Publications

2021
Fabian Fröhlich, Daniel Weindl, Yannik Schälte, Dilan Pathirana, Łukasz Paszkowski, Glenn Terje Lines, Paul Stapor, and Jan Hasenauer. 4/2/2021. “AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models.” Bioinformatics. Publisher's Version Froehlich_et_al_2020.pdf
Leonard Schmiester, Yannik Schälte, Frank T Bergman, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L Stapor, Philipp Städter, Danton Wang, Frang-Georg Wieland, Julio R Banga, Jens Timmer, Alejandro F Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, and Daniel Weindl. 1/26/2021. “PEtab – Interoperable specification of parameter estimation problems in systems biology.” PLoS Computation Biology, 17, 1, Pp. e1008646. Publisher's Version Schmiester_et_al_2021.pdf
2020
Luca Gerosa, Christopher Chidley, Fabian Fröhlich, Gabriela Sanchez, Sang Kyun Lim, Jeremy Muhlich, Jia-Yun Chen, Sreeram Vallabhaneni, Gregory J. Baker, Deni Schapiro, Mariya I Atanasova, Lily A. Chylek, Tujin Shi, Lian Yi, Carrie D. Nicora, Allison Claas, Thomas S.C. Ng, Rainer H. Kohler, Douglas A. Lauffenburger, Ralph Weissleder, Miles A. Miller, Wei-Jun Qian, H. Steven Wiley, and Peter K. Sorger. 2020. “Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells.” Cell Systems, 11, 5, Pp. 478-494. Publisher's Version Gerosa_et_al_2020.pdf
Robin Schmucker, Gabriele Farina, James Faeder, Fabian Fröhlich, Ali Sinan Saglam, and Tuomas Sandholm. 2020. “Combination Treatment Optimization Using a Pan-Cancer Pathway Model.” bioRxiv. Publisher's Version Schmucker_et_al_2020.pdf
Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, and Daniel Weindl. 2020. “Efficient parameterization of large-scale dynamic models based on relative measurements.” Bioinformatics, 36, 2, Pp. 594-602. Publisher's Version Schmiester_et_al_2020a.pdf
2019
Fabian Fröhlich, Carolin Loos, and Jan Hasenauer. 2019. “Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes.” In Gene Regulatory Networks: Methods and Protocols, Pp. 385-422. New York, NY: Springer New York. Publisher's Version
Alejandro F Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, and Julio R Banga. 2019. “Benchmarking optimization methods for parameter estimation in large kinetic models.” Bioinformatics, 35, 5, Pp. 830-838. Publisher's Version Villaverde_et_al_2018.pdf
2018
Fabian Fröhlich, Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan, Moritz Schütte, Ji-Hyun Lim, Matthias Heinig, Fabian J Theis, Hans Lehrach, Christoph Wierling, Bodo Lange, and Jan Hasenauer. 2018. “Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model.” Cell Systems, 7, 6, Pp. 567-579. Publisher's Version Froehlich_et_al_2018b.pdf
Thomas S Ligon, Fabian Fröhlich, Oana T Chi, Julio R Banga, Eva Balsa-Canto, and Jan Hasenauer. 2018. “GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models.” Bioinformatics, 34, 8, Pp. 1421-1423. Publisher's Version Ligon_et_al_2018.pdf
Carolin Loos, Katharina Moeller, Fabian Fröhlich, Tim Hucho, and Jan Hasenauer. 2018. “A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability.” Cell Systems, 6, 5, Pp. 593-603. Publisher's Version Loos_et_al_2018.pdf
Fabian Fröhlich, Anita Reiser, Laura Fink, Daniel Woschée, Thomas Ligon, Fabian J Theis, Joachim O Rädler, and Jan Hasenauer. 2018. “Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.” NPJ systems biology and applications, 5, 1, Pp. 42. Publisher's Version Froehlich_et_al_2018c.pdf
Paul Stapor, Fabian Fröhlich, and Jan Hasenauer. 2018. “Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.” Bioinformatics, 34, 13, Pp. i151-i159. Publisher's Version Stapor_et_al_2018b.pdf
Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hroß, Fabian Fröhlich, and Jan Hasenauer. 2018. “PESTO: Parameter EStimation TOolbox.” Bioinformatics, 34, 4, Pp. 705-707. Publisher's Version Stapor_et_al_2018a.pdf
2017
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J Theis, and Jan Hasenauer. 2017. “Scalable parameter estimation for genome-scale biochemical reaction networks.” PLoS computational biology, 13, 1, Pp. e1005331. Publisher's Version Froehlich_et_al_2017.pdf
Fabian Fröhlich, Fabian J Theis, Joachim O Rädler, and Jan Hasenauer. 2017. “Parameter estimation for dynamical systems with discrete events and logical operations.” Bioinformatics, 33, 7. Publisher's Version Froehlich_et_al_2016b.pdf
2016
Atefeh Kazeroonian, Fabian Fröhlich, Andreas Raue, Fabian J Theis, and Jan Hasenauer. 2016. “CERENA: chemical reaction network analyzer—a toolbox for the simulation and analysis of stochastic chemical kinetics.” PloS one, 11, 1, Pp. e0146732. Publisher's Version Kazeroonian_et_al_2016.pdf
Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J Theis, Ramon Grima, and Jan Hasenauer. 2016. “Inference for stochastic chemical kinetics using moment equations and system size expansion.” PLoS computational biology, 12, 7, Pp. e1005030. Publisher's Version Froehlich_et_al_2016a.pdf
2014
Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, and Jan Hasenauer. 11/2014. “Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis.” Computational Methods in Systems Biology 8859. Manchester: Springer International Publishing. Fröhlich_et_al_2014b.pdf
Fabian Fröhlich, Fabian J. Theis, and Jan Hasenauer. 11/2014. “Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More.” Computational Methods in Systems Biology 8859, Pp. 61-72. Manchester: Springer International Publishing. Fröhlich_et_al_2014a.pdf