Linus Schumacher

- Centre for Regenerative Medicine
Contact details
- Tel: +44 (0)131 651 9526
- Email: Linus.Schumacher@ed.ac.uk
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Address
- Street
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Centre for Regenerative Medicine,
Institute for Regeneration and Repair,
The University of Edinburgh,
Edinburgh BioQuarter,
5 Little France Drive, - City
- Edinburgh
- Post code
- EH16 4UU
Background
I moved to Edinburgh as a Chancellor’s Fellow in 2018. Previously I was a postdoctoral researcher at Imperial College London and the University of Oxford, where I also obtained my DPhil, based at the Wolfson Centre for Mathematical Biology. For my undergraduate degree I read Natural Sciences at the University of Cambridge.
Open to PhD supervision enquiries?
Yes
Areas of interest for supervision
Applicants requiring funding should also consider the following doctoral programmes: MAC-MIGS (https://www.mac-migs.ac.uk), Biomedical AI (http://web.inf.ed.ac.uk/cdt/biomedical-ai), Precision Medicine (https://www.ed.ac.uk/usher/precision-medicine)
Current PhD students supervised
- Rodrigo Garcia. Development of mathematical tools for identifying hallmarks of regulatory mechanisms in stem cell lineages (co-supervised with Ramon Grima)
- Thanakorn Jaemthaworn. Integrating network state representations for modelling cell state dynamics (co-supervised with Tamir Chandra)
- Viktoria Freingruber. Collective chemotaxis: how cells work together to migrate more efficiently (co-supervised with Kevin Painter & Mariya Ptashnyk)
- Alex Richardson. Learning the rules of biological pattern formation (co-supervised with Richard Blythe and Tibor Antal)
Past PhD students supervised
- Jorge Lemos. Computational modelling of human stem cell fitness in ageing blood (co-supervised with Tamir Chandra and Kristina Kirschner)
Research summary
Computational biology of cell populations
Tissue development and regeneration can be seen as group behaviours of cell populations. To understand development and regeneration, we need to consider the interactions between stem cells and the rest of the cells that make up a tissue. We use mathematical models and computational simulations to predict tissue behaviour from the behaviour of cells. This allows us to develop and test hypotheses in complex biological systems and discern informative patterns in experimental data.
Read an accessible description of Linus Schumacher’s research on the Data-Driven Innovation website: https://ddi.ac.uk/chancellors/linus-schumacher/
Aims and areas of interest
The dynamics of a tissue in development and regeneration arises from the behaviour of its constituent cells and their interactions. In embryo development, initially homogeneous populations of cells have to acquire cell fates in specific proportions and spatial arrangements to enable tissue function. How do individual cells coordinate with their neighbours to achieve this? In adult tissues, cell populations have to self-regulate so as to enable regeneration after injury without over-proliferating in a malignant manner. How does regeneration only happen when needed, and how does it know when to stop?
We use mathematical models and statistical inference methods to infer from various experimental data the most likely cellular behaviours and regulatory mechanisms underlying changing tissue states. Example methods include birth-death process models of stem cell dynamics, extending such models by incorporating regulatory interactions and additional or intermediate cell states, and machine learning tools to learn cell-cell interaction models directly from data in interpretable ways. The applications range from in vitro models of embryo development to adult tissue regeneration that is disrupted in ageing or cancer.
By developing theoretical models we also bring new perspectives on how to interrogate experimental data. We work closely with experimental collaborators with the aims to formulate principles that apply to multiple biological systems, gain insight into misregulation in disease, and inform improvements to regenerative therapy.
Current research interests
Bayesian inference of cell state transitions, Data-driven modelling of immune cell interactions in tissue regeneration and repair, Quantitative analysis and modelling of immune cell migration in wound response, Clonal dynamics under homeostatic feedback, mutation competition, and ageingPast research interests
Neural crest cell migration, Collective behaviour of C. elegans nematodes, Noise-induced phenomena in stochastic pattern formationAffiliated research centres
Current project grants
University of Edinburgh Chancellor's Fellowship
Academy of Medical Sciences Springboard Award
Wellcome Leap Delta Tissue grant (as co-I)
Leverhulme research grant (as co-I)
Past project grants
EPSRC Doctoral Prize
Wellcome Trust Institutional Strategic Support Fund
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Modelling the Dynamics of Senescence Spread
In:
Aging Cell
Research output: Contribution to Journal › Article (Accepted/In press) -
Regulation of stem cell dynamics through volume exclusion
(22 pages)
In:
Proceedings of the royal society of london series a-Mathematical and physical sciences, vol. 478
DOI: https://doi.org/10.1098/rspa.2022.0376
Research output: Contribution to Journal › Article (Published) -
Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects
In:
Nature Medicine
DOI: https://doi.org//10.1038/s41591-022-01
Research output: Contribution to Journal › Article (Published) -
Live cell tracking of macrophage efferocytosis during Drosophila embryo development in vivo
In:
Science, vol. 375, pp. 1182-1187
DOI: https://doi.org/10.1126/science.abl4430
Research output: Contribution to Journal › Article (Published) -
Regenerative medicine meets mathematical modelling: developing symbiotic relationships
(8 pages)
In:
npj Regenerative Medicine, vol. 6
DOI: https://doi.org/10.1038/s41536-021-00134-2
Research output: Contribution to Journal › Review article (Published) -
Comparison of solitary and collective foraging strategies of Caenorhabditis elegans in patchy food distributions
In:
Philosophical Transactions of the Royal Society B: Biological Sciences
DOI: https://doi.org/10.1098/rstb.2019.0382
Research output: Contribution to Journal › Article (Published) -
Coupled differentiation and division of embryonic stem cells inferred from clonal snapshots
In:
Physical Biology
DOI: https://doi.org/10.1088/1478-3975/aba041
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Persistent and polarised global actin flow is essential for directionality during cell migration
(12 pages)
In:
Nature Cell Biology, vol. 21, pp. 1370–1381
DOI: https://doi.org/10.1038/s41556-019-0411-5
Research output: Contribution to Journal › Article (Published) -
Shared behavioral mechanisms underlie C. elegans aggregation and swarming
(32 pages)
In:
eLIFE, vol. 8
DOI: https://doi.org/10.7554/eLife.43318
Research output: Contribution to Journal › Article (Published) -
Neural crest migration with continuous cell states
In:
Journal of Theoretical Biology
DOI: https://doi.org/10.1016/j.jtbi.2019.01.029
Research output: Contribution to Journal › Article (E-pub ahead of print) -
The devil is in the mesoscale: Mechanical and behavioural heterogeneity in collective cell movement
In:
Seminars in Cell and Developmental Biology
DOI: https://doi.org/10.1016/j.semcdb.2018.06.003
Research output: Contribution to Journal › Review article (E-pub ahead of print) -
DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion
(16 pages)
In:
Journal of Cell Biology, vol. 216, pp. 3339-3354
DOI: https://doi.org/10.1083/jcb.201612169
Research output: Contribution to Journal › Article (Published) -
Self-organization process in newborn skin organoid formation inspires strategy to restore hair regeneration of adult cells
(10 pages)
In:
Proceedings of the National Academy of Sciences (PNAS), vol. 114, pp. E7101-E7110
DOI: https://doi.org/10.1073/pnas.1700475114
Research output: Contribution to Journal › Article (Published) -
Semblance of Heterogeneity in Collective Cell Migration
(10 pages)
In:
Cell Systems, vol. 5, pp. 119-+
DOI: https://doi.org/10.1016/j.cels.2017.06.006
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Multidisciplinary approaches to understanding collective cell migration in developmental biology
(10 pages)
In:
Open Biology, vol. 6
DOI: https://doi.org/10.1098/rsob.160056
Research output: Contribution to Journal › Review article (Published) -
VEGF signals induce trailblazer cell identity that drives neural crest migration
(14 pages)
In:
Developmental Biology, vol. 407, pp. 12-25
DOI: https://doi.org/10.1016/j.ydbio.2015.08.011
Research output: Contribution to Journal › Article (Published) -
Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front
(12 pages)
In:
Development, vol. 142, pp. 2014-2025
DOI: https://doi.org/10.1242/dev.117507
Research output: Contribution to Journal › Article (Published) -
Noise-induced temporal dynamics in Turing systems
(10 pages)
In:
Physical Review E, vol. 87
DOI: https://doi.org/10.1103/PhysRevE.87.042719
Research output: Contribution to Journal › Article (Published) -
How liquid is biological signalling?
(10 pages)
In:
Theoretical Computer Science, vol. 410, pp. 1003-1012
DOI: https://doi.org/10.1016/j.tcs.2008.10.037
Research output: Contribution to Journal › Article (Published) -
A statistical analysis of receptor clustering using random graphs
(4 pages)
Research output: › Conference contribution (Published)
Guillaume Blin (University of Edinburgh)
Tamir Chandra (University of Edinburgh)
Yi Feng (University of Edinburgh)
Alex Fletcher (University of Sheffield)
Kristina Kirschner (University of Glasgow)
Jochen Kursawe (University of St Andrews)
Anestis Tsakiridis (University of Sheffield)
Will Wood (University of Edinburgh)
Val Wilson (University of Edinburgh)