Jan Hasenauer

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 45

Top Topics

Parameter Estimation

Dynamical Systems

Top Venues

PLoS Comput. Biol.

Briefings Bioinform.

Publications

Nina Schmid, David Fernandes del Pozo, Willem Waegeman, Jan Hasenauer
Assessment of Uncertainty Quantification in Universal Differential Equations. CoRR (2024)
Maren Philipps, Antonia Körner, Jakob Vanhoefer, Dilan Pathirana, Jan Hasenauer
Non-Negative Universal Differential Equations With Applications in Systems Biology. CoRR (2024)
Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß, Nils Bundgaard, Frederik Graw, Lutz Brusch, Jan Hasenauer
FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes. Bioinform. 39 (11) (2023)
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)
Lorenzo Contento, Paul Stapor, Daniel Weindl, Jan Hasenauer
A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI. CMSB (2023)
Marc Vaisband, Maria Schubert, Franz Josef Gassner, Roland Geisberger, Richard Greil, Nadja Zaborsky, Jan Hasenauer
Validation of genetic variants from NGS data using deep convolutional neural networks. BMC Bioinform. 24 (1) (2023)
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)
Alejandro F. Villaverde, Elba Raimúndez-Álvarez, Jan Hasenauer, Julio R. Banga
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Manuel Huth, Jonas Arruda, Roy Gusinow, Lorenzo Contento, Evelina Tacconelli, Jan Hasenauer
Accessibility of covariance information creates vulnerability in Federated Learning frameworks. Bioinform. 39 (9) (2023)
Altay Yuzeir, David Alejandro Bejarano, Stephan Grein, Jan Hasenauer, Andreas Schlitzer, Jiangyan Yu
IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line. Bioinform. 39 (4) (2023)
Yannik Schälte, Emmanuel Klinger, Emad Alamoudi, Jan Hasenauer
pyABC: Efficient and robust easy-to-use approximate Bayesian computation. J. Open Source Softw. 7 (74) (2022)
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 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 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 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) (2022)
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga
A protocol for dynamic model calibration. Briefings Bioinform. 23 (1) (2022)
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) (2021)
Leonard Schmiester, Daniel Weindl, Jan Hasenauer
Efficient gradient-based parameter estimation for dynamic models using qualitative data. Bioinform. 37 (23) (2021)
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 L. 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)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 22 (1) (2021)
Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte, Jan Hasenauer
yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. J. Open Source Softw. 6 (61) (2021)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37 (21) (2021)
Yannik Schälte, Jan Hasenauer
Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. Bioinform. 36 (Supplement-1) (2020)
Elba Raimúndez-Álvarez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J. Theis, Dieter Maier, Birgit Luber, Jan Hasenauer
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. PLoS Comput. Biol. 16 (3) (2020)
Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl
Efficient parameterization of large-scale dynamic models based on relative measurements. Bioinform. 36 (2) (2020)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 21 (4) (2020)
Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz
Benchmark problems for dynamic modeling of intracellular processes. Bioinform. 35 (17) (2019)
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) (2019)
Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20 (2) (2019)
Paul Stapor, Fabian Fröhlich, Jan Hasenauer
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. Bioinform. 34 (13) (2018)
Justin Feigelman, Daniel Weindl, Fabian J. Theis, Carsten Marr, Jan Hasenauer
LNA++: Linear Noise Approximation with First and Second Order Sensitivities. CMSB (2018)
Benjamin Ballnus, Steffen Schaper, Fabian J. Theis, Jan Hasenauer
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. Bioinform. 34 (13) (2018)
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) (2018)
Carolin Loos, Sabrina Krause, Jan Hasenauer
Hierarchical optimization for the efficient parametrization of ODE models. Bioinform. 34 (24) (2018)
Emmanuel Klinger, Dennis Rickert, Jan Hasenauer
pyABC: distributed, likelihood-free inference. Bioinform. 34 (20) (2018)
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) (2018)
Emmanuel Klinger, Jan Hasenauer
A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo. CMSB (2017)
Corinna Maier, Carolin Loos, Jan Hasenauer
Robust parameter estimation for dynamical systems from outlier-corrupted data. Bioinform. 33 (5) (2017)
Fabian Fröhlich, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer
Parameter estimation for dynamical systems with discrete events and logical operations. Bioinform. 33 (7) (2017)
Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J. Theis
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. BMC Syst. Biol. 11 (1) (2017)
Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer
A scalable moment-closure approximation for large-scale biochemical reaction networks. Bioinform. 33 (14) (2017)
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput. Biol. 13 (1) (2017)
Anna Fiedler, Sebastian Raeth, Fabian J. Theis, Angelika Hausser, Jan Hasenauer
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. BMC Syst. Biol. 10 (2016)
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)
Carolin Loos, Anna Fiedler, Jan Hasenauer
Parameter Estimation for Reaction Rate Equation Constrained Mixture Models. CMSB (2016)
Eva-Maria Geissen, Jan Hasenauer, Stephanie Heinrich, Silke Hauf, Fabian J. Theis, Nicole Radde
MEMO: multi-experiment mixture model analysis of censored data. Bioinform. 32 (16) (2016)
Sabine Hug, Michael Schwarzfischer, Jan Hasenauer, Carsten Marr, Fabian J. Theis
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule. Stat. Comput. 26 (3) (2016)
Sabrina Hross, Jan Hasenauer
Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinform. 32 (15) (2016)
Carolin Loos, Carsten Marr, Fabian J. Theis, Jan Hasenauer
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. CMSB (2015)
Andreas Raue, Bernhard Steiert, Max Schelker, Clemens Kreutz, Tim Maiwald, Helge Hass, Joep Vanlier, Christian Tönsing, Lorenz Adlung, Raphael Engesser, Wolfgang Mader, Tim Heinemann, Jan Hasenauer, Marcel Schilling, Thomas Höfer, Edda Klipp, Fabian J. Theis, Ursula Klingmüller, Birgit Schoeberl, Jens Timmer
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinform. 31 (21) (2015)
Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. PLoS Comput. Biol. 10 (7) (2014)
Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, Jan Hasenauer
Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. CMSB (2014)
Fabian Fröhlich, Fabian J. Theis, Jan Hasenauer
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. CMSB (2014)
Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf
iVUN: interactive Visualization of Uncertain biochemical reaction Networks. BMC Bioinform. 14 (S-19) (2013)
Sabrina Hock, Jan Hasenauer, Fabian J. Theis
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. BMC Bioinform. 14 (S-10) (2013)
Sabrina Hock, Yen-Kar Ng, Jan Hasenauer, Dominik M. Wittmann, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. BMC Syst. Biol. 7 (2013)
Corinna Vehlow, Jan Hasenauer, Fabian J. Theis, Daniel Weiskopf
Visualizing edge-edge relations in graphs. PacificVis (2013)
Jan Hasenauer, Julian Heinrich, Malgorzata Doszczak, Peter Scheurich, Daniel Weiskopf, Frank Allgöwer
A visual analytics approach for models of heterogeneous cell populations. EURASIP J. Bioinform. Syst. Biol. 2012 (2012)
Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Julian Heinrich, Nicole Radde, Frank Allgöwer, Daniel Weiskopf
Uncertainty-aware visual analysis of biochemical reaction networks. BioVis (2012)
Martin Lohning, Jan Hasenauer, Frank Allgöwer
Steady state stability preserving nonlinear model reduction using sequential convex optimization. CDC/ECC (2011)
Jan Hasenauer, Steffen Waldherr, Malgorzata Doszczak, Nicole Radde, Peter Scheurich, Frank Allgöwer
Identification of models of heterogeneous cell populations from population snapshot data. BMC Bioinform. 12 (2011)
Jan Hasenauer, Steffen Waldherr, Nicole Radde, Malgorzata Doszczak, Peter Scheurich, Frank Allgöwer
A maximum likelihood estimator for parameter distributions in heterogeneous cell populations. ICCS (1) (2010)
Jan Hasenauer, Christian Breindl, Steffen Waldherr, Frank Allgöwer
Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior. CDC (2010)
Andrei Kramer, Jan Hasenauer, Frank Allgöwer, Nicole Radde
Computation of the Posterior Entropy in a Bayesian Framework for Parameter Estimation in Biological Networks. CCA (2010)