Paul Kirk

Please see my new webpage:

Work in the Theoretical Systems Biology group

While in the Theoretical Systems Biology group, I was employed on a Human Frontier Science Program (HFSP) grant, on a project entitled “Cellular Information Processing and Decision Making: from Noise to Robust Phenotypes”. This was an international collaboration between the groups of Profs. Michael Stumpf (Imperial), David Klug (Imperial), Mustafa Khammash (ETH Zurich) and Shinya Kuroda (Tokyo).

Brief bio

From November 2010 to April 2012, I was employed at the University of Warwick, working on Bayesian data integration approaches for functional genomics data. This was another collaborative project, involving researchers from the groups of Profs. David Wild (Warwick), Jim Griffin (Kent) and Zoubin Ghahramani (Cambridge).

Prior to this, I was a Wellcome Trust funded 1+3 year (MSc+PhD) doctoral student at Imperial College, supervised by Profs. Michael Stumpf and Sylvia Richardson. After completing the MSc component with Distinction, I started my PhD in October 2007. Additionally working with Charles Bangham (Immunology) and Alexandra Lewin (Biostatistics), I investigated and developed stability selection approaches for proteomic biomarker discovery in the context of HTLV-1 associated myelopathy/tropical spastic paraparesis. I also considered the use of Gaussian process regression models for quantifying the robustness of inferences drawn from biological time course data. For my PhD, I was awarded the Centenary Prize for Research in the Molecular Biosciences.

Before starting my PhD, I completed the MSc in Computational Science and Modelling at Exeter (with Distinction), winning the Mathematics Research Institute prize for best MSc project. Before that, I was an MSci Mathematics undergraduate at Imperial College, graduating with First Class Honours and winning the Royal College of Science Association prize.

Journal publications

Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB.
Jovanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MP.
Mol Biosyst. 2015 Apr 21;11(5):1348-59. doi: 10.1039/c4mb00720d.

SYSBIONS: nested sampling for systems biology.
Johnson R*, Kirk P*, Stumpf MP.
Bioinformatics. 2015 Feb 15;31(4):604-5. doi: 10.1093/bioinformatics/btu675. Epub 2014 Oct 16.
*Joint first authors

Topological sensitivity analysis for systems biology.
Babtie AC*, Kirk P*, Stumpf MP.
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18507-12. doi: 10.1073/pnas.1414026112. Epub 2014 Dec 15.
*Joint first authors

Model selection in systems biology depends on experimental design.
Silk D, Kirk PD, Barnes CP, Toni T, Stumpf MP.
PLoS Comput Biol. 2014 Jun 12;10(6):e1003650. doi: 10.1371/journal.pcbi.1003650. eCollection 2014 Jun.

Derivative processes for modelling metabolic fluxes.
Zurauskienė J, Kirk P, Thorne T, Pinney J, Stumpf M.
Bioinformatics. 2014 Jul 1;30(13):1892-8. doi: 10.1093/bioinformatics/btu069. Epub 2014 Feb 26.

Bayesian nonparametric approaches to reconstructing oscillatory systems and the Nyquist limit.
Zurauskienė J, Kirk P, Thorne T, Stumpf MP.
Physica A: Statistical Mechanics and its Applications. 2014 March 26. [Epub ahead of print]

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.
Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP.
Nat Protoc. 2014 Feb;9(2):439-56. doi: 10.1038/nprot.2014.025. Epub 2014 Jan 23.

Balancing the Robustness and Predictive Performance of Biomarkers.
Kirk P, Witkover A, Bangham CR, Richardson S, Lewin AM, Stumpf MP.
J Comput Biol. 2013 Dec;20(12):979-89. doi: 10.1089/cmb.2013.0018

A general moment expansion method for stochastic kinetic models.
Ale A*, Kirk P*, Stumpf MP.
The Journal of Chemical Physics. 2013; 138(17). doi:10.1063/1.4802475
*Joint first authors

Model selection in systems and synthetic biology.
Kirk P*, Thorne T*, Stumpf MP.
Current Opinion in Biotechnology. 2013, doi:10.1016/j.copbio.2013.03.012
*Joint first authors

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.
Darkins R, Cooke EJ, Ghahramani Z, Kirk PD, Wild DL, Savage RS.
PLOS ONE. 2013; 8(4), e59795. doi:10.1371/journal.pone.0059795

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.
Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ.
Immunol Cell Biol. 2013 Jan;91(1):60-9. doi: 10.1038/icb.2012.57.

Bayesian correlated clustering to integrate multiple datasets.
Kirk P, Griffin JE, Savage RS, Ghahramani Z, Wild DL.
Bioinformatics. 2012 Dec 15;28(24):3290-7. doi: 10.1093/bioinformatics/bts595.

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.
Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP.
Mol Biosyst. 2012 Jul 6;8(7):1921-9. doi: 10.1039/c2mb05493k.

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements.
Cooke EJ, Savage RS, Kirk PD, Darkins R, Wild DL.
BMC Bioinformatics. 2011 Oct 13;12:399. doi: 10.1186/1471-2105-12-399.

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis.
Kirk PD*, Witkover A*, Courtney A, Lewin AM, Wait R, Stumpf MP, Richardson S, Taylor GP, Bangham CR.
Retrovirology. 2011 Oct 12;8:81. doi: 10.1186/1742-4690-8-81.
*Joint first authors

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes.
Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP.
Nat Commun. 2011 Oct 4;2:489. doi: 10.1038/ncomms1496.

Discussion of “Stability Selection” by Meinshausen and Buhlmann
Kirk PD, Lewin A, Stumpf MP
J. Roy. Statist. Soc., Ser. B 2010 Sept; 72(4), 456-458

ABC-SysBio–approximate Bayesian computation in Python with GPU support.
Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.
Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.
Kirk PD, Stumpf MP.
Bioinformatics. 2009 May 15;25(10):1300-6. doi: 10.1093/bioinformatics/btp139.

Parameter inference for biochemical systems that undergo a Hopf bifurcation.
Kirk PD, Toni T, Stumpf MP.
Biophys J. 2008 Jul;95(2):540-9. doi: 10.1529/biophysj.107.126086.

Conference proceedings

Automated detection of chaotic and oscillatory regimes
Silk D, Kirk PD, Barnes C, Stumpf MP
Proceedings of the Fourth International Workshop on Machine Learning in Systems Biology. 2010, pp. 59-66.