To what extent can large-scale approaches accurately reconstruct classic signaling pathways? Here, authors revisit the EGF pathway using phosphoproteomics and kinase-substrate interactions

To what extent can large-scale approaches accurately reconstruct classic signaling pathways? Here, authors revisit the EGF pathway using phosphoproteomics and kinase-substrate interactions

Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...

New tool combines biological knowledge with machine learning to help researchers extract meaningful insights from complex omics data.

The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...

Nature Reviews Nephrology, Published online: 19 June 2025; doi:10.1038/s41581-025-00968-9The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability have led to frustration, collaboration bodes well for a future in which patients will have access to more personalized information.

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

Here the authors present deep quantitative glycoprofiling (DQGlyco), a method that enables high-throughput analysis of protein glycosylation dynamics. Using DQGlyco, they link gut microbiome compositi...

Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...

Recently, someone asked PRIDE support how to get the number of RAW files from all PRIDE projects. Here, is the best solution: Before anything, you have to install pridepy: > pip install --upgrade p...

GitHub is where people build software. More than 150 million people use GitHub to discover, fork, and contribute to over 420 million projects.

AbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage

Post-translational modifications are important regulators of cellular pathways, but our understanding of these processes is limited. Here, the authors present a web tool that integrates various databa...