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publications
Crypt fusion as a homeostatic mechanism in the human colon
Published in Gut, 2019
In this study, evidence is presented for the existence of crypt fusion in the human colon, a novel homeostatic mechanism whereby two neighbouring intestinal crypts can merge to form a single daughter crypt. Joint first author.
Recommended citation: Baker A, Gabbutt C, Williams MJ, et al (2019). "Crypt fusion as a homeostatic mechanism in the human colon " Gut . 2019;68:1986-1993. http://dx.doi.org/10.1136/gutjnl-2018-317540
AFM nanoindentation reveals decrease of elastic modulus of lipid bilayers near freezing point of water.
Published in Scientific Reports, 2019
A study applying atomic force microscopy to lipid membrane across a range of temperatures, probing the effect of freezing on the mechanical properties of lipid membranes. Research undertaken during MPhys project.
Recommended citation: Gabbutt, C., Shen, W., Seifert, J. et al. (2019). "AFM nanoindentation reveals decrease of elastic modulus of lipid bilayers near freezing point of water." Sci Rep. 9, 19473. https://doi.org/10.1038/s41598-019-55519-7
Evolution’s cartographer: Mapping the fitness landscape in cancer
Published in Cancer Cell, 2021
A spotlight highlighting Salehi et al. (2021) and discussing the potential impact that probing the cancer fitness landscape and how it changes in response to drug could have on predicting tumour evolution through therapy.
Recommended citation: Gabbutt, C, and Graham, T. A. (2021). "Evolution's Cartographer: Mapping the Fitness Landscape in Cancer." Cancer Cell. 39 (10): 1311-13. https://doi.org/10.1016/J.CCELL.2021.09.002.
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues
Published in Nature Biotechnology, 2022
This study presents fluctuating methylation clocks (FMCs) as a novel lineage tracing marker and demonstrates how they can be employed to quantitively infer the clonal dynamics of healthy tissue.
Recommended citation: Gabbutt, C., Schenck, R.O., Weisenberger, D.J. et al. (2022). "Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues." Nat Biotechnol. 40, 720-730. https://doi.org/10.1038/s41587-021-01109-w
Lineage tracing in human tissues
Published in Journal of Pathology, 2022
A review article outlining the various approaches to learning about dynamic biological processes from naturally occurring lineage markers. This included a discussion of historical approaches, such as the use of germline mutations, to gold standard modern approaches like multi-region whole genome sequencing.
Recommended citation: Gabbutt, C., Wright, N.A., Baker, A.-M., Shibata, D. and Graham, T.A. (2022). "Lineage tracing in human tissues." J. Pathol.. 257: 501-51. https://doi.org/10.1002/path.5911
Phenotypic plasticity and genetic control in colorectal cancer evolution.
Published in Nature, 2022
Research investigating the genotype-pheotype map in colorectal cancer, and the effect of phenotypic plasticity on cancer evolution.
Recommended citation: Househam, J., Heide, T., Cresswell, G.D. et al. (2022). "Phenotypic plasticity and genetic control in colorectal cancer evolution." Nature. 611, 744-753. https://doi.org/10.1038/s41586-022-05311-x
Evolutionary dynamics of 1,976 lymphoid malignancies predict clinical outcome.
Published in medRxiv, 2023
This study presents fluctuating methylation clocks (FMCs) as a novel lineage tracing marker and demonstrates how they can be employed to quantitively infer the clonal dynamics of healthy tissue.
Recommended citation: Gabbutt, C., Duran-Ferrer, M., Grant, H et al. (2023). "Evolutionary dynamics of 1,976 lymphoid malignancies predict clinical outcome." medRxiv. https://doi.org/10.1101/2023.11.10.23298336
talks
Integrated Mathematical Oncology - Evolutionary Therapy
Published:
A week-long workshop focused on mathematical and computational modelling of evolutionary therapeutic approaches.
‘The tick-tock clock’ - Exploiting the distribution of methylation patterns within single colonic crypts to infer intra-crypt dynamics.
Published:
Presented a poster detailing proof-of-principle that the methylation patterns at specific sites across the genome encode the stem cell dynamics of an intestinal crypt.
Cell Imaging Hackathon
Published:
A hackathon surrounding image analysis in the context of cancer research, particularly focused on cell segmentation and cell type identification.
Reconstructing Contemporary Human Stem Cell Dynamics with Oscillatory Molecular Clocks
Published:
A minisymposium talk presenting work in progress applying methylation based lineage marks to uncover stem cell dynamics in human colon.
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues
Published:
A short talk presenting our work on measuring contemporary cell dynamics with fluctuating methylation clocks (FMCs).
Dynamics and Statistics of Cancer Evolution
Published:
Attended an interactive summer school focused on cancer evolution, specifically applying mathematics to experimental and clinical data.
Lineage tracing methods to measure evolutionary dynamics in cancer
Published:
Organised a minisymposium to spotlight recent attempts to quantitatively interpret lineage tracing data in cancer.
Fluctuating methylations clocks allow for the quantification of the evolutionary dynamics in blood cancers
Published:
Presented recent work on measuring the evolutionary history of lymphoid cancers.
Fluctuating methylation clocks are a flexible tool for measuring ongoing somatic evolution in healthy tissue and cancer
Published:
An extended talk covering the full breadth of our fluctuating methylation clock research, including their use to probe clonal dynamics in intestinal tissue (doi.org/10.1038/s41587-021-01109-w), and unpublished research extending this to multi-region samples using phylogenetic approaches and to assay the evolutionary history of blood cancers.
Methylation-based lineage markers as a novel method to measure a cancer’s evolutionary dynamics.
Published:
A talk describing our recent work to measure a cancer’s evolutionary history using low-cost, readily availible methylation array data.
Timing copy number alterations in Barrett’s oesophagus in absolute time.
Published:
A talk focused on our new tool, CARBINE, which uses the frequency of point mutations to time copy number changes in real time. Awarded 1st prize.
Fluctuating methylation as a high temporal-resolution molecular clock to track lineages in vivo.
Published:
A talk focused on our discovery of fCpGs as a powerful and general tool to track lineages in vivo using low-cost, bulk methylation samples.
Quantification of the evolutionary history of a cancer from bulk methylation data using stochastic modelling and Bayesian inference.
Published:
A talk on our work using stochastic modelling of epigenetic data to infer a cancer’s evolutionary history at scale.
Learning a cancer’s evolutionary history from bulk methylation data using Bayesian inference.
Published:
A discussion of our research coupling Bayesian inference and methylation-based lineage markers to learn the evolutionary history of a cancer.
teaching
Fitting Mathematical Models to Data
Summer School, Evolutionary Biology and Ecology of Cancer, Wellcome Genome Campus, 2022
Delivered an interactive session introducing a mixed audience of cancer reserachers to the theory and practice of fitting mathematical models to data.
Evolution, Modelling and AI
Workshop, Institute of Cancer Research, MRC DTP, 2023
A workshop on cancer evolution and mathematical modelling for the new MRC doctoral training centre at ICR