Continuous Clonal Labeling Reveals Small Numbers of Functional Stem Cells in Intestinal Crypts and Adenomas

Identification of stem cells in small intestine and colon by marker gene Lgr5

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A human colon cancer cell capable of initiating tumour growth in immunodeficient mice

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A Direct Measurement of the Radiation Sensitivity of Normal Mouse Bone Marrow Cells1

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A Direct Measurement of the Radiation Sensitivity of Normal Mouse Bone Marrow Cells

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Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells

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Bmi1 is expressed in vivo in intestinal stem cells

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Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution

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Cell intrinsic alterations underlie hematopoietic stem cell aging

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Lineage Tracing Reveals Lgr5 + Stem Cell Activity in Mouse Intestinal Adenomas

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Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16INK4a

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Multiscale modelling of intestinal crypt organization and carcinogenesis

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Predominant Asymmetrical Stem Cell Fate Outcome Limits the Rate of Niche Succession in Human Colonic Crypts

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GI stem cells – new insights into roles in physiology and pathophysiology

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The Induction of Selected Wnt Target Genes by Tcf1 Mediates Generation of Tumorigenic Colon Stem Cells

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Stem cell heterogeneity, plasticity, and regulation

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Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation

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A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

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Engineered epithelial curvature controls Paneth cell localization in intestinal organoids

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Initiation of Cancer: The Journey From Mutations in Somatic Cells to Epigenetic Changes in Tissue-resident VSELs

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Adult stem cell lineage tracing and deep tissue imaging

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In vivosensitivity of the embryonic and adult neural stem cell compartments to low-dose radiation

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The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts

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Stem cell competition in the gut: insights from multi-scale computational modelling

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Predicting colorectal cancer risk from adenoma detection via a two-type branching process model

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Lineage tracing in human tissues

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Somatic Mutations in Normal Tissues: New Perspectives on Early Carcinogenesis

Herms, A., & Jones, P. H. (2023) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-061421-012447 · Cited by 18

The implications of small stem cell niche sizes and the distribution of fitness effects of new mutations in aging and tumorigenesis

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Control of cell fraction and population recovery during tissue regeneration in stem cell lineages

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The evolutionary trade‐off between stem cell niche size, aging, and tumorigenesis

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Decay of driver mutations shapes the landscape of intestinal transformation

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Protein-level mutant p53 reporters identify druggable rare precancerous clones in noncancerous tissues

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Wound-healing plasticity enables clonal expansion of founder progenitor cells in colitis

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The Complex, Clonal, and Controversial Nature of Barrett’s Esophagus

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The role of gene mutations and gene products in intestinal tissue reactions from ionising radiation

Hendry, J. H., & Otsuka, K. (2016) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2016.07.006 · Cited by 14

Stem Cells in Pituitary Tumors: Experimental Evidence Supporting Their Existence and Their Role in Tumor Clinical Behavior

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Metabolic Regulation of Stem Cells in Aging

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A contemporary snapshot of intestinal stem cells and their regulation

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Mutation, clonal fitness and field change in epithelial carcinogenesis

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Quantifying cell divisions along evolutionary lineages in cancer

Blohmer, M., Cheek, D. M., Hung, W.-T., Kessler, M., Chatzidimitriou, F., Wang, J., Hung, W., Lee, I., Gorelick, A. N., Wassenaar, E. C. E., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02078-5 · Cited by 12

Location, location, location! The reality of life for an intestinal stem cell in the crypt

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Age-Associated Loss in Renal Nestin-Positive Progenitor Cells

Buyan, M. I., Andrianova, N. V., Popkov, V. A., Zorova, L. D., Pevzner, I. B., Silachev, D. N., Zorov, D. B., & Plotnikov, E. Y. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231911015 · Cited by 14

The intricate interplay between cancer stem cells and cell-of-origin of cancer: implications for therapeutic strategies

Bamodu, O. A., Chung, C., Pisanic, T. R., & Wu, A. T. H. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1404628 · Cited by 13

In situ monitoring of barrier function on-chip via automated, non-invasive luminescence sensing

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Intravital microscopy to illuminate cell state plasticity during metastasis

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Computer simulation of neutral drift among limbal epithelial stem cells of mosaic mice

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Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt

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Reduced adhesion of aged intestinal stem cells contributes to an accelerated clonal drift

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Inferring average generation via division-linked labeling

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Mathematical Modeling of Normal and Cancer Stem Cells

Weiss, L. D., Komarova, N. L., & Rodriguez-Brenes, I. A. (2017) · Current Stem Cell Reports · doi:10.1007/s40778-017-0094-4 · Cited by 11

Microenvironmental cues in cancer stemness

Flanagan, D. J., Hodder, M. C., & Sansom, O. J. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0210-4 · Cited by 10

Inferring average generation via division-linked labeling

Weber, T. S., Perié, L., & Duffy, K. R. (2015) · Maynooth University ePrints and eTheses Archive (Maynooth University) · Cited by 10

Cell and tissue reprogramming: Unlocking a new era in medical drug discovery

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Molecular and cellular basis of the dose-rate-dependent adverse effects of radiation exposure in animal models. Part I: Mammary gland and digestive tract

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Investigating Adult Stem Cells Through Lineage analyses

Kalderon, D. (2021) · Stem Cell Reviews and Reports · doi:10.1007/s12015-021-10282-z · Cited by 8

Boveri at 100: cancer evolution, from preneoplasia to malignancy

Wright, N. A. (2014) · The Journal of Pathology · doi:10.1002/path.4408 · Cited by 9

Revealing human intestinal stem cell and crypt dynamics

Baker, A., & Graham, T. A. (2014) · Molecular & Cellular Oncology · doi:10.4161/23723548.2014.970069 · Cited by 9

Quantifying Lgr5-positive stem cell behaviour in the pyloric epithelium

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A van der Waals-like Transition Between Normal and Cancerous Phases in Cell Populations Dynamics of Colorectal Cancer

Qiu, K., Wang, L., Shen, J. G., Yousif, A. A. M., He, P., Shao, D.-D., Zhang, X.-M., Kirunda, J. B., & Jia, Y. (2016) · Scientific Reports · doi:10.1038/srep36620 · Cited by 8

Clonal selection parallels between normal and cancer tissues

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Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers

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Insights into radiation carcinogenesis based on dose-rate effects in tissue stem cells

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Stem cell competition: how speeding mutants beat the rest

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Defining key concepts of intestinal and epithelial cancer biology through the use of mouse models

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Defining the mucosal ecosystem: epithelial–mesenchymal interdependence in gastrointestinal health and disease

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Modelling the dynamics of mammalian gut homeostasis

Corominas‐Murtra, B., & Hannezo, É. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.11.005 · Cited by 6

Clonal Evolution of Stem Cells in the Gastrointestinal Tract

Fink, J., & Koo, B. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-41388-4_2 · Cited by 6

Immune modulatory stem cells represent a significant component of the immune system

Karpenko, D. V. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1543495 · Cited by 5

Emerging Prospects for the Study of Colorectal Cancer Stem Cells using Patient-derived Organoids

Ding, L., Yang, Y., Lu, Q., Cao, Z., & Weygant, N. (2022) · Current Cancer Drug Targets · doi:10.2174/1568009622666220117124546 · Cited by 5

Construction of high coverage whole-genome sequencing libraries from single colon crypts without DNA extraction or whole-genome amplification

Manojlovic, Z., Wlodarczyk, J. R., Okitsu, C. Y., Jin, Y., Berg, D. V. D., Lieber, M. R., & Hsieh, C. (2023) · BMC Research Notes · doi:10.1186/s13104-023-06333-y · Cited by 5

Stochastic model for cell population dynamics quantifies homeostasis in colonic crypts and its disruption in early tumorigenesis

Mamis, K., Zhang, R., & Božić, I. (2023) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.1020 · Cited by 4

Cancer Stem Cells: Concepts, Challenges, and Opportunities for Cancer Therapy

Lee, M. Y., Giraddi, R. R., & Tam, W. L. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9524-0_4 · Cited by 7

Protein–protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer

Yu, Z., Chen, Y., Zheng, B., Cai, Z., Zou, Y., Ke, J., Lan, P., Gao, F., & Wu, X. (2021) · Cancer Cell International · doi:10.1186/s12935-021-01794-2 · Cited by 5

Bunched and Madm Function Downstream of Tuberous Sclerosis Complex to Regulate the Growth of Intestinal Stem Cells in Drosophila

Nie, Y., Li, Q., Amcheslavsky, A., Duhart, J. C., Veraksa, A. N., Stocker, H., Raftery, L. A., & Ip, Y. T. (2015) · Stem Cell Reviews and Reports · doi:10.1007/s12015-015-9617-5 · Cited by 5

Ballroom Dancing with Stem Cells: Placement and Displacement in the Intestinal Crypt

Tajbakhsh, S. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.02.011 · Cited by 5

Stem cell dynamics and pretumor progression in the intestinal tract

Ma, H., Morsink, F. H. M., Offerhaus, G. J. A., & de Leng, W. W. J. (2016) · Journal of Gastroenterology · doi:10.1007/s00535-016-1211-3 · Cited by 5

Intestinal Stem Cell Dynamics: A Story of Mice and Humans

Hodder, M. C., Flanagan, D. J., & Sansom, O. J. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.05.005 · Cited by 4

Potential protective effect of ALDH-1 stromal expression against early recurrence of operable breast cancers

Lee, J. S., & Kim, W. G. (2018) · Stem Cell Investigation · doi:10.21037/sci.2018.11.03 · Cited by 4

Quantifying Microsatellite Mutation Rates from Intestinal Stem Cell Dynamics in Msh2-Deficient Murine Epithelium

Christopher, J., Thorsen, A.-S., Abujudeh, S., Lourenço, F. C., Kemp, R., Potter, P. K., Morrissey, E. R., Hazelwood, L. D., & Winton, D. J. (2019) · Genetics · doi:10.1534/genetics.119.302268 · Cited by 5

Cell competition as an emerging mechanism and therapeutic target in cancer

Yang, D., Sun, W., Gao, L., Zhao, K., Zhuang, Q., & Cai, Y. (2025) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2025.167769 · Cited by 3

Heterogeneity in clone dynamics within and adjacent to intestinal tumours identified by Dre-mediated lineage tracing

Thorsen, A.-S., Khamis, D., Kemp, R., Colombé, M., Lourenço, F. C., Morrissey, E. R., & Winton, D. J. (2020) · Disease Models & Mechanisms · doi:10.1242/dmm.046706 · Cited by 3

Modeling Cell Dynamics in Colon and Intestinal Crypts: The Significance of Central Stem Cells in Tumorigenesis

Mahdipour–Shirayeh, A., & Shahriyari, L. (2018) · Bulletin of Mathematical Biology · doi:10.1007/s11538-018-0457-8 · Cited by 3

Quantifying human intestinal stem cell and crypt dynamics: the implications for cancer screening and prevention

Baker, A., & Graham, T. A. (2015) · Expert Review of Gastroenterology & Hepatology · doi:10.1586/17474124.2016.1134314 · Cited by 3

Counting Cells by Age Tells Us About How, and Why, and When, We Grow, and Become Old and IllPreprint

Citi, L., Lasky-Su, J. A., Huang, L., & Michaelson, J. S. (2023) · medRxiv · doi:10.1101/2023.01.05.23284244 · Cited by 3

Bayesian inference of fitness landscapes via tree-structured branching processes

Luo, X. G., Kuipers, J., Rupp, K., Takahashi, K., & Beerenwinkel, N. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf193 · Cited by 5

Aging: Lifespan and the evolution of somatic mutation rates

Galeota-Sprung, B., & Sniegowski, P. (2022) · Current Biology · doi:10.1016/j.cub.2022.06.002 · Cited by 2

Relocation sustains intestinal stem-cell numbers

Ellis, S. J., & Fuchs, E. V. (2022) · Nature · doi:10.1038/d41586-022-01596-0 · Cited by 2

Cancer stem cells: here, there, and everywhere

Lodestijn, S. C., Lenos, K., Miedema, D. M., Bijlsma, M. F., & Vermeulen, L. (2018) · Molecular & Cellular Oncology · doi:10.1080/23723556.2018.1540235 · Cited by 2

Cell division can accelerate the loss of a heteroplasmic mitochondrial DNA mutation in a mouse model of mitochondrial diseasePreprint

Su, T., Gomes, T. M. B., Smith, A. L. M., Whitehall, J. C., Blain, A. P., Simard, M., Scholten, L., Stewart, J. B., Turnbull, D. M., Lawless, C., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.06.535821 · Cited by 2

Age-Related Changes in Kidney and Loss of Resistance to Damage: The Role of the Decrease in the Number of Kidney Progenitor Cells during Aging

Buyan, M. I., Andrianova, N. V., & Plotnikov, E. Y. (2023) · Problems of Geroscience · doi:10.37586/2949-4745-3-2023-127-133 · Cited by 1

Stem and immune cells in colorectal primary tumour: Number and function of subsets may diagnose metastasis

Varela‐Calviño, R. (2015) · World Journal of Immunology · doi:10.5411/wji.v5.i2.68 · Cited by 1

Bioengineered ‘mini-colons’ shed light on cancer progression

Riggi, N., & Melo, F. D. S. E. (2024) · Nature · doi:10.1038/d41586-024-01018-3 · Cited by 1

Shaping intestinal organoids: Engineering crypt curvature to guide stem cell niches

Barrile, R., & Kasendra, M. J. (2025) · Cell stem cell · doi:10.1016/j.stem.2025.03.015 · Cited by 1

Testing Three Hypotheses of the Contribution of Geometry and Migration Dynamics to Intestine Crypt Evolution

Araujo, A., Rübben, A., Bentley, P. J., & Basanta, D. (2018) · Conference on Artificial Life (ALIFE) · doi:10.1162/isal_a_00080 · Cited by 1

A Cancer Stem Cell Perspective on Minimal Residual Disease in Solid Malignancies

van der Heijden, M., & Vermeulen, L. (2019) · Resistance to targeted anti-cancer therapeutics · doi:10.1007/978-3-030-16624-3_2 · Cited by 2

Replicative history marks transcriptional and functional disparity in the CD8+ T cell memory poolPreprint

Schumacher, T. N., Bresser, K., Kok, L., Swain, A. C., King, L. A., Jacobs, L., Weber, T., Perié, L., Duffy, K. R., Scheeren, F. A., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-310238/v1 · Cited by 1

Supplementary Materials for Variation in cancer incidence among tissues can be explained by the number of stem cell divisions

Tomasetti, C., & Vogelstein, B. (2015)

Biomedical Applications of Gut Stem Cells: Gaining First-Hand Insights for Developing Therapy for the Future

Kar, U. K. (2016) · Journal of Stem Cell Research & Therapeutics · doi:10.15406/jsrt.2016.01.00023

Delayed activation of the DNA replication licensing system in Lgr5(+) intestinal stem cellsPreprint

Carroll, T. D., Newton, I. P., Chen, Y., Blow, J. J., & Näthke, I. S. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/177477

CANCER STEM CELL BIOLOGY

Göktuna, S. İ., Chau, T. L., & Xhafa, E. (2019) · Trakya University Journal of Natural Sciences · doi:10.23902/trkjnat.483577

Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cellsPreprint

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Effect of Modeling Intestinal Crypts as Cylinders for Simulating Stem Cell Dynamics within Mouse and Human Colonic Crypts

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