BibTeX records: Jörg Stelling

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@inproceedings{DBLP:conf/cmsb/StallvikKS25,
  author       = {Andrea Stallvik and
                  Hans{-}Michael Kaltenbach and
                  J{\"{o}}rg Stelling},
  editor       = {Fran{\c{c}}ois Fages and
                  Sabine P{\'{e}}r{\`{e}}s},
  title        = {Optimal Input Design for Model Selection in Systems with Cell-to-Cell
                  Variability},
  booktitle    = {Computational Methods in Systems Biology - 23rd International Conference,
                  {CMSB} 2025, Lyon, France, September 10-12, 2025, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {15959},
  pages        = {240--257},
  publisher    = {Springer},
  year         = {2025},
  url          = {https://doi.org/10.1007/978-3-032-01436-8\_13},
  doi          = {10.1007/978-3-032-01436-8\_13},
  timestamp    = {Sat, 30 Aug 2025 20:22:30 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/StallvikKS25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/cmsb/MoawadS25,
  author       = {Alix Moawad and
                  J{\"{o}}rg Stelling},
  editor       = {Fran{\c{c}}ois Fages and
                  Sabine P{\'{e}}r{\`{e}}s},
  title        = {Minimal Metabolic Exchanges for Microbial Communities in a Chemostat
                  at Steady State},
  booktitle    = {Computational Methods in Systems Biology - 23rd International Conference,
                  {CMSB} 2025, Lyon, France, September 10-12, 2025, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {15959},
  pages        = {356--369},
  publisher    = {Springer},
  year         = {2025},
  url          = {https://doi.org/10.1007/978-3-032-01436-8\_19},
  doi          = {10.1007/978-3-032-01436-8\_19},
  timestamp    = {Sat, 30 Aug 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/MoawadS25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/GollubBKS24,
  author       = {Mattia G. Gollub and
                  Thierry Backes and
                  Hans{-}Michael Kaltenbach and
                  J{\"{o}}rg Stelling},
  title        = {{ENKIE:} a package for predicting enzyme kinetic parameter values
                  and their uncertainties},
  journal      = {Bioinform.},
  volume       = {40},
  number       = {11},
  year         = {2024},
  url          = {https://doi.org/10.1093/bioinformatics/btae652},
  doi          = {10.1093/BIOINFORMATICS/BTAE652},
  timestamp    = {Wed, 25 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GollubBKS24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/TheorellS23,
  author       = {Axel Theorell and
                  J{\"{o}}rg Stelling},
  title        = {Assumptions on decision making and environment can yield multiple
                  steady states in microbial community models},
  journal      = {{BMC} Bioinform.},
  volume       = {24-S},
  number       = {1},
  pages        = {262},
  year         = {2023},
  url          = {https://doi.org/10.1186/s12859-023-05325-w},
  doi          = {10.1186/S12859-023-05325-W},
  timestamp    = {Fri, 07 Jul 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/TheorellS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/TurpinBKS23,
  author       = {Baptiste Turpin and
                  Eline Y. Bijman and
                  Hans{-}Michael Kaltenbach and
                  J{\"{o}}rg Stelling},
  title        = {Efficient design of synthetic gene circuits under cell-to-cell variability},
  journal      = {{BMC} Bioinform.},
  volume       = {24},
  number       = {1},
  pages        = {460},
  year         = {2023},
  url          = {https://doi.org/10.1186/s12859-023-05538-z},
  doi          = {10.1186/S12859-023-05538-Z},
  timestamp    = {Mon, 03 Mar 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/TurpinBKS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/TheorellJNS22,
  author       = {Axel Theorell and
                  Johann F. Jadebeck and
                  Katharina N{\"{o}}h and
                  J{\"{o}}rg Stelling},
  title        = {PolyRound: polytope rounding for random sampling in metabolic networks},
  journal      = {Bioinform.},
  volume       = {38},
  number       = {2},
  pages        = {566--567},
  year         = {2022},
  url          = {https://doi.org/10.1093/bioinformatics/btab552},
  doi          = {10.1093/BIOINFORMATICS/BTAB552},
  timestamp    = {Tue, 07 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/TheorellJNS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/pieee/KhammashS22,
  author       = {Mustafa Hani Khammash and
                  J{\"{o}}rg Stelling},
  title        = {Systems and Synthetic Biology},
  journal      = {Proc. {IEEE}},
  volume       = {110},
  number       = {5},
  pages        = {518--522},
  year         = {2022},
  url          = {https://doi.org/10.1109/JPROC.2022.3173798},
  doi          = {10.1109/JPROC.2022.3173798},
  timestamp    = {Mon, 13 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/pieee/KhammashS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/pieee/TheorellS22,
  author       = {Axel Theorell and
                  J{\"{o}}rg Stelling},
  title        = {Metabolic Networks, Microbial Consortia, and Analogies to Smart Grids},
  journal      = {Proc. {IEEE}},
  volume       = {110},
  number       = {5},
  pages        = {541--556},
  year         = {2022},
  url          = {https://doi.org/10.1109/JPROC.2022.3158396},
  doi          = {10.1109/JPROC.2022.3158396},
  timestamp    = {Thu, 27 Jul 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/pieee/TheorellS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/GollubKS21,
  author       = {Mattia G. Gollub and
                  Hans{-}Michael Kaltenbach and
                  J{\"{o}}rg Stelling},
  title        = {Probabilistic thermodynamic analysis of metabolic networks},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {18},
  pages        = {2938--2945},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btab194},
  doi          = {10.1093/BIOINFORMATICS/BTAB194},
  timestamp    = {Tue, 12 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GollubKS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/cmsb/TheorellS21,
  author       = {Axel Theorell and
                  J{\"{o}}rg Stelling},
  editor       = {Eugenio Cinquemani and
                  Lo{\"{\i}}c Paulev{\'{e}}},
  title        = {Microbial Community Decision Making Models in Batch and Chemostat
                  Cultures},
  booktitle    = {Computational Methods in Systems Biology - 19th International Conference,
                  {CMSB} 2021, Bordeaux, France, September 22-24, 2021, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {12881},
  pages        = {141--158},
  publisher    = {Springer},
  year         = {2021},
  url          = {https://doi.org/10.1007/978-3-030-85633-5\_9},
  doi          = {10.1007/978-3-030-85633-5\_9},
  timestamp    = {Tue, 28 Feb 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/cmsb/TheorellS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/cmsb/TurpinBKS21,
  author       = {Baptiste Turpin and
                  Eline Y. Bijman and
                  Hans{-}Michael Kaltenbach and
                  J{\"{o}}rg Stelling},
  editor       = {Eugenio Cinquemani and
                  Lo{\"{\i}}c Paulev{\'{e}}},
  title        = {Population Design for Synthetic Gene Circuits},
  booktitle    = {Computational Methods in Systems Biology - 19th International Conference,
                  {CMSB} 2021, Bordeaux, France, September 22-24, 2021, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {12881},
  pages        = {181--197},
  publisher    = {Springer},
  year         = {2021},
  url          = {https://doi.org/10.1007/978-3-030-85633-5\_11},
  doi          = {10.1007/978-3-030-85633-5\_11},
  timestamp    = {Mon, 03 Mar 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/cmsb/TurpinBKS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/YordanovSO20,
  author       = {Pencho Yordanov and
                  J{\"{o}}rg Stelling and
                  Irene Otero{-}Muras},
  title        = {BioSwitch: a tool for the detection of bistability and multi-steady
                  state behaviour in signalling and gene regulatory networks},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {5},
  pages        = {1640--1641},
  year         = {2020},
  url          = {https://doi.org/10.1093/bioinformatics/btz746},
  doi          = {10.1093/BIOINFORMATICS/BTZ746},
  timestamp    = {Sat, 30 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/YordanovSO20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/RybinskiMSLS20,
  author       = {Mikolaj Rybinski and
                  Simon M{\"{o}}ller and
                  Mikael Sunn{\aa}ker and
                  Claude Lormeau and
                  J{\"{o}}rg Stelling},
  title        = {TopoFilter: a {MATLAB} package for mechanistic model identification
                  in systems biology},
  journal      = {{BMC} Bioinform.},
  volume       = {21},
  number       = {1},
  pages        = {34},
  year         = {2020},
  url          = {https://doi.org/10.1186/s12859-020-3343-y},
  doi          = {10.1186/S12859-020-3343-Y},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/RybinskiMSLS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/Otero-MurasYS17,
  author       = {Irene Otero{-}Muras and
                  Pencho Yordanov and
                  J{\"{o}}rg Stelling},
  title        = {Chemical Reaction Network Theory elucidates sources of multistability
                  in interferon signaling},
  journal      = {PLoS Comput. Biol.},
  volume       = {13},
  number       = {4},
  year         = {2017},
  url          = {https://doi.org/10.1371/journal.pcbi.1005454},
  doi          = {10.1371/JOURNAL.PCBI.1005454},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/Otero-MurasYS17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/HeckGSS16,
  author       = {Ruben G. A. van Heck and
                  Mathias Ganter and
                  V{\'{\i}}tor A. P. Martins dos Santos and
                  J{\"{o}}rg Stelling},
  title        = {Efficient Reconstruction of Predictive Consensus Metabolic Network
                  Models},
  journal      = {PLoS Comput. Biol.},
  volume       = {12},
  number       = {8},
  year         = {2016},
  url          = {https://doi.org/10.1371/journal.pcbi.1005085},
  doi          = {10.1371/JOURNAL.PCBI.1005085},
  timestamp    = {Tue, 07 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/HeckGSS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/siamsc/LangS16,
  author       = {Moritz Lang and
                  J{\"{o}}rg Stelling},
  title        = {Modular Parameter Identification of Biomolecular Networks},
  journal      = {{SIAM} J. Sci. Comput.},
  volume       = {38},
  number       = {6},
  year         = {2016},
  url          = {https://doi.org/10.1137/15M103306X},
  doi          = {10.1137/15M103306X},
  timestamp    = {Thu, 30 Jul 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/siamsc/LangS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/SchillingsSSS15,
  author       = {Claudia Schillings and
                  Mikael Sunn{\aa}ker and
                  J{\"{o}}rg Stelling and
                  Christoph Schwab},
  title        = {Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical
                  Networks},
  journal      = {PLoS Comput. Biol.},
  volume       = {11},
  number       = {8},
  year         = {2015},
  url          = {https://doi.org/10.1371/journal.pcbi.1004457},
  doi          = {10.1371/JOURNAL.PCBI.1004457},
  timestamp    = {Sun, 06 Oct 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/SchillingsSSS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@incollection{DBLP:reference/sc/StellingK15,
  author       = {J{\"{o}}rg Stelling and
                  Hans{-}Michael Kaltenbach},
  editor       = {John Baillieul and
                  Tariq Samad},
  title        = {Deterministic Description of Biochemical Networks},
  booktitle    = {Encyclopedia of Systems and Control},
  publisher    = {Springer},
  year         = {2015},
  url          = {https://doi.org/10.1007/978-1-4471-5102-9\_87-1},
  doi          = {10.1007/978-1-4471-5102-9\_87-1},
  timestamp    = {Wed, 12 Jul 2017 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/reference/sc/StellingK15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/SunnakerZLRSSW14,
  author       = {Mikael Sunn{\aa}ker and
                  El{\'{\i}}as Zamora{-}Sillero and
                  Adri{\'{a}}n L{\'{o}}pez Garc{\'{\i}}a de Lomana and
                  Florian Rudroff and
                  Uwe Sauer and
                  J{\"{o}}rg Stelling and
                  Andreas Wagner},
  title        = {Topological augmentation to infer hidden processes in biological systems},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {2},
  pages        = {221--227},
  year         = {2014},
  url          = {https://doi.org/10.1093/bioinformatics/btt638},
  doi          = {10.1093/BIOINFORMATICS/BTT638},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SunnakerZLRSSW14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/DimopoulosMRS14,
  author       = {Sotiris Dimopoulos and
                  Christian E. Mayer and
                  Fabian Rudolf and
                  J{\"{o}}rg Stelling},
  title        = {Accurate cell segmentation in microscopy images using membrane patterns},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {18},
  pages        = {2644--2651},
  year         = {2014},
  url          = {https://doi.org/10.1093/bioinformatics/btu302},
  doi          = {10.1093/BIOINFORMATICS/BTU302},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DimopoulosMRS14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/Otero-MurasYS14,
  author       = {Irene Otero{-}Muras and
                  Pencho Yordanov and
                  J{\"{o}}rg Stelling},
  title        = {A method for inverse bifurcation of biochemical switches: inferring
                  parameters from dose response curves},
  journal      = {{BMC} Syst. Biol.},
  volume       = {8},
  pages        = {114},
  year         = {2014},
  url          = {https://doi.org/10.1186/s12918-014-0114-2},
  doi          = {10.1186/S12918-014-0114-2},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/Otero-MurasYS14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/GanterBMSP13,
  author       = {Mathias Ganter and
                  Thomas Bernard and
                  S{\'{e}}bastien Moretti and
                  J{\"{o}}rg Stelling and
                  Marco Pagni},
  title        = {MetaNetX.org: a website and repository for accessing, analysing and
                  manipulating metabolic networks},
  journal      = {Bioinform.},
  volume       = {29},
  number       = {6},
  pages        = {815--816},
  year         = {2013},
  url          = {https://doi.org/10.1093/bioinformatics/btt036},
  doi          = {10.1093/BIOINFORMATICS/BTT036},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GanterBMSP13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/BusettoHKSDOSB13,
  author       = {Alberto Giovanni Busetto and
                  Alain Hauser and
                  Gabriel Krummenacher and
                  Mikael Sunn{\aa}ker and
                  Sotiris Dimopoulos and
                  Cheng Soon Ong and
                  J{\"{o}}rg Stelling and
                  Joachim M. Buhmann},
  title        = {Near-optimal experimental design for model selection in systems biology},
  journal      = {Bioinform.},
  volume       = {29},
  number       = {20},
  pages        = {2625--2632},
  year         = {2013},
  url          = {https://doi.org/10.1093/bioinformatics/btt436},
  doi          = {10.1093/BIOINFORMATICS/BTT436},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BusettoHKSDOSB13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/MarchisioCWS13,
  author       = {Mario Andrea Marchisio and
                  Moreno Colaiacovo and
                  Ellis Whitehead and
                  J{\"{o}}rg Stelling},
  title        = {Modular, rule-based modeling for the design of eukaryotic synthetic
                  gene circuits},
  journal      = {{BMC} Syst. Biol.},
  volume       = {7},
  pages        = {42},
  year         = {2013},
  url          = {https://doi.org/10.1186/1752-0509-7-42},
  doi          = {10.1186/1752-0509-7-42},
  timestamp    = {Mon, 03 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcsb/MarchisioCWS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/GonnetDWS12,
  author       = {Pedro Gonnet and
                  Sotiris Dimopoulos and
                  Lukas Widmer and
                  J{\"{o}}rg Stelling},
  title        = {A specialized {ODE} integrator for the efficient computation of parameter
                  sensitivities},
  journal      = {{BMC} Syst. Biol.},
  volume       = {6},
  pages        = {46},
  year         = {2012},
  url          = {https://doi.org/10.1186/1752-0509-6-46},
  doi          = {10.1186/1752-0509-6-46},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/GonnetDWS12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/JolKTSH12,
  author       = {Stefan J. Jol and
                  Anne K{\"{u}}mmel and
                  Marco Terzer and
                  J{\"{o}}rg Stelling and
                  Matthias Heinemann},
  title        = {System-Level Insights into Yeast Metabolism by Thermodynamic Analysis
                  of Elementary Flux Modes},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {3},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002415},
  doi          = {10.1371/JOURNAL.PCBI.1002415},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/JolKTSH12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/Zamora-SilleroHISW11,
  author       = {El{\'{\i}}as Zamora{-}Sillero and
                  Marc Hafner and
                  Ariane Ibig and
                  J{\"{o}}rg Stelling and
                  Andreas Wagner},
  title        = {Efficient characterization of high-dimensional parameter spaces for
                  systems biology},
  journal      = {{BMC} Syst. Biol.},
  volume       = {5},
  pages        = {142},
  year         = {2011},
  url          = {https://doi.org/10.1186/1752-0509-5-142},
  doi          = {10.1186/1752-0509-5-142},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/Zamora-SilleroHISW11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/MarchisioS11,
  author       = {Mario Andrea Marchisio and
                  J{\"{o}}rg Stelling},
  title        = {Automatic Design of Digital Synthetic Gene Circuits},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {2},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1001083},
  doi          = {10.1371/JOURNAL.PCBI.1001083},
  timestamp    = {Mon, 03 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/MarchisioS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/wabi/KaltenbachCFS11,
  author       = {Hans{-}Michael Kaltenbach and
                  Simona Constantinescu and
                  Justin Feigelman and
                  J{\"{o}}rg Stelling},
  editor       = {Teresa M. Przytycka and
                  Marie{-}France Sagot},
  title        = {Graph-Based Decomposition of Biochemical Reaction Networks into Monotone
                  Subsystems},
  booktitle    = {Algorithms in Bioinformatics - 11th International Workshop, {WABI}
                  2011, Saarbr{\"{u}}cken, Germany, September 5-7, 2011. Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {6833},
  pages        = {139--150},
  publisher    = {Springer},
  year         = {2011},
  url          = {https://doi.org/10.1007/978-3-642-23038-7\_13},
  doi          = {10.1007/978-3-642-23038-7\_13},
  timestamp    = {Sun, 25 Oct 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/wabi/KaltenbachCFS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/MullerS09,
  author       = {Dirk M{\"{u}}ller and
                  J{\"{o}}rg Stelling},
  title        = {Precise Regulation of Gene Expression Dynamics Favors Complex Promoter
                  Architectures},
  journal      = {PLoS Comput. Biol.},
  volume       = {5},
  number       = {1},
  year         = {2009},
  url          = {https://doi.org/10.1371/journal.pcbi.1000279},
  doi          = {10.1371/JOURNAL.PCBI.1000279},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/MullerS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/iscas/MarchisioS09,
  author       = {Mario Andrea Marchisio and
                  J{\"{o}}rg Stelling},
  title        = {Synthetic Gene Network Computational Design},
  booktitle    = {International Symposium on Circuits and Systems {(ISCAS} 2009), 24-17
                  May 2009, Taipei, Taiwan},
  pages        = {309--312},
  publisher    = {{IEEE}},
  year         = {2009},
  url          = {https://doi.org/10.1109/ISCAS.2009.5117747},
  doi          = {10.1109/ISCAS.2009.5117747},
  timestamp    = {Mon, 03 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/iscas/MarchisioS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ppam/TerzerS09,
  author       = {Marco Terzer and
                  J{\"{o}}rg Stelling},
  editor       = {Roman Wyrzykowski and
                  Jack J. Dongarra and
                  Konrad Karczewski and
                  Jerzy Wasniewski},
  title        = {Parallel Extreme Ray and Pathway Computation},
  booktitle    = {Parallel Processing and Applied Mathematics, 8th International Conference,
                  {PPAM} 2009, Wroclaw, Poland, September 13-16, 2009, Revised Selected
                  Papers, Part {II}},
  series       = {Lecture Notes in Computer Science},
  volume       = {6068},
  pages        = {300--309},
  publisher    = {Springer},
  year         = {2009},
  url          = {https://doi.org/10.1007/978-3-642-14403-5\_32},
  doi          = {10.1007/978-3-642-14403-5\_32},
  timestamp    = {Tue, 14 May 2019 10:00:45 +0200},
  biburl       = {https://dblp.org/rec/conf/ppam/TerzerS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@incollection{DBLP:reference/auto/MirskySGBTKSD09,
  author       = {Henry Mirsky and
                  J{\"{o}}rg Stelling and
                  Rudiyanto Gunawan and
                  Neda Bagheri and
                  Stephanie R. Taylor and
                  Eric Kwei and
                  Jason E. Shoemaker and
                  Francis J. Doyle III},
  editor       = {Shimon Y. Nof},
  title        = {Automatic Control in Systems Biology},
  booktitle    = {Springer Handbook of Automation},
  series       = {Springer Handbooks},
  pages        = {1335--1360},
  publisher    = {Springer},
  year         = {2009},
  url          = {https://doi.org/10.1007/978-3-540-78831-7\_75},
  doi          = {10.1007/978-3-540-78831-7\_75},
  timestamp    = {Tue, 12 Nov 2019 17:14:07 +0100},
  biburl       = {https://dblp.org/rec/reference/auto/MirskySGBTKSD09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/MarchisioS08,
  author       = {Mario Andrea Marchisio and
                  J{\"{o}}rg Stelling},
  title        = {Computational design of synthetic gene circuits with composable parts},
  journal      = {Bioinform.},
  volume       = {24},
  number       = {17},
  pages        = {1903--1910},
  year         = {2008},
  url          = {https://doi.org/10.1093/bioinformatics/btn330},
  doi          = {10.1093/BIOINFORMATICS/BTN330},
  timestamp    = {Mon, 03 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MarchisioS08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/TerzerS08,
  author       = {Marco Terzer and
                  J{\"{o}}rg Stelling},
  title        = {Large-scale computation of elementary flux modes with bit pattern
                  trees},
  journal      = {Bioinform.},
  volume       = {24},
  number       = {19},
  pages        = {2229--2235},
  year         = {2008},
  url          = {https://doi.org/10.1093/bioinformatics/btn401},
  doi          = {10.1093/BIOINFORMATICS/BTN401},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/TerzerS08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/BagheriSD08,
  author       = {Neda Bagheri and
                  J{\"{o}}rg Stelling and
                  Francis J. Doyle III},
  title        = {Circadian Phase Resetting via Single and Multiple Control Targets},
  journal      = {PLoS Comput. Biol.},
  volume       = {4},
  number       = {7},
  year         = {2008},
  url          = {https://doi.org/10.1371/journal.pcbi.1000104},
  doi          = {10.1371/JOURNAL.PCBI.1000104},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/BagheriSD08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/BagheriSD07,
  author       = {Neda Bagheri and
                  J{\"{o}}rg Stelling and
                  Francis J. Doyle III},
  title        = {Quantitative performance metrics for robustness in circadian rhythms},
  journal      = {Bioinform.},
  volume       = {23},
  number       = {3},
  pages        = {358--364},
  year         = {2007},
  url          = {https://doi.org/10.1093/bioinformatics/btl627},
  doi          = {10.1093/BIOINFORMATICS/BTL627},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BagheriSD07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/TerzerS07,
  author       = {Marco Terzer and
                  J{\"{o}}rg Stelling},
  title        = {Elementary flux modes - state-of-the-art implementation and scope
                  of application},
  journal      = {{BMC} Syst. Biol.},
  volume       = {1},
  number       = {{S-1}},
  pages        = {P2},
  year         = {2007},
  url          = {https://doi.org/10.1186/1752-0509-1-S1-P2},
  doi          = {10.1186/1752-0509-1-S1-P2},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/TerzerS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/wabi/TerzerS06,
  author       = {Marco Terzer and
                  J{\"{o}}rg Stelling},
  editor       = {Philipp Bucher and
                  Bernard M. E. Moret},
  title        = {Accelerating the Computation of Elementary Modes Using Pattern Trees},
  booktitle    = {Algorithms in Bioinformatics, 6th International Workshop, {WABI} 2006,
                  Zurich, Switzerland, September 11-13, 2006, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {4175},
  pages        = {333--343},
  publisher    = {Springer},
  year         = {2006},
  url          = {https://doi.org/10.1007/11851561\_31},
  doi          = {10.1007/11851561\_31},
  timestamp    = {Tue, 14 May 2019 10:00:40 +0200},
  biburl       = {https://dblp.org/rec/conf/wabi/TerzerS06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/cce/ZakSD05,
  author       = {Daniel E. Zak and
                  J{\"{o}}rg Stelling and
                  Francis J. Doyle III},
  title        = {Sensitivity analysis of oscillatory (bio)chemical systems},
  journal      = {Comput. Chem. Eng.},
  volume       = {29},
  number       = {3},
  pages        = {663--673},
  year         = {2005},
  url          = {https://doi.org/10.1016/j.compchemeng.2004.08.021},
  doi          = {10.1016/J.COMPCHEMENG.2004.08.021},
  timestamp    = {Mon, 18 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/cce/ZakSD05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/amcc/BagheriSD05,
  author       = {Neda Bagheri and
                  J{\"{o}}rg Stelling and
                  Francis J. Doyle},
  title        = {Optimal phase-tracking of the nonlinear circadian oscillator},
  booktitle    = {American Control Conference, {ACC} 2005, Portland, OR, USA, 8-10 June,
                  2005},
  pages        = {3235--3240},
  publisher    = {{IEEE}},
  year         = {2005},
  url          = {https://doi.org/10.1109/ACC.2005.1470470},
  doi          = {10.1109/ACC.2005.1470470},
  timestamp    = {Fri, 07 Oct 2022 18:48:01 +0200},
  biburl       = {https://dblp.org/rec/conf/amcc/BagheriSD05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/KlamtSGG03,
  author       = {Steffen Klamt and
                  J{\"{o}}rg Stelling and
                  Martin Ginkel and
                  Ernst Dieter Gilles},
  title        = {FluxAnalyzer: exploring structure, pathways, and flux distributions
                  in metabolic networks on interactive flux maps},
  journal      = {Bioinform.},
  volume       = {19},
  number       = {2},
  pages        = {261--269},
  year         = {2003},
  url          = {https://doi.org/10.1093/bioinformatics/19.2.261},
  doi          = {10.1093/BIOINFORMATICS/19.2.261},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KlamtSGG03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/HuckaFS03,
  author       = {Michael Hucka and
                  Andrew Finney and
                  Herbert M. Sauro and
                  H. Bolouri and
                  John C. Doyle and
                  Hiroaki Kitano and
                  Adam P. Arkin and
                  Benjamin J. Bornstein and
                  Dennis Bray and
                  Athel Cornish{-}Bowden and
                  Autumn A. Cuellar and
                  Serge Dronov and
                  Ernst Dieter Gilles and
                  Martin Ginkel and
                  Victoria Gor and
                  Igor Goryanin and
                  W. J. Hedley and
                  T. Charles Hodgman and
                  Jan{-}Hendrik S. Hofmeyr and
                  Peter J. Hunter and
                  Nick S. Juty and
                  J. L. Kasberger and
                  Andreas Kremling and
                  Ursula Kummer and
                  Nicolas Le Nov{\`{e}}re and
                  Leslie M. Loew and
                  D. Lucio and
                  Pedro Mendes and
                  E. Minch and
                  Eric Mjolsness and
                  Yoichi Nakayama and
                  M. R. Nelson and
                  Poul M. F. Nielsen and
                  T. Sakurada and
                  James C. Schaff and
                  Bruce E. Shapiro and
                  Thomas Simon Shimizu and
                  Hugh D. Spence and
                  J{\"{o}}rg Stelling and
                  Koichi Takahashi and
                  Masaru Tomita and
                  J. Wagner and
                  J. Wang},
  title        = {The systems biology markup language {(SBML):} a medium for representation
                  and exchange of biochemical network models},
  journal      = {Bioinform.},
  volume       = {19},
  number       = {4},
  pages        = {524--531},
  year         = {2003},
  url          = {https://doi.org/10.1093/bioinformatics/btg015},
  doi          = {10.1093/BIOINFORMATICS/BTG015},
  timestamp    = {Sat, 31 May 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HuckaFS03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/gcb/SchusterKS03,
  author       = {Stefan Schuster and
                  Steffen Klamt and
                  J{\"{o}}rg Stelling},
  title        = {Making predictions about robustness and flexibility from metabolic
                  network structure},
  booktitle    = {Proceedings of the German Conference on Bioinformatics, {GCB} 2003,
                  October 12-14, 2003, Neuherberg/Garching near Munich, Germany},
  pages        = {129--134},
  year         = {2003},
  timestamp    = {Tue, 15 Mar 2005 13:11:15 +0100},
  biburl       = {https://dblp.org/rec/conf/gcb/SchusterKS03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

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