Liam Shaw

Email: liam [dot] philip [dot] shaw [at]

Hello! I'm a computational biologist. My research focuses on analysing and modelling bacterial communities. I'm particularly interested in the development and spread of antimicrobial resistance (AMR).

As of 20th August 2018 I work in the Modernising Medical Microbiology consortium in the Nuffield Department of Medicine, University of Oxford. I'm trying to understand the spread of AMR between humans, animals, and the environment within Oxfordshire.

I completed my PhD at UCL in the Computational Biology Group (2014-2018) after an MRes in Modelling Biological Complexity (2013-2014). Prior to this, my undergraduate degree at Oxford was in physics (2009-2013).

My academic CV is available for download here.


† = equal contribution.
I sporadically update this reverse chronological list, but my Google scholar profile is probably more up-to-date.


Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles
L. P. Shaw, R. M. Doyle, E. Kavaliunaite, H. Spencer, F. Balloux, G. Dixon, K. A Harris (2018)
bioRxiv doi: 10.1101/436261

Modelling microbiome recovery after antibiotics using a stability landscape framework
L. P. Shaw, H. Bassam, C. Barnes, N. Klein, A. Sarah Walker, F. Balloux (2018)
bioRxiv doi: 10.1101/222398


The microbial ecology of human-associated bacterial communities
PhD thesis. Supervisors: Francois Balloux, Nigel Klein, A. Sarah Walker, Robin Callard. Available here

Microbial translocation does not drive immune activation in Ugandan children with HIV.
F. C. Fitzgerald, E. L’homme, K. Harris, J. Kenny, R. Doyle, C. Kityo, L. P Shaw, G. Abongomera, V. Musiime, A. Cook, J. R. Brown, A. Brooks, E. Owen-Powell, D. M. Gibb, A. J. Prendergast, A. S. Walker, R. Thiebaut, N. Klein, The CHAPAS-3 Trial Team.(2018)
Journal of Infectious Diseases (2018) doi: 10.1093/infdis/jiy495

From theory to practice: translating whole-genome sequencing (WGS) into the clinic.
F. Balloux†, O. B. Brynildsrud†, L. van Dorp†, L. P. Shaw, H. Chen, K. A. Harris, H. Wang, V. Eldholm.
Trends in Microbiology (2018) doi: 10.1016/j.tim.2018.08.004

The global distribution and spread of the mobilized colistin resistance gene mcr-1.
R. Wang†, L. van Dorp†, L. P. Shaw†, P. Bradley, Q. Wang, X. Wang, L. Jin, Q. Zhang, Y. Liu, A. Rieux, T. Dorai-Schneiders, L. Weinert, Z. Iqbal, X. Didelot, H. Wang, F. Balloux (2018)
Nature Communications doi: 10.1101/220921

Periapical infection may affect birth outcomes via systemic inflammation.
U. Harjunmaa, R. Doyle, J. Järnstedt, S. Kamiz, J.M. Jorgensen, C.P. Stewart, L. P. Shaw, L. Hallamaa, U. Ashorn, N. Klein, K.G. Dewey, K. Maleta, P. Ashorn (2018)
Oral Diseases doi: 10.1111/odi.12817

Deep sequencing of oral microbiomes from hunter-gatherers and traditional agriculturalists reveals shifts in commensal taxon balance and pathogen load linked to subsistence strategy.
F. Lassalle†, M. Spagnoletti†, M. Fumagalli, L. P. Shaw, M. Dyble, C. Walker, M.G. Thomas, A. Bamberg Migliano, F. Balloux (2018)
Molecular Ecology doi: 10.1111/mec.14435


The oral microbiome.
L. P. Shaw, A. Smith, A. Roberts (2017)
Emerging Topics in Life Sciences doi: 10.1042/ETLS20170040

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals
L. P. Shaw†, A. Ribeiro†, A. Levine, N. Pontikos, F. Balloux, A. Segal, A. Roberts, A. Smith (2017)
mBio doi: 10.1101/131086


Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
D. Jeffares, C. Jolly, M. Hoti, D. Speed, C. Rallis, L. P. Shaw, F. Balloux, C. Dessimoz, J. Bahler, F. Sedlazeck (2016)
Nature Communications doi: 10.1038/ncomms14061

Distinguishing the signals of gingivitis and periodontitis in supragingival plaque: a cross-sectional cohort study in Malawi
L. P. Shaw, U. Harjunmaa, R. Doyle, S. Mulewa, D. Charlie, K. Maleta, R. Callard, A. S. Walker, F. Balloux, P. Ashorn, N. Klein (2016)
Applied and Environmental Microbiology doi: 10.1128/AEM.01756-16


DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization
J. Schreck, T. Ouldridge, F. Romano, P. Sulc, L. P. Shaw, A. Louis, J. Doye (2015)
Nucleic Acids Research doi: 10.1093/nar/gkv582


Here are some lectures I've given:

The human microbiome and antibiotic resistance (1st year undergraduate)

The human microbiome and disease (graduate)


Since 2016 I've been an ambassador for Ask for Evidence, a campaign to try and make companies, politicians, commentators and official bodies more accountable for factual claims. I give talks about this organised by Sense about Science. I also quite occasionally give more general talks about science, society, statistics, and even things not beginning with 's', such as pallets. If you want me to give a talk, feel free to get in touch.

Alongside my academic work, I'm interested in the social and political aspects of science and technology. I also enjoy thinking about the prospects for improving healthcare with technology (particularly in the context of the evidence-based medicine movement), as well as the possibilities of making healthcare significantly worse.

Outside my academic work, I have other interests.

Website theme courtesy of here.