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ORCIDJan Hasenauer
- > Home > Persons > Jan Hasenauer
Publications
- 2023
[j43]Yannik Schälte
, Fabian Fröhlich, Paul J. Jost, Jakob Vanhoefer, Dilan Pathirana, Paul Stapor, Polina A. Lakrisenko, Dantong Wang, Elba Raimúndez-Álvarez, Simon Merkt, Leonard Schmiester, Philipp Städter, Stephan Grein, Erika Dudkin, Domagoj Doresic, Daniel Weindl, Jan Hasenauer:
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models. Bioinform. 39(11) (2023)- [j41]Polina A. Lakrisenko, Paul Stapor, Stephan Grein, Lukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer:
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. PLoS Comput. Biol. 19(1) (2023) - 2022
- [j39]Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga:
A protocol for dynamic model calibration. Briefings Bioinform. 23(1) (2022) - [j37]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - 2021
- [j35]Fabian Fröhlich, Daniel Weindl, Yannik Schälte, Dilan Pathirana, Lukasz Paszkowski, Glenn Terje Lines, Paul Stapor, Jan Hasenauer:
AMICI: high-performance sensitivity analysis for large ordinary differential equation models. Bioinform. 37(20): 3676-3677 (2021) - [j31]Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl:
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j29]Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl:
Efficient parameterization of large-scale dynamic models based on relative measurements. Bioinform. 36(2): 594-602 (2020) - 2019
- [j25]Alejandro Fernández Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R. Banga:
Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinform. 35(5): 830-838 (2019) - 2018
- [j23]Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hross, Fabian Fröhlich, Jan Hasenauer:
PESTO: Parameter EStimation TOolbox. Bioinform. 34(4): 705-707 (2018) - [j22]Thomas S. Ligon, Fabian Fröhlich, Oana Chis, Julio R. Banga, Eva Balsa-Canto, Jan Hasenauer:
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. Bioinform. 34(8): 1421-1423 (2018) - [j21]Paul Stapor, Fabian Fröhlich, Jan Hasenauer:
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. Bioinform. 34(13): i151-i159 (2018) - 2017
- [j16]Fabian Fröhlich, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer:
Parameter estimation for dynamical systems with discrete events and logical operations. Bioinform. 33(7): 1049-1056 (2017) - [j13]Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer:
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput. Biol. 13(1) (2017) - 2016
- [j9]Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J. Theis, Ramon Grima, Jan Hasenauer:
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLoS Comput. Biol. 12(7) (2016) - 2014
- [c8]Fabian Fröhlich, Fabian J. Theis, Jan Hasenauer:
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. CMSB 2014: 61-72 - [c7]Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, Jan Hasenauer:
Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. CMSB 2014: 73-85
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