CERENA: chemical reaction network analyzer—a toolbox for the simulation and analysis of stochastic chemical kinetics

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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

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Fabian Fröhlich, PhD

Laboratory of Systems Pharmacology

Department of Systems Biology

Harvard Medical School
Warren Alpert Building 444
Boston, MA 02115 USA

Recent Publications

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

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

Fabian Fröhlich, Phd

Large-Scale Kinetic Modeling for Cancer Precision Medicine

CERENA: chemical reaction network analyzer—a toolbox for the simulation and analysis of stochastic chemical kinetics

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