Project Description
Public­ations
A. Hass H, Loos C, Alvarez ER, Timmer J, Hasenauer J, Kreutz C. 2019. Benchmark Problems for Dy-namic Modeling of Intracellular Processes. Bioinformatics. Bioinformatics 35: 3073-3082.
B. Kaschek D, Mader W, Fehling-Kaschek M, Rosenblatt M, Timmer J. 2019. Dynamic Modeling, Parame-ter Estimation, and Uncertainty Analysis in R. Journal of Statistical Software. 10: 1-32.
C. Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U. 2018. Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. Cell Syst. 6(1):75-89.
D. Oppelt A, Kaschek D, Huppelschoten S, Sison-Young R, Zhang F, Buck-Wiese M, Herrmann F, Malkusch S, Krüger CL, Meub M, Merkt B, Zimmermann L, Schofield A, Jones RP, Malik H, Schilling M, Heilemann M, van de Water B, Goldring CE, Park BK, Timmer J, Klingmüller U. 2018. Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduc-tion as a tool to quantify the impact of drug-induced liver injury compounds. NPJ Syst Biol Appl. 4:23.
E. Sobotta S, Raue A, Huang X, Vanlier J, Jünger A, Bohl S, Albrecht U, Hahnel MJ, Wolf S, Mueller NS, D'Alessandro LA, Mueller-Bohl S, Boehm ME, Lucarelli P, Bonefas S, Damm G, Seehofer D, Lehmann WD, Rose-John S, van der Hoeven F, Gretz N, Theis FJ, Ehlting C, Bode JG, Timmer J, Schilling M, Klingmüller U. 2017. Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Pri-mary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib. Front Physiol. 8:775
F. Rosenblatt M, Timmer J, Kaschek D. 2016. Customized Steady-State Constraints for Parameter Esti-mation in Non-Linear Ordinary Differential Equation Models. Front Cell Dev Biol. 4:41.
G. Maiwald T, Hass H, Steiert B, Vanlier J, Engesser R, Raue A, Kipkeew F, Bock HH, Kaschek D, Kreutz C, Timmer J. 2016. Driving the Model to Its Limit: Profile Likelihood Based Model Reduction. PLoS One. 11(9):e0162366.
H. D'Alessandro LA, Samaga R, Maiwald T, Rho SH, Bonefas S, Raue A, Iwamoto N, Kienast A, Waldow K, Meyer R, Schilling M, Timmer J, Klamt S, Klingmüller U. 2015. Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Comput Biol. 11(4):e1004192.
I. Mueller S, Huard J, Waldow K, Huang X, D'Alessandro LA, Bohl S, Börner K, Grimm D, Klamt S, Klingmüller U, Schilling M. 2015. T160-phosphorylated CDK2 defines threshold for HGF dependent proliferation in primary hepatocytes. Mol Syst Biol. 11(3):795.
J. 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, Schö-berl B, Timmer J. 2015. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics. 31(21):3558-60.