ArticlePLoS computational biology2007
The stem cell population of the human colon crypt: analysis via methylation patterns.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- DNA methylation meets lineage tracing: History, recent progress, and future directions.Quantitative biology (Beijing, China) · 2026Article
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
- Stochastic model for cell population dynamics quantifies homeostasis in colonic crypts and its disruption in early tumorigenesis.Proceedings. Biological sciences · 2023Article
- Construction of high coverage whole-genome sequencing libraries from single colon crypts without DNA extraction or whole-genome amplification.BMC research notes · 2023Article
- Human Stem Cells for Ophthalmology: Recent Advances in Diagnostic Image Analysis and Computational Modelling.Current stem cell reports · 2023Review
- Article
- Lineage tracing in human tissues.The Journal of pathology · 2022Review
- Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues.Nature biotechnology · 2022Article
- Spatial dynamics of feedback and feedforward regulation in cell lineages.PLoS computational biology · 2022Article
- Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization.Nature communications · 2022Article
- Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking.Nature communications · 2020Article
- A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Effect of cellular de-differentiation on the dynamics and evolution of tissue and tumor cells in mathematical models with feedback regulation.Journal of theoretical biology · 2018Article
- Spatial Patterning from an Integrated Wnt/β-catenin and Notch/Delta Gene Circuit.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2018Article
- The evolutionary trade-off between stem cell niche size, aging, and tumorigenesis.Evolutionary applications · 2017Article
- PhyloOncology: Understanding cancer through phylogenetic analysis.Biochimica et biophysica acta. Reviews on cancer · 2017Review
- A population genetics perspective on the determinants of intra-tumor heterogeneity.Biochimica et biophysica acta. Reviews on cancer · 2017Review
- The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt.PLoS computational biology · 2017Article
- Stem cell dynamics and pretumor progression in the intestinal tract.Journal of gastroenterology · 2016Review
- Mice lacking functional CD95-ligand display reduced proliferation of the intestinal epithelium without gross homeostatic alterations.Medical molecular morphology · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The analysis of methylation patterns is a promising approach to investigate the genealogy of cell populations in an organism. In a stem cell-niche scenario, sampled methylation patterns are the stochastic outcome of a complex interplay between niche structural features such as the number of stem cells within a niche and the niche succession time, the methylation/demethylation process, and the randomness due to sampling. As a consequence, methylation pattern studies can reveal niche characteristics but also require appropriate statistical methods. The analysis of methylation patterns sampled from colon crypts is a prototype of such a study. Previous analyses were based on forward simulation of the cell content of the whole crypt and subsequent comparisons between simulated and experimental data using a few statistics as a proxy to summarize the data. In this paper we develop a more powerful method to analyze these data based on coalescent modelling and Bayesian inference. Results support a scenario where the colon crypt is maintained by a high number of stem cells; the posterior indicates a number greater than eight and the posterior mode is between 15 and 20. The results also provide further evidence for synergistic effects in the methylation/demethylation process that could for the first time be quantitatively assessed through their long-term consequences such as the coexistence of hypermethylated and hypomethylated patterns in the same colon crypt.
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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.