Jan Hasenauer

71 papers A* 1B 2C 1Misc 1Journal 56Unranked 10
YearRankTypeTitle / Venue / Authors
2026 J jnl
Efficient numerical computation of traveler states in explicit mobility-based metapopulation models: Mathematical theory and application to epidemics.
CoRR
Henrik Zunker, René Schmieding, Jan Hasenauer, Martin J. Kühn
2026 J jnl
MEmilio - A high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics.
CoRR
Julia Bicker, Carlotta Gerstein, David Kerkmann, Sascha Korf, René Schmieding, Anna Wendler, Henrik Zunker, Daniel Abele, Maximilian Betz, Khoa Nguyen, Lena Plötzke, Kilian Volmer, Agatha Schmidt, Nils Waßmuth, Patrick Lenz, Daniel Richter, Hannah Tritzschak, Ralf Hannemann-Tamas, Julian Litz, Paul Johannssen, Marielena Borges, Annika Jungklaus, Manuel Heger, Annalena Lange, Elisabeth Kluth, Kathrin Rack, Vincent Wieland, Jonas Arruda, Sebastian Binder, Margrit Klitz, Martin Siggel, Manuel Dahmen, Achim Basermann, Michael Meyer-Hermann, Jan Hasenauer, Martin J. Kühn
2026 J jnl
PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.
Bioinform.
Paul J. Jost, Frank T. Bergmann, Daniel Weindl, Jan Hasenauer
2025 J jnl
Diffusion Models in Simulation-Based Inference: A Tutorial Review.
CoRR
Jonas Arruda, Niels Bracher, Ullrich Köthe, Jan Hasenauer, Stefan T. Radev
2025 J jnl
PEtab.jl: advancing the efficiency and utility of dynamic modelling.
Bioinform.
Sebastian Persson, Fabian Fröhlich, Stephan Grein, Torkel Loman, Damiano Ognissanti, Viktor Hasselgren, Jan Hasenauer, Marija Cvijovic
2024 A* conf
An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation.
ICML
Jonas Arruda, Yannik Schälte, Clemens Peiter, Olga Teplytska, Ulrich Jaehde, Jan Hasenauer
2024 J jnl
Assessment of Uncertainty Quantification in Universal Differential Equations.
CoRR
Nina Schmid, David Fernandes del Pozo, Willem Waegeman, Jan Hasenauer
2024 B conf
Data infrastructure for integrating clinical data in the large-scale international ORCHESTRA cohort: from data import to federated analysis.
IEEE Big Data
Miroslav Puskaric, Hammam Abu Attieh, Fabian Prasser, Roy Gusinow, Chiara Dellacasa, Elisa Rossi, Juan Mata Naranjo, Lorenzo Maria Canziani, Anna Górska, Jan Hasenauer
2024 J jnl
Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data.
Bioinform.
Domagoj Doresic, Stephan Grein, Jan Hasenauer
2024 J jnl
Hawkes Process Modelling for Chemical Reaction Networks in a Random Environment.
SIAM J. Appl. Dyn. Syst.
Mark Sinzger-D'Angelo, Jan Hasenauer, Heinz Koeppl
2024 J jnl
Missing data in amortized simulation-based neural posterior estimation.
PLoS Comput. Biol.
Zijian Wang, Jan Hasenauer, Yannik Schälte
2024 J jnl
Non-Negative Universal Differential Equations With Applications in Systems Biology.
CoRR
Maren Philipps, Antonia Körner, Jakob Vanhoefer, Dilan Pathirana, Jan Hasenauer
2023 — conf
A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI.
CMSB
Lorenzo Contento, Paul Stapor, Daniel Weindl, Jan Hasenauer
2023 J jnl
Accessibility of covariance information creates vulnerability in Federated Learning frameworks.
Bioinform.
Manuel Huth, Jonas Arruda, Roy Gusinow, Lorenzo Contento, Evelina Tacconelli, Jan Hasenauer
2023 J jnl
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alejandro F. Villaverde, Elba Raimúndez-Álvarez, Jan Hasenauer, Julio R. Banga
2023 J jnl
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks.
PLoS Comput. Biol.
Polina A. Lakrisenko, Paul Stapor, Stephan Grein, Lukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer
2023 J jnl
FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes.
Bioinform.
Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß, Nils Bundgaard, Frederik Graw, Lutz Brusch, Jan Hasenauer
2023 J jnl
IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.
Bioinform.
Altay Yuzeir, David Alejandro Bejarano, Stephan Grein, Jan Hasenauer, Andreas Schlitzer, Jiangyan Yu
2023 J jnl
Validation of genetic variants from NGS data using deep convolutional neural networks.
BMC Bioinform.
Marc Vaisband, Maria Schubert, Franz Josef Gassner, Roland Geisberger, Richard Greil, Nadja Zaborsky, Jan Hasenauer
2023 J jnl
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models.
Bioinform.
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
2022 J jnl
A protocol for dynamic model calibration.
Briefings Bioinform.
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga
2022 J jnl
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res.
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 Sinan 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
2022 J jnl
pyABC: Efficient and robust easy-to-use approximate Bayesian computation.
J. Open Source Softw.
Yannik Schälte, Emmanuel Klinger, Emad Alamoudi, Jan Hasenauer
2021 J jnl
AMICI: high-performance sensitivity analysis for large ordinary differential equation models.
Bioinform.
Fabian Fröhlich, Daniel Weindl, Yannik Schälte, Dilan Pathirana, Lukasz Paszkowski, Glenn Terje Lines, Paul Stapor, Jan Hasenauer
2021 J jnl
Closing the gap between formats for storing layout information in systems biology.
Briefings Bioinform.
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2021 J jnl
Efficient gradient-based parameter estimation for dynamic models using qualitative data.
Bioinform.
Leonard Schmiester, Daniel Weindl, Jan Hasenauer
2021 J jnl
PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol.
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
2021 J jnl
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.
Bioinform.
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
2021 J jnl
yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML.
J. Open Source Softw.
Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte, Jan Hasenauer
2020 J jnl
Closing the gap between formats for storing layout information in systems biology.
Briefings Bioinform.
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2020 J jnl
Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation.
Bioinform.
Yannik Schälte, Jan Hasenauer
2020 J jnl
Efficient parameterization of large-scale dynamic models based on relative measurements.
Bioinform.
Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl
2020 J jnl
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.
PLoS Comput. Biol.
Elba Raimúndez-Álvarez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J. Theis, Dieter Maier, Birgit Luber, Jan Hasenauer
2019 J jnl
Benchmark problems for dynamic modeling of intracellular processes.
Bioinform.
Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz
2019 J jnl
Benchmarking optimization methods for parameter estimation in large kinetic models.
Bioinform.
Alejandro Fernández Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R. Banga
2019 J jnl
Community-driven roadmap for integrated disease maps.
Briefings Bioinform.
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
2018 J jnl
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.
Bioinform.
Benjamin Ballnus, Steffen Schaper, Fabian J. Theis, Jan Hasenauer
2018 J jnl
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.
Bioinform.
Thomas S. Ligon, Fabian Fröhlich, Oana Chis, Julio R. Banga, Eva Balsa-Canto, Jan Hasenauer
2018 J jnl
Hierarchical optimization for the efficient parametrization of ODE models.
Bioinform.
Carolin Loos, Sabrina Krause, Jan Hasenauer
2018 — conf
LNA++: Linear Noise Approximation with First and Second Order Sensitivities.
CMSB
Justin Feigelman, Daniel Weindl, Fabian J. Theis, Carsten Marr, Jan Hasenauer
2018 J jnl
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.
Bioinform.
Paul Stapor, Fabian Fröhlich, Jan Hasenauer
2018 J jnl
PESTO: Parameter EStimation TOolbox.
Bioinform.
Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hross, Fabian Fröhlich, Jan Hasenauer
2018 J jnl
pyABC: distributed, likelihood-free inference.
Bioinform.
Emmanuel Klinger, Dennis Rickert, Jan Hasenauer
2017 — conf
A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo.
CMSB
Emmanuel Klinger, Jan Hasenauer
2017 J jnl
A scalable moment-closure approximation for large-scale biochemical reaction networks.
Bioinform.
Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer
2017 J jnl
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.
BMC Syst. Biol.
Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J. Theis
2017 J jnl
Parameter estimation for dynamical systems with discrete events and logical operations.
Bioinform.
Fabian Fröhlich, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer
2017 J jnl
Robust parameter estimation for dynamical systems from outlier-corrupted data.
Bioinform.
Corinna Maier, Carolin Loos, Jan Hasenauer
2017 J jnl
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
PLoS Comput. Biol.
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer
2016 J jnl
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule.
Stat. Comput.
Sabine Hug, Michael Schwarzfischer, Jan Hasenauer, Carsten Marr, Fabian J. Theis
2016 J jnl
Analysis of CFSE time-series data using division-, age- and label-structured population models.
Bioinform.
Sabrina Hross, Jan Hasenauer
2016 J jnl
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.
PLoS Comput. Biol.
Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J. Theis, Ramon Grima, Jan Hasenauer
2016 J jnl
MEMO: multi-experiment mixture model analysis of censored data.
Bioinform.
Eva-Maria Geissen, Jan Hasenauer, Stephanie Heinrich, Silke Hauf, Fabian J. Theis, Nicole Radde
2016 — conf
Parameter Estimation for Reaction Rate Equation Constrained Mixture Models.
CMSB
Carolin Loos, Anna Fiedler, Jan Hasenauer
2016 J jnl
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.
BMC Syst. Biol.
Anna Fiedler, Sebastian Raeth, Fabian J. Theis, Angelika Hausser, Jan Hasenauer
2015 — conf
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics.
CMSB
Carolin Loos, Carsten Marr, Fabian J. Theis, Jan Hasenauer
2015 J jnl
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Bioinform.
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
2014 J jnl
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics.
PLoS Comput. Biol.
Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis
2014 — conf
Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis.
CMSB
Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, Jan Hasenauer
2014 — conf
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More.
CMSB
Fabian Fröhlich, Fabian J. Theis, Jan Hasenauer
2013 J jnl
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis.
BMC Bioinform.
Sabrina Hock, Jan Hasenauer, Fabian J. Theis
2013 J jnl
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation.
BMC Syst. Biol.
Sabrina Hock, Yen-Kar Ng, Jan Hasenauer, Dominik M. Wittmann, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis
2013 B conf
Visualizing edge-edge relations in graphs.
PacificVis
Corinna Vehlow, Jan Hasenauer, Fabian J. Theis, Daniel Weiskopf
2013 J jnl
iVUN: interactive Visualization of Uncertain biochemical reaction Networks.
BMC Bioinform.
Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf
2012 J jnl
A visual analytics approach for models of heterogeneous cell populations.
EURASIP J. Bioinform. Syst. Biol.
Jan Hasenauer, Julian Heinrich, Malgorzata Doszczak, Peter Scheurich, Daniel Weiskopf, Frank Allgöwer
2012 — conf
Uncertainty-aware visual analysis of biochemical reaction networks.
BioVis
Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Julian Heinrich, Nicole Radde, Frank Allgöwer, Daniel Weiskopf
2011 J jnl
Identification of models of heterogeneous cell populations from population snapshot data.
BMC Bioinform.
Jan Hasenauer, Steffen Waldherr, Malgorzata Doszczak, Nicole Radde, Peter Scheurich, Frank Allgöwer
2011 — conf
Steady state stability preserving nonlinear model reduction using sequential convex optimization.
CDC/ECC
Martin Löhning, Jan Hasenauer, Frank Allgöwer
2010 Misc conf
A maximum likelihood estimator for parameter distributions in heterogeneous cell populations.
ICCS
Jan Hasenauer, Steffen Waldherr, Nicole Radde, Malgorzata Doszczak, Peter Scheurich, Frank Allgöwer
2010 — conf
Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior.
CDC
Jan Hasenauer, Christian Breindl, Steffen Waldherr, Frank Allgöwer
2010 C conf
Computation of the Posterior Entropy in a Bayesian Framework for Parameter Estimation in Biological Networks.
CCA
Andrei Kramer, Jan Hasenauer, Frank Allgöwer, Nicole Radde