Search Results - "Kaschek, Daniel"

Lessons learned from quantitative dynamical modeling in systems biology by Raue, Andreas, Schilling, Marcel, Bachmann, Julie, Matteson, Andrew, Schelker, Max, Schelke, Max, Kaschek, Daniel, Hug, Sabine, Kreutz, Clemens, Harms, Brian D, Theis, Fabian J, Klingmüller, Ursula, Timmer, Jens

“…Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A…”
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Local Riemannian geometry of model manifolds and its implications for practical parameter identifiability by Lill, Daniel, Timmer, Jens, Kaschek, Daniel

“…When non-linear models are fitted to experimental data, parameter estimates can be poorly constrained albeit being identifiable in principle. This means that…”
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BlotIt—Optimal alignment of Western blot and qPCR experiments by Kemmer, Svenja, Bang, Severin, Rosenblatt, Marcus, Timmer, Jens, Kaschek, Daniel

“…Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can…”
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Driving the Model to Its Limit: Profile Likelihood Based Model Reduction by Maiwald, Tim, Hass, Helge, Steiert, Bernhard, Vanlier, Joep, Engesser, Raphael, Raue, Andreas, Kipkeew, Friederike, Bock, Hans H, Kaschek, Daniel, Kreutz, Clemens, Timmer, Jens

“…In systems biology, one of the major tasks is to tailor model complexity to information content of the data. A useful model should describe the data and…”
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Dynamic Modeling, Parameter Estimation, and Uncertainty Analysis in R by Kaschek, Daniel, Mader, Wolfgang, Fehling-Kaschek, Mirjam, Rosenblatt, Marcus, Timmer, Jens

“…In a wide variety of research fields, dynamic modeling is employed as an instrument to learn and understand complex systems. The differential equations…”
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Dynamic modeling of Nrf2 pathway activation in liver cells after toxicant exposure by Hiemstra, Steven, Fehling-Kaschek, Mirjam, Kuijper, Isoude A., Bischoff, Luc J. M., Wijaya, Lukas S., Rosenblatt, Marcus, Esselink, Jeroen, van Egmond, Allard, Mos, Jornt, Beltman, Joost B., Timmer, Jens, van de Water, Bob, Kaschek, Daniel

“…Cells are exposed to oxidative stress and reactive metabolites every day. The Nrf2 signaling pathway responds to oxidative stress by upregulation of…”
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Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range by Bachmann, Julie, Raue, Andreas, Schilling, Marcel, Böhm, Martin E, Kreutz, Clemens, Kaschek, Daniel, Busch, Hauke, Gretz, Norbert, Lehmann, Wolf D, Timmer, Jens, Klingmüller, Ursula

“…Cellular signal transduction is governed by multiple feedback mechanisms to elicit robust cellular decisions. The specific contributions of individual feedback…”
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Quantitative Systems Pharmacology: An Exemplar Model‐Building Workflow With Applications in Cardiovascular, Metabolic, and Oncology Drug Development by Helmlinger, Gabriel, Sokolov, Victor, Peskov, Kirill, Hallow, Karen M., Kosinsky, Yuri, Voronova, Veronika, Chu, Lulu, Yakovleva, Tatiana, Azarov, Ivan, Kaschek, Daniel, Dolgun, Artem, Schmidt, Henning, Boulton, David W., Penland, Robert C.

“…Quantitative systems pharmacology (QSP), a mechanistically oriented form of drug and disease modeling, seeks to address a diverse set of problems in the…”
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Efficient simulation of clinical target response surfaces by Lill, Daniel, Kümmel, Anne, Mitov, Venelin, Kaschek, Daniel, Gobeau, Nathalie, Schmidt, Henning, Timmer, Jens

“…Simulation of combination therapies is challenging due to computational complexity. Either a simple model is used to simulate the response for many…”
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RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data by von der Heyde, Silvia, Sonntag, Johanna, Kaschek, Daniel, Bender, Christian, Bues, Johannes, Wachter, Astrid, Timmer, Jens, Korf, Ulrike, Beißbarth, Tim

“…Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce…”
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Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology by Raue, Andreas, Schilling, Marcel, Bachmann, Julie, Matteson, Andrew, Schelker, Max, Kaschek, Daniel, Hug, Sabine, Kreutz, Clemens, Harms, Brian D., Theis, Fabian J., Klingmüller, Ursula, Timmer, Jens

“…(2013) Lessons Learned from Quantitative Dynamical Modeling in Systems Biology. (2013) Correction: Lessons Learned from Quantitative Dynamical Modeling in…”
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Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration by Meyer, René, D'Alessandro, Lorenza A, Kar, Sandip, Kramer, Bernhard, She, Bin, Kaschek, Daniel, Hahn, Bettina, Wrangborg, David, Karlsson, Johan, Kvarnström, Mats, Jirstrand, Mats, Lehmann, Wolf-Dieter, Timmer, Jens, Höfer, Thomas, Klingmüller, Ursula

“…In most solid cancers, cells harboring oncogenic mutations represent only a sub-fraction of the entire population. Within this sub-fraction the expression…”
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Profile likelihood in systems biology by Kreutz, Clemens, Raue, Andreas, Kaschek, Daniel, Timmer, Jens

“…Inferring knowledge about biological processes by a mathematical description is a major characteristic of Systems Biology. To understand and predict system's…”
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Nonlinear Parameter Optimization Using R Tools. J. C.Nash (2014). Chichester, UK: John Wiley & Sons. 304 pages, ISBN: 978‐1‐118‐56928‐3 by Kaschek, Daniel

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Population Pharmacokinetic Modeling of Adavosertib (AZD1775) in Patients with Solid Tumors by Johnson, Martin, Kaschek, Daniel, Ghiorghiu, Dana, Lanke, Shankar, Miah, Kowser, Schmidt, Henning, Mugundu, Ganesh M.

“…Adavosertib (AZD1775) is a potent small‐molecule inhibitor of Wee1 kinase. This analysis utilized pharmacokinetic data from 8 Phase I/II studies of adavosertib…”
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Fast integration-based prediction bands for ordinary differential equation models by Hass, Helge, Kreutz, Clemens, Timmer, Jens, Kaschek, Daniel

“…To gain a deeper understanding of biological processes and their relevance in disease, mathematical models are built upon experimental data. Uncertainty in the…”
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Mathematical modeling of drug-induced receptor internalization in the HER2-positive SKBR3 breast cancer cell-line by Fehling-Kaschek, Mirjam, Peckys, Diana B., Kaschek, Daniel, Timmer, Jens, Jonge, Niels de

“…About 20% of breast cancer tumors over-express the HER2 receptor. Trastuzumab, an approved drug to treat this type of breast cancer, is a monoclonal antibody…”
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A variational approach to parameter estimation in ordinary differential equations by Kaschek, Daniel, Timmer, Jens

“…Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous…”
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Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models by Rosenblatt, Marcus, Timmer, Jens, Kaschek, Daniel

“…Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters…”
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A Dynamic Mathematical Model of Bile Acid Clearance in HepaRG Cells by Kaschek, Daniel, Sharanek, Ahmad, Guillouzo, André, Timmer, Jens, Weaver, Richard J

“…Abstract A dynamic model based on ordinary differential equations that describes uptake, basolateral and canalicular export of taurocholic acid (TCA) in human…”
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