Mathematical sciences
University of Göteborg
SE-412 96 Göteborg
Phone: +46-(0)31-772 5334
E-mail: peterg...chalmers.se
Department of mathematics
Uppsala University
SE-751 06 Uppsala
Phone: +46-(0)18-471 3259
E-mail: peterg...math.uu.se
We maintain a collection of benchmark problems for identification of ordinary differential equations from time series data at www.odeidentification.org
LICS Workshop on Logic and Systems Biology, 10 July 2010, Edinburgh, U.K.
Improved parameter estimation for completely observed ordinary differential equations with application to biological systems. CMSB 2009, Bologna.
Formal pepresentation of the High Osmolarity Glycerol pathway in Yeast. ISMB/ECCB BioPathways SIG, 2009, Stockholm.
Gennemark P. 2005. Modeling and identification of biological systems with emphasis on osmoregulation in yeast, ISBN 91-7291-647-8.
Kattas, GD, Gennemark, P. and Wedelin, D. 2010. Structural identification of GMA models: algorithm and model comparison. Accepted paper for Computational methods in systems biology, Trento, Italy.
Kühn C., Prasad K.V.S., Klipp E., Gennemark P. 2010. Formal representation of the High Osmolarity Glycerol pathway. Genome informatics 22:69-83
Gennemark, P. and Wedelin, D. 2009. Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems. In Computational methods in systems biology, LNCS 5688, 205-217. ISBN 978-3-642-03844-0.
Gennemark P. and Wedelin D. 2009. D. Benchmarks for identification of ordinary differential equations from time series data. Bioinformatics 25(6):780-6.
Nelander S., Wang W., Nilsson B., She Q-B., Pratilas C., Rosen N., Gennemark P. and Sander C. 2008. Models from experiments: combinatorial drug perturbations of cancer cells, Molecular Systems Biology 4:216.
Wedelin, D. and Gennemark, P. 2008. On the design and evaluation of identification algorithms for ordinary differential equations. 5th Workshop on Computation of Biochemical Pathways and Genetic Networks. BIOQUANT, Heidelberg, p. 35-41. ISBN/ISSN: 978-3-8325-1993-3
Gennemark, P. and Wedelin, D. 2007. Efficient algorithms for ordinary differential equation model identification of biological systems. IET Systems Biology, 1 (2) pp. 120-129. (submitted pdf, submitted supplement)
Gennemark P., Nordlander B., Hohmann S. and Wedelin D. 2006. A simple mathematical model of adaptation to high osmolarity in yeast. In Silico Biology 6, 0018 (pdf).
Klipp E, Nordlander B, Kruger R, Gennemark P, Hohmann S. 2005. Integrative model of the response of yeast to osmotic shock. Nature Biotechnology. 23(8):975-82.
Gennemark P. 2010. Modelling Yeast Osmoregulation at Different Levels of Resolution LICS Workshop on Logic and Systems Biology, Edinburgh, U.K.
Gennemark P. 2010. Lärande i interdisciplinära miljöer.
Gennemark P. 2002. A model identification algorithm for cell signalling pathways. Licentiate thesis.
Gennemark P. Nyman M. 2000. Interactions between [poly(R)-3-hydroxybutyrate] (PHB) and in vitro cultured macrophages and fibroblasts. Master thesis.