Email Address: firstname.lastname@example.org
Other Research Theme Collaborations: ESH
Current researchI joined the BSU in April 2015, working within the Statistical Genomics (SGX) theme. I am currently developing methods for the unsupervised integration of (big) genomics datasets.
I am a member of the Cambridge Big Data Initiative: http://www.bigdata.cam.ac.uk/directory/paul-kirk.
I also have a Google scholar profile.
Brief BioBetween June 2014 and March 2015, I was a senior postdoc in the Yau group (Applied Statistical Genomics) at the Wellcome Trust Centre for Human Genetics, University of Oxford. During this time, I worked on Bayesian approaches for the deconvolution of tumour heterogeneity.
For 2 years, starting in May 2012, I was a postdoc in the Theoretical Systems Biology group, Imperial College London, working with Prof Michael Stumpf. 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).
From November 2010 to April 2012, I was employed at the University of Warwick, working on Bayesian 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 my MSc project “Bayesian Approaches to Active Learning” (supervised by Prof Richard Everson). Before that, I was an MSci Mathematics undergraduate at Imperial College London, graduating with First Class Honours and winning the Royal College of Science Association prize. While an undergraduate at Imperial, I was predominantly interested in Pure Mathematics (particularly Algebra, and especially Group Theory), and submitted an MSci dissertation entitled "The Extension Problem and the Extension of Vn(2) by GLn(2)” (supervised by Prof Alexander Ivanov).
Outreach, Public Engagement, and Communication
Retroviruses integrate into a shared, non-palindromic DNA motifI recently wrote a lay summary of our Nature Microbiology paper "Retroviruses integrate into a shared, non-palindromic DNA motif" for the BSU website.
Modelling in biology: certainties and consequencesTogether with Ann Babtie and Michael Stumpf from the TheoSysBio group at Imperial College London, I wrote a Perspective that appeared in Science on October 23rd 2015. A lay summary is provided on the BSU website.
The author's version of the article may be downloaded here.
This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science on 23 October 2015: Vol. 350 no. 6259 pp. 386-388, DOI: 10.1126/science.aac9505.
Will a realistic complex system be stable?Together with collaborators from the Stumpf group at Imperial College London, I put together a video abstract to accompany our NJP article Conditional random matrix ensembles and the stability of dynamical systems, which is available here.
I also wrote a lay summary of the paper for the BSU website.
A more reliable method for working with mathematical modelsHere is a description and lay summary of the PNAS article Topological sensitivity analysis for systems biology by Babtie*, Kirk*, and Stumpf (*Joint first authors): Imperial College Press Release.
Wimbledon College InterviewDuring the Royal Society Summer Science Exhibition (2013), I had a stab at answering the question "How do bacteria make decisions without brains?", which was posed by students from Wimbledon College who won the "Ask a Scientist" competition. You can hear my answer on the Royal Society's R.Science podcast here.
I subsequently visited Wimbledon College, where I chatted to some of the students about the exhibit and also answered some of their questions. My grilling by the students appeared on a "Skills for Scientists -- Careers Special" podcast from the Royal Society, available from here.
Royal Society Summer Science Exhibition (2013)I took part in the 2013 Royal Society Summer Science Exhibition, as one of the team leaders for the Clever Microbes exhibit. As part of this, I took part in a video interview, and also had a go at some scientific stand up during one of the "Show and Tell" sessions at the Royal Society.
I was also part of the team that produced the animated video "The life of COLIn", which tells the story of a day in the life of an E. coli bacterium.
My First Academic TalkThe first academic talk I ever gave was in 2009, at the "Learning and Inference in Computational and Systems Biology" workshop. Luckily enough, the whole experience was captured for posterity and appears on the videolectures.net website! And here it is: http://videolectures.net/licsb09_kirk_gprb/.
Book chaptersReverse engineering under uncertainty. Kirk P, Silk D, Stumpf MP. In: D Gomez-Cabrero and L Geris (eds.), Uncertainty in Biology: a Computational Modeling Approach. Switzerland:Springer International Publishing, Chapter 2 (2016, in press)
Journal publicationsA comprehensive evaluation of nasal and bronchial cytokines and chemokines following experimental rhinovirus infection in asthma: increased interferons (IFN-γ and IFN-λ) and type 2 inflammation (IL-5 and IL-13). Hansel TT, Tunstall T, Trujillo-Torralbo M-B, Shamji B, del-Rosario J, Dhariwal J, Kirk PDW, et al. eBioMedicine. 2017.
Retroviruses integrate into a shared, non-palindromic motif. Kirk PDW, Huvet M, Melamed A, Maertens GN, Bangham CRM Nature Microbiology. 2016; 2, 16212.
Inferring extrinsic noise from single-cell gene expression data using Approximate Bayesian Computation. Lenive O, Kirk PDW, Stumpf MPH BMC Systems Biology. 2016; 10(1), 1–17.
Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling. Filippi S, Barnes CP, Kirk PDW, Kudo T, Kunida K, McMahon SS, et al. Cell Reports. 2016.
MEANS: python package for Moment Expansion Approximation, iNference and Simulation Fan S, Geissman Q, Lakatos E, Lukauskas S, Ale A, Babtie A, Kirk PDW, Stumpf MPH Bioinformatics. First published online May 5, 2016 Software: theosysbio GitHub page.
MDI-GPU: Accelerating integrative modelling for genomic-scale data using GP-GPU computing. Mason S, Sayyid F, Kirk PDW, Starr C, Wild D Statistical Applications in Genetics and Molecular Biology. 2016; 15(1), 83–86. Software: Warwick Systems Biology software page.
A Graph Theoretical Approach to Data Fusion. Zurauskiene J*, Kirk PDW*, Stumpf MPH Statistical Applications in Genetics and Molecular Biology. 2016. *Joint first authors
Systems biology (un)certainties. Kirk PDW*, Babtie AC*, Stumpf MP*. Science. 2015 Oct 23;350(6259):386-8. *Corresponding authors and equal contributors
Cellular Population Dynamics Control the Robustness of the Stem Cell Niche. MacLean AL*, Kirk PDW*, Stumpf MPH Biol Open. 2015 Oct 9. pii: bio.013714. *Joint first authors
Multivariate moment closure techniques for stochastic kinetic models. Lakatos E, Ale A, Kirk PDW, Stumpf MPH J Chem Phys. 2015 Sep 7;143(9):094107.
Conditional random matrix ensembles and the stability of dynamical systems. Kirk P*, Rolando DMY*, MacLean AL, Stumpf MPH. New Journal of Physics. 2015 August;17(8):083025. *Joint first authors
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 May;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.