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Jan Hasenauer
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2020 – today
- 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 - 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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last updated on 2024-08-05 20:20 CEST by the dblp team
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