Honors & Awards

  • Simons Foundation Postdoctoral Fellowship, Life Sciences Research Foundation (August 2017 - August 2020)
  • Long-term Postdoctoral Fellowship (accepted as non-stipendiary), EMBO (July 2017 - June 2019)

Professional Education

  • BA, The University of Cambridge, Cambridge, Natural Sciences (2011)
  • PhD, The Francis Crick Institute, London, Cell and Molecular Biology (Supervisor: Sir Paul Nurse) (2016)

Stanford Advisors

Lab Affiliations

All Publications

  • Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe CELL REPORTS Swaffer, M. P., Jones, A. W., Flynn, H. R., Snijders, A. P., Nurse, P. 2018; 24 (2): 503–14


    Multiple protein kinases regulate cell-cycle progression, of which the cyclin-dependent kinases (CDKs) are thought to act as upstream master regulators. We have used quantitative phosphoproteomics to analyze the fission yeast cell cycle at sufficiently high temporal resolution to distinguish fine-grain differences in substrate phosphorylation dynamics on a proteome-wide scale. This dataset provides a useful resource for investigating the regulatory dynamics of cell-cycle kinases and their substrates. For example, our analysis indicates that the substrates of different mitotic kinases (CDK, NIMA-related, Polo-like, and Aurora) are phosphorylated in sequential, kinase-specific waves during mitosis. Phosphoproteomics analysis after chemical-genetic manipulation of CDK activity suggests that the timing of these waves is established by the differential dependency of the downstream kinases on upstream CDK. We have also examined the temporal organization of phosphorylation during G1/S, as well as the coordination between the NDR-related kinase Orb6, which controls polarized growth, and other cell-cycle kinases.

    View details for DOI 10.1016/j.celrep.2018.06.036

    View details for Web of Science ID 000438422700022

    View details for PubMedID 29996109

    View details for PubMedCentralID PMC6057490

  • CDK Substrate Phosphorylation and Ordering the Cell Cycle Cell Swaffer, M. P., Jones, A. W., Flynn, H. R., Snijders, A. P., Nurse, P. 2016; 167: 1750–1761
  • Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods Shipony, Z., Marinov, G. K., Swaffer, M. P., Sinnott-Armstrong, N. A., Skotheim, J. M., Kundaje, A., Greenleaf, W. J. 2020


    Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.

    View details for DOI 10.1038/s41592-019-0730-2

    View details for PubMedID 32042188

  • An Imaging Flow Cytometry-based approach to analyse the fission yeast cell cycle in fixed cells METHODS Patterson, J. O., Swaffer, M., Filby, A. 2015; 82: 74–84


    Fission yeast (Schizosaccharomyces pombe) is an excellent model organism for studying eukaryotic cell division because many of the underlying principles and key regulators of cell cycle biology are conserved from yeast to humans. As such it can be employed as tool for understanding complex human diseases that arise from dis-regulation in cell cycle controls, including cancers. Conventional Flow Cytometry (CFC) is a high-throughput, multi-parameter, fluorescence-based single cell analysis technology. It is widely used for studying the mammalian cell cycle both in the context of the normal and disease states by measuring changes in DNA content during the transition through G1, S and G2/M using fluorescent DNA-binding dyes. Unfortunately analysis of the fission yeast cell cycle by CFC is not straightforward because, unlike mammalian cells, cytokinesis occurs after S-phase meaning that bi-nucleated G1 cells have the same DNA content as mono-nucleated G2 cells and cannot be distinguished using total integrated fluorescence (pulse area). It has been elegantly shown that the width of the DNA pulse can be used to distinguish G2 cells with a single 2C foci versus G1 cells with two 1C foci, however the accuracy of this measurement is dependent on the orientation of the cell as it traverses the laser beam. To this end we sought to improve the accuracy of the fission yeast cell cycle analysis and have developed an Imaging Flow Cytometry (IFC)-based method that is able to preserve the high throughput, objective analysis afforded by CFC in combination with the spatial and morphometric information provide by microscopy. We have been able to derive an analysis framework for subdividing the yeast cell cycle that is based on intensiometric and morphometric measurements and is thus robust against orientation-based miss-classification. In addition we can employ image-based metrics to define populations of septated/bi-nucleated cells and measure cellular dimensions. To our knowledge, this is the first use of IFC to study fission yeast and we are confident that this will provide a springboard for further IFC-based analysis across all aspects of fission yeast biology.

    View details for DOI 10.1016/j.ymeth.2015.04.026

    View details for Web of Science ID 000356910700010

    View details for PubMedID 25952947

  • What determines cell size? BMC BIOLOGY Marshall, W. F., Young, K. D., Swaffer, M., Wood, E., Nurse, P., Kimura, A., Frankel, J., Wallingford, J., Walbot, V., Qu, X., Roeder, A. H. 2012; 10

    View details for DOI 10.1186/1741-7007-10-101

    View details for Web of Science ID 000312301200001

    View details for PubMedID 23241366

    View details for PubMedCentralID PMC3522064