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Large-scale assignment of orthology: back to phylogenetics?
Reliable orthology prediction is central to comparative genomics. Although orthology is
defined by phylogenetic criteria, most automated prediction methods are based on pairwise …
defined by phylogenetic criteria, most automated prediction methods are based on pairwise …
Models, algorithms and programs for phylogeny reconciliation
Gene sequences contain a gold mine of phylogenetic information. But unfortunately for
taxonomists this information does not only tell the story of the species from which it was …
taxonomists this information does not only tell the story of the species from which it was …
Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells
T regulatory cells that express the transcription factor Foxp3 (Foxp3+ Tregs) promote tissue
homeostasis in several settings. We now report that symbiotic members of the human gut …
homeostasis in several settings. We now report that symbiotic members of the human gut …
[HTML][HTML] A recently evolved transcriptional network controls biofilm development in Candida albicans
A biofilm is an organized, resilient group of microbes in which individual cells acquire
properties, such as drug resistance, that are distinct from those observed in suspension …
properties, such as drug resistance, that are distinct from those observed in suspension …
eggNOG v3. 0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Orthologous relationships form the basis of most comparative genomic and metagenomic
studies and are essential for proper phylogenetic and functional analyses. The third version …
studies and are essential for proper phylogenetic and functional analyses. The third version …
eggNOG: automated construction and annotation of orthologous groups of genes
The identification of orthologous genes forms the basis for most comparative genomics
studies. Existing approaches either lack functional annotation of the identified orthologous …
studies. Existing approaches either lack functional annotation of the identified orthologous …
A Phenotypic Profile of the Candida albicans Regulatory Network
Candida albicans is a normal resident of the gastrointestinal tract and also the most
prevalent fungal pathogen of humans. It last shared a common ancestor with the model …
prevalent fungal pathogen of humans. It last shared a common ancestor with the model …
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus
High-quality, well-annotated genome sequences and standardized laboratory strains fuel
experimental and evolutionary research. We present improved genome sequences of three …
experimental and evolutionary research. We present improved genome sequences of three …
Natural history and evolutionary principles of gene duplication in fungi
Gene duplication and loss is a powerful source of functional innovation. However, the
general principles that govern this process are still largely unknown. With the growing …
general principles that govern this process are still largely unknown. With the growing …
Computational methods for Gene Orthology inference
Accurate inference of orthologous genes is a pre-requisite for most comparative genomics
studies, and is also important for functional annotation of new genomes. Identification of …
studies, and is also important for functional annotation of new genomes. Identification of …