diff --git a/bib/dealb.bib b/bib/dealb.bib new file mode 100644 index 0000000..cee5114 --- /dev/null +++ b/bib/dealb.bib @@ -0,0 +1,298 @@ +@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} +}