Dustin Ebert
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View article: Updates to the Alliance of Genome Resources central infrastructure
Updates to the Alliance of Genome Resources central infrastructure Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: Enrichment on steps, not genes, improves inference of differentially expressed pathways
Enrichment on steps, not genes, improves inference of differentially expressed pathways Open
Enrichment analysis is frequently used in combination with differential expression data to investigate potential commonalities amongst lists of genes and generate hypotheses for further experiments. However, current enrichment analysis app…
View article: Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium
Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: The Gene Ontology knowledgebase in 2023
The Gene Ontology knowledgebase in 2023 Open
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life…
View article: Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation Open
The Annotation Query (AnnoQ) (http://annoq.org/) is designed to provide comprehensive and up-to-date functional annotations for human genetic variants. The system is supported by an annotation database with ∼39 million human variants from …
View article: Harmonizing model organism data in the Alliance of Genome Resources
Harmonizing model organism data in the Alliance of Genome Resources Open
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene…
View article: <scp>PANTHER</scp>: Making genome‐scale phylogenetics accessible to all
<span>PANTHER</span>: Making genome‐scale phylogenetics accessible to all Open
Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics analyses can be challenging: they are computationally expensive and must be performed…
View article: Gene family data from the PhyloGenes (release version 2.2, phylogenes.org)
Gene family data from the PhyloGenes (release version 2.2, phylogenes.org) Open
About the two zip files: 1. phyloXML.zip PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. .xml). The following information is provided for each node of a tree: 1) leaf node: branch length name taxonomy scientific…
View article: Gene family data from the PhyloGenes (release version 2.2, phylogenes.org)
Gene family data from the PhyloGenes (release version 2.2, phylogenes.org) Open
About the two zip files: 1. phyloXML.zip PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. .xml). The following information is provided for each node of a tree: 1) leaf node: branch length name taxonomy scientific…
View article: PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence Open
Enhancers are powerful and versatile agents of cell-type specific gene regulation, which are thought to play key roles in human disease. Enhancers are short DNA elements that function primarily as clusters of transcription factor binding s…
View article: The Gene Ontology resource: enriching a GOld mine
The Gene Ontology resource: enriching a GOld mine Open
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two y…
View article: PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference
PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference Open
We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to dup…
View article: PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API Open
PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is b…
View article: Alliance of Genome Resources Portal: unified model organism research platform
Alliance of Genome Resources Portal: unified model organism research platform Open
The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by …
View article: PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Open
PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made t…