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start [2019/11/01 14:48] Nicolas Schabanel [My current researches include] |
start [2022/05/31 09:42] Nicolas Schabanel [Publications] |
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France\\ | France\\ | ||
Office: **322** //(Site Monnod - Main building - 3rd floor - South)//\\ | Office: **322** //(Site Monnod - Main building - 3rd floor - South)//\\ | ||
- | Phone: +33 4 72 72 80 00 / +33 4 26 23 39 67 / +33 4 72 72 87 42 | + | Phone: +33 4 72 72 80 00 / +33 4 26 73 14 55 |
Resident member of the\\ | Resident member of the\\ | ||
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==== Internship proposal ==== | ==== Internship proposal ==== | ||
- | **2020 M2 Internship proposal: [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2020_M2_Internship.pdf|DNA computing: Theory, Models and wet lab experiments]]** | + | :!: **__2022 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]** |
==== Students ==== | ==== Students ==== | ||
+ | * Amaury **Jacques** (M1, 2021) | ||
+ | * Octave **Hazard** (M2, 2021) | ||
+ | * Nicolas **Levy** (M2, 2020; PhD advisor 2020-) | ||
+ | * Pierre **Marcus** (M2, 2020; 4A, 2021) | ||
* Daria **Pchelina** (M1, 2019) [ [[http://perso.ens-lyon.fr/nicolas.schabanel/publications/2019/2019-M1-report-Pchelina.pdf|Report]] ] | * Daria **Pchelina** (M1, 2019) [ [[http://perso.ens-lyon.fr/nicolas.schabanel/publications/2019/2019-M1-report-Pchelina.pdf|Report]] ] | ||
- | * Nikola **Blanchard** (M2, 2015; PhD advisor 2016-2019) | + | * Enka (Nikola) **Blanchard** (M2, 2015; PhD co-advisor with Ted Selker 2016-2019) **:!: Prix de thèse PSL SHS //"Interface Sciences/Humanités"//** [ [[http://www.ens-lyon.fr/actualite/recherche/enka-blanchard-laureate-du-prix-de-these-psl-shs?ctx=contexte|web]] | [[https://www.youtube.com/watch?v=Rlps2gkKb-A&feature=youtu.be|Remise du prix]] ] |
* Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015) | * Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015) | ||
* Damien **Regnault** (PhD co-advisor with Éric Thierry, 2005-2008) | * Damien **Regnault** (PhD co-advisor with Éric Thierry, 2005-2008) | ||
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* **[[http://www.ens-lyon.fr/DI/en/informations-m2-2019-2020/|M2IF]] SCR1 [[lecturemolecularprogramming|Molecular programming: Theory & wet-lab experiments]]** [ [[lecturemolecularprogramming#past_lectures_summary|past lectures]] ] | * **[[http://www.ens-lyon.fr/DI/en/informations-m2-2019-2020/|M2IF]] SCR1 [[lecturemolecularprogramming|Molecular programming: Theory & wet-lab experiments]]** [ [[lecturemolecularprogramming#past_lectures_summary|past lectures]] ] | ||
* **[[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=start|MPRI]] 2.11.1 [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1|Approximation Algorithms & Molecular Algorithms]]** [ [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1#course_summary_2019-20molecular_programming_lectures_5-8|past lectures]] ] | * **[[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=start|MPRI]] 2.11.1 [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1|Approximation Algorithms & Molecular Algorithms]]** [ [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1#course_summary_2019-20molecular_programming_lectures_5-8|past lectures]] ] | ||
+ | * :!: **__2022 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]** | ||
+ | ==== Softwares ==== | ||
+ | * :!: **[[http://www.ens-lyon.fr/ensnano|ENSnano]]**: a 3D DNA nanostructure design software for Windows, Mac OS and linux\\ codeveloped with [[http://perso.ens-lyon.fr/nicolas.levy|Nicolas Levy]], 2021 [ [[http://www.ens-lyon.fr/ensnano|website]] | [[https://www.youtube.com/channel/UC-5XMNJouMPsB9pW5Q9UVcA|youtube channel]] ] | ||
+ | * :!: **[[http://perso.ens-lyon.fr/nicolas.schabanel/OSsimulator|OS simulator]]**: a fast and memory-efficient iPad app that simulates arbitrary Oritatami Systems //(works with limitations on Apple silicon M1 too)//, 2021 [ [[http://perso.ens-lyon.fr/nicolas.schabanel/OSsimulator|website]] | [[https://apps.apple.com/us/app/simple-os-simulator/id1530162352|download]] ] | ||
+ | * **[[https://apps.apple.com/us/app/caos-simulator/id1488203962|CAOS simulator]]**: an iOS app implementing our Oritatami cellular automata simulation, 2020 \\ [ [[https://hub.darcs.net/nikaoOoOoO/CAOSSimulator|source code]] ] | ||
+ | * **[[https://itunes.apple.com/us/app/id1335581323|Scary Pacman]]**: an iOS app implementing our Oritatami scaling algorihms, 2018\\ [ [[https://hub.darcs.net/nikaoOoOoO/OritatamiScaling|source code]] ] | ||
+ | * **[[https://apps.apple.com/app/clean-scan/id995830264|Clean scan]]**: an iOS app to take printable pictures of white, green and black board, 2015 | ||
==== Publications ==== | ==== Publications ==== | ||
+ | * **2022** | ||
+ | * **Rule-of-thumb-free geometry-driven design of arbitrary complex curved DNA origami with ENSnano (Abstract)**\\ Nicolas Levy, Allan Mills, Gaëtan Bellot*, Nicolas Schabanel*. //[[https://dna28.cs.unm.edu/|DNA28]]//, New Mexico, 2022. \\ | ||
+ | * **[[%%publiRoot%%/2022/2022-PchelinaSchabanelSekiTheyssier-STACS.pdf|Oritatami systems assemble shapes no less | ||
+ | complex than tile assembly model (aTAM)]]** \\ Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier. //[[https://stacs2022.sciencesconf.org/|STACS]]//, 26:1-23, 2022. \\ Supplementary material: [ [[https://hub.darcs.net/turedo2oritatami/turedo2oritatami/python|Turedo2oritatami compiler]] | [[%%publiRoot%%/2021/2021-PchelinaSchabanelSekiTheyssier.pdf|Full version]] ] | ||
+ | * **2021** | ||
+ | * **[[%%publiRoot%%/2021/2021-LevySchabanel.pdf|ENSnano: a 3D modeling software for DNA nanostructures]]** \\ Nicolas Levy, Nicolas Schabanel. //In [[http://dna27.iopconfs.org/home|DNA27]]//, LIPIcs, vol. 205, pp.5:1-23, doi:10.4230/LIPIcs.DNA.27.5, 2021.\\ **:!: best student paper & best presentation award.** \\ :!: Download ENSnano at: [ [[https://www.ens-lyon.fr/ensnano|ENSnano website]] ] [ [[https://www.youtube.com/channel/UC-5XMNJouMPsB9pW5Q9UVcA|Youtube channel]] ] | ||
+ | * **2020** | ||
+ | * **[[%%publiRoot%%/2020/2020-LATIN-PchelinaSchabanelSekiUbukata.pdf|Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model]]** [ [[https://hal.archives-ouvertes.fr/hal-02410874/document|Full version]] ] \\ Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata. In //[[http://latin2020.ime.usp.br/|LATIN]]//, LNCS 12118:425-436, Sao Paulo, 2020. doi:10.1007/978-3-030-61792-9_34 [[https://hal.archives-ouvertes.fr/hal-02410874v1|hal-02410874]]\\ //:!: Download the iOS app [[https://apps.apple.com/us/app/caos-simulator/id1488203962|CAOS simulator]] implementing our simulation [ [[https://hub.darcs.net/nikaoOoOoO/CAOSSimulator|source code]] ]// | ||
* **2019** | * **2019** | ||
* **[[https://www.mdpi.com/1422-0067/20/9/2259|Oritatami: A Computational Model for Molecular Co-Transcriptional Folding ]]** [ [[%%publiRoot%%/2019/2019-IJMS-GearyMeunierSchabanelSeki.pdf|PDF]] & [[%%publiRoot%%/2019/2019-IJMS-GearyMeunierSchabanelSeki-s1.pdf|supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[https://www.mdpi.com/journal/ijms|IJMS (Int. J. of Molecular Sciences)]], Special Issue Nucleic Acid Nanotechnology, 2019, 20(9), 2259.\\ [[https://doi.org/10.3390/ijms20092259]] | * **[[https://www.mdpi.com/1422-0067/20/9/2259|Oritatami: A Computational Model for Molecular Co-Transcriptional Folding ]]** [ [[%%publiRoot%%/2019/2019-IJMS-GearyMeunierSchabanelSeki.pdf|PDF]] & [[%%publiRoot%%/2019/2019-IJMS-GearyMeunierSchabanelSeki-s1.pdf|supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[https://www.mdpi.com/journal/ijms|IJMS (Int. J. of Molecular Sciences)]], Special Issue Nucleic Acid Nanotechnology, 2019, 20(9), 2259.\\ [[https://doi.org/10.3390/ijms20092259]] | ||
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* **2015** | * **2015** | ||
- | * **[[%%publiRoot%%/2015/2015-DNA21-GearyMeunierSchabanelSeki.pdf|Efficient universal computation by molecular co-transcriptional folding (Short announcement)]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //[[http://dna21.wyss.harvard.edu/|DNA21]]//, 1 page, 2015. (Full version in submission, see above) | + | * **[[%%publiRoot%%/2015/2015-DNA21-GearyMeunierSchabanelSeki.pdf|Efficient universal computation by molecular co-transcriptional folding (Short announcement)]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //[[http://dna21.wyss.harvard.edu/|DNA21]]//, 1 page, 2015. |
- | + | ||
- | * **2014** | + | |
* **[[%%publiRoot%%/2014/2014-ICALP-EisenstatMathieuSchabanel.pdf|Facility Location in Evolving Metrics]]**\\ with David Eisenstat and Claire Mathieu. //ICALP,// pages 459-470, 2014. | * **[[%%publiRoot%%/2014/2014-ICALP-EisenstatMathieuSchabanel.pdf|Facility Location in Evolving Metrics]]**\\ with David Eisenstat and Claire Mathieu. //ICALP,// pages 459-470, 2014. | ||