ArticleNature communications2023
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
20 citing papers in PubMed, 24 citations in OpenAlex.
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.Bioinformatics (Oxford, England) · 2026Article
- Intrinsic cellular heterogeneity directs divergent epithelial-to-mesenchymal transition outcomes.The FEBS journal · 2026Article
- Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.Cell systems · 2026Article
- A single-cell atlas revealing cellular heterogeneity across healthy and diseased human thymus.Nature communications · 2026Article
- Partial EMT Drives Persistent Collective Migration via Collision Guidance in Heterogeneous Populations.bioRxiv : the preprint server for biology · 2026Article
- Tumor exosomes impact functional hallmarks of cancer.Cancer metastasis reviews · 2026Review
- OmNI: a modular open-source framework for interactive multi-omics data integration and visualization.NAR genomics and bioinformatics · 2026Article
- Phosphorylation-dependent modulation of the Lamin A/C-EZH2 complex regulates epithelial-mesenchymal plasticity.Nucleic acids research · 2026Article
- Association between vitamin D levels and psychological stress-induced asthma prevalence: an untargeted metabolomics study combined with the NHANES database.Frontiers in nutrition · 2026Article
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.bioRxiv : the preprint server for biology · 2025Article
- Microenvironmental regulation and remodeling of breast cancer angiogenesis: from basic mechanisms to clinical therapeutic implications.Discover oncology · 2025Review
- Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells.iScience · 2025Article
- Single-Cell Expression Analysis of Ductal Carcinoma In Situ Identifies Complex Genotypic-Phenotypic Relationships Altering Epithelial Composition.Cancer research · 2025Article
- Transcriptional responses to direct and indirect TGFB1 stimulation in cancerous and noncancerous mammary epithelial cells.Cell communication and signaling : CCS · 2024Article
- Exosomal circ-0100519 promotes breast cancer progression via inducing M2 macrophage polarisation by USP7/NRF2 axis.Clinical and translational medicine · 2024Article
- DESP demixes cell-state profiles from dynamic bulk molecular measurements.Cell reports methods · 2024Article
- Composition, functions, and applications of exosomal membrane proteins.Frontiers in immunology · 2024Review
- Article
- Review
- Learning Causal Biological Networks with Parallel Ant Colony Optimization Algorithm.Bioengineering (Basel, Switzerland) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 9 institutions in 3 countries.
Funding
Abstract
A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.
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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.