Ann Babtie

Email

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 Ph.D. 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 and theoretical systems biology at Imperial College in 2013, before joining the Theoretical Systems Biology Group as a postdoctoral researcher.

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Publications

Empirical Bayes Meets Information Theoretical Network Reconstruction From Single Cell Data ➟
Chan TE, Pallaseni A, Babtie AC, McEwen K, Stumpf MPH (2018). bioRxiv. DOI: 10.1101/264853

Learning Regulatory Models for Cell Development From Single Cell Transcriptomic Data ➟
Babtie AC+, Chan TE, Stumpf MPH (2017). Current Opinion in Systems Biology, 5:72-81. DOI: 10.1016/j.coisb.2017.07.013
+ Corresponding author

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 (2017). Cell Systems. 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*+ (2017). Cell Systems. DOI: 10.1016/j.cels.2017.08.014
* Equal contributions
+ Corresponding author

How to Deal With Parameters for Whole-Cell Modelling ➟
Babtie AC+, Stumpf MPH+ (2017). Journal of the Royal Society Interface, 14:20170237. DOI: 10.1098/rsif.2017.0237
+ Corresponding author

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 (2017). Infection and Immunity. 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 (2016). Bioinformatics. DOI: 10.1093/bioinformatics/btw229

Systems Biology (Un)Certainties ➟
Kirk PDW*+, Babtie AC*+, Stumpf MPH*+ (2015). Science, 350:386-388. DOI: 10.1126/science.aac9505.
* Equal contributions
+ Corresponding author

Topological Sensitivity Analysis for Systems Biology ➟
Babtie AC*, Kirk PDW*, Stumpf MPH (2014). PNAS, 111(52):18507-18512. DOI: 10.1073/pnas.1414026112.
* Equal contributions

Metabolic Engineering: Enabling Technology of a Bio-Based Economy ➟
Zhang J, Babtie AC, Stephanopoulos G (2012). Current Opinion in Chemical Engineering, 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 (2012). Organic & Biomolecular Chemistry, 10:8095-8101. DOI: 10.1039/C2OB25699A.

What Makes an Enzyme Promiscuous? ➟
Babtie AC, Tokuriki N, Hollfelder F (2010). Current Opinion in Chemical Biology, 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 (2010). PNAS, 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 (2009). Journal of the American Chemical Society, 131(42):15251–15256. DOI: 10.1021/ja904823z

Efficient Catalytic Promiscuity for Chemically Distinct Reactions ➟
Babtie AC, Bandyopadhyay S, Olguin LF, Hollfelder F (2009). Angew. Chem. Int. Ed., 48(20):3692-3694. DOI: 10.1002/anie.200805843

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Conferences, Workshops and 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 and 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)