I am a BBSRC-funded research fellow based in the Theoretical Systems Biology group at Imperial College. I use a variety of mathematical and statistical approaches to study the structure and regulation of biological networks. My current research focuses on developing methods to analyse single-cell transcriptomic data, and approaches to assess uncertainty in mathematical models of biological systems. This work involves collaborations with a number of experimental groups studying development of neural and immune cells, and protein signalling pathways in cancer cell lines.
I received a PhD in Biochemistry from Cambridge University in 2010, where I studied the mechanisms and evolution of catalytically promiscuous enzymes. Following this, I did postdoctoral research in the Department of Chemical Engineering at MIT (2011-2012) developing synthetic metabolic pathways for the production of new biofuels in yeast and bacteria. I received an MSc in Bioinformatics & Theoretical Systems Biology at Imperial College in 2013, before joining the Theoretical Systems Biology group as a postdoctoral researcher.
Stem cell differentiation is a stochastic process with memory.
Stumpf PS, Smith RCG, Lenz M, Schubert A, Mueller F-J, Babtie AC, Chan TE, Stumpf MPH, Please CP, Howison SD, Arai F, MacArthur BD.
bioRxiv (2017). DOI: 10.1101/101048.
Network inference and hypotheses-generation from single-cell transcriptomic data using multivariate information measures.
Chan TE, Stumpf MPH, Babtie AC.
bioRxiv (2016). DOI: 10.1101/082099.
Model of host-pathogen interaction dynamics links in vivo optical imaging and immune responses.
Ale A, Crepin VF, Collins JW, Constantinou N, Habibzay M, Babtie AC, Frankel G, Stumpf MPH.
Infect Immun (2017). DOI: 10.1128/IAI.00606-16
MEANS: python package for Moment Expansion Approximation, iNference and Simulation.
Fan S, Geissmann Q, Lakatos E, Lukauskas S, Ale A, Babtie AC, Kirk PDW, Stumpf MPH.
Bioinformatics (2016). DOI: 10.1093/bioinformatics/btw229
Systems biology (un)certainties.
Kirk PDW*, Babtie AC*, Stumpf MPH*.
Science (2015) 350:386-388. DOI: 10.1126/science.aac9505.
Topological sensitivity analysis for systems biology.
Babtie AC*, Kirk PDW*, Stumpf MPH.
PNAS (2014) 111(52):18507-18512. DOI: 10.1073/pnas.1414026112.
Metabolic engineering: enabling technology of a bio-based economy.
Zhang J, Babtie AC, Stephanopoulos G.
Curr Opin Chem Eng (2012) 1(4):355-362. DOI: 10.1016/j.coche.2012.09.003.
Kinetic and computational evidence for an intermediate in the hydrolysis of sultanate esters.
Babtie AC, Lima MF, Kirby AJ, Hollfelder F.
Org Biomol Chem (2012) 10:8095-8101. DOI: 10.1039/C2OB25699A.
What makes an enzyme promiscuous?
Babtie AC, Tokuriki N, Hollfelder F.
Curr Opin Chem Biol (2010) 14(12):200-207. DOI: 10.1016/j.cbpa.2009.11.028.
An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily.
van Loo B, Jonas S, Babtie AC, Benjdia A, Berteau O, Hyvönen M, Hollfelder F.
PNAS (2010) 107(7):2740-2745. DOI: 10.1073/pnas.0903951107.
Simultaneous Determination of Gene Expression and Enzymatic Activity in Individual Bacterial Cells in Microdroplet Compartments.
Shim J, Olguin LF, Whyte G, Scott D, Babtie AC, Abell C, Huck WTS, Rollfelder F.
J Am Chem Soc (2009) 131(42):15251–15256. DOI: 10.1021/ja904823z
Efficient Catalytic Promiscuity for Chemically Distinct Reactions.
Babtie AC, Bandyopadhyay S, Olguin LF, Hollfelder F.
Angew Chem Int Ed (2009) 48(20):3692-3694. DOI: 10.1002/anie.200805843
(* indicates equal contributions)
Conferences, workshops & seminars
Applied Mathematics group seminar (Southampton University, 2016)
Mathematics & Statistical Aspects of Molecular Biology (Cambridge, 2016)
Bridging Scales in Models of Cell to Tissue Behaviour workshop (Oxford, 2016)
Model Parameter Estimation for Predictive Medicine workshop (Birmingham, 2016)
Modelling from Structures to Systems symposium (Imperial, London, 2016)
Biomathematics seminar (Imperial, London, 2015)
An Uncertain Cardiac Modelling workshop (KCL, London, 2015)
Physics of Biological Systems workshop (Francis Crick Institute, London, 2015)
SIAM Conference on Computational Science & Engineering (Utah, USA, 2015)
Calculating & Communicating Uncertainty (London, 2015)
Workshop on Statistical Systems Biology (Warwick, 2014)
Mathematics & Statistical Aspects of Molecular Biology (Sheffield, 2014)
International Conference on Systems Biology (poster; Melbourne, Australia, 2014)
Mathematics & Statistical Aspects of Molecular Biology (poster; London, 2013)
Enzyme Engineering Conference (poster; Groningen, Netherlands, 2009)
European Symposium of the Protein Society (poster; Zurich, Switzerland, 2009)