Systems Biology University of Freiburg
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  Dr. Joep Vanlier



Dr. Ir. Joep Vanlier

University of Freiburg
Institute of Physics
Hermann-Herder-Str. 3, Room 2011
79104 Freiburg i.Br.
joep.vanlier at fdm.uni-freiburg.de
phone: ++49 761 203 8531

Private Address:
Dunantstrasse 1a
79110 Freiburg

 

 

Research Summary

 
  • Dynamical Systems
  • Inference
  • Optimal Experimental Design
  • Model Selection
  • Statistical Methodology
  • Signal Transduction
 

PhD Thesis


Uncertainty Analysis in Systems Biology
Eindhoven University of Technology (2014).
ISBN 978-94-6191-995-3

Publications



Maiwald, T, Hass, H, Steiert, B, Vanlier, J, Engesser, R, Raue, A, Kipkeew, F, Bock, HH, Kaschek, D, Kreutz, C, Timmer, J. Driving the Model to Its Limit: Profile Likelihood Based Model Reduction., PloS one (2016), 11(9), e0162366.

Raue, A, Steiert, B, Schelker, M, Kreutz, C, Maiwald, T, Hass, H, Vanlier, J, Tönsing, C, Adlung, L, Engesser, R, Mader, W, Heinemann, T, Hasenauer, J, Schilling, M, Höfer, T, Klipp, E, Theis, F, Klingmüller, U, Schöberl, B, Timmer, J, Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems, Bioinformatics, 31:3558-3560 (2015)

Vanlier, J, Tiemann, CA, Hilbers, Peter AJ, van Riel, Natal AW, Optimal experiment design for model selection in biochemical networks, BMC systems biology, 8:20 (2014)

Vanlier, J, Tiemann, CA, Hilbers, Peter AJ, van Riel, Natal AW, An integrated strategy for prediction uncertainty analysis, Bioinformatics, 8:1130--1135 (2012)

Vanlier, J, Tiemann, CA, Hilbers, Peter AJ, van Riel, Natal AW, A Bayesian approach to targeted experiment design Vanlier, J, Tiemann, CA, Hilbers, PAJ, van Riel, NAW, Parameter uncertainty in biochemical models described by ordinary differential equations, Mathematical biosciences (2013)

Tiemann, Christian A, Vanlier, Joep, Oosterveer, Maaike H, Groen, Albert K, Hilbers, Peter AJ, van Riel, Natal AW, Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions, PLoS computational biology, 8:e1003166 (2013)

van Riel, Natal, Vanlier, Joep, Tiemann, Christian, Hilbers, Peter, Prediction uncertainty analysis and targeted experiment design in systems biology (2013)

Vanlier, J, Tiemann, CA, Hilbers, Peter AJ, van Riel, Natal AW, An integrated strategy for prediction uncertainty analysis, Bioinformatics, 8:1130--1135 (2012)

Vanlier, J, Tiemann, CA, Hilbers, Peter AJ, van Riel, Natal AW, A Bayesian approach to targeted experiment design, Bioinformatics, 8:1136--1142 (2012)

Tiemann, Christian, Vanlier, Joep, Hilbers, Peter, van Riel, Natal, Parameter adaptations during phenotype transitions in progressive diseases, BMC systems biology, 1:174 (2011)

Schmitz, JPJ, Vanlier, J, van Riel, NAW, Jeneson, Jeroen AL, Computational modeling of mitochondrial energy transduction, Critical Reviews in Biomedical Engineering, 5:363 (2011)

Vanlier, Joep, Wu, Fan, Qi, Feng, Vinnakota, KC, Han, Yu, Dash, Ranjan K, Yang, F, Beard, Daniel A, BISEN: Biochemical simulation environment, Bioinformatics, 6:836--837 (2009)

Software



I have contributed to the following software packages:
NL2SOL mex - MATLAB wrapper to NL2SOL (syntax compatible with lsqnonlin)
Data 2 Dynamics - MATLAB software package for modelling with differential equations.

Older:
CVode Wrapper - MATLAB wrapper around the SUNDIALS' CVODES.
Prediction Uncertainty Analysis Package - MATLAB software package for computing likelihood profiles and performing Bayesian sampling on ODEs (superseded by D2D)
Bayesian Approach to Experimental Design Package with Sequential Monte Carlo sampler - MATLAB package for optimal experiment design based on Posterior Probability distributions.
Optimal Experimental Design for Model Selection - MATLAB package for optimal experiment design based on Posterior Probability distributions.

Hobbies



Running
Electronic music production
Game development (C++/OpenGL/GLSL)
Fluid sim
Procedural generation
Lighting models

Curriculum Vitae



Full CV can be downloaded here