Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models von Fröhlich, Fabian, Sorger, Peter K

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Benchmarking optimization methods for parameter estimation in large kinetic models von Villaverde, Alejandro F, Fröhlich, Fabian, Weindl, Daniel, Hasenauer, Jan, Banga, Julio R

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Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance von Fröhlich, Fabian, Gerosa, Luca, Muhlich, Jeremy, Sorger, Peter K

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Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks von Lakrisenko, Polina, Stapor, Paul, Grein, Stephan, Paszkowski, Łukasz, Pathirana, Dilan, Fröhlich, Fabian, Lines, Glenn Terje, Weindl, Daniel, Hasenauer, Jan

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PESTO: Parameter EStimation TOolbox von Stapor, Paul, Weindl, Daniel, Ballnus, Benjamin, Hug, Sabine, Loos, Carolin, Fiedler, Anna, Krause, Sabrina, Hroß, Sabrina, Fröhlich, Fabian, Hasenauer, Jan

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Linking patient-specific basal MET phosphorylation levels to liver health von Fröhlich, Fabian

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CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics von Kazeroonian, Atefeh, Fröhlich, Fabian, Raue, Andreas, Theis, Fabian J, Hasenauer, Jan

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Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model von Fröhlich, Fabian, Kessler, Thomas, Weindl, Daniel, Shadrin, Alexey, Schmiester, Leonard, Hache, Hendrik, Muradyan, Artur, Schütte, Moritz, Lim, Ji-Hyun, Heinig, Matthias, Theis, Fabian J., Lehrach, Hans, Wierling, Christoph, Lange, Bodo, Hasenauer, Jan

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Combination treatment optimization using a pan-cancer pathway model von Schmucker, Robin, Farina, Gabriele, Faeder, James, Fröhlich, Fabian, Saglam, Ali Sinan, Sandholm, Tuomas

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A Practical Guide for the Efficient Formulation and Calibration of Large, Energy- and Rule-Based Models of Cellular Signal Transduction von Fröhlich, Fabian

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Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks von Fröhlich, Fabian, Kaltenbacher, Barbara, Theis, Fabian J, Hasenauer, Jan

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Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion von Fröhlich, Fabian, Thomas, Philipp, Kazeroonian, Atefeh, Theis, Fabian J, Grima, Ramon, Hasenauer, Jan

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PEtab-Interoperable specification of parameter estimation problems in systems biology von Schmiester, Leonard, Schälte, Yannik, Bergmann, Frank T, Camba, Tacio, Dudkin, Erika, Egert, Janine, Fröhlich, Fabian, Fuhrmann, Lara, Hauber, Adrian L, Kemmer, Svenja, Lakrisenko, Polina, Loos, Carolin, Merkt, Simon, Müller, Wolfgang, Pathirana, Dilan, Raimúndez, Elba, Refisch, Lukas, Rosenblatt, Marcus, Stapor, Paul L, Städter, Philipp, Wang, Dantong, Wieland, Franz-Georg, Banga, Julio R, Timmer, Jens, Villaverde, Alejandro F, Sahle, Sven, Kreutz, Clemens, Hasenauer, Jan, Weindl, Daniel

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A protocol for dynamic model calibration von Villaverde, Alejandro F, Pathirana, Dilan, Fröhlich, Fabian, Hasenauer, Jan, Banga, Julio R

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AMICI: high-performance sensitivity analysis for large ordinary differential equation models von Fröhlich, Fabian, Weindl, Daniel, Schälte, Yannik, Pathirana, Dilan, Paszkowski, Łukasz, Lines, Glenn Terje, Stapor, Paul, Hasenauer, Jan

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Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection von Fröhlich, Fabian, Reiser, Anita, Fink, Laura, Woschée, Daniel, Ligon, Thomas, Theis, Fabian Joachim, Rädler, Joachim Oskar, Hasenauer, Jan

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GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models von Ligon, Thomas S, Fröhlich, Fabian, Chiş, Oana T, Banga, Julio R, Balsa-Canto, Eva, Hasenauer, Jan

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Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction von Chen, Jia-Yun, Hug, Clemens, Reyes, José, Tian, Chengzhe, Gerosa, Luca, Fröhlich, Fabian, Ponsioen, Bas, Snippert, Hugo J.G., Spencer, Sabrina L., Jambhekar, Ashwini, Sorger, Peter K., Lahav, Galit

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Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes von Fröhlich, Fabian, Loos, Carolin, Hasenauer, Jan

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Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis von Stapor, Paul, Fröhlich, Fabian, Hasenauer, Jan

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