Phosphoproteomics in the age of rapid and deep proteome profiling

NM Riley, JJ Coon - Analytical chemistry, 2016 - ACS Publications
Protein phosphorylation is a post-translational modification (PTM) that orchestrates a diverse
array of cellular processes. Because this modification serves as a rapid and reversible …

A compendium of ERK targets

EB Ünal, F Uhlitz, N Blüthgen - FEBS letters, 2017 - Wiley Online Library
The RAF‐MEK‐ERK cascade is one of the most studied signaling pathways as it controls
many vital cellular programs. There has been an immense amount of effort to determine …

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

L Xu, Z Dong, L Fang, Y Luo, Z Wei, H Guo… - Nucleic acids …, 2019 - academic.oup.com
OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome
orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new …

[HTML][HTML] Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates

NJ Hoffman, BL Parker, R Chaudhuri… - Cell metabolism, 2015 - cell.com
Exercise is essential in regulating energy metabolism and whole-body insulin sensitivity. To
explore the exercise signaling network, we undertook a global analysis of protein …

[HTML][HTML] Protein post-translational modifications: In silico prediction tools and molecular modeling

M Audagnotto, M Dal Peraro - Computational and structural biotechnology …, 2017 - Elsevier
Post-translational modifications (PTMs) occur in almost all proteins and play an important
role in numerous biological processes by significantly affecting proteins' structure and …

New tools in orthology analysis: a brief review of promising perspectives

BTL Nichio, JN Marchaukoski, RT Raittz - Frontiers in genetics, 2017 - frontiersin.org
Nowadays defying homology relationships among sequences is essential for biological
research. Within homology the analysis of orthologs sequences is of great importance for …

Phosphoproteomics reveals conserved exercise‐stimulated signaling and AMPK regulation of store‐operated calcium entry

ME Nelson, BL Parker, JG Burchfield… - The EMBO …, 2019 - embopress.org
Exercise stimulates cellular and physiological adaptations that are associated with
widespread health benefits. To uncover conserved protein phosphorylation events …

Protein phosphorylation database and prediction tools

MX Zhao, Q Chen, F Li, S Fu, B Huang… - Briefings in …, 2023 - academic.oup.com
Protein phosphorylation, one of the main protein post-translational modifications, is required
for regulating various life activities. Kinases and phosphatases that regulate protein …

Omics and exercise: global approaches for mapping exercise biological networks

NJ Hoffman - Cold Spring Harbor perspectives in …, 2017 - perspectivesinmedicine.cshlp.org
The application of global “-omics” technologies to exercise has introduced new opportunities
to map the complexity and interconnectedness of biological networks underlying the tissue …

[HTML][HTML] Decoding the PTM-switchboard of Notch

D Antfolk, C Antila, K Kemppainen, SKJ Landor… - … et Biophysica Acta (BBA …, 2019 - Elsevier
The developmentally indispensable Notch pathway exhibits a high grade of pleiotropism in
its biological output. Emerging evidence supports the notion of post-translational …