Ann Babtie

ABpic (394x400)
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.



Learning regulatory models for cell development from single cell transcriptomic data.
Babtie AC†, Chan TE, Stumpf MPH.
Curr Opin Syst Biol (2017) 5:72-81. DOI: 10.1016/j.coisb.2017.07.013

Stem cell differentiation as a non-Markov stochastic process.
Stumpf PS, Smith RCG, Lenz M, Schuppert A, Mueller F-J, Babtie AC, Chan TE, Stumpf MPH, Please CP, Howison SD, Arai F, MacArthur BD.
Cell Systems (2017). DOI: 10.1016/j.cels.2017.08.009

Gene regulatory network inference from single-cell data using multivariate information measures.
Chan TE*, Stumpf MPH*†, Babtie AC*†.
Cell Systems (2017). DOI: 10.1016/j.cels.2017.08.014

How to deal with parameters for whole-cell modelling.
Babtie AC†, Stumpf MPH†.
J R Soc Interface (2017) 14:20170237. DOI:10.1098/rsif.2017.0237

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, † indicates corresponding author)



Empirical Bayes meets information theoretical network reconstruction from single cell data.
Chan TE, Pallaseni A, Babtie AC, McEwen K, Stumpf MPH.
bioRxiv (2018). DOI: 10.1101/264853


Conferences, workshops & seminars

Invited talks
MathBioFest (Imperial, London, 2018)
Advanced Lecture Course on Computational Systems Biology (Aussois, France, 2017)
Applied Mathematics group seminar (Southampton University, 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)

Contributed talks & posters
Mathematics & Statistical Aspects of Molecular Biology (Cambridge, 2016)
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)