ArticleMolecular systems biology2020
The transcriptome dynamics of single cells during the cell cycle.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 87 citations in OpenAlex.
- Drought and salinity stress remodel Asian rice (Oryza sativa) leaf development through cell-type-specific regulatory programs.The New phytologist · 2026Article
- Cell-cycle-driven noncanonical ubiquitination of METTL14 orchestrates RNA methylation.Nature chemical biology · 2026Article
- OscillomeR infers ultradian oscillations and targets of the Hes family.Patterns (New York, N.Y.) · 2026Article
- Multiscale learning of gene network-driven phenotypic dynamics of single cells.Molecular systems biology · 2026Article
- Deep learning models for cell cycle phase prediction from single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Cell Cycle Sensing Shapes Human T Cell Fate and Exhaustion Programs.bioRxiv : the preprint server for biology · 2026Article
- Metab8D: a metabolic regulome network from multiomics and machine learning.Communications biology · 2026Article
- CycleVI: isolating cell cycle variation with an interpretable deep generative model.Bioinformatics (Oxford, England) · 2026Article
- Cell Cycle Control of Nuclear Metabolism Couples Phosphatidylinositol Signaling to Histone Methylation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunity.bioRxiv : the preprint server for biology · 2026Article
- CDK4/6 inhibition mitigates chemotherapy-induced expansion of TP53-mutant clonal hematopoiesis.Nature genetics · 2026Article
- CellUntangler: Separating distinct biological signals in single-cell data with deep generative models.Cell genomics · 2026Article
- Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.Communications biology · 2026Article
- Article
- Characterizing the Impact of the Cell Cycle on mRNA Lipid Nanoparticles.Journal of the American Chemical Society · 2026Article
- The role of FRUITFULL controlling cell cycle during early flower development revealed by time-series snRNA-seq experiments.Genome biology · 2025Article
- Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review.Briefings in bioinformatics · 2025Review
- Mapping cells through time and space with moscot.Nature · 2025Article
- Inferring metabolic objectives and trade-offs in single cells during embryogenesis.Cell systems · 2025Article
- Classifying cell cycle states and a quiescent-like G0 state using single-cell transcriptomics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The cell cycle is among the most basic phenomena in biology. Despite advances in single-cell analysis, dynamics and topology of the cell cycle in high-dimensional gene expression space remain largely unknown. We developed a linear analysis of transcriptome data which reveals that cells move along a planar circular trajectory in transcriptome space during the cycle. Non-cycling gene expression adds a third dimension causing helical motion on a cylinder. We find in immortalized cell lines that cell cycle transcriptome dynamics occur largely independently from other cellular processes. We offer a simple method ("Revelio") to order unsynchronized cells in time. Precise removal of cell cycle effects from the data becomes a straightforward operation. The shape of the trajectory implies that each gene is upregulated only once during the cycle, and only two dynamic components represented by groups of genes drive transcriptome dynamics. It indicates that the cell cycle has evolved to minimize changes of transcriptional activity and the related regulatory effort. This design principle of the cell cycle may be of relevance to many other cellular differentiation processes.
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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 OpenQuestion graph.