Computation of the Posterior Entropy in a Bayesian Framework for Parameter Estimation in Biological Networks. - Andrei Kramer; Jan Hasenauer; Frank Allgöwer; Nicole Radde (CCA, 2010)

Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior. - Jan Hasenauer; Christian Breindl; Steffen Waldherr; Frank Allgöwer (CDC, 2010)

A maximum likelihood estimator for parameter distributions in heterogeneous cell populations. - Jan Hasenauer; Steffen Waldherr; Nicole Radde; Malgorzata Doszczak; Peter Scheurich; Frank Allgöwer (ICCS, 2010)

Steady state stability preserving nonlinear model reduction using sequential convex optimization. - Martin Löhning; Jan Hasenauer; Frank Allgöwer (CDC/ECC, 2011)

Identification of models of heterogeneous cell populations from population snapshot data. - Jan Hasenauer; Steffen Waldherr; Malgorzata Doszczak; Nicole Radde; Peter Scheurich; Frank Allgöwer (BMC Bioinform., 2011)

Uncertainty-aware visual analysis of biochemical reaction networks. - Corinna Vehlow; Jan Hasenauer; Andrei Kramer; Julian Heinrich; Nicole Radde; Frank Allgöwer; Daniel Weiskopf (BioVis, 2012)

A visual analytics approach for models of heterogeneous cell populations. - Jan Hasenauer; Julian Heinrich; Malgorzata Doszczak; Peter Scheurich; Daniel Weiskopf; Frank Allgöwer (EURASIP J. Bioinform. Syst. Biol., 2012)

Visualizing edge-edge relations in graphs. - Corinna Vehlow; Jan Hasenauer; Fabian J. Theis; Daniel Weiskopf (PacificVis, 2013)

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. - Sabrina Hock; Jan Hasenauer; Fabian J. Theis (BMC Bioinform., 2013)

iVUN: interactive Visualization of Uncertain biochemical reaction Networks. - Corinna Vehlow; Jan Hasenauer; Andrei Kramer; Andreas Raue; Sabine Hug; Jens Timmer; Nicole Radde; Fabian J. Theis; Daniel Weiskopf (BMC Bioinform., 2013)

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. - Sabrina Hock; Yen-Kar Ng; Jan Hasenauer; Dominik M. Wittmann; Dominik Lutter; Dietrich Trümbach; Wolfgang Wurst; Nilima Prakash; Fabian J. Theis (BMC Syst. Biol., 2013)

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. - Fabian Fröhlich; Sabrina Hross; Fabian J. Theis; Jan Hasenauer (CMSB, 2014)

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. - Fabian Fröhlich; Fabian J. Theis; Jan Hasenauer (CMSB, 2014)

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. - Jan Hasenauer; Christine Hasenauer; Tim Hucho; Fabian J. Theis (PLoS Comput. Biol., 2014)

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. - Carolin Loos; Carsten Marr; Fabian J. Theis; Jan Hasenauer (CMSB, 2015)

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. - Andreas Raue; Bernhard Steiert; Max Schelker; Clemens Kreutz; Tim Maiwald; Helge Hass; Joep Vanlier; Christian Tönsing; Lorenz Adlung; Raphael Engesser; Wolfgang Mader 002; Tim Heinemann; et al. (Bioinform., 2015)

Parameter Estimation for Reaction Rate Equation Constrained Mixture Models. - Carolin Loos; Anna Fiedler; Jan Hasenauer (CMSB, 2016)

MEMO: multi-experiment mixture model analysis of censored data. - Eva-Maria Geissen; Jan Hasenauer; Stephanie Heinrich; Silke Hauf; Fabian J. Theis; Nicole Radde (Bioinform., 2016)

Analysis of CFSE time-series data using division-, age- and label-structured population models. - Sabrina Hross; Jan Hasenauer (Bioinform., 2016)

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. - Anna Fiedler; Sebastian Raeth; Fabian J. Theis; Angelika Hausser; Jan Hasenauer (BMC Syst. Biol., 2016)

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. - Fabian Fröhlich; Philipp Thomas; Atefeh Kazeroonian; Fabian J. Theis; Ramon Grima; Jan Hasenauer (PLoS Comput. Biol., 2016)

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule. - Sabine Hug; Michael Schwarzfischer; Jan Hasenauer; Carsten Marr; Fabian J. Theis (Stat. Comput., 2016)

A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo. - Emmanuel Klinger; Jan Hasenauer (CMSB, 2017)

Parameter estimation for dynamical systems with discrete events and logical operations. - Fabian Fröhlich; Fabian J. Theis; Joachim O. Rädler; Jan Hasenauer (Bioinform., 2017)

A scalable moment-closure approximation for large-scale biochemical reaction networks. - Atefeh Kazeroonian; Fabian J. Theis; Jan Hasenauer (Bioinform., 2017)

Robust parameter estimation for dynamical systems from outlier-corrupted data. - Corinna Maier; Carolin Loos; Jan Hasenauer (Bioinform., 2017)

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. - Benjamin Ballnus; Sabine Hug; Kathrin Hatz; Linus Görlitz; Jan Hasenauer; Fabian J. Theis (BMC Syst. Biol., 2017)

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. - Fabian Fröhlich; Barbara Kaltenbacher; Fabian J. Theis; Jan Hasenauer (PLoS Comput. Biol., 2017)

LNA++: Linear Noise Approximation with First and Second Order Sensitivities. - Justin Feigelman; Daniel Weindl; Fabian J. Theis; Carsten Marr; Jan Hasenauer (CMSB, 2018)

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. - Benjamin Ballnus; Steffen Schaper; Fabian J. Theis; Jan Hasenauer (Bioinform., 2018)

pyABC: distributed, likelihood-free inference. - Emmanuel Klinger; Dennis Rickert; Jan Hasenauer (Bioinform., 2018)

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. - Thomas S. Ligon; Fabian Fröhlich; Oana Chis; Julio R. Banga; Eva Balsa-Canto; Jan Hasenauer (Bioinform., 2018)

Hierarchical optimization for the efficient parametrization of ODE models. - Carolin Loos; Sabrina Krause; Jan Hasenauer (Bioinform., 2018)

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. - Paul Stapor; Fabian Fröhlich; Jan Hasenauer (Bioinform., 2018)

PESTO: Parameter EStimation TOolbox. - Paul Stapor; Daniel Weindl; Benjamin Ballnus; Sabine Hug; Carolin Loos; Anna Fiedler; Sabrina Krause; Sabrina Hross; Fabian Fröhlich; Jan Hasenauer (Bioinform., 2018)

Supplementary Code to Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. - Fabian Fröhlich; Anita Reiser; Laura Fink; Daniel Woschée; Thomas S. Ligon; Fabian J. Theis; Joachim O. Rädler; Jan Hasenauer (Zenodo, 2018)

Community-driven roadmap for integrated disease maps. - 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; et al. (Briefings Bioinform., 2019)

Benchmark problems for dynamic modeling of intracellular processes. - Helge Hass; Carolin Loos; Elba Raimúndez-Álvarez; Jens Timmer; Jan Hasenauer; Clemens Kreutz (Bioinform., 2019)

Benchmarking optimization methods for parameter estimation in large kinetic models. - Alejandro Fernández Villaverde; Fabian Fröhlich; Daniel Weindl; Jan Hasenauer; Julio R. Banga (Bioinform., 2019)

Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. - Yannik Schälte; Jan Hasenauer (Bioinform., 2020)

Efficient parameterization of large-scale dynamic models based on relative measurements. - Leonard Schmiester; Yannik Schälte; Fabian Fröhlich; Jan Hasenauer; Daniel Weindl (Bioinform., 2020)

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. - Elba Raimúndez-Álvarez; Simone Keller; Gwen Zwingenberger; Karolin Ebert; Sabine Hug; Fabian J. Theis; Dieter Maier; Birgit Luber; Jan Hasenauer (PLoS Comput. Biol., 2020)

Closing the gap between formats for storing layout information in systems biology. - David Hoksza; Piotr Gawron; Marek Ostaszewski; Jan Hasenauer; Reinhard Schneider 002 (Briefings Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - 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 (Bioinform., 2021)

AMICI: high-performance sensitivity analysis for large ordinary differential equation models. - Fabian Fröhlich; Daniel Weindl; Yannik Schälte; Dilan Pathirana; Lukasz Paszkowski; Glenn Terje Lines; Paul Stapor; Jan Hasenauer (Bioinform., 2021)

Efficient gradient-based parameter estimation for dynamic models using qualitative data. - Leonard Schmiester; Daniel Weindl; Jan Hasenauer (Bioinform., 2021)

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. - Jakob Vanhoefer; Marta R. A. Matos; Dilan Pathirana; Yannik Schälte; Jan Hasenauer (J. Open Source Softw., 2021)

PEtab - Interoperable specification of parameter estimation problems in systems biology. - 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; et al. (PLoS Comput. Biol., 2021)

A protocol for dynamic model calibration. - Alejandro F. Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R. Banga (Briefings Bioinform., 2022)

pyABC: Efficient and robust easy-to-use approximate Bayesian computation. - Yannik Schälte; Emmanuel Klinger; Emad Alamoudi; Jan Hasenauer (J. Open Source Softw., 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (Nucleic Acids Res., 2022)

A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI. - Lorenzo Contento; Paul Stapor; Daniel Weindl; Jan Hasenauer (CMSB, 2023)

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. - Alejandro F. Villaverde; Elba Raimúndez-Álvarez; Jan Hasenauer; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. - Polina A. Lakrisenko; Paul Stapor; Stephan Grein; Lukasz Paszkowski; Dilan Pathirana; Fabian Fröhlich; Glenn Terje Lines; Daniel Weindl; Jan Hasenauer (PLoS Comput. Biol., 2023)

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line. - Altay Yuzeir; David Alejandro Bejarano; Stephan Grein; Jan Hasenauer; Andreas Schlitzer; Jiangyan Yu (Bioinform., 2023)

Accessibility of covariance information creates vulnerability in Federated Learning frameworks. - Manuel Huth; Jonas Arruda; Roy Gusinow; Lorenzo Contento; Evelina Tacconelli; Jan Hasenauer (Bioinform., 2023)

FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes. - Emad Alamoudi; Yannik Schälte; Robert Müller; Jörn Starruß; Nils Bundgaard; Frederik Graw; Lutz Brusch; Jan Hasenauer (Bioinform., 2023)

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models. - 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; et al. (Bioinform., 2023)

Validation of genetic variants from NGS data using deep convolutional neural networks. - Marc Vaisband; Maria Schubert; Franz Josef Gassner; Roland Geisberger; Richard Greil; Nadja Zaborsky; Jan Hasenauer (BMC Bioinform., 2023)

Data infrastructure for integrating clinical data in the large-scale international ORCHESTRA cohort: from data import to federated analysis. - Miroslav Puskaric; Hammam Abu Attieh; Fabian Prasser; Roy Gusinow; Chiara Dellacasa; Elisa Rossi; Juan Mata Naranjo; Lorenzo Maria Canziani; Anna Górska; Jan Hasenauer (IEEE Big Data, 2024)

An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation. - Jonas Arruda; Yannik Schälte; Clemens Peiter; Olga Teplytska; Ulrich Jaehde; Jan Hasenauer (ICML, 2024)

Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. - Domagoj Doresic; Stephan Grein; Jan Hasenauer (Bioinform., 2024)

Assessment of Uncertainty Quantification in Universal Differential Equations. - Nina Schmid; David Fernandes del Pozo; Willem Waegeman; Jan Hasenauer (CoRR, 2024)

Non-Negative Universal Differential Equations With Applications in Systems Biology. - Maren Philipps; Antonia Körner; Jakob Vanhoefer; Dilan Pathirana; Jan Hasenauer (CoRR, 2024)

Missing data in amortized simulation-based neural posterior estimation. - Zijian Wang; Jan Hasenauer; Yannik Schälte (PLoS Comput. Biol., 2024)

Hawkes Process Modelling for Chemical Reaction Networks in a Random Environment. - Mark Sinzger-D'Angelo; Jan Hasenauer; Heinz Koeppl (SIAM J. Appl. Dyn. Syst., 2024)