:623. 2013..bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts...
- Eukaryotic cold shock domain proteins: highly versatile regulators of gene expressionMarija Mihailovich
Gene Regulation Programme, Centre de Regulació Genòmica CRG UPF, Barcelona, Spain
Bioessays 32:109-18. 2010..This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD...