Theoretical Systems Biology

I am a Wellcome Trust funded PhD student supervised by Prof. Michael Stumpf, Prof. Jonathan Lamb and Prof. Rob Krams. After I received an MSc degree in Biochemistry from the University of Potsdam in 2008 I completed the MSc in Bioinformatics and Theoretical Systems Biology with distinction at Imperial College as part of my 1+3 year PhD programme.

The aim of my research is to develop novel mathematical and computational techniques to model the spatio-temporal signalling processes during the innate immune response.

 

Maximizing the Information Content of Experiments in Systems Biology.
Liepe J, Filippi S, Komorowski M, Stumpf MPH
PLoS Comput Biol. 2013 Jan;9(1):e1002888. doi: 10.1371/journal.pcbi.1002888. Epub 2013 Jan 31.

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. Epub 2012 Nov 20.

Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation.
Liepe J, Taylor H, Barnes CP, Huvet M, Bugeon L, Thorne T, Lamb JR, Dallman MJ, Stumpf MP.
Integr Biol (Camb). 2012 Mar;4(3):335-45. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

GPU accelerated biochemical network simulation.
Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.
Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

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.

The 20S proteasome splicing activity discovered by SpliceMet.
Liepe J, Mishto M, Textoris-Taube K, Janek K, Keller C, Henklein P, Kloetzel PM, Zaikin A.
PLoS Comput Biol. 2010 Jun 24;6(6):e1000830. doi: 10.1371/journal.pcbi.1000830.

Microtubule tracking from stochastic optical reconstruction microscopy images.
J. Liepe, F. Felizzi, A. Pernus and M. Hanulova
Proceedings of the 8th WCSB, 2011

Variety of dynamical regimes in a population of coupled synthetic genetic oscillators.
A. Koseska, A. Zaikin, J. Liepe, and J. Kurths
Proceedings of the 3rd International Conference “Physics and Control” (PhysCon), 2007

 

ABC-SysBio : A tool for parameter inference and model selection.

 

Inference of signalling pathway models.
T. Toni, J. Liepe and M. Stumpf.
Handbook of Statistical Systems Biology, Wiley, 2011

 

“Method for identification of proteasome generated spliced peptides”. 2010,
Application number: EP10075087.6. Application date: 25.02.2010. Applicant: Charité – Berlin.

 

Oral presentation
“Bayesian experimental design to probe cellular decision making processes”. 2012,
MASAMB (Workshop on Mathematical & Statistical Aspects of Molecular Biology),
Berlin, Germany

Oral presentation
“Calibrating multi-scale models of macrophage dynamics”. 2011,
PICA (Physics of Immunity: Complexity Approach),
Dresden, Germany.

Oral presentation
“Quantitative imaging reveals p38 MAP kinase mediated chemotactic variability in leukocytes”. 2010,
MASAMB (Mathematical and Statistical Aspects of Molecular Biology),
University of Warwick, UK.

Poster presentation
EMBO Workshop on Visualizing Biological Data, 2010
Heidelberg, Germany

Poster presentation
International Symposium for Topical Problems of Biophotonics,2009
Nichninovgorod, Russia.