@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\%27s_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} }