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 …

SBML Level 3: an extensible format for the exchange and reuse of biological models

SM Keating, D Waltemath, M König, F Zhang… - Molecular systems …, 2020‏ - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

The BioCyc collection of microbial genomes and metabolic pathways

PD Karp, R Billington, R Caspi… - Briefings in …, 2019‏ - academic.oup.com
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 …

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 …

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

I Rodchenkov, O Babur, A Luna, BA Aksoy… - Nucleic acids …, 2020‏ - academic.oup.com
Abstract Pathway Commons (https://www. pathwaycommons. org) is an integrated resource
of publicly available information about biological pathways including biochemical reactions …

A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020‏ - frontiersin.org
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 …

[HTML][HTML] Artificial intelligence and early detection of pancreatic cancer: 2020 summative review

B Kenner, ST Chari, D Kelsen, DS Klimstra, SJ Pandol… - Pancreas, 2021‏ - journals.lww.com
Despite considerable research efforts, pancreatic cancer is associated with a dire prognosis
and a 5-year survival rate of only 10%. Early symptoms of the disease are mostly …

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 …

Large-scale gene function analysis with the PANTHER classification system

H Mi, A Muruganujan, JT Casagrande, PD Thomas - Nature protocols, 2013‏ - nature.com
The PANTHER (protein annotation through evolutionary relationship) classification system
(http://www. pantherdb. org/) is a comprehensive system that combines gene function …

The Reactome pathway knowledgebase

D Croft, AF Mundo, R Haw, M Milacic… - Nucleic acids …, 2014‏ - academic.oup.com
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 …