% Bibliography for "Exact interfaces for modular autocatalytic reaction networks".
% Style: unsrtnat (numeric, citation order). DOIs are placed in the note
% field as \href links because plain/unsrt styles do not print a doi field.

@article{kauffman1986,
  author  = {Kauffman, Stuart A.},
  title   = {Autocatalytic sets of proteins},
  journal = {Journal of Theoretical Biology},
  volume  = {119},
  number  = {1},
  pages   = {1--24},
  year    = {1986},
  note    = {\href{https://doi.org/10.1016/S0022-5193(86)80047-9}{doi:10.1016/S0022-5193(86)80047-9}}
}

@article{hordijk2004,
  author  = {Hordijk, Wim and Steel, Mike},
  title   = {Detecting autocatalytic, self-sustaining sets in chemical reaction systems},
  journal = {Journal of Theoretical Biology},
  volume  = {227},
  number  = {4},
  pages   = {451--461},
  year    = {2004},
  note    = {\href{https://doi.org/10.1016/j.jtbi.2003.11.020}{doi:10.1016/j.jtbi.2003.11.020}}
}

@article{hordijk2014,
  author  = {Hordijk, Wim and Wills, Peter R. and Steel, Mike},
  title   = {Autocatalytic sets and biological specificity},
  journal = {Bulletin of Mathematical Biology},
  volume  = {76},
  pages   = {201--224},
  year    = {2014},
  note    = {\href{https://doi.org/10.1007/s11538-013-9916-4}{doi:10.1007/s11538-013-9916-4}}
}

@article{steel2019,
  author  = {Steel, Mike and Hordijk, Wim and Xavier, Joana C.},
  title   = {Autocatalytic networks in biology: structural theory and algorithms},
  journal = {Journal of the Royal Society Interface},
  volume  = {16},
  pages   = {20180808},
  year    = {2019},
  note    = {\href{https://doi.org/10.1098/rsif.2018.0808}{doi:10.1098/rsif.2018.0808}}
}

@article{blokhuis2020,
  author  = {Blokhuis, Alex and Lacoste, David and Nghe, Philippe},
  title   = {Universal motifs and the diversity of autocatalytic systems},
  journal = {Proceedings of the National Academy of Sciences},
  volume  = {117},
  number  = {41},
  pages   = {25230--25236},
  year    = {2020},
  note    = {\href{https://doi.org/10.1073/pnas.2013527117}{doi:10.1073/pnas.2013527117}}
}

@article{unterberger2022,
  author  = {Unterberger, J{\'e}r{\'e}mie and Nghe, Philippe},
  title   = {Stoechiometric and dynamical autocatalysis for diluted chemical reaction networks},
  journal = {Journal of Mathematical Biology},
  volume  = {85},
  pages   = {26},
  year    = {2022},
  note    = {\href{https://doi.org/10.1007/s00285-022-01791-x}{doi:10.1007/s00285-022-01791-x}}
}

@article{nandan2026,
  author  = {Nandan, Praneet and Nghe, Philippe and Unterberger, J{\'e}r{\'e}mie},
  title   = {Autocatalytic cores in the diluted regime: classification and properties},
  journal = {Journal of Mathematical Biology},
  volume  = {92},
  pages   = {36},
  year    = {2026},
  note    = {\href{https://doi.org/10.1007/s00285-026-02357-7}{doi:10.1007/s00285-026-02357-7}; preprint arXiv:2507.15546}
}

@misc{golnik2026cores,
  author        = {Golnik, Richard and Gatter, Thomas and Stadler, Peter F. and Vassena, Nicola},
  title         = {Autocatalytic cores in reaction networks with explicit catalysis},
  year          = {2026},
  howpublished  = {arXiv preprint arXiv:2603.02770 [math.CO]},
  note          = {\href{https://doi.org/10.48550/arXiv.2603.02770}{doi:10.48550/arXiv.2603.02770}}
}

@misc{golnik2026bridging,
  author        = {Golnik, Richard and Gatter, Thomas and Hordijk, Wim and Stadler, Peter F. and Vassena, Nicola},
  title         = {Bridging two theoretical frameworks of autocatalysis: {RAF} sets and stoichiometric autocatalysis},
  year          = {2026},
  howpublished  = {arXiv preprint arXiv:2605.25523},
  note          = {\href{https://doi.org/10.48550/arXiv.2605.25523}{doi:10.48550/arXiv.2605.25523}}
}

@misc{gagrani2026maf,
  author        = {Gagrani, Praful and Wang, Jiwei and De Decker, Yannick and Lacoste, David},
  title         = {Topological bounds on the dynamical growth rate of chemical reaction networks},
  year          = {2026},
  howpublished  = {arXiv preprint arXiv:2603.02627},
  note          = {\href{https://doi.org/10.48550/arXiv.2603.02627}{doi:10.48550/arXiv.2603.02627}}
}

@article{gagrani2024,
  author  = {Gagrani, Praful and Blanco, Victor and Smith, Eric and Baum, David},
  title   = {Polyhedral geometry and combinatorics of an autocatalytic ecosystem},
  journal = {Journal of Mathematical Chemistry},
  volume  = {62},
  pages   = {1012--1078},
  year    = {2024},
  note    = {\href{https://doi.org/10.1007/s10910-024-01576-x}{doi:10.1007/s10910-024-01576-x}}
}

@article{andersen2012,
  author  = {Andersen, Jakob L. and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.},
  title   = {Maximizing output and recognizing autocatalysis in chemical reaction networks is {NP}-complete},
  journal = {Journal of Systems Chemistry},
  volume  = {3},
  pages   = {1},
  year    = {2012},
  note    = {\href{https://doi.org/10.1186/1759-2208-3-1}{doi:10.1186/1759-2208-3-1}}
}

@article{vassena2024,
  author  = {Vassena, Nicola and Stadler, Peter F.},
  title   = {Unstable cores are the source of instability in chemical reaction networks},
  journal = {Proceedings of the Royal Society A},
  volume  = {480},
  pages   = {20230694},
  year    = {2024},
  note    = {\href{https://doi.org/10.1098/rspa.2023.0694}{doi:10.1098/rspa.2023.0694}}
}

@article{kosc2025,
  author  = {Kosc, Thomas and Kuperberg, Denis and Rajon, Etienne and Charlat, Sylvain},
  title   = {Thermodynamic consistency of autocatalytic cycles},
  journal = {Proceedings of the National Academy of Sciences},
  volume  = {122},
  number  = {18},
  pages   = {e2421274122},
  year    = {2025},
  note    = {\href{https://doi.org/10.1073/pnas.2421274122}{doi:10.1073/pnas.2421274122}}
}

@article{ofir2022,
  author  = {Ofir, Ron and Bullo, Francesco and Margaliot, Michael},
  title   = {Minimum effort decentralized control design for contracting network systems},
  journal = {IEEE Control Systems Letters},
  volume  = {6},
  pages   = {2731--2736},
  year    = {2022},
  note    = {\href{https://doi.org/10.1109/LCSYS.2022.3176196}{doi:10.1109/LCSYS.2022.3176196}; preprint arXiv:2203.10392}
}

@book{bermanplemmons1994,
  author    = {Berman, Abraham and Plemmons, Robert J.},
  title     = {Nonnegative Matrices in the Mathematical Sciences},
  publisher = {SIAM},
  series    = {Classics in Applied Mathematics},
  volume    = {9},
  year      = {1994},
  note      = {\href{https://doi.org/10.1137/1.9781611971262}{doi:10.1137/1.9781611971262}}
}

@book{farinarinaldi2000,
  author    = {Farina, Lorenzo and Rinaldi, Sergio},
  title     = {Positive Linear Systems: Theory and Applications},
  publisher = {Wiley},
  year      = {2000},
  note      = {\href{https://doi.org/10.1002/9781118033029}{doi:10.1002/9781118033029}}
}

@article{vonneumann1945,
  author  = {von Neumann, John},
  title   = {A model of general economic equilibrium},
  journal = {The Review of Economic Studies},
  volume  = {13},
  number  = {1},
  pages   = {1--9},
  year    = {1945},
  note    = {\href{https://doi.org/10.2307/2296111}{doi:10.2307/2296111}}
}

@article{kemeny1956,
  author  = {Kemeny, John G. and Morgenstern, Oskar and Thompson, Gerald L.},
  title   = {A generalization of the von {N}eumann model of an expanding economy},
  journal = {Econometrica},
  volume  = {24},
  number  = {2},
  pages   = {115--135},
  year    = {1956},
  note    = {\href{https://doi.org/10.2307/1905746}{doi:10.2307/1905746}}
}

@article{gordan1873,
  author  = {Gordan, Paul},
  title   = {Ueber die {A}ufl\"osung linearer {G}leichungen mit reellen {C}oefficienten},
  journal = {Mathematische Annalen},
  volume  = {6},
  pages   = {23--28},
  year    = {1873},
  note    = {\href{https://doi.org/10.1007/BF01442864}{doi:10.1007/BF01442864}}
}

@book{schrijver1986,
  author    = {Schrijver, Alexander},
  title     = {Theory of Linear and Integer Programming},
  publisher = {Wiley},
  address   = {Chichester},
  year      = {1986}
}

@article{schauder1930,
  author  = {Schauder, Juliusz},
  title   = {Der {F}ixpunktsatz in {F}unktionalr\"aumen},
  journal = {Studia Mathematica},
  volume  = {2},
  pages   = {171--180},
  year    = {1930},
  note    = {\url{https://eudml.org/doc/217247}}
}

@article{lauritzen1988,
  author  = {Lauritzen, Steffen L. and Spiegelhalter, David J.},
  title   = {Local computations with probabilities on graphical structures and their application to expert systems},
  journal = {Journal of the Royal Statistical Society: Series B},
  volume  = {50},
  number  = {2},
  pages   = {157--194},
  year    = {1988},
  note    = {\href{https://doi.org/10.1111/j.2517-6161.1988.tb01721.x}{doi:10.1111/j.2517-6161.1988.tb01721.x}}
}

@inproceedings{freuder1990,
  author    = {Freuder, Eugene C.},
  title     = {Complexity of {K}-tree structured constraint satisfaction problems},
  booktitle = {Proceedings of the Eighth National Conference on Artificial Intelligence (AAAI-90)},
  pages     = {4--9},
  year      = {1990},
  note      = {\url{https://www.aaai.org/Papers/AAAI/1990/AAAI90-001.pdf}}
}

@article{beeri1983,
  author  = {Beeri, Catriel and Fagin, Ronald and Maier, David and Yannakakis, Mihalis},
  title   = {On the desirability of acyclic database schemes},
  journal = {Journal of the ACM},
  volume  = {30},
  number  = {3},
  pages   = {479--513},
  year    = {1983},
  note    = {\href{https://doi.org/10.1145/2402.322389}{doi:10.1145/2402.322389}}
}

@article{kschischang2001,
  author  = {Kschischang, Frank R. and Frey, Brendan J. and Loeliger, Hans-Andrea},
  title   = {Factor graphs and the sum-product algorithm},
  journal = {IEEE Transactions on Information Theory},
  volume  = {47},
  number  = {2},
  pages   = {498--519},
  year    = {2001},
  note    = {\href{https://doi.org/10.1109/18.910572}{doi:10.1109/18.910572}}
}

@article{willems2007,
  author  = {Willems, Jan C.},
  title   = {The behavioral approach to open and interconnected systems},
  journal = {IEEE Control Systems Magazine},
  volume  = {27},
  number  = {6},
  pages   = {46--99},
  year    = {2007},
  note    = {\href{https://doi.org/10.1109/MCS.2007.906923}{doi:10.1109/MCS.2007.906923}}
}

@article{baezpollard2017,
  author  = {Baez, John C. and Pollard, Blake S.},
  title   = {A compositional framework for reaction networks},
  journal = {Reviews in Mathematical Physics},
  volume  = {29},
  number  = {9},
  pages   = {1750028},
  year    = {2017},
  note    = {\href{https://doi.org/10.1142/S0129055X17500283}{doi:10.1142/S0129055X17500283}}
}

@inproceedings{demoura2021,
  author    = {de Moura, Leonardo and Ullrich, Sebastian},
  title     = {The {L}ean 4 theorem prover and programming language},
  booktitle = {Automated Deduction -- CADE 28},
  series    = {Lecture Notes in Computer Science},
  volume    = {12699},
  pages     = {625--635},
  publisher = {Springer},
  year      = {2021},
  note      = {\href{https://doi.org/10.1007/978-3-030-79876-5_37}{doi:10.1007/978-3-030-79876-5\_37}}
}

@inproceedings{mathlib2020,
  author    = {{The mathlib Community}},
  title     = {The {L}ean mathematical library},
  booktitle = {Proceedings of the 9th ACM SIGPLAN International Conference on Certified Programs and Proofs (CPP 2020)},
  pages     = {367--381},
  publisher = {ACM},
  year      = {2020},
  note      = {\href{https://doi.org/10.1145/3372885.3373824}{doi:10.1145/3372885.3373824}}
}