ArticleFrontiers in genetics2020
Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 45 citations in OpenAlex.
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data.NPJ systems biology and applications · 2025Review
- Modeling the dynamics of EMT reveals genes associated with pan-cancer intermediate states and plasticity.NPJ systems biology and applications · 2025Article
- Targeting persistently activated inflammatory microenvironment to promote chronic wound healing.Frontiers in immunology · 2025Review
- The tumor microenvironment across four dimensions: assessing space and time in cancer biology.Frontiers in immunology · 2025Review
- Leveraging gene correlations in single cell transcriptomic data.BMC bioinformatics · 2024Article
- Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data.Biophysical journal · 2024Article
- Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- Leveraging gene correlations in single cell transcriptomic data.bioRxiv : the preprint server for biology · 2023Article
- From time-series transcriptomics to gene regulatory networks: A review on inference methods.PLoS computational biology · 2023Review
- Deciphering functional tumor states at single-cell resolution.The EMBO journal · 2022Review
- spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.Molecular systems biology · 2022Article
- Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.Nucleic acids research · 2022Article
- DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data.Briefings in bioinformatics · 2022Article
- Review
- Enhancing the diversity of self-replicating structures using active self-adapting mechanisms.Frontiers in genetics · 2022Article
- Article
- Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition.Biophysical journal · 2021Article
- A Coagulation-Related Gene-Based Prognostic Model for Invasive Ductal Carcinoma.Frontiers in genetics · 2021Article
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5 authors at 1 institution in 1 country.
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Abstract
Epithelial-to-mesenchymal transition (EMT) plays an important role in many biological processes during development and cancer. The advent of single-cell transcriptome sequencing techniques allows the dissection of dynamical details underlying EMT with unprecedented resolution. Despite several single-cell data analysis on EMT, how cell communicates and regulates dynamics along the EMT trajectory remains elusive. Using single-cell transcriptomic datasets, here we infer the cell-cell communications and the multilayer gene-gene regulation networks to analyze and visualize the complex cellular crosstalk and the underlying gene regulatory dynamics along EMT. Combining with trajectory analysis, our approach reveals the existence of multiple intermediate cell states (ICSs) with hybrid epithelial and mesenchymal features. Analyses on the time-series datasets from cancer cell lines with different inducing factors show that the induced EMTs are context-specific: the EMT induced by transforming growth factor B1 (TGFB1) is synchronous, whereas the EMTs induced by epidermal growth factor and tumor necrosis factor are asynchronous, and the responses of TGF-β pathway in terms of gene expression regulations are heterogeneous under different treatments or among various cell states. Meanwhile, network topology analysis suggests that the ICSs during EMT serve as the signaling in cellular communication under different conditions. Interestingly, our analysis of a mouse skin squamous cell carcinoma dataset also suggests regardless of the significant discrepancy in concrete genes between
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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 OpenQuestion graph.