hdr/bib/dealb.bib

@book{Glade22,
  author       = {Nicolas Glade},
  title        = {Le Vivant Rare, Faible et Amorphe - {\'{E}}volution depuis les
                  Origines jusqu'{\`{a}} la Vie telle qu'elle nous Appara{\^{\i}}t.
                  (Rare, Weak and Amorphous Life - Evolution of Life from the Origins
                  until Life as it Appears Nowadays)},
  year         = {2022},
  url          = {https://tel.archives-ouvertes.fr/tel-04075075},
  timestamp    = {Sun, 23 Apr 2023 00:55:01 +0200},
  biburl       = {https://dblp.org/rec/books/hal/Glade22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org},
  publisher    = {Habilitation thesis (HDR)}
}

@book{Howe1858,
author = {Henry Howe},
title = {Memoirs of the most eminent {A}merican mechanics},
year = {1858},
publisher = {New York: Derby \& Jackson},
note = {Page 450}
}

@book{Lilienthal1911,
author = {Otto Lilienthal},
title = {Birdflight as the Basis of Aviation},
year = {1911},
publisher = {Berlin},
note = {Table of contents: \url{http://www.lilienthal-museum.de/olma/e6.htm}}
}

@article{RamamoorthyT22,
  author       = {Raghu Ramamoorthy and
                  Menakadevi Thangavelu},
  title        = {An enhanced hybrid ant colony optimization routing protocol for vehicular
                  ad-hoc networks},
  journal      = {Journal of Ambient Intelligence and Humanized Computing},
  volume       = {13},
  number       = {8},
  pages        = {3837--3868},
  year         = {2022},
  url          = {https://doi.org/10.1007/s12652-021-03176-y},
  doi          = {10.1007/s12652-021-03176-y},
  timestamp    = {Sun, 02 Oct 2022 15:39:55 +0200},
  biburl       = {https://dblp.org/rec/journals/jaihc/RamamoorthyT22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{Hopfield1982,
  author = {John J. Hopfield},
  title = {Neural networks and physical systems with emergent collective computational abilities},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {79},
  pages = {2554--2558},
  year = {1982}
}

@article{Woese2004,
author = {Carl R. Woese},
title = {A new biology for a new century},
journal = {Microbiology and molecular biology reviews},
volume = {68(2)},
pages = {173--186},
year = {2004}
}

@article{Nicholson2019,
title = {Is the cell really a machine?},
journal = {Journal of Theoretical Biology},
volume = {477},
pages = {108--126},
year = {2019},
issn = {0022-5193},
doi = {https://doi.org/10.1016/j.jtbi.2019.06.002},
url = {https://www.sciencedirect.com/science/article/pii/S0022519319302292},
author = {Daniel J. Nicholson}
}

@article{CornishBowdenCLSA2007,
author = {Athel Cornish-Bowden and Mar\'{i}a Luz C\'{a}rdenas and Juan-Carlos Letelier and Jorge Soto-Andrade},
title = {Beyond reductionism: metabolic circularity as a guiding vision for a real biology of systems},
journal = {Proteomics},
volume = {7(6)},
pages = {839--845},
year = {2007}
}

@inproceedings{RonaldSC99,
  author       = {Edmund M. A. Ronald and
                  Moshe Sipper and
                  Mathieu S. Capcarr{\`{e}}re},
  editor       = {Dario Floreano and
                  Jean{-}Daniel Nicoud and
                  Francesco Mondada},
  title        = {Testing for Emergence in Artificial Life},
  booktitle    = {Advances in Artificial Life, 5th European Conference, ECAL'99, Lausanne,
                  Switzerland, September 13-17, 1999, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {1674},
  pages        = {13--20},
  publisher    = {Springer},
  year         = {1999},
  url          = {https://doi.org/10.1007/3-540-48304-7\_5},
  doi          = {10.1007/3-540-48304-7\_5},
  timestamp    = {Wed, 07 Dec 2022 23:10:50 +0100},
  biburl       = {https://dblp.org/rec/conf/ecal/RonaldSC99.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@misc{wikiLaplace,
    author = "{Wikipedia contributors}",
    title = "Laplace's demon --- {Wikipedia}{,} The Free Encyclopedia",
    year = "2023",
    howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Laplace's_demon&oldid=1163265214}",
    note = "[Online; accessed 26-July-2023]"
}

@misc{Carroll,
author = {Sean Carroll},
title = {{S}ean {C}arroll's {M}indscape {P}odcast},
year = {Retrieved on 2023-07-25},
howpublished = {\url{https://www.preposterousuniverse.com/podcast/}}
}

@misc{wikiEntropy,
    author = "{Wikipedia contributors}",
    title = "Entropy (statistical thermodynamics) --- {Wikipedia}{,} The Free Encyclopedia",
    year = "2023",
    howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Entropy_(statistical_thermodynamics)&oldid=1143513230}",
    note = "[Online; accessed 26-July-2023]"
}

@misc{SusskindCourse,
author = {Leonard Susskind},
title = {Modern Physics: Statistical Mechanics},
misc = {Standford Lecture Collection},
howpublished = {\url{https://www.youtube.com/playlist?list=PLB72416C707D85AB0}}
}

@misc{wikiMotors,
    author = "{Wikipedia contributors}",
    title = "Molecular motor --- {Wikipedia}{,} The Free Encyclopedia",
    year = "2023",
    howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Molecular_motor&oldid=1130929229}",
    note = "[Online; accessed 26-July-2023]"
}

@misc{lifeOfTheCell,
author = {John Liebler},
title = {The Inner Life of the Cell},
note = {Guidance of Robert Lue and Alain Viel},
year = {2006},
howpublished = {\url{https://www.artofthecell.com/in-the-beginning-there-was-the-inner-life-of-the-cell/}}
}

@article{Mayer2009,
author = {Bruce J. Mayer and Michael L. Blinov and Leslie M. Loew},
title = {Molecular machines or pleiomorphic ensembles: signaling complexes revisited},
journal = {Journal of biology},
volume = {8(9)},
page = {81},
year = {2009}
}

@article{Kurakin2006,
title = {Self-organization versus Watchmaker: Molecular motors and protein translocation},
journal = {Biosystems},
volume = {84},
number = {1},
pages = {15-23},
year = {2006},
issn = {0303-2647},
doi = {https://doi.org/10.1016/j.biosystems.2005.09.007},
url = {https://www.sciencedirect.com/science/article/pii/S030326470500153X},
author = {Alexei Kurakin},
keywords = {Self-organization, Stochasticity, Determinism, Molecular motors, Brownian ratchet, Protein translocation},
}

@misc{berkleyBio,
author = {Berkley Bioengineering},
title = {What is Bioengineering?},
year = {Retrieved on 2023-07-29},
howpublished = {\url{https://bioeng.berkeley.edu/about-us/what-is-bioengineering}}
}

@article{PardoID21,
  author    = {J{\'{e}}r{\'{e}}mie Pardo and
               Sergiu Ivanov and
               Franck Delaplace},
  title     = {Sequential reprogramming of biological network fate},
  journal   = {Theor. Comput. Sci.},
  volume    = {872},
  pages     = {97--116},
  year      = {2021},
  url       = {https://doi.org/10.1016/j.tcs.2021.03.013},
  doi       = {10.1016/j.tcs.2021.03.013},
  timestamp = {Tue, 01 Jun 2021 08:35:28 +0200},
  biburl    = {https://dblp.org/rec/journals/tcs/PardoID21.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{MandonSH0P19,
  author    = {Hugues Mandon and
               Cui Su and
               Stefan Haar and
               Jun Pang and
               Lo{\"{\i}}c Paulev{\'{e}}},
  editor    = {Luca Bortolussi and
               Guido Sanguinetti},
  title     = {Sequential Reprogramming of {B}oolean Networks Made Practical},
  booktitle = {Computational Methods in Systems Biology - 17th International Conference,
               {CMSB} 2019, Trieste, Italy, September 18-20, 2019, Proceedings},
  series    = {Lecture Notes in Computer Science},
  volume    = {11773},
  pages     = {3--19},
  publisher = {Springer},
  year      = {2019},
  url       = {https://doi.org/10.1007/978-3-030-31304-3\_1},
  doi       = {10.1007/978-3-030-31304-3\_1},
  timestamp = {Tue, 17 Sep 2019 12:55:34 +0200},
  biburl    = {https://dblp.org/rec/conf/cmsb/MandonSH0P19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{BianeD19,
  author    = {C{\'{e}}lia Biane and
               Franck Delaplace},
  title     = {Causal Reasoning on {B}oolean Control Networks Based on Abduction: Theory
               and Application to Cancer Drug Discovery},
  journal   = {{IEEE} {ACM} Transactions on Computational Biology and Bioinformatics},
  volume    = {16},
  number    = {5},
  pages     = {1574--1585},
  year      = {2019},
  url       = {https://doi.org/10.1109/TCBB.2018.2889102},
  doi       = {10.1109/TCBB.2018.2889102},
  timestamp = {Sun, 06 Sep 2020 16:55:36 +0200},
  biburl    = {https://dblp.org/rec/journals/tcbb/BianeD19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@Article{Zanudo2015,
  Title                    = {Cell fate reprogramming by control of intracellular network dynamics},
  Author                   = {Za{\~n}udo, Jorge G.T. and Albert, R{\'e}ka},
  Journal                  = {PLoS Computational Biology},
  Year                     = {2015},
  Number                   = {4},
  Pages                    = {e1004193},
  Volume                   = {11},

  Owner                    = {FD LAPTOP},
  Publisher                = {Public Library of Science},
  Timestamp                = {2017.01.24}
}

@Article{Vogel2008,
  author    = {Vogel, Gretchen},
  title     = {Reprogramming cells},
  journal   = {Science},
  year      = {2008},
  volume    = {322},
  number    = {5909},
  pages     = {1766--1767},
  publisher = {American Association for the Advancement of Science},
}

@article{AlhazovFDFGI2023,
title = {A {P} systems variant for reasoning about sequential controllability of Boolean networks},
journal = {Theoretical Computer Science},
volume = {970},
pages = {114056},
year = {2023},
issn = {0304-3975},
doi = {https://doi.org/10.1016/j.tcs.2023.114056},
url = {https://www.sciencedirect.com/science/article/pii/S0304397523003699},
author = {Artiom Alhazov and Vincent Ferrari-Dominguez and Rudolf Freund and Nicolas Glade and Sergiu Ivanov},
keywords = {Boolean P systems, Boolean networks, Reachability, Complexity},
}

@book{handMC,
  editor =	 {{\relax Gh}eorghe P\u{a}un and Grzegorz Rozenberg
                  and Arto Salomaa},
  title =	 {The Oxford Handbook of Membrane Computing},
  publisher =	 {Oxford University Press},
  year =	 {2010}
}

@book{DassowP89,
  author =	 {J{\"{u}}rgen Dassow and Gheorghe Paun},
  title =	 {Regulated Rewriting in Formal Language Theory},
  publisher =	 {Springer},
  year =	 {1989},
  url =		 {https://www.springer.com/de/book/9783642749346},
  isbn =	 {978-3-642-74934-6},
  timestamp =	 {Tue, 21 May 2019 16:47:56 +0200},
  biburl =	 {https://dblp.org/rec/books/sp/DassowP89.bib},
  bibsource =	 {dblp computer science bibliography,
                  https://dblp.org}
}

@article{BjornbergKGH2017,
  title =	 {Climate and environmental science denial: A review
                  of the scientific literature published in 1990–2015},
  journal =	 {Journal of Cleaner Production},
  volume =	 167,
  pages =	 {229--241},
  year =	 2017,
  issn =	 {0959-6526},
  doi =		 {https://doi.org/10.1016/j.jclepro.2017.08.066},
  url =
                  {https://www.sciencedirect.com/science/article/pii/S0959652617317821},
  author =	 {Karin Edvardsson Björnberg and Mikael Karlsson and
                  Michael Gilek and Sven Ove Hansson}
}

@article{ONeillB2010,
  author =	 {Saffron J. O’Neill and Max Boykoffb},
  title =	 {Climate denier, skeptic, or contrarian?},
  journal =	 {Proceedings of the National Academy of Sciences of
                  the United States of America},
  volume =	 {107(39):E151},
  doi =		 {doi:10.1073/pnas.1010507107},
  year =	 {2010}
}

@misc{wikiClimate,
  author =	 "{Wikipedia contributors}",
  title =	 "Climate change --- {Wikipedia}{,} The Free
                  Encyclopedia",
  year =	 "2024",
  howpublished =
                  "\url{https://en.wikipedia.org/w/index.php?title=Climate_change&oldid=1210314463}",
  note =	 "[Online; accessed 26-February-2024]"
}

@book{DryzekNS2011,
  author =	 {Dryzek, John S. and Norgaard, Richard B. and
                  Schlosberg, David},
  title =	 "{The Oxford Handbook of Climate Change and Society}",
  publisher =	 {Oxford University Press},
  year =	 {2011},
  month =	 {08},
  isbn =	 {9780199566600},
  doi =		 {10.1093/oxfordhb/9780199566600.001.0001},
  url =
                  {https://doi.org/10.1093/oxfordhb/9780199566600.001.0001},
}

@article{Zeeman1976,
  author =	 {Erik C. Zeeman},
  title =	 {Catastrophe theory},
  journal =	 {Scientific American},
  volume =	 {234(4)},
  pages =	 {65--83},
  year =	 {1976}
}

@misc{wikiDS,
  author =	 "{Wikipedia contributors}",
  title =	 "Dynamical system --- {Wikipedia}{,} The Free
                  Encyclopedia",
  year =	 "2024",
  howpublished =
                  "\url{https://en.wikipedia.org/w/index.php?title=Dynamical_system&oldid=1208607435}",
  note =	 "[Online; accessed 27-February-2024]"
}

@article{Thom1974,
  title =	 {Stabilité structurelle et morphogenèse},
  journal =	 {Poetics},
  volume =	 {3},
  number =	 {2},
  pages =	 {7-19},
  year =	 {1974},
  issn =	 {0304-422X},
  doi =		 {https://doi.org/10.1016/0304-422X(74)90010-2},
  url =
                  {https://www.sciencedirect.com/science/article/pii/0304422X74900102},
  author =	 {René Thom}
}

@book{Brown2018,
  title =	 {A Modern Introduction to Dynamical Systems},
  author =	 {Richard J. Brown},
  isbn =	 {978-0198743286},
  publisher =	 {Oxford University Press},
  year =	 {2018}
}

@phdthesis{Riva22,
  author       = {Sara Riva},
  title        = {Factorisation of discrete dynamical systems. (Factorisation de syst{\`{e}}mes
                  dynamiques discrets)},
  school       = {C{\^{o}}te d'Azur University, Nice, France},
  year         = {2022},
  url          = {https://tel.archives-ouvertes.fr/tel-03937258},
  timestamp    = {Wed, 25 Jan 2023 22:01:27 +0100},
  biburl       = {https://dblp.org/rec/phd/hal/Riva22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DotyKLOSW2023,
  author       = {David Doty and
                  Niels Kornerup and
                  Austin Luchsinger and
                  Leo Orshansky and
                  David Soloveichik and
                  Damien Woods},
  title        = {Harvesting Brownian Motion: Zero Energy Computational Sampling},
  journal      = {CoRR},
  volume       = {abs/2309.06957},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2309.06957},
  doi          = {10.48550/ARXIV.2309.06957},
  eprinttype    = {arXiv},
  eprint       = {2309.06957},
  timestamp    = {Mon, 05 Feb 2024 20:19:04 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2309-06957.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{Bennett1973,
  author =	 {Charles H. Bennett},
  title =	 {Logical reversibility of computation},
  journal =	 {IBM Journal of Research and Development},
  volume =	 {17(6)},
  pages =	 {525--532},
  year =	 {1973}
}

@misc{CarrollArrowFAQ2007,
  author =	 {Sean Carroll},
  title =	 {Arrow of Time {FAQ}},
  howpublished =
                  {\url{https://www.preposterousuniverse.com/blog/2007/12/03/arrow-of-time-faq/}},
  year =	 {2007}
}

@misc{wikiStochastic,
  author =	 "{Wikipedia contributors}",
  title =	 "Stochastic process --- {Wikipedia}{,} The Free
                  Encyclopedia",
  year =	 "2024",
  howpublished =
                  "\url{https://en.wikipedia.org/w/index.php?title=Stochastic_process&oldid=1194369849}",
  note =	 "[Online; accessed 9-April-2024]"
}