PANTHER: Making genome‐scale phylogenetics accessible to all
PD Thomas, D Ebert, A Muruganujan… - Protein …, 2022 - Wiley Online Library
Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their
evolutionary relationships to other proteins. However, phylogenetics analyses can be …
evolutionary relationships to other proteins. However, phylogenetics analyses can be …
SBML Level 3: an extensible format for the exchange and reuse of biological models
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …
complexity of computational models. To reproduce simulation results and reuse models …
The BioCyc collection of microbial genomes and metabolic pathways
BioCyc. org is a microbial genome Web portal that combines thousands of genomes with
additional information inferred by computer programs, imported from other databases and …
additional information inferred by computer programs, imported from other databases and …
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
Abstract Pathway Commons (https://www. pathwaycommons. org) is an integrated resource
of publicly available information about biological pathways including biochemical reactions …
of publicly available information about biological pathways including biochemical reactions …
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
MV Kuleshov, MR Jones, AD Rouillard… - Nucleic acids …, 2016 - academic.oup.com
Enrichment analysis is a popular method for analyzing gene sets generated by genome-
wide experiments. Here we present a significant update to one of the tools in this domain …
wide experiments. Here we present a significant update to one of the tools in this domain …
[HTML][HTML] A guide to conquer the biological network era using graph theory
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …
of binary interactions or relations between different bioentities. In this article, we discuss the …
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis
CS Abhinand, R Raju, SJ Soumya, PS Arya… - Journal of cell …, 2016 - Springer
Vascular endothelial growth factor-A (VEGF-A) is essential for endothelial cell functions
associated with angiogenesis. Signal transduction networks initiated by VEGFA/VEGFR2 …
associated with angiogenesis. Signal transduction networks initiated by VEGFA/VEGFR2 …
Large-scale gene function analysis with the PANTHER classification system
The PANTHER (protein annotation through evolutionary relationship) classification system
(http://www. pantherdb. org/) is a comprehensive system that combines gene function …
(http://www. pantherdb. org/) is a comprehensive system that combines gene function …
The Reactome pathway knowledgebase
Abstract Reactome (http://www. reactome. org) is a manually curated open-source open-
data resource of human pathways and reactions. The current version 46 describes 7088 …
data resource of human pathways and reactions. The current version 46 describes 7088 …
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
The data and tools in PANTHER—a comprehensive, curated database of protein families,
trees, subfamilies and functions available at http://pantherdb. org—have undergone …
trees, subfamilies and functions available at http://pantherdb. org—have undergone …