BibTeX records: Jan Hasenauer

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@article{DBLP:journals/bioinformatics/YuzeirBGHSY23,
  author       = {Altay Yuzeir and
                  David Alejandro Bejarano and
                  Stephan Grein and
                  Jan Hasenauer and
                  Andreas Schlitzer and
                  Jiangyan Yu},
  title        = {IntestLine: a shiny-based application to map the rolled intestinal
                  tissue onto a line},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {4},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad140},
  doi          = {10.1093/BIOINFORMATICS/BTAD140},
  timestamp    = {Fri, 15 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/YuzeirBGHSY23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuthAGCTH23,
  author       = {Manuel Huth and
                  Jonas Arruda and
                  Roy Gusinow and
                  Lorenzo Contento and
                  Evelina Tacconelli and
                  Jan Hasenauer},
  title        = {Accessibility of covariance information creates vulnerability in Federated
                  Learning frameworks},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {9},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad531},
  doi          = {10.1093/BIOINFORMATICS/BTAD531},
  timestamp    = {Fri, 15 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HuthAGCTH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlamoudiSMSBGBH23,
  author       = {Emad Alamoudi and
                  Yannik Sch{\"{a}}lte and
                  Robert M{\"{u}}ller and
                  J{\"{o}}rn Starru{\ss} and
                  Nils Bundgaard and
                  Frederik Graw and
                  Lutz Brusch and
                  Jan Hasenauer},
  title        = {FitMultiCell: simulating and parameterizing computational models of
                  multi-scale and multi-cellular processes},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {11},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad674},
  doi          = {10.1093/BIOINFORMATICS/BTAD674},
  timestamp    = {Mon, 05 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/AlamoudiSMSBGBH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchalteFJVPSLWRMSSGDDWH23,
  author       = {Yannik Sch{\"{a}}lte and
                  Fabian Fr{\"{o}}hlich and
                  Paul J. Jost and
                  Jakob Vanhoefer and
                  Dilan Pathirana and
                  Paul Stapor and
                  Polina A. Lakrisenko and
                  Dantong Wang and
                  Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
                  Simon Merkt and
                  Leonard Schmiester and
                  Philipp St{\"{a}}dter and
                  Stephan Grein and
                  Erika Dudkin and
                  Domagoj Doresic and
                  Daniel Weindl and
                  Jan Hasenauer},
  title        = {pyPESTO: a modular and scalable tool for parameter estimation for
                  dynamic models},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {11},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad711},
  doi          = {10.1093/BIOINFORMATICS/BTAD711},
  timestamp    = {Mon, 05 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SchalteFJVPSLWRMSSGDDWH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VaisbandSGGGZH23,
  author       = {Marc Vaisband and
                  Maria Schubert and
                  Franz Josef Gassner and
                  Roland Geisberger and
                  Richard Greil and
                  Nadja Zaborsky and
                  Jan Hasenauer},
  title        = {Validation of genetic variants from {NGS} data using deep convolutional
                  neural networks},
  journal      = {{BMC} Bioinform.},
  volume       = {24},
  number       = {1},
  pages        = {158},
  year         = {2023},
  url          = {https://doi.org/10.1186/s12859-023-05255-7},
  doi          = {10.1186/S12859-023-05255-7},
  timestamp    = {Mon, 24 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/VaisbandSGGGZH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LakrisenkoSGPPFLWH23,
  author       = {Polina A. Lakrisenko and
                  Paul Stapor and
                  Stephan Grein and
                  Lukasz Paszkowski and
                  Dilan Pathirana and
                  Fabian Fr{\"{o}}hlich and
                  Glenn Terje Lines and
                  Daniel Weindl and
                  Jan Hasenauer},
  title        = {Efficient computation of adjoint sensitivities at steady-state in
                  {ODE} models of biochemical reaction networks},
  journal      = {PLoS Comput. Biol.},
  volume       = {19},
  number       = {1},
  year         = {2023},
  url          = {https://doi.org/10.1371/journal.pcbi.1010783},
  doi          = {10.1371/JOURNAL.PCBI.1010783},
  timestamp    = {Sat, 29 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/LakrisenkoSGPPFLWH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/VillaverdeRHB23,
  author       = {Alejandro F. Villaverde and
                  Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
                  Jan Hasenauer and
                  Julio R. Banga},
  title        = {Assessment of Prediction Uncertainty Quantification Methods in Systems
                  Biology},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {20},
  number       = {3},
  pages        = {1725--1736},
  year         = {2023},
  url          = {https://doi.org/10.1109/TCBB.2022.3213914},
  doi          = {10.1109/TCBB.2022.3213914},
  timestamp    = {Thu, 27 Jul 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/VillaverdeRHB23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/ContentoSWH23,
  author       = {Lorenzo Contento and
                  Paul Stapor and
                  Daniel Weindl and
                  Jan Hasenauer},
  editor       = {Jun Pang and
                  Joachim Niehren},
  title        = {A More Expressive Spline Representation for {SBML} Models Improves
                  Code Generation Performance in {AMICI}},
  booktitle    = {Computational Methods in Systems Biology - 21st International Conference,
                  {CMSB} 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {14137},
  pages        = {36--43},
  publisher    = {Springer},
  year         = {2023},
  url          = {https://doi.org/10.1007/978-3-031-42697-1\_3},
  doi          = {10.1007/978-3-031-42697-1\_3},
  timestamp    = {Sun, 24 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/ContentoSWH23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/VillaverdePFHB22,
  author       = {Alejandro F. Villaverde and
                  Dilan Pathirana and
                  Fabian Fr{\"{o}}hlich and
                  Jan Hasenauer and
                  Julio R. Banga},
  title        = {A protocol for dynamic model calibration},
  journal      = {Briefings Bioinform.},
  volume       = {23},
  number       = {1},
  year         = {2022},
  url          = {https://doi.org/10.1093/bib/bbab387},
  doi          = {10.1093/BIB/BBAB387},
  timestamp    = {Sat, 13 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/VillaverdePFHB22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jossw/SchalteKAH22,
  author       = {Yannik Sch{\"{a}}lte and
                  Emmanuel Klinger and
                  Emad Alamoudi and
                  Jan Hasenauer},
  title        = {pyABC: Efficient and robust easy-to-use approximate Bayesian computation},
  journal      = {J. Open Source Softw.},
  volume       = {7},
  number       = {74},
  pages        = {4304},
  year         = {2022},
  url          = {https://doi.org/10.21105/joss.04304},
  doi          = {10.21105/JOSS.04304},
  timestamp    = {Mon, 25 Jul 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jossw/SchalteKAH22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShaikhSVMWAAAAB22,
  author       = {Bilal Shaikh and
                  Lucian P. Smith and
                  Dan Vasilescu and
                  Gnaneswara Marupilla and
                  Michael Wilson and
                  Eran Agmon and
                  Henry Agnew and
                  Steven S. Andrews and
                  Azraf Anwar and
                  Moritz E. Beber and
                  Frank T. Bergmann and
                  David Brooks and
                  Lutz Brusch and
                  Laurence Calzone and
                  Kiri Choi and
                  Joshua Cooper and
                  John Detloff and
                  Brian Drawert and
                  Michel Dumontier and
                  G. Bard Ermentrout and
                  James R. Faeder and
                  Andrew P. Freiburger and
                  Fabian Fr{\"{o}}hlich and
                  Akira Funahashi and
                  Alan Garny and
                  John H. Gennari and
                  Padraig Gleeson and
                  Anne Goelzer and
                  Zachary B. Haiman and
                  Jan Hasenauer and
                  Joseph L. Hellerstein and
                  Henning Hermjakob and
                  Stefan Hoops and
                  Jon C. Ison and
                  Diego Jahn and
                  Henry V. Jakubowski and
                  Ryann Jordan and
                  Mat{\'{u}}s Kalas and
                  Matthias K{\"{o}}nig and
                  Wolfram Liebermeister and
                  Rahuman S. Malik{-}Sheriff and
                  Synchon Mandal and
                  Robert A. McDougal and
                  J. Kyle Medley and
                  Pedro Mendes and
                  Robert M{\"{u}}ller and
                  Chris J. Myers and
                  Aur{\'{e}}lien Naldi and
                  Tung V. N. Nguyen and
                  David P. Nickerson and
                  Brett G. Olivier and
                  Drashti Patoliya and
                  Lo{\"{\i}}c Paulev{\'{e}} and
                  Linda R. Petzold and
                  Ankita Priya and
                  Anand K. Rampadarath and
                  Johann M. Rohwer and
                  Ali S. Saglam and
                  Dilawar Singh and
                  Ankur Sinha and
                  Jacky L. Snoep and
                  Hugh Sorby and
                  Ryan K. Spangler and
                  J{\"{o}}rn Starru{\ss} and
                  Payton J. Thomas and
                  David D. van Niekerk and
                  Daniel Weindl and
                  Fengkai Zhang and
                  Anna Zhukova and
                  Arthur P. Goldberg and
                  James C. Schaff and
                  Michael L. Blinov and
                  Herbert M. Sauro and
                  Ion I. Moraru and
                  Jonathan R. Karr},
  title        = {BioSimulators: a central registry of simulation engines and services
                  for recommending specific tools},
  journal      = {Nucleic Acids Res.},
  volume       = {50},
  number       = {{W1}},
  pages        = {108--114},
  year         = {2022},
  url          = {https://doi.org/10.1093/nar/gkac331},
  doi          = {10.1093/NAR/GKAC331},
  timestamp    = {Tue, 24 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/ShaikhSVMWAAAAB22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HokszaGOHS21,
  author       = {David Hoksza and
                  Piotr Gawron and
                  Marek Ostaszewski and
                  Jan Hasenauer and
                  Reinhard Schneider},
  title        = {Closing the gap between formats for storing layout information in
                  systems biology},
  journal      = {Briefings Bioinform.},
  volume       = {22},
  number       = {1},
  pages        = {608},
  year         = {2021},
  url          = {https://doi.org/10.1093/bib/bbaa030},
  doi          = {10.1093/BIB/BBAA030},
  timestamp    = {Wed, 07 Dec 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/HokszaGOHS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FrohlichWSPPLSH21,
  author       = {Fabian Fr{\"{o}}hlich and
                  Daniel Weindl and
                  Yannik Sch{\"{a}}lte and
                  Dilan Pathirana and
                  Lukasz Paszkowski and
                  Glenn Terje Lines and
                  Paul Stapor and
                  Jan Hasenauer},
  title        = {{AMICI:} high-performance sensitivity analysis for large ordinary
                  differential equation models},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {20},
  pages        = {3676--3677},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btab227},
  doi          = {10.1093/BIOINFORMATICS/BTAB227},
  timestamp    = {Tue, 12 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/FrohlichWSPPLSH21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DragerHBBCCHKNM21,
  author       = {Andreas Dr{\"{a}}ger and
                  Tom{\'{a}}s Helikar and
                  Matteo Barberis and
                  Marc R. Birtwistle and
                  Laurence Calzone and
                  Claudine Chaouiya and
                  Jan Hasenauer and
                  Jonathan R. Karr and
                  Anna Niarakis and
                  Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez and
                  Julio Saez{-}Rodriguez and
                  Juilee Thakar},
  title        = {SysMod: the {ISCB} community for data-driven computational modelling
                  and multi-scale analysis of biological systems},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {21},
  pages        = {3702--3706},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btab229},
  doi          = {10.1093/BIOINFORMATICS/BTAB229},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DragerHBBCCHKNM21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchmiesterWH21,
  author       = {Leonard Schmiester and
                  Daniel Weindl and
                  Jan Hasenauer},
  title        = {Efficient gradient-based parameter estimation for dynamic models using
                  qualitative data},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {23},
  pages        = {4493--4500},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btab512},
  doi          = {10.1093/BIOINFORMATICS/BTAB512},
  timestamp    = {Tue, 12 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SchmiesterWH21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jossw/VanhoeferMPSH21,
  author       = {Jakob Vanhoefer and
                  Marta R. A. Matos and
                  Dilan Pathirana and
                  Yannik Sch{\"{a}}lte and
                  Jan Hasenauer},
  title        = {yaml2sbml: Human-readable and -writable specification of {ODE} models
                  and their conversion to {SBML}},
  journal      = {J. Open Source Softw.},
  volume       = {6},
  number       = {61},
  pages        = {3215},
  year         = {2021},
  url          = {https://doi.org/10.21105/joss.03215},
  doi          = {10.21105/JOSS.03215},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jossw/VanhoeferMPSH21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SchmiesterSBCDE21,
  author       = {Leonard Schmiester and
                  Yannik Sch{\"{a}}lte and
                  Frank T. Bergmann and
                  Tacio Camba and
                  Erika Dudkin and
                  Janine Egert and
                  Fabian Fr{\"{o}}hlich and
                  Lara Fuhrmann and
                  Adrian L. Hauber and
                  Svenja Kemmer and
                  Polina A. Lakrisenko and
                  Carolin Loos and
                  Simon Merkt and
                  Wolfgang M{\"{u}}ller and
                  Dilan Pathirana and
                  Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
                  Lukas Refisch and
                  Marcus Rosenblatt and
                  Paul Stapor and
                  Philipp St{\"{a}}dter and
                  Dantong Wang and
                  Franz{-}Georg Wieland and
                  Julio R. Banga and
                  Jens Timmer and
                  Alejandro F. Villaverde and
                  Sven Sahle and
                  Clemens Kreutz and
                  Jan Hasenauer and
                  Daniel Weindl},
  title        = {PEtab - Interoperable specification of parameter estimation problems
                  in systems biology},
  journal      = {PLoS Comput. Biol.},
  volume       = {17},
  number       = {1},
  year         = {2021},
  url          = {https://doi.org/10.1371/journal.pcbi.1008646},
  doi          = {10.1371/JOURNAL.PCBI.1008646},
  timestamp    = {Wed, 07 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/SchmiesterSBCDE21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HokszaGOHS20,
  author       = {David Hoksza and
                  Piotr Gawron and
                  Marek Ostaszewski and
                  Jan Hasenauer and
                  Reinhard Schneider},
  title        = {Closing the gap between formats for storing layout information in
                  systems biology},
  journal      = {Briefings Bioinform.},
  volume       = {21},
  number       = {4},
  pages        = {1249--1260},
  year         = {2020},
  url          = {https://doi.org/10.1093/bib/bbz067},
  doi          = {10.1093/BIB/BBZ067},
  timestamp    = {Wed, 07 Dec 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/HokszaGOHS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchmiesterSFHW20,
  author       = {Leonard Schmiester and
                  Yannik Sch{\"{a}}lte and
                  Fabian Fr{\"{o}}hlich and
                  Jan Hasenauer and
                  Daniel Weindl},
  title        = {Efficient parameterization of large-scale dynamic models based on
                  relative measurements},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {2},
  pages        = {594--602},
  year         = {2020},
  url          = {https://doi.org/10.1093/bioinformatics/btz581},
  doi          = {10.1093/BIOINFORMATICS/BTZ581},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SchmiesterSFHW20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchalteH20,
  author       = {Yannik Sch{\"{a}}lte and
                  Jan Hasenauer},
  title        = {Efficient exact inference for dynamical systems with noisy measurements
                  using sequential approximate Bayesian computation},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {Supplement-1},
  pages        = {i551--i559},
  year         = {2020},
  url          = {https://doi.org/10.1093/bioinformatics/btaa397},
  doi          = {10.1093/BIOINFORMATICS/BTAA397},
  timestamp    = {Fri, 25 Dec 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SchalteH20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Raimundez-Alvarez20,
  author       = {Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
                  Simone Keller and
                  Gwen Zwingenberger and
                  Karolin Ebert and
                  Sabine Hug and
                  Fabian J. Theis and
                  Dieter Maier and
                  Birgit Luber and
                  Jan Hasenauer},
  title        = {Model-based analysis of response and resistance factors of cetuximab
                  treatment in gastric cancer cell lines},
  journal      = {PLoS Comput. Biol.},
  volume       = {16},
  number       = {3},
  year         = {2020},
  url          = {https://doi.org/10.1371/journal.pcbi.1007147},
  doi          = {10.1371/JOURNAL.PCBI.1007147},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/Raimundez-Alvarez20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OstaszewskiGKMZ19,
  author       = {Marek Ostaszewski and
                  Stephan Gebel and
                  Inna Kuperstein and
                  Alexander Mazein and
                  Andrei Yu. Zinovyev and
                  Ugur Dogrusoz and
                  Jan Hasenauer and
                  Ronan M. T. Fleming and
                  Nicolas Le Nov{\`{e}}re and
                  Piotr Gawron and
                  Thomas S. Ligon and
                  Anna Niarakis and
                  David P. Nickerson and
                  Daniel Weindl and
                  Rudi Balling and
                  Emmanuel Barillot and
                  Charles Auffray and
                  Reinhard Schneider},
  title        = {Community-driven roadmap for integrated disease maps},
  journal      = {Briefings Bioinform.},
  volume       = {20},
  number       = {2},
  pages        = {659--670},
  year         = {2019},
  url          = {https://doi.org/10.1093/bib/bby024},
  doi          = {10.1093/BIB/BBY024},
  timestamp    = {Wed, 07 Dec 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/OstaszewskiGKMZ19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VillaverdeFWHB19,
  author       = {Alejandro Fern{\'{a}}ndez Villaverde and
                  Fabian Fr{\"{o}}hlich and
                  Daniel Weindl and
                  Jan Hasenauer and
                  Julio R. Banga},
  title        = {Benchmarking optimization methods for parameter estimation in large
                  kinetic models},
  journal      = {Bioinform.},
  volume       = {35},
  number       = {5},
  pages        = {830--838},
  year         = {2019},
  url          = {https://doi.org/10.1093/bioinformatics/bty736},
  doi          = {10.1093/BIOINFORMATICS/BTY736},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/VillaverdeFWHB19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HassLRTHK19,
  author       = {Helge Hass and
                  Carolin Loos and
                  Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
                  Jens Timmer and
                  Jan Hasenauer and
                  Clemens Kreutz},
  title        = {Benchmark problems for dynamic modeling of intracellular processes},
  journal      = {Bioinform.},
  volume       = {35},
  number       = {17},
  pages        = {3073--3082},
  year         = {2019},
  url          = {https://doi.org/10.1093/bioinformatics/btz020},
  doi          = {10.1093/BIOINFORMATICS/BTZ020},
  timestamp    = {Sun, 25 Jul 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HassLRTHK19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StaporWBHLFKHFH18,
  author       = {Paul Stapor and
                  Daniel Weindl and
                  Benjamin Ballnus and
                  Sabine Hug and
                  Carolin Loos and
                  Anna Fiedler and
                  Sabrina Krause and
                  Sabrina Hross and
                  Fabian Fr{\"{o}}hlich and
                  Jan Hasenauer},
  title        = {{PESTO:} Parameter EStimation TOolbox},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {4},
  pages        = {705--707},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/btx676},
  doi          = {10.1093/BIOINFORMATICS/BTX676},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/StaporWBHLFKHFH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LigonFCBBH18,
  author       = {Thomas S. Ligon and
                  Fabian Fr{\"{o}}hlich and
                  Oana Chis and
                  Julio R. Banga and
                  Eva Balsa{-}Canto and
                  Jan Hasenauer},
  title        = {GenSSI 2.0: multi-experiment structural identifiability analysis of
                  {SBML} models},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {8},
  pages        = {1421--1423},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/btx735},
  doi          = {10.1093/BIOINFORMATICS/BTX735},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/LigonFCBBH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StaporFH18,
  author       = {Paul Stapor and
                  Fabian Fr{\"{o}}hlich and
                  Jan Hasenauer},
  title        = {Optimization and profile calculation of {ODE} models using second
                  order adjoint sensitivity analysis},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {13},
  pages        = {i151--i159},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty230},
  doi          = {10.1093/BIOINFORMATICS/BTY230},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/StaporFH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BallnusSTH18,
  author       = {Benjamin Ballnus and
                  Steffen Schaper and
                  Fabian J. Theis and
                  Jan Hasenauer},
  title        = {Bayesian parameter estimation for biochemical reaction networks using
                  region-based adaptive parallel tempering},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {13},
  pages        = {i494--i501},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty229},
  doi          = {10.1093/BIOINFORMATICS/BTY229},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BallnusSTH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlingerRH18,
  author       = {Emmanuel Klinger and
                  Dennis Rickert and
                  Jan Hasenauer},
  title        = {pyABC: distributed, likelihood-free inference},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {20},
  pages        = {3591--3593},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty361},
  doi          = {10.1093/BIOINFORMATICS/BTY361},
  timestamp    = {Sat, 30 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KlingerRH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LoosKH18,
  author       = {Carolin Loos and
                  Sabrina Krause and
                  Jan Hasenauer},
  title        = {Hierarchical optimization for the efficient parametrization of {ODE}
                  models},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {24},
  pages        = {4266--4273},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty514},
  doi          = {10.1093/BIOINFORMATICS/BTY514},
  timestamp    = {Sat, 30 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/LoosKH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/FeigelmanWTMH18,
  author       = {Justin Feigelman and
                  Daniel Weindl and
                  Fabian J. Theis and
                  Carsten Marr and
                  Jan Hasenauer},
  editor       = {Milan Ceska and
                  David Safr{\'{a}}nek},
  title        = {{LNA++:} Linear Noise Approximation with First and Second Order Sensitivities},
  booktitle    = {Computational Methods in Systems Biology - 16th International Conference,
                  {CMSB} 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {11095},
  pages        = {300--306},
  publisher    = {Springer},
  year         = {2018},
  url          = {https://doi.org/10.1007/978-3-319-99429-1\_19},
  doi          = {10.1007/978-3-319-99429-1\_19},
  timestamp    = {Wed, 30 Oct 2019 16:34:37 +0100},
  biburl       = {https://dblp.org/rec/conf/cmsb/FeigelmanWTMH18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaierLH17,
  author       = {Corinna Maier and
                  Carolin Loos and
                  Jan Hasenauer},
  title        = {Robust parameter estimation for dynamical systems from outlier-corrupted
                  data},
  journal      = {Bioinform.},
  volume       = {33},
  number       = {5},
  pages        = {718--725},
  year         = {2017},
  url          = {https://doi.org/10.1093/bioinformatics/btw703},
  doi          = {10.1093/BIOINFORMATICS/BTW703},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MaierLH17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FrohlichTRH17,
  author       = {Fabian Fr{\"{o}}hlich and
                  Fabian J. Theis and
                  Joachim O. R{\"{a}}dler and
                  Jan Hasenauer},
  title        = {Parameter estimation for dynamical systems with discrete events and
                  logical operations},
  journal      = {Bioinform.},
  volume       = {33},
  number       = {7},
  pages        = {1049--1056},
  year         = {2017},
  url          = {https://doi.org/10.1093/bioinformatics/btw764},
  doi          = {10.1093/BIOINFORMATICS/BTW764},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/FrohlichTRH17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KazeroonianTH17,
  author       = {Atefeh Kazeroonian and
                  Fabian J. Theis and
                  Jan Hasenauer},
  title        = {A scalable moment-closure approximation for large-scale biochemical
                  reaction networks},
  journal      = {Bioinform.},
  volume       = {33},
  number       = {14},
  pages        = {i293--i300},
  year         = {2017},
  url          = {https://doi.org/10.1093/bioinformatics/btx249},
  doi          = {10.1093/BIOINFORMATICS/BTX249},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KazeroonianTH17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/BallnusHHGHT17,
  author       = {Benjamin Ballnus and
                  Sabine Hug and
                  Kathrin Hatz and
                  Linus G{\"{o}}rlitz and
                  Jan Hasenauer and
                  Fabian J. Theis},
  title        = {Comprehensive benchmarking of Markov chain Monte Carlo methods for
                  dynamical systems},
  journal      = {{BMC} Syst. Biol.},
  volume       = {11},
  number       = {1},
  pages        = {63:1--63:18},
  year         = {2017},
  url          = {https://doi.org/10.1186/s12918-017-0433-1},
  doi          = {10.1186/S12918-017-0433-1},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/BallnusHHGHT17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/FrohlichKTH17,
  author       = {Fabian Fr{\"{o}}hlich and
                  Barbara Kaltenbacher and
                  Fabian J. Theis and
                  Jan Hasenauer},
  title        = {Scalable Parameter Estimation for Genome-Scale Biochemical Reaction
                  Networks},
  journal      = {PLoS Comput. Biol.},
  volume       = {13},
  number       = {1},
  year         = {2017},
  url          = {https://doi.org/10.1371/journal.pcbi.1005331},
  doi          = {10.1371/JOURNAL.PCBI.1005331},
  timestamp    = {Thu, 23 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/FrohlichKTH17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/KlingerH17,
  author       = {Emmanuel Klinger and
                  Jan Hasenauer},
  editor       = {J{\'{e}}r{\^{o}}me Feret and
                  Heinz Koeppl},
  title        = {A Scheme for Adaptive Selection of Population Sizes in Approximate
                  Bayesian Computation - Sequential Monte Carlo},
  booktitle    = {Computational Methods in Systems Biology - 15th International Conference,
                  {CMSB} 2017, Darmstadt, Germany, September 27-29, 2017, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {10545},
  pages        = {128--144},
  publisher    = {Springer},
  year         = {2017},
  url          = {https://doi.org/10.1007/978-3-319-67471-1\_8},
  doi          = {10.1007/978-3-319-67471-1\_8},
  timestamp    = {Tue, 14 May 2019 10:00:49 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/KlingerH17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HrossH16,
  author       = {Sabrina Hross and
                  Jan Hasenauer},
  title        = {Analysis of {CFSE} time-series data using division-, age- and label-structured
                  population models},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {15},
  pages        = {2321--2329},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btw131},
  doi          = {10.1093/BIOINFORMATICS/BTW131},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HrossH16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GeissenHHHTR16,
  author       = {Eva{-}Maria Geissen and
                  Jan Hasenauer and
                  Stephanie Heinrich and
                  Silke Hauf and
                  Fabian J. Theis and
                  Nicole Radde},
  title        = {{MEMO:} multi-experiment mixture model analysis of censored data},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {16},
  pages        = {2464--2472},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btw190},
  doi          = {10.1093/BIOINFORMATICS/BTW190},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GeissenHHHTR16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/FiedlerRTHH16,
  author       = {Anna Fiedler and
                  Sebastian Raeth and
                  Fabian J. Theis and
                  Angelika Hausser and
                  Jan Hasenauer},
  title        = {Tailored parameter optimization methods for ordinary differential
                  equation models with steady-state constraints},
  journal      = {{BMC} Syst. Biol.},
  volume       = {10},
  pages        = {80},
  year         = {2016},
  url          = {https://doi.org/10.1186/s12918-016-0319-7},
  doi          = {10.1186/S12918-016-0319-7},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/FiedlerRTHH16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/FrohlichTKTGH16,
  author       = {Fabian Fr{\"{o}}hlich and
                  Philipp Thomas and
                  Atefeh Kazeroonian and
                  Fabian J. Theis and
                  Ramon Grima and
                  Jan Hasenauer},
  title        = {Inference for Stochastic Chemical Kinetics Using Moment Equations
                  and System Size Expansion},
  journal      = {PLoS Comput. Biol.},
  volume       = {12},
  number       = {7},
  year         = {2016},
  url          = {https://doi.org/10.1371/journal.pcbi.1005030},
  doi          = {10.1371/JOURNAL.PCBI.1005030},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/FrohlichTKTGH16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sac/HugSHMT16,
  author       = {Sabine Hug and
                  Michael Schwarzfischer and
                  Jan Hasenauer and
                  Carsten Marr and
                  Fabian J. Theis},
  title        = {An adaptive scheduling scheme for calculating Bayes factors with thermodynamic
                  integration using Simpson's rule},
  journal      = {Stat. Comput.},
  volume       = {26},
  number       = {3},
  pages        = {663--677},
  year         = {2016},
  url          = {https://doi.org/10.1007/s11222-015-9550-0},
  doi          = {10.1007/S11222-015-9550-0},
  timestamp    = {Wed, 25 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/sac/HugSHMT16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/LoosFH16,
  author       = {Carolin Loos and
                  Anna Fiedler and
                  Jan Hasenauer},
  editor       = {Ezio Bartocci and
                  Pietro Li{\`{o}} and
                  Nicola Paoletti},
  title        = {Parameter Estimation for Reaction Rate Equation Constrained Mixture
                  Models},
  booktitle    = {Computational Methods in Systems Biology - 14th International Conference,
                  {CMSB} 2016, Cambridge, UK, September 21-23, 2016, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {9859},
  pages        = {186--200},
  publisher    = {Springer},
  year         = {2016},
  url          = {https://doi.org/10.1007/978-3-319-45177-0\_12},
  doi          = {10.1007/978-3-319-45177-0\_12},
  timestamp    = {Sun, 02 Jun 2019 21:13:15 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/LoosFH16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaueSSKMHVTAEMH15,
  author       = {Andreas Raue and
                  Bernhard Steiert and
                  Max Schelker and
                  Clemens Kreutz and
                  Tim Maiwald and
                  Helge Hass and
                  Joep Vanlier and
                  Christian T{\"{o}}nsing and
                  Lorenz Adlung and
                  Raphael Engesser and
                  Wolfgang Mader and
                  Tim Heinemann and
                  Jan Hasenauer and
                  Marcel Schilling and
                  Thomas H{\"{o}}fer and
                  Edda Klipp and
                  Fabian J. Theis and
                  Ursula Klingm{\"{u}}ller and
                  Birgit Schoeberl and
                  Jens Timmer},
  title        = {Data2Dynamics: a modeling environment tailored to parameter estimation
                  in dynamical systems},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {21},
  pages        = {3558--3560},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btv405},
  doi          = {10.1093/BIOINFORMATICS/BTV405},
  timestamp    = {Sat, 10 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/RaueSSKMHVTAEMH15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/LoosMTH15,
  author       = {Carolin Loos and
                  Carsten Marr and
                  Fabian J. Theis and
                  Jan Hasenauer},
  editor       = {Olivier F. Roux and
                  J{\'{e}}r{\'{e}}mie Bourdon},
  title        = {Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse
                  Data Using Multivariate Test Statistics},
  booktitle    = {Computational Methods in Systems Biology - 13th International Conference,
                  {CMSB} 2015, Nantes, France, September 16-18, 2015, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {9308},
  pages        = {52--63},
  publisher    = {Springer},
  year         = {2015},
  url          = {https://doi.org/10.1007/978-3-319-23401-4\_6},
  doi          = {10.1007/978-3-319-23401-4\_6},
  timestamp    = {Sun, 02 Jun 2019 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/LoosMTH15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HasenauerHHT14,
  author       = {Jan Hasenauer and
                  Christine Hasenauer and
                  Tim Hucho and
                  Fabian J. Theis},
  title        = {{ODE} Constrained Mixture Modelling: {A} Method for Unraveling Subpopulation
                  Structures and Dynamics},
  journal      = {PLoS Comput. Biol.},
  volume       = {10},
  number       = {7},
  year         = {2014},
  url          = {https://doi.org/10.1371/journal.pcbi.1003686},
  doi          = {10.1371/JOURNAL.PCBI.1003686},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/HasenauerHHT14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/FrohlichTH14,
  author       = {Fabian Fr{\"{o}}hlich and
                  Fabian J. Theis and
                  Jan Hasenauer},
  editor       = {Pedro Mendes and
                  Joseph O. Dada and
                  Kieran Smallbone},
  title        = {Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile
                  Likelihoods, Bootstrapping and More},
  booktitle    = {Computational Methods in Systems Biology - 12th International Conference,
                  {CMSB} 2014, Manchester, UK, November 17-19, 2014, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {8859},
  pages        = {61--72},
  publisher    = {Springer},
  year         = {2014},
  url          = {https://doi.org/10.1007/978-3-319-12982-2\_5},
  doi          = {10.1007/978-3-319-12982-2\_5},
  timestamp    = {Sat, 09 Apr 2022 12:36:34 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/FrohlichTH14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/FrohlichHTH14,
  author       = {Fabian Fr{\"{o}}hlich and
                  Sabrina Hross and
                  Fabian J. Theis and
                  Jan Hasenauer},
  editor       = {Pedro Mendes and
                  Joseph O. Dada and
                  Kieran Smallbone},
  title        = {Radial Basis Function Approximations of Bayesian Parameter Posterior
                  Densities for Uncertainty Analysis},
  booktitle    = {Computational Methods in Systems Biology - 12th International Conference,
                  {CMSB} 2014, Manchester, UK, November 17-19, 2014, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {8859},
  pages        = {73--85},
  publisher    = {Springer},
  year         = {2014},
  url          = {https://doi.org/10.1007/978-3-319-12982-2\_6},
  doi          = {10.1007/978-3-319-12982-2\_6},
  timestamp    = {Sun, 02 Jun 2019 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/FrohlichHTH14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HockHT13,
  author       = {Sabrina Hock and
                  Jan Hasenauer and
                  Fabian J. Theis},
  title        = {Modeling of 2D diffusion processes based on microscopy data: parameter
                  estimation and practical identifiability analysis},
  journal      = {{BMC} Bioinform.},
  volume       = {14},
  number       = {{S-10}},
  pages        = {S7},
  year         = {2013},
  url          = {https://doi.org/10.1186/1471-2105-14-S10-S7},
  doi          = {10.1186/1471-2105-14-S10-S7},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/HockHT13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VehlowHKRHTRTW13,
  author       = {Corinna Vehlow and
                  Jan Hasenauer and
                  Andrei Kramer and
                  Andreas Raue and
                  Sabine Hug and
                  Jens Timmer and
                  Nicole Radde and
                  Fabian J. Theis and
                  Daniel Weiskopf},
  title        = {iVUN: interactive Visualization of Uncertain biochemical reaction
                  Networks},
  journal      = {{BMC} Bioinform.},
  volume       = {14},
  number       = {{S-19}},
  pages        = {S2},
  year         = {2013},
  url          = {https://doi.org/10.1186/1471-2105-14-S19-S2},
  doi          = {10.1186/1471-2105-14-S19-S2},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/VehlowHKRHTRTW13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HockNHWLTWPT13,
  author       = {Sabrina Hock and
                  Yen{-}Kar Ng and
                  Jan Hasenauer and
                  Dominik M. Wittmann and
                  Dominik Lutter and
                  Dietrich Tr{\"{u}}mbach and
                  Wolfgang Wurst and
                  Nilima Prakash and
                  Fabian J. Theis},
  title        = {Sharpening of expression domains induced by transcription and microRNA
                  regulation within a spatio-temporal model of mid-hindbrain boundary
                  formation},
  journal      = {{BMC} Syst. Biol.},
  volume       = {7},
  pages        = {48},
  year         = {2013},
  url          = {https://doi.org/10.1186/1752-0509-7-48},
  doi          = {10.1186/1752-0509-7-48},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcsb/HockNHWLTWPT13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apvis/VehlowHTW13,
  author       = {Corinna Vehlow and
                  Jan Hasenauer and
                  Fabian J. Theis and
                  Daniel Weiskopf},
  editor       = {Sheelagh Carpendale and
                  Wei Chen and
                  Seok{-}Hee Hong},
  title        = {Visualizing edge-edge relations in graphs},
  booktitle    = {{IEEE} Pacific Visualization Symposium, PacificVis 2013, February
                  27 2013-March 1, 2013, Sydney, NSW, Australia},
  pages        = {201--208},
  publisher    = {{IEEE} Computer Society},
  year         = {2013},
  url          = {https://doi.org/10.1109/PacificVis.2013.6596146},
  doi          = {10.1109/PACIFICVIS.2013.6596146},
  timestamp    = {Thu, 27 Apr 2023 14:57:18 +0200},
  biburl       = {https://dblp.org/rec/conf/apvis/VehlowHTW13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/HasenauerHDSWA12,
  author       = {Jan Hasenauer and
                  Julian Heinrich and
                  Malgorzata Doszczak and
                  Peter Scheurich and
                  Daniel Weiskopf and
                  Frank Allg{\"{o}}wer},
  title        = {A visual analytics approach for models of heterogeneous cell populations},
  journal      = {{EURASIP} J. Bioinform. Syst. Biol.},
  volume       = {2012},
  pages        = {4},
  year         = {2012},
  url          = {https://doi.org/10.1186/1687-4153-2012-4},
  doi          = {10.1186/1687-4153-2012-4},
  timestamp    = {Thu, 18 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ejbsb/HasenauerHDSWA12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biovis/VehlowHKHRAW12,
  author       = {Corinna Vehlow and
                  Jan Hasenauer and
                  Andrei Kramer and
                  Julian Heinrich and
                  Nicole Radde and
                  Frank Allg{\"{o}}wer and
                  Daniel Weiskopf},
  title        = {Uncertainty-aware visual analysis of biochemical reaction networks},
  booktitle    = {2012 {IEEE} Symposium on Biological Data Visualization, BioVis 2011,
                  Seattle, WA, USA, October 14-15, 2012},
  pages        = {91--98},
  publisher    = {{IEEE} Computer Society},
  year         = {2012},
  url          = {https://doi.org/10.1109/BioVis.2012.6378598},
  doi          = {10.1109/BIOVIS.2012.6378598},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/biovis/VehlowHKHRAW12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HasenauerWDRSA11,
  author       = {Jan Hasenauer and
                  Steffen Waldherr and
                  Malgorzata Doszczak and
                  Nicole Radde and
                  Peter Scheurich and
                  Frank Allg{\"{o}}wer},
  title        = {Identification of models of heterogeneous cell populations from population
                  snapshot data},
  journal      = {{BMC} Bioinform.},
  volume       = {12},
  pages        = {125},
  year         = {2011},
  url          = {https://doi.org/10.1186/1471-2105-12-125},
  doi          = {10.1186/1471-2105-12-125},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/HasenauerWDRSA11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cdc/LohningHA11,
  author       = {Martin L{\"{o}}hning and
                  Jan Hasenauer and
                  Frank Allg{\"{o}}wer},
  title        = {Steady state stability preserving nonlinear model reduction using
                  sequential convex optimization},
  booktitle    = {50th {IEEE} Conference on Decision and Control and European Control
                  Conference, 11th European Control Conference, {CDC/ECC} 2011, Orlando,
                  FL, USA, December 12-15, 2011},
  pages        = {7158--7163},
  publisher    = {{IEEE}},
  year         = {2011},
  url          = {https://doi.org/10.1109/CDC.2011.6161227},
  doi          = {10.1109/CDC.2011.6161227},
  timestamp    = {Tue, 25 Jul 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/cdc/LohningHA11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/IEEEcca/KramerHAR10,
  author       = {Andrei Kramer and
                  Jan Hasenauer and
                  Frank Allg{\"{o}}wer and
                  Nicole Radde},
  title        = {Computation of the Posterior Entropy in a Bayesian Framework for Parameter
                  Estimation in Biological Networks},
  booktitle    = {Proceedings of the {IEEE} International Conference on Control Applications,
                  {CCA} 2010, Yokohama, Japan, September 8-10, 2010},
  pages        = {493--498},
  publisher    = {{IEEE}},
  year         = {2010},
  url          = {https://doi.org/10.1109/CCA.2010.5611198},
  doi          = {10.1109/CCA.2010.5611198},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/IEEEcca/KramerHAR10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cdc/HasenauerBWA10,
  author       = {Jan Hasenauer and
                  Christian Breindl and
                  Steffen Waldherr and
                  Frank Allg{\"{o}}wer},
  title        = {Approximative classification of regions in parameter spaces of nonlinear
                  ODEs yielding different qualitative behavior},
  booktitle    = {Proceedings of the 49th {IEEE} Conference on Decision and Control,
                  {CDC} 2010, December 15-17, 2010, Atlanta, Georgia, {USA}},
  pages        = {4114--4119},
  publisher    = {{IEEE}},
  year         = {2010},
  url          = {https://doi.org/10.1109/CDC.2010.5718044},
  doi          = {10.1109/CDC.2010.5718044},
  timestamp    = {Fri, 04 Mar 2022 13:28:01 +0100},
  biburl       = {https://dblp.org/rec/conf/cdc/HasenauerBWA10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/HasenauerWRDSA10,
  author       = {Jan Hasenauer and
                  Steffen Waldherr and
                  Nicole Radde and
                  Malgorzata Doszczak and
                  Peter Scheurich and
                  Frank Allg{\"{o}}wer},
  editor       = {Peter M. A. Sloot and
                  G. Dick van Albada and
                  Jack J. Dongarra},
  title        = {A maximum likelihood estimator for parameter distributions in heterogeneous
                  cell populations},
  booktitle    = {Proceedings of the International Conference on Computational Science,
                  {ICCS} 2010, University of Amsterdam, The Netherlands, May 31 - June
                  2, 2010},
  series       = {Procedia Computer Science},
  volume       = {1},
  number       = {1},
  pages        = {1655--1663},
  publisher    = {Elsevier},
  year         = {2010},
  url          = {https://doi.org/10.1016/j.procs.2010.04.185},
  doi          = {10.1016/J.PROCS.2010.04.185},
  timestamp    = {Wed, 27 Jul 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/procedia/HasenauerWRDSA10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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