BioPreDyn

From Data to Models
New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications

publication

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology (2015)

Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger and Julio R Banga

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Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach (2015)

Henriques, D., Rocha, M., Saez-Rodriguez, J., and Banga, J. R

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Stochastic Collocatation for Correlated Inputs (2015)

Maria Navarro, Jeroen Witteveen and Joke Blom

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High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita (2015)

Wotton, Karl R, Jimenez-Guri, Eva, Crombach, Anton, Cicin-Sain, Damjan and Jaeger, Johannes

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A consensus approach for estimating the predictive accuracy of dynamic models in biology (2015)

Villaverde, A. F., Bongard, S., Mauch, K.,Muller, D.. Balsa-Canto, E., Schmid, J. and Banga, J. R.

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SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos (2015)

Cicin-Sain, Damjan, Pulido, Antonio Hermoso, Crombach, Anton, Wotton, Karl R, Jimenez-Guri, Eva, Taly, Jean-Francois, Roma, Guglielmo, and Jaeger, Johannes

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Cooperative development of logical modelling standards and tools with CoLoMoTo (2015)

Naldi, A., Monteiro, P. T., Mussel, C., the Consortium for Logical, Models, Tools,, Kestler, H. A., Thieffry, D., Xenarios, I., Saez-Rodriguez, J., Helikar, T., and Chaouiya, C. (2015)

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Uncertainty Propagation in Nerve Impulses Through the Action Potential Mechanism (2015)

Valderrama, Aldemar T., Witteveen, Jeroen, Navarro, Maria, and Blom, Joke

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Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model (2014)

Rybakova, K. N., Tomaszewska, A., van Mourik, S., Blom, J., Westerhoff, H. V., Carlberg, C.and Bruggeman, F. J.

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publication

A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis (2014)

Botman, D., Rottinger, E., Martindale, M.Q., de Jong, J., and Kaandorp, J.A.

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publication
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