Add the bib/dealb.bib.
Copy it over from the draft paper on the Deal.
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Sergiu Ivanov
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@book{Glade22,
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author = {Nicolas Glade},
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title = {Le Vivant Rare, Faible et Amorphe - {\'{E}}volution depuis les
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Origines jusqu'{\`{a}} la Vie telle qu'elle nous Appara{\^{\i}}t.
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(Rare, Weak and Amorphous Life - Evolution of Life from the Origins
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until Life as it Appears Nowadays)},
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year = {2022},
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url = {https://tel.archives-ouvertes.fr/tel-04075075},
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timestamp = {Sun, 23 Apr 2023 00:55:01 +0200},
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biburl = {https://dblp.org/rec/books/hal/Glade22.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org},
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publisher = {Habilitation thesis (HDR)}
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}
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@book{Howe1858,
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author = {Henry Howe},
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title = {Memoirs of the most eminent {A}merican mechanics},
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year = {1858},
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publisher = {New York: Derby \& Jackson},
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note = {Page 450}
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}
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@book{Lilienthal1911,
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author = {Otto Lilienthal},
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title = {Birdflight as the Basis of Aviation},
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year = {1911},
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publisher = {Berlin},
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note = {Table of contents: \url{http://www.lilienthal-museum.de/olma/e6.htm}}
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}
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@article{RamamoorthyT22,
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author = {Raghu Ramamoorthy and
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Menakadevi Thangavelu},
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title = {An enhanced hybrid ant colony optimization routing protocol for vehicular
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ad-hoc networks},
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journal = {Journal of Ambient Intelligence and Humanized Computing},
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volume = {13},
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number = {8},
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pages = {3837--3868},
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year = {2022},
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url = {https://doi.org/10.1007/s12652-021-03176-y},
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doi = {10.1007/s12652-021-03176-y},
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timestamp = {Sun, 02 Oct 2022 15:39:55 +0200},
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biburl = {https://dblp.org/rec/journals/jaihc/RamamoorthyT22.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@article{Hopfield1982,
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author = {John J. Hopfield},
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title = {Neural networks and physical systems with emergent collective computational abilities},
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journal = {Proceedings of the National Academy of Sciences of the United States of America},
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volume = {79},
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pages = {2554--2558},
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year = {1982}
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}
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@article{Woese2004,
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author = {Carl R. Woese},
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title = {A new biology for a new century},
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journal = {Microbiology and molecular biology reviews},
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volume = {68(2)},
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pages = {173--186},
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year = {2004}
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}
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@article{Nicholson2019,
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title = {Is the cell really a machine?},
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journal = {Journal of Theoretical Biology},
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volume = {477},
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pages = {108--126},
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year = {2019},
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issn = {0022-5193},
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doi = {https://doi.org/10.1016/j.jtbi.2019.06.002},
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url = {https://www.sciencedirect.com/science/article/pii/S0022519319302292},
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author = {Daniel J. Nicholson}
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}
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@article{CornishBowdenCLSA2007,
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author = {Athel Cornish-Bowden and Mar\'{i}a Luz C\'{a}rdenas and Juan-Carlos Letelier and Jorge Soto-Andrade},
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title = {Beyond reductionism: metabolic circularity as a guiding vision for a real biology of systems},
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journal = {Proteomics},
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volume = {7(6)},
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pages = {839--845},
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year = {2007}
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}
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@inproceedings{RonaldSC99,
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author = {Edmund M. A. Ronald and
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Moshe Sipper and
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Mathieu S. Capcarr{\`{e}}re},
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editor = {Dario Floreano and
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Jean{-}Daniel Nicoud and
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Francesco Mondada},
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title = {Testing for Emergence in Artificial Life},
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booktitle = {Advances in Artificial Life, 5th European Conference, ECAL'99, Lausanne,
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Switzerland, September 13-17, 1999, Proceedings},
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series = {Lecture Notes in Computer Science},
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volume = {1674},
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pages = {13--20},
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publisher = {Springer},
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year = {1999},
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url = {https://doi.org/10.1007/3-540-48304-7\_5},
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doi = {10.1007/3-540-48304-7\_5},
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timestamp = {Wed, 07 Dec 2022 23:10:50 +0100},
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biburl = {https://dblp.org/rec/conf/ecal/RonaldSC99.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@misc{wikiLaplace,
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author = "{Wikipedia contributors}",
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title = "Laplace's demon --- {Wikipedia}{,} The Free Encyclopedia",
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year = "2023",
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howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Laplace\%27s_demon&oldid=1163265214}",
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note = "[Online; accessed 26-July-2023]"
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}
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@misc{Carroll,
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author = {Sean Carroll},
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title = {{S}ean {C}arroll's {M}indscape {P}odcast},
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year = {Retrieved on 2023-07-25},
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howpublished = {\url{https://www.preposterousuniverse.com/podcast/}}
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}
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@misc{wikiEntropy,
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author = "{Wikipedia contributors}",
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title = "Entropy (statistical thermodynamics) --- {Wikipedia}{,} The Free Encyclopedia",
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year = "2023",
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howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Entropy_(statistical_thermodynamics)&oldid=1143513230}",
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note = "[Online; accessed 26-July-2023]"
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}
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@misc{SusskindCourse,
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author = {Leonard Susskind},
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title = {Modern Physics: Statistical Mechanics},
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misc = {Standford Lecture Collection},
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howpublished = {\url{https://www.youtube.com/playlist?list=PLB72416C707D85AB0}}
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}
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@misc{wikiMotors,
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author = "{Wikipedia contributors}",
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title = "Molecular motor --- {Wikipedia}{,} The Free Encyclopedia",
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year = "2023",
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howpublished = "\url{https://en.wikipedia.org/w/index.php?title=Molecular_motor&oldid=1130929229}",
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note = "[Online; accessed 26-July-2023]"
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}
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@misc{lifeOfTheCell,
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author = {John Liebler},
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title = {The Inner Life of the Cell},
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note = {Guidance of Robert Lue and Alain Viel},
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year = {2006},
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howpublished = {\url{https://www.artofthecell.com/in-the-beginning-there-was-the-inner-life-of-the-cell/}}
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}
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@article{Mayer2009,
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author = {Bruce J. Mayer and Michael L. Blinov and Leslie M. Loew},
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title = {Molecular machines or pleiomorphic ensembles: signaling complexes revisited},
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journal = {Journal of biology},
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volume = {8(9)},
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page = {81},
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year = {2009}
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}
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@article{Kurakin2006,
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title = {Self-organization versus Watchmaker: Molecular motors and protein translocation},
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journal = {Biosystems},
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volume = {84},
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number = {1},
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pages = {15-23},
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year = {2006},
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issn = {0303-2647},
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doi = {https://doi.org/10.1016/j.biosystems.2005.09.007},
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url = {https://www.sciencedirect.com/science/article/pii/S030326470500153X},
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author = {Alexei Kurakin},
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keywords = {Self-organization, Stochasticity, Determinism, Molecular motors, Brownian ratchet, Protein translocation},
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}
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@misc{berkleyBio,
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author = {Berkley Bioengineering},
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title = {What is Bioengineering?},
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year = {Retrieved on 2023-07-29},
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howpublished = {\url{https://bioeng.berkeley.edu/about-us/what-is-bioengineering}}
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}
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@article{PardoID21,
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author = {J{\'{e}}r{\'{e}}mie Pardo and
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Sergiu Ivanov and
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Franck Delaplace},
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title = {Sequential reprogramming of biological network fate},
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journal = {Theor. Comput. Sci.},
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volume = {872},
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pages = {97--116},
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year = {2021},
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url = {https://doi.org/10.1016/j.tcs.2021.03.013},
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doi = {10.1016/j.tcs.2021.03.013},
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timestamp = {Tue, 01 Jun 2021 08:35:28 +0200},
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biburl = {https://dblp.org/rec/journals/tcs/PardoID21.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@inproceedings{MandonSH0P19,
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author = {Hugues Mandon and
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Cui Su and
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Stefan Haar and
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Jun Pang and
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Lo{\"{\i}}c Paulev{\'{e}}},
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editor = {Luca Bortolussi and
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Guido Sanguinetti},
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title = {Sequential Reprogramming of {B}oolean Networks Made Practical},
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booktitle = {Computational Methods in Systems Biology - 17th International Conference,
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{CMSB} 2019, Trieste, Italy, September 18-20, 2019, Proceedings},
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series = {Lecture Notes in Computer Science},
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volume = {11773},
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pages = {3--19},
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publisher = {Springer},
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year = {2019},
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url = {https://doi.org/10.1007/978-3-030-31304-3\_1},
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doi = {10.1007/978-3-030-31304-3\_1},
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timestamp = {Tue, 17 Sep 2019 12:55:34 +0200},
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biburl = {https://dblp.org/rec/conf/cmsb/MandonSH0P19.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@article{BianeD19,
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author = {C{\'{e}}lia Biane and
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Franck Delaplace},
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title = {Causal Reasoning on {B}oolean Control Networks Based on Abduction: Theory
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and Application to Cancer Drug Discovery},
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journal = {{IEEE} {ACM} Transactions on Computational Biology and Bioinformatics},
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volume = {16},
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number = {5},
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pages = {1574--1585},
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year = {2019},
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url = {https://doi.org/10.1109/TCBB.2018.2889102},
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doi = {10.1109/TCBB.2018.2889102},
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timestamp = {Sun, 06 Sep 2020 16:55:36 +0200},
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biburl = {https://dblp.org/rec/journals/tcbb/BianeD19.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@Article{Zanudo2015,
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Title = {Cell fate reprogramming by control of intracellular network dynamics},
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Author = {Za{\~n}udo, Jorge G.T. and Albert, R{\'e}ka},
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Journal = {PLoS Computational Biology},
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Year = {2015},
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Number = {4},
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Pages = {e1004193},
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Volume = {11},
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Owner = {FD LAPTOP},
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Publisher = {Public Library of Science},
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Timestamp = {2017.01.24}
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}
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@Article{Vogel2008,
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author = {Vogel, Gretchen},
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title = {Reprogramming cells},
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journal = {Science},
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year = {2008},
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volume = {322},
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number = {5909},
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pages = {1766--1767},
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publisher = {American Association for the Advancement of Science},
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}
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@article{AlhazovFDFGI2023,
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title = {A {P} systems variant for reasoning about sequential controllability of Boolean networks},
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journal = {Theoretical Computer Science},
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volume = {970},
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pages = {114056},
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year = {2023},
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issn = {0304-3975},
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doi = {https://doi.org/10.1016/j.tcs.2023.114056},
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url = {https://www.sciencedirect.com/science/article/pii/S0304397523003699},
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author = {Artiom Alhazov and Vincent Ferrari-Dominguez and Rudolf Freund and Nicolas Glade and Sergiu Ivanov},
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keywords = {Boolean P systems, Boolean networks, Reachability, Complexity},
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}
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@book{handMC,
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editor = {{\relax Gh}eorghe P\u{a}un and Grzegorz Rozenberg
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and Arto Salomaa},
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title = {The Oxford Handbook of Membrane Computing},
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publisher = {Oxford University Press},
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year = {2010}
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}
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@book{DassowP89,
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author = {J{\"{u}}rgen Dassow and Gheorghe Paun},
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title = {Regulated Rewriting in Formal Language Theory},
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publisher = {Springer},
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year = {1989},
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url = {https://www.springer.com/de/book/9783642749346},
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isbn = {978-3-642-74934-6},
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timestamp = {Tue, 21 May 2019 16:47:56 +0200},
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biburl = {https://dblp.org/rec/books/sp/DassowP89.bib},
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bibsource = {dblp computer science bibliography,
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https://dblp.org}
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}
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