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2020 – today
- 2024
[j47]Mark Sinzger-D'Angelo
, Jan Hasenauer, Heinz Koeppl:
Hawkes Process Modelling for Chemical Reaction Networks in a Random Environment. SIAM J. Appl. Dyn. Syst. 23(3): 2444-2488 (2024)- [c14]Jonas Arruda, Yannik Schälte, Clemens Peiter, Olga Teplytska, Ulrich Jaehde, Jan Hasenauer:
An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation. ICML 2024 - [i2]Nina Schmid, David Fernandes del Pozo, Willem Waegeman, Jan Hasenauer:
Assessment of Uncertainty Quantification in Universal Differential Equations. CoRR abs/2406.08853 (2024) - [i1]Maren Philipps, Antonia Körner, Jakob Vanhoefer, Dilan Pathirana, Jan Hasenauer:
Non-Negative Universal Differential Equations With Applications in Systems Biology. CoRR abs/2406.14246 (2024) - 2023
- [j46]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) - [j45]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) - [j44]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) - [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) - [j42]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): 158 (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) - [j40]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): 1725-1736 (2023) - [c13]Lorenzo Contento, Paul Stapor, Daniel Weindl, Jan Hasenauer:
A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI. CMSB 2023: 36-43 - 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) - [j38]Yannik Schälte, Emmanuel Klinger, Emad Alamoudi, Jan Hasenauer:
pyABC: Efficient and robust easy-to-use approximate Bayesian computation. J. Open Source Softw. 7(74): 4304 (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 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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - 2021
- [j36]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): 608 (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) - [j34]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:
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37(21): 3702-3706 (2021) - [j33]Leonard Schmiester, Daniel Weindl, Jan Hasenauer:
Efficient gradient-based parameter estimation for dynamic models using qualitative data. Bioinform. 37(23): 4493-4500 (2021) - [j32]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): 3215 (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
- [j30]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): 1249-1260 (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) - [j28]Yannik Schälte, Jan Hasenauer:
Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. Bioinform. 36(Supplement-1): i551-i559 (2020) - [j27]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)
2010 – 2019
- 2019
- [j26]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): 659-670 (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) - [j24]Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz:
Benchmark problems for dynamic modeling of intracellular processes. Bioinform. 35(17): 3073-3082 (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) - [j20]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): i494-i501 (2018) - [j19]Emmanuel Klinger, Dennis Rickert, Jan Hasenauer:
pyABC: distributed, likelihood-free inference. Bioinform. 34(20): 3591-3593 (2018) - [j18]Carolin Loos, Sabrina Krause, Jan Hasenauer:
Hierarchical optimization for the efficient parametrization of ODE models. Bioinform. 34(24): 4266-4273 (2018) - [c12]Justin Feigelman, Daniel Weindl, Fabian J. Theis, Carsten Marr, Jan Hasenauer:
LNA++: Linear Noise Approximation with First and Second Order Sensitivities. CMSB 2018: 300-306 - [d1]Fabian Fröhlich, Anita Reiser, Laura Fink, Daniel Woschée, Thomas S. Ligon, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer:
Supplementary Code to Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. Zenodo, 2018
- 2017
- [j17]Corinna Maier, Carolin Loos, Jan Hasenauer:
Robust parameter estimation for dynamical systems from outlier-corrupted data. Bioinform. 33(5): 718-725 (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) - [j15]Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer:
A scalable moment-closure approximation for large-scale biochemical reaction networks. Bioinform. 33(14): i293-i300 (2017) - [j14]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): 63:1-63:18 (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) - [c11]Emmanuel Klinger, Jan Hasenauer:
A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo. CMSB 2017: 128-144 - 2016
- [j12]Sabrina Hross, Jan Hasenauer:
Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinform. 32(15): 2321-2329 (2016) - [j11]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): 2464-2472 (2016) - [j10]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: 80 (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) - [j8]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): 663-677 (2016) - [c10]Carolin Loos, Anna Fiedler, Jan Hasenauer:
Parameter Estimation for Reaction Rate Equation Constrained Mixture Models. CMSB 2016: 186-200 - 2015
- [j7]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): 3558-3560 (2015) - [c9]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: 52-63 - 2014
- [j6]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) - [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 - 2013
- [j5]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): S7 (2013) - [j4]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): S2 (2013) - [j3]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: 48 (2013) - [c6]Corinna Vehlow, Jan Hasenauer, Fabian J. Theis, Daniel Weiskopf:
Visualizing edge-edge relations in graphs. PacificVis 2013: 201-208 - 2012
- [j2]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: 4 (2012) - [c5]Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Julian Heinrich, Nicole Radde, Frank Allgöwer, Daniel Weiskopf:
Uncertainty-aware visual analysis of biochemical reaction networks. BioVis 2012: 91-98 - 2011
- [j1]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: 125 (2011) - [c4]Martin Löhning, Jan Hasenauer, Frank Allgöwer:
Steady state stability preserving nonlinear model reduction using sequential convex optimization. CDC/ECC 2011: 7158-7163 - 2010
- [c3]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: 493-498 - [c2]Jan Hasenauer, Christian Breindl, Steffen Waldherr, Frank Allgöwer:
Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior. CDC 2010: 4114-4119 - [c1]Jan Hasenauer, Steffen Waldherr, Nicole Radde, Malgorzata Doszczak, Peter Scheurich, Frank Allgöwer:
A maximum likelihood estimator for parameter distributions in heterogeneous cell populations. ICCS 2010: 1655-1663
Coauthor Index
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