ArticleGenome biology2013
Temporal dynamics and transcriptional control using single-cell gene expression analysis.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- CRISPR-Enabled functional genomics in hPSCs-derived neural models for autism spectrum disorder.Metabolic brain disease · 2026Review
- Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.Molecular systems biology · 2026Article
- CeSpGRN: inferring cell-specific gene regulatory networks from single-cell multi-omics and spatial data.Bioinformatics (Oxford, England) · 2026Article
- Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data.Biostatistics (Oxford, England) · 2026Article
- Pseudotime-conditioned diffusion models for imputing time-series single-cell data.Bioinformatics advances · 2026Article
- Blue Noise-based Generative Models for the Imputation of Time-series Data.International Conference on Information Science and Technology. International Conference on Information Science and Technology · 2025Article
- Gene Regulatory Network Inference from Pseudotime-Ordered scRNA-seq Data via Time-Lagged Divergence Measures.Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference) · 2025Article
- TRENDY: gene regulatory network inference enhanced by transformer.Bioinformatics (Oxford, England) · 2025Article
- Reconstructing Dynamic Gene Regulatory Networks Using f-Divergence from Time-Series scRNA-Seq Data.Current issues in molecular biology · 2025Article
- Time-Varying Gene Regulatory Networks Inference Using KL Divergence from Single Cell Data.Proceedings of the ... International Conference on Bioinformatics and Biomedical Technology · 2025Article
- Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation.PLoS computational biology · 2025Article
- tBN-CSDI: a time-varying blue noise-based diffusion model for time-series imputation.Bioinformatics advances · 2025Article
- Reversal of MYB-dependent suppression of MAFB expression overrides leukaemia phenotype in MLL-rearranged AML.Cell death & disease · 2023Article
- Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics.Frontiers in plant science · 2023Review
- A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA.Nature communications · 2022Article
- Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments.Patterns (New York, N.Y.) · 2021Article
- Affinity proteomic dissection of the human nuclear cap-binding complex interactome.Nucleic acids research · 2020Article
- A comparison of single-cell trajectory inference methods.Nature biotechnology · 2019Article
- Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Highly Multiplexed Single-Cell Protein Profiling with Large-Scale Convertible DNA-Antibody Barcoded Arrays.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChanges in environmental conditions lead to expression variation that manifest at the level of gene regulatory networks. Despite a strong understanding of the role noise plays in synthetic biological systems, it remains unclear how propagation of expression heterogeneity in an endogenous regulatory network is distributed and utilized by cells transitioning through a key developmental event.
resultsHere we investigate the temporal dynamics of a single-cell transcriptional network of 45 transcription factors in THP-1 human myeloid monocytic leukemia cells undergoing differentiation to macrophages. We systematically measure temporal regulation of expression and variation by profiling 120 single cells at eight distinct time points, and infer highly controlled regulatory modules through which signaling operates with stochastic effects. This reveals dynamic and specific rewiring as a cellular strategy for differentiation. The integration of both positive and negative co-expression networks further identifies the proto-oncogene MYB as a network hinge to modulate both the pro- and anti-differentiation pathways.
conclusionsCompared to averaged cell populations, temporal single-cell expression profiling provides a much more powerful technique to probe for mechanistic insights underlying cellular differentiation. We believe that our approach will form the basis of novel strategies to study the regulation of transcription at a single-cell level.
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