Large-scale assignment of orthology: back to phylogenetics?

T Gabaldón - Genome biology, 2008‏ - Springer
Reliable orthology prediction is central to comparative genomics. Although orthology is
defined by phylogenetic criteria, most automated prediction methods are based on pairwise …

Models, algorithms and programs for phylogeny reconciliation

JP Doyon, V Ranwez, V Daubin… - Briefings in …, 2011‏ - academic.oup.com
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 …

Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells

E Sefik, N Geva-Zatorsky, S Oh, L Konnikova… - Science, 2015‏ - science.org
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 …

[HTML][HTML] A recently evolved transcriptional network controls biofilm development in Candida albicans

CJ Nobile, EP Fox, JE Nett, TR Sorrells, QM Mitrovich… - Cell, 2012‏ - cell.com
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 …

eggNOG v3. 0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

S Powell, D Szklarczyk, K Trachana, A Roth… - Nucleic acids …, 2012‏ - academic.oup.com
Orthologous relationships form the basis of most comparative genomic and metagenomic
studies and are essential for proper phylogenetic and functional analyses. The third version …

eggNOG: automated construction and annotation of orthologous groups of genes

LJ Jensen, P Julien, M Kuhn, C von Mering… - Nucleic acids …, 2007‏ - academic.oup.com
The identification of orthologous genes forms the basis for most comparative genomics
studies. Existing approaches either lack functional annotation of the identified orthologous …

A Phenotypic Profile of the Candida albicans Regulatory Network

OR Homann, J Dea, SM Noble, AD Johnson - PLoS genetics, 2009‏ - journals.plos.org
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 …

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

DR Scannell, OA Zill, A Rokas, C Payen… - G3: Genes …, 2011‏ - academic.oup.com
High-quality, well-annotated genome sequences and standardized laboratory strains fuel
experimental and evolutionary research. We present improved genome sequences of three …

Natural history and evolutionary principles of gene duplication in fungi

I Wapinski, A Pfeffer, N Friedman, A Regev - Nature, 2007‏ - nature.com
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 …

Computational methods for Gene Orthology inference

DM Kristensen, YI Wolf, AR Mushegian… - Briefings in …, 2011‏ - academic.oup.com
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 …