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 …

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

H Mi, D Ebert, A Muruganujan, C Mills… - Nucleic acids …, 2021‏ - academic.oup.com
Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.
pantherdb. org) is a resource for the evolutionary and functional classification of protein …

WikiPathways: connecting communities

M Martens, A Ammar, A Riutta… - Nucleic acids …, 2021‏ - academic.oup.com
Abstract WikiPathways (https://www. wikipathways. org) is a biological pathway database
known for its collaborative nature and open science approaches. With the core idea of the …

From hype to reality: data science enabling personalized medicine

H Fröhlich, R Balling, N Beerenwinkel, O Kohlbacher… - BMC medicine, 2018‏ - Springer
Abstract Background Personalized, precision, P4, or stratified medicine is understood as a
medical approach in which patients are stratified based on their disease subtype, risk …

[HTML][HTML] Oxylipin profiling for clinical research: Current status and future perspectives

K Parchem, S Letsiou, T Petan, O Oskolkova… - Progress in Lipid …, 2024‏ - Elsevier
Oxylipins are potent lipid mediators with increasing interest in clinical research. They are
usually measured in systemic circulation and can provide a wealth of information regarding …

Quantitative and logic modelling of molecular and gene networks

N Le Novere - Nature Reviews Genetics, 2015‏ - nature.com
Behaviours of complex biomolecular systems are often irreducible to the elementary
properties of their individual components. Explanatory and predictive mathematical models …

Cytoscape: software for visualization and analysis of biological networks

M Kohl, S Wiese, B Warscheid - Data mining in proteomics: from standards …, 2011‏ - Springer
Substantial progress has been made in the field of “omics” research (eg, Genomics,
Transcriptomics, Proteomics, and Metabolomics), leading to a vast amount of biological …

Integration of biological networks and gene expression data using Cytoscape

MS Cline, M Smoot, E Cerami, A Kuchinsky… - Nature protocols, 2007‏ - nature.com
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …

A comprehensive pathway map of epidermal growth factor receptor signaling

K Oda, Y Matsuoka, A Funahashi… - Molecular systems …, 2005‏ - embopress.org
The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important
pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells …