BibTeX records: Sven Sahle

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@article{DBLP:journals/ploscb/MaierASMKDBBK22,
  author       = {Benjamin D. Maier and
                  Luis U. Aguilera and
                  Sven Sahle and
                  Pascal Mutz and
                  Priyata Kalra and
                  Christopher D{\"{a}}chert and
                  Ralf Bartenschlager and
                  Marco Binder and
                  Ursula Kummer},
  title        = {Stochastic dynamics of Type-I interferon responses},
  journal      = {PLoS Comput. Biol.},
  volume       = {18},
  number       = {10},
  pages        = {1010623},
  year         = {2022},
  url          = {https://doi.org/10.1371/journal.pcbi.1010623},
  doi          = {10.1371/JOURNAL.PCBI.1010623},
  timestamp    = {Wed, 17 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/MaierASMKDBBK22.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/jib/HuckaBCDHKKNMOS19,
  author       = {Michael Hucka and
                  Frank T. Bergmann and
                  Claudine Chaouiya and
                  Andreas Dr{\"{a}}ger and
                  Stefan Hoops and
                  Sarah M. Keating and
                  Matthias K{\"{o}}nig and
                  Nicolas Le Nov{\`{e}}re and
                  Chris J. Myers and
                  Brett G. Olivier and
                  Sven Sahle and
                  James C. Schaff and
                  Rahuman S. Malik{-}Sheriff and
                  Lucian P. Smith and
                  Dagmar Waltemath and
                  Darren J. Wilkinson and
                  Fengkai Zhang},
  title        = {The Systems Biology Markup Language {(SBML):} Language Specification
                  for Level 3 Version 2 Core Release 2},
  journal      = {J. Integr. Bioinform.},
  volume       = {16},
  number       = {2},
  year         = {2019},
  url          = {https://doi.org/10.1515/jib-2019-0021},
  doi          = {10.1515/JIB-2019-0021},
  timestamp    = {Fri, 14 May 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/HuckaBCDHKKNMOS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannCKMNNOS18,
  author       = {Frank T. Bergmann and
                  Jonathan Cooper and
                  Matthias K{\"{o}}nig and
                  Ion I. Moraru and
                  David P. Nickerson and
                  Nicolas Le Nov{\`{e}}re and
                  Brett G. Olivier and
                  Sven Sahle and
                  Lucian P. Smith and
                  Dagmar Waltemath},
  title        = {Simulation Experiment Description Markup Language {(SED-ML)} Level
                  1 Version 3 {(L1V3)}},
  journal      = {J. Integr. Bioinform.},
  volume       = {15},
  number       = {1},
  year         = {2018},
  url          = {https://doi.org/10.1515/jib-2017-0086},
  doi          = {10.1515/JIB-2017-0086},
  timestamp    = {Fri, 14 May 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/BergmannCKMNNOS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannKGSW18,
  author       = {Frank T. Bergmann and
                  Sarah M. Keating and
                  Ralph Gauges and
                  Sven Sahle and
                  Katja Wengler},
  title        = {{SBML} Level 3 package: Render, Version 1, Release 1},
  journal      = {J. Integr. Bioinform.},
  volume       = {15},
  number       = {1},
  year         = {2018},
  url          = {https://doi.org/10.1515/jib-2017-0078},
  doi          = {10.1515/JIB-2017-0078},
  timestamp    = {Tue, 14 Jul 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/BergmannKGSW18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS18,
  author       = {Michael Hucka and
                  Frank T. Bergmann and
                  Andreas Dr{\"{a}}ger and
                  Stefan Hoops and
                  Sarah M. Keating and
                  Nicolas Le Nov{\`{e}}re and
                  Chris J. Myers and
                  Brett G. Olivier and
                  Sven Sahle and
                  James C. Schaff and
                  Lucian P. Smith and
                  Dagmar Waltemath and
                  Darren J. Wilkinson},
  title        = {The Systems Biology Markup Language {(SBML):} Language Specification
                  for Level 3 Version 1 Core},
  journal      = {J. Integr. Bioinform.},
  volume       = {15},
  number       = {1},
  year         = {2018},
  url          = {https://doi.org/10.1515/jib-2017-0080},
  doi          = {10.1515/JIB-2017-0080},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS18a,
  author       = {Michael Hucka and
                  Frank T. Bergmann and
                  Andreas Dr{\"{a}}ger and
                  Stefan Hoops and
                  Sarah M. Keating and
                  Nicolas Le Nov{\`{e}}re and
                  Chris J. Myers and
                  Brett G. Olivier and
                  Sven Sahle and
                  James C. Schaff and
                  Lucian P. Smith and
                  Dagmar Waltemath and
                  Darren J. Wilkinson},
  title        = {The Systems Biology Markup Language {(SBML):} Language Specification
                  for Level 3 Version 2 Core},
  journal      = {J. Integr. Bioinform.},
  volume       = {15},
  number       = {1},
  year         = {2018},
  url          = {https://doi.org/10.1515/jib-2017-0081},
  doi          = {10.1515/JIB-2017-0081},
  timestamp    = {Tue, 14 Jul 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS18a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergmannSZ16,
  author       = {Frank T. Bergmann and
                  Sven Sahle and
                  Christoph Zimmer},
  title        = {Piecewise parameter estimation for stochastic models in {COPASI}},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {10},
  pages        = {1586--1588},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btv759},
  doi          = {10.1093/BIOINFORMATICS/BTV759},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BergmannSZ16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ZimmerS16,
  author       = {Christoph Zimmer and
                  Sven Sahle},
  title        = {Comparison of approaches for parameter estimation on stochastic models:
                  Generic least squares versus specialized approaches},
  journal      = {Comput. Biol. Chem.},
  volume       = {61},
  pages        = {75--85},
  year         = {2016},
  url          = {https://doi.org/10.1016/j.compbiolchem.2015.10.003},
  doi          = {10.1016/J.COMPBIOLCHEM.2015.10.003},
  timestamp    = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/candc/ZimmerS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ZimmerBS16,
  author       = {Christoph Zimmer and
                  Frank T. Bergmann and
                  Sven Sahle},
  title        = {Reducing local minima in fitness landscapes of parameter estimation
                  by using piecewise evaluation and state estimation},
  journal      = {CoRR},
  volume       = {abs/1601.04458},
  year         = {2016},
  url          = {http://arxiv.org/abs/1601.04458},
  eprinttype    = {arXiv},
  eprint       = {1601.04458},
  timestamp    = {Mon, 13 Aug 2018 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/ZimmerBS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/ZimmerS15,
  author       = {Christoph Zimmer and
                  Sven Sahle},
  title        = {A termination criterion for parameter estimation in stochastic models
                  in systems biology},
  journal      = {Biosyst.},
  volume       = {137},
  pages        = {55--63},
  year         = {2015},
  url          = {https://doi.org/10.1016/j.biosystems.2015.08.003},
  doi          = {10.1016/J.BIOSYSTEMS.2015.08.003},
  timestamp    = {Thu, 20 Feb 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/biosystems/ZimmerS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/GaugesRSWB15,
  author       = {Ralph Gauges and
                  Ursula Rost and
                  Sven Sahle and
                  Katja Wengler and
                  Frank Thomas Bergmann},
  title        = {The Systems Biology Markup Language {(SBML)} Level 3 Package: Layout,
                  Version 1 Core},
  journal      = {J. Integr. Bioinform.},
  volume       = {12},
  number       = {2},
  year         = {2015},
  url          = {https://doi.org/10.2390/biecoll-jib-2015-267},
  doi          = {10.2390/BIECOLL-JIB-2015-267},
  timestamp    = {Tue, 14 Jul 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/GaugesRSWB15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS15,
  author       = {Michael Hucka and
                  Frank T. Bergmann and
                  Andreas Dr{\"{a}}ger and
                  Stefan Hoops and
                  Sarah M. Keating and
                  Nicolas Le Nov{\`{e}}re and
                  Chris J. Myers and
                  Brett G. Olivier and
                  Sven Sahle and
                  James C. Schaff and
                  Lucian P. Smith and
                  Dagmar Waltemath and
                  Darren J. Wilkinson},
  title        = {Systems Biology Markup Language {(SBML)} Level 2 Version 5: Structures
                  and Facilities for Model Definitions},
  journal      = {J. Integr. Bioinform.},
  volume       = {12},
  number       = {2},
  year         = {2015},
  url          = {https://doi.org/10.2390/biecoll-jib-2015-271},
  doi          = {10.2390/BIECOLL-JIB-2015-271},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBHKSSSW15,
  author       = {Michael Hucka and
                  Frank T. Bergmann and
                  Stefan Hoops and
                  Sarah M. Keating and
                  Sven Sahle and
                  James C. Schaff and
                  Lucian P. Smith and
                  Darren J. Wilkinson},
  title        = {The Systems Biology Markup Language {(SBML):} Language Specification
                  for Level 3 Version 1 Core},
  journal      = {J. Integr. Bioinform.},
  volume       = {12},
  number       = {2},
  year         = {2015},
  url          = {https://doi.org/10.2390/biecoll-jib-2015-266},
  doi          = {10.2390/BIECOLL-JIB-2015-266},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jib/HuckaBHKSSSW15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/SurovtsovaSHSK12,
  author       = {Irina Surovtsova and
                  Natalia Simus and
                  Katrin H{\"{u}}bner and
                  Sven Sahle and
                  Ursula Kummer},
  title        = {Simplification of biochemical models: a general approach based on
                  the analysis of the impact of individual species and reactions on
                  the systems dynamics},
  journal      = {{BMC} Syst. Biol.},
  volume       = {6},
  pages        = {14},
  year         = {2012},
  url          = {https://doi.org/10.1186/1752-0509-6-14},
  doi          = {10.1186/1752-0509-6-14},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/SurovtsovaSHSK12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WaltemathABHKMMNSSN11,
  author       = {Dagmar Waltemath and
                  Richard R. Adams and
                  Frank T. Bergmann and
                  Michael Hucka and
                  Fedor A. Kolpakov and
                  Andrew K. Miller and
                  Ion I. Moraru and
                  David P. Nickerson and
                  Sven Sahle and
                  Jacky L. Snoep and
                  Nicolas Le Nov{\`{e}}re},
  title        = {Reproducible computational biology experiments with {SED-ML} - The
                  Simulation Experiment Description Markup Language},
  journal      = {{BMC} Syst. Biol.},
  volume       = {5},
  pages        = {198},
  year         = {2011},
  url          = {https://doi.org/10.1186/1752-0509-5-198},
  doi          = {10.1186/1752-0509-5-198},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/WaltemathABHKMMNSSN11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WaltemathABBBBCCCCGHHHKLMMNNNSSSSTWN11,
  author       = {Dagmar Waltemath and
                  Richard R. Adams and
                  Daniel A. Beard and
                  Frank T. Bergmann and
                  Upinder S. Bhalla and
                  Randall Britten and
                  Vijayalakshmi Chelliah and
                  Mike T. Cooling and
                  Jonathan Cooper and
                  Edmund J. Crampin and
                  Alan Garny and
                  Stefan Hoops and
                  Michael Hucka and
                  Peter J. Hunter and
                  Edda Klipp and
                  Camille Laibe and
                  Andrew K. Miller and
                  Ion I. Moraru and
                  David P. Nickerson and
                  Poul M. F. Nielsen and
                  Macha Nikolski and
                  Sven Sahle and
                  Herbert M. Sauro and
                  Henning Schmidt and
                  Jacky L. Snoep and
                  Dominic P. Tolle and
                  Olaf Wolkenhauer and
                  Nicolas Le Nov{\`{e}}re},
  title        = {Minimum Information About a Simulation Experiment {(MIASE)}},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {4},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1001122},
  doi          = {10.1371/JOURNAL.PCBI.1001122},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/WaltemathABBBBCCCCGHHHKLMMNNNSSSSTWN11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SurovtsovaSLKSK09,
  author       = {Irina Surovtsova and
                  Natalia Simus and
                  Thomas Lorenz and
                  Artjom K{\"{o}}nig and
                  Sven Sahle and
                  Ursula Kummer},
  title        = {Accessible methods for the dynamic time-scale decomposition of biochemical
                  systems},
  journal      = {Bioinform.},
  volume       = {25},
  number       = {21},
  pages        = {2816--2823},
  year         = {2009},
  url          = {https://doi.org/10.1093/bioinformatics/btp451},
  doi          = {10.1093/BIOINFORMATICS/BTP451},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SurovtsovaSLKSK09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeidemannRSSGGSSBRWK08,
  author       = {Andreas Weidemann and
                  Stefan Richter and
                  Matthias Stein and
                  Sven Sahle and
                  Ralph Gauges and
                  Razif R. Gabdoulline and
                  Irina Surovtsova and
                  Nils Semmelrock and
                  Bruno Besson and
                  Isabel Rojas and
                  Rebecca C. Wade and
                  Ursula Kummer},
  title        = {{SYCAMORE} - a systems biology computational analysis and modeling
                  research environment},
  journal      = {Bioinform.},
  volume       = {24},
  number       = {12},
  pages        = {1463--1464},
  year         = {2008},
  url          = {https://doi.org/10.1093/bioinformatics/btn207},
  doi          = {10.1093/BIOINFORMATICS/BTN207},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WeidemannRSSGGSSBRWK08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GaugesRSW06,
  author       = {Ralph Gauges and
                  Ursula Rost and
                  Sven Sahle and
                  Katja Wegner},
  title        = {A model diagram layout extension for {SBML}},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {15},
  pages        = {1879--1885},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl195},
  doi          = {10.1093/BIOINFORMATICS/BTL195},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GaugesRSW06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoopsSGLPSSXMK06,
  author       = {Stefan Hoops and
                  Sven Sahle and
                  Ralph Gauges and
                  Christine Lee and
                  J{\"{u}}rgen Pahle and
                  Natalia Simus and
                  Mudita Singhal and
                  Liang Xu and
                  Pedro Mendes and
                  Ursula Kummer},
  title        = {{COPASI} - a COmplex PAthway SImulator},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {24},
  pages        = {3067--3074},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl485},
  doi          = {10.1093/BIOINFORMATICS/BTL485},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HoopsSGLPSSXMK06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wsc/SurovtsovaSPK06,
  author       = {Irina Surovtsova and
                  Sven Sahle and
                  J{\"{u}}rgen Pahle and
                  Ursula Kummer},
  editor       = {L. Felipe Perrone and
                  Barry Lawson and
                  Jason Liu and
                  Frederick P. Wieland},
  title        = {Approaches to complexity reduction in a systems biology research environment
                  {(SYCAMORE)}},
  booktitle    = {Proceedings of the Winter Simulation Conference {WSC} 2006, Monterey,
                  California, USA, December 3-6, 2006},
  pages        = {1683--1689},
  publisher    = {{IEEE} Computer Society},
  year         = {2006},
  url          = {https://doi.org/10.1109/WSC.2006.322943},
  doi          = {10.1109/WSC.2006.322943},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/wsc/SurovtsovaSPK06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wsc/SahleGPSKHLSXM06,
  author       = {Sven Sahle and
                  Ralph Gauges and
                  J{\"{u}}rgen Pahle and
                  Natalia Simus and
                  Ursula Kummer and
                  Stefan Hoops and
                  Christine Lee and
                  Mudita Singhal and
                  Liang Xu and
                  Pedro Mendes},
  editor       = {L. Felipe Perrone and
                  Barry Lawson and
                  Jason Liu and
                  Frederick P. Wieland},
  title        = {Simulation of biochemical networks using {COPASI:} a complex pathway
                  simulator},
  booktitle    = {Proceedings of the Winter Simulation Conference {WSC} 2006, Monterey,
                  California, USA, December 3-6, 2006},
  pages        = {1698--1706},
  publisher    = {{IEEE} Computer Society},
  year         = {2006},
  url          = {https://doi.org/10.1109/WSC.2006.322945},
  doi          = {10.1109/WSC.2006.322945},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/wsc/SahleGPSKHLSXM06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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