ArticleNature methods2023
A computational framework for the inference of protein complex remodeling from whole-proteome measurements.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- PCIPG: A comprehensive framework for protein complex identification based on a probabilistic graphical model.PLoS computational biology · 2026Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- A journey through the molecular networks of endomyocardial biopsies to explore ATTR and ALiScience · 2026Article
- The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.NPJ systems biology and applications · 2026Article
- A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.Nature biotechnology · 2026Article
- LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis.Nature communications · 2026Article
- Synthetic tunable promoters for flexible control of multi-gene expression in mammalian cells.Journal of advanced research · 2025Article
- CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditions.Briefings in bioinformatics · 2025Article
- π-HuB: the proteomic navigator of the human body.Nature · 2024Review
- Distinct Regions within SAP25 Recruit O-Linked Glycosylation, DNA Demethylation, and Ubiquitin Ligase and Hydrolase Activities to the Sin3/HDAC Complex.Journal of proteome research · 2024Article
- Proteomic studies of VEGFR2 in human placentas reveal protein associations with preeclampsia, diabetes, gravidity, and labor.Cell communication and signaling : CCS · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
Protein complexes are responsible for the enactment of most cellular functions. For the protein complex to form and function, its subunits often need to be present at defined quantitative ratios. Typically, global changes in protein complex composition are assessed with experimental approaches that tend to be time consuming. Here, we have developed a computational algorithm for the detection of altered protein complexes based on the systematic assessment of subunit ratios from quantitative proteomic measurements. We applied it to measurements from breast cancer cell lines and patient biopsies and were able to identify strong remodeling of HDAC2 epigenetic complexes in more aggressive forms of cancer. The presented algorithm is available as an R package and enables the inference of changes in protein complex states by extracting functionally relevant information from bottom-up proteomic datasets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.