Dr Michael Stubbington | Principal Staff Scientist

Stubbington, Michael

Mike leads the team at Sanger working on the Human Cell Atlas project. Mike is using his experience in single-cell analyses to develop enabling technologies for this effort as well as working to generate pilot data for the first draft of the Atlas.

I started my research career at the laboratory bench and first worked in the field of high-containment microbiology before moving to molecular immunology for my PhD. I realised during my PhD that I really enjoyed computational biology and bioinformatics and so moved to purely computational projects for a postdoctoral fellowship with Dr. Sarah Teichmann at EMBL-EBI and then as a Senior Staff Scientist when the Teichmann Group moved to WTSI. I am fascinated by the potential of single-cell analysis methods to reveal novel insights about cellular populations. I enjoy developing and implementing new methods in this area and I have been focusing on the analysis of immune cell populations and antigen-receptor repertoires. I am looking forward to applying single-cell techniques to across all human cell types as part of the Human Cell Atlas projects at Sanger. I hope that we will be able to develop new and effective protocols for large-scale surveys of individual cells and to make important contributions to this major international effort.

Publications

  • Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

    Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I et al.

    Science immunology 2017;2;9

  • T cell fate and clonality inference from single-cell transcriptomes.

    Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO et al.

    Nature methods 2016;13;4;329-332

  • The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.

    Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D et al.

    PLoS genetics 2015;11;6;e1005251

  • An atlas of mouse CD4(+) T cell transcriptomes.

    Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK et al.

    Biology direct 2015;10;14

  • Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

    Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F et al.

    Cell reports 2016;15;11;2475-87

  • Circulating and Tissue-resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function is Altered During Inflammation.

    Hegazy AN, West NR, Stubbington MJT, Wendt E, Suijker KIM et al.

    Gastroenterology 2017

  • Aging increases cell-to-cell transcriptional variability upon immune stimulation.

    Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA et al.

    Science (New York, N.Y.) 2017;355;6332;1433-1436

  • Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments.

    Vieira Braga FA, Teichmann SA and Stubbington MJ

    Genome biology 2017;18;1;54

  • Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

    Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I et al.

    Science immunology 2017;2;9

  • Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.

    Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ et al.

    Genome research 2017;27;3;451-461

  • Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.

    Wu YL, Stubbington MJ, Daly M, Teichmann SA and Rada C

    The Journal of experimental medicine 2017;214;1;183-196

  • Single-cell analysis at the threshold.

    Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ et al.

    Nature biotechnology 2016;34;11;1111-1118

  • Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

    Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F et al.

    Cell reports 2016;15;11;2475-87

  • T cell fate and clonality inference from single-cell transcriptomes.

    Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO et al.

    Nature methods 2016;13;4;329-332

  • The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.

    Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D et al.

    PLoS genetics 2015;11;6;e1005251

  • An atlas of mouse CD4(+) T cell transcriptomes.

    Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK et al.

    Biology direct 2015;10;14

  • Non-coding transcription and large-scale nuclear organisation of immunoglobulin recombination.

    Stubbington MJ and Corcoran AE

    Current opinion in genetics & development 2013;23;2;81-8

Stubbington, Michael
Michael's Timeline
2016

Became Principal Staff Scientist leading the Human Cell Atlas team at WTSI

Became Senior Staff Scientist in the Teichmann Group at WTSI

2013

Started postdoctoral fellowship in the Teichmann Group at EMBL-EBI

2009

Started PhD in the Corcoran Lab at the Babraham Institute, Cambridge, UK

2004

Started work as a research scientist at the Health Protection Agency, Porton Down, UK.

Completed MSci in Natural Sciences at University of Cambridge.