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start [2018/03/16 10:57] Nicolas Schabanel |
start [2021/06/18 17:09] Nicolas Schabanel [Publications] |
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{{ :ma_pomme.png?440x348 |Ma pomme}}\\ | {{ :ma_pomme.png?440x348 |Ma pomme}}\\ | ||
- | {{ :email-cnrs.png?250x70 |Courriel}} | + | {{::email-ens.png?300x88|}} |
<newcolumn> | <newcolumn> | ||
- | === Directeur de recherches CNRS === | + | ==== Directeur de recherches CNRS ==== |
**[[http://www.cnrs.fr/|CNRS]] - [[http://www.ens-lyon.fr/LIP|LIP]]**\\ | **[[http://www.cnrs.fr/|CNRS]] - [[http://www.ens-lyon.fr/LIP|LIP]]**\\ | ||
**[[http://www.ens-lyon.fr/|École Normale Supérieure de Lyon]]**\\ | **[[http://www.ens-lyon.fr/|École Normale Supérieure de Lyon]]**\\ | ||
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69364 Lyon Cedex 07\\ | 69364 Lyon Cedex 07\\ | ||
France\\ | France\\ | ||
- | Office: **332** //(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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- | [ [[#My current researches include|Research]] | [[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/|GT CoA]] | [[#Students|Students]] | [[#Publications|Publications]] | [[#Popularization|Popularization]] | [[#Teaching|Teaching]] | [[#Other|Other]] ] | + | [ [[#My current researches include|Research]] | [[http://www.irif.fr/gt-coa/|GT CoA]] | [[#Students|Students]] | [[#Publications|Publications]] | [[#Popularization|Popularization]] | [[#Teaching|Teaching]] | [[#Other|Other]] ] |
- | === Upcoming Event === | + | ==== Upcoming Event ==== |
- | === Past Event === | + | ==== Past Event ==== |
+ | * **[[https://remila60.sciencesconf.org/|Conférence en l'honneur d'Éric Rémila pour ses 60 ans]]**, ÉNS de Lyon, France, May 28, 2019\\ //(Co-organizer with Kevin Perrot) Founded by ANR, LIP and Codrin Nichitiu.// | ||
* **[[%%siteRoot%%/workshop/ComputingWithMolecularGeometry/|Workshop: Computing with molecular geometry]]**, Villa Finaly, Florence, Italie, Nov. 20-23, 2017\\ //(Co-organizer with Claire Lesieur and Damien Woods) Founded by [[http://www.ixxi.fr|IXXI]], [[https://tapdance.inria.fr/|Tapdance]] and la [[http://www.cnrs.fr/mi/|mission pour l'interdisciplinarité du CNRS]]// | * **[[%%siteRoot%%/workshop/ComputingWithMolecularGeometry/|Workshop: Computing with molecular geometry]]**, Villa Finaly, Florence, Italie, Nov. 20-23, 2017\\ //(Co-organizer with Claire Lesieur and Damien Woods) Founded by [[http://www.ixxi.fr|IXXI]], [[https://tapdance.inria.fr/|Tapdance]] and la [[http://www.cnrs.fr/mi/|mission pour l'interdisciplinarité du CNRS]]// | ||
* **[[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/Journees_2017|6èmes journées]] du [[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/|GT CoA]]** (Complexités et Algorithmes), LIP, Lyon, Nov. 27-28, 2017 | * **[[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/Journees_2017|6èmes journées]] du [[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/|GT CoA]]** (Complexités et Algorithmes), LIP, Lyon, Nov. 27-28, 2017 | ||
* **Research school on [[%%siteRoot%%/enseignement/2017-ER02/|Molecular Programming: Theory & Wet Lab Nano-Scale Computation]]** at **[[http://www.ens-lyon.fr/DI/?cat=77|ENS Lyon]]**, Jan 16-20, 2017. :!: Free to register and open to everyone :!: | * **Research school on [[%%siteRoot%%/enseignement/2017-ER02/|Molecular Programming: Theory & Wet Lab Nano-Scale Computation]]** at **[[http://www.ens-lyon.fr/DI/?cat=77|ENS Lyon]]**, Jan 16-20, 2017. :!: Free to register and open to everyone :!: | ||
- | === My current researches include === | + | ==== My current researches include ==== |
* **DNA Computing:** Algorithmic self-assembly, Molecular folding, Experiments (to come!) | * **DNA Computing:** Algorithmic self-assembly, Molecular folding, Experiments (to come!) | ||
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* **Random systems** | * **Random systems** | ||
- | My work is currently supported by the LIP Installation BQR and MOPREXPROGMOL CNRS MI grants. | + | My work is currently supported by the LIP Installation BQR (2017-18), MoPrExProgMol (2018) and AMARP (2018-20) by CNRS Mission pour l'interdisplinarité, and IXXI CalcASMol (2018-19) grants. |
- | === Students === | + | ==== Internship proposal ==== |
- | * Nicolas **Blanchard** (M2, 2015; PhD advisor 2016-) | + | |
+ | :!: **__2021 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]** | ||
+ | ==== 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]] ] | ||
+ | * 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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* Sandeep **Dey** (Master thesis advisor, 2005) | * Sandeep **Dey** (Master thesis advisor, 2005) | ||
- | === Publications === | + | ==== Teaching ==== |
+ | * **[[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]] ] | ||
+ | * :!: **__2021 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]] ] | ||
+ | * **[[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 ==== | ||
+ | * **2021** | ||
+ | * **[[%%publiRoot%%/2021/2021-LevySchabanel.pdf|ENSnano: a 3D modeling software for DNA nanostructures]]** \\ Nicolas Levy, Nicolas Schabanel. Accepted to //[[http://dna27.iopconfs.org/home|DNA27]]//, 2021. \\ :!: Download ENSnano at: [ [[https://www.ens-lyon.fr/ensnano|ENSnano website]] ] [ [[https://www.youtube.com/channel/UC-5XMNJouMPsB9pW5Q9UVcA|Youtube channel]] ] | ||
+ | * **[[%%publiRoot%%/2021/2021-PchelinaSchabanelSekiTheyssier.pdf|Oritatami simulates self-avoiding 2D Turing machines]]** \\ Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier. Submitted, 2021. [[%%publiRoot%%/2021/oritatami-turedo-rule.pdf|Supplementary material]] | ||
+ | * **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]]//, Sao Paulo, 2020. [[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** | ||
+ | * **[[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]] | ||
+ | * **2018** | ||
+ | * **[[%%publiRoot%%/2018/2018-ISAAC-OritatamiTuring-GearyMeunierSchabanelSeki.pdf|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]** {{anchor:oritatamituring2018:}} [ [[http://www.irif.fr/~nschaban/oritatami/|Supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[http://isaac2018.ie.nthu.edu.tw/|ISAAC 2018]], LIPIcs.ISAAC.2018.23:1-23:13, Jiaoxi, Yilan County, Taiwan, Dec. 2018. [ [[https://arxiv.org/abs/1508.00510|Arxiv]] ] | ||
+ | * **[[%%publiRoot%%/2018/2018-DNA24-OritatamiShapes-DemaineHendricksOlsenPatitzRogersSchabanelSekiThomas.pdf|Know When to Fold ’Em: Self-Assembly of Shapes by Folding in Oritatami]]**\\ Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thomas. [[http://dna24sdnu.com/|DNA24]], LNCS 11145:19-36, Jinan, China, Oct. 2018.\\ Invited talk at [[https://ucnc2018.lacl.fr/self-assembly/|UCNC2018 Self-assembly, geometry and computation workshop]], Fontainebleau, June 2018. \\ //:!: Download the iOS app [[https://itunes.apple.com/us/app/id1335581323|Scary Pacman]] implementing our algorithms [ [[https://hub.darcs.net/nikaoOoOoO/OritatamiScaling|source code]] ]// | ||
* **2017** | * **2017** | ||
- | * **[[%%publiRoot%%/2017/2017-Oritatami-GearyMeunierSchabanelSeki|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //Submitted//, 65 pages, july 2017. [ [[http://perso.ens-lyon.fr/nicolas.schabanel/oritatami/|Supplementary materials]] ] | ||
* **[[%%publiRoot%%/2017/2017-Walcom-BlanchardSchabanel.pdf|Dynamic Facility Location: Minimizing the Sum of Radii]]**\\ Nicolas K. Blanchard, Nicolas Schabanel. //[[http://walcom2017.nctu.edu.tw/index.html|WALCOM]]//, LNCS 10167:30-41, march 2017. | * **[[%%publiRoot%%/2017/2017-Walcom-BlanchardSchabanel.pdf|Dynamic Facility Location: Minimizing the Sum of Radii]]**\\ Nicolas K. Blanchard, Nicolas Schabanel. //[[http://walcom2017.nctu.edu.tw/index.html|WALCOM]]//, LNCS 10167:30-41, march 2017. | ||
* **2016** | * **2016** | ||
* **[[%%publiRoot%%/2016/2016-Automata-Schabanel.pdf|Oritatami systems: a computational model for co-transcriptional folding]]**\\ Nicolas Schabanel. **Invited plenary talk** at //[[http://automata2016.ini.uzh.ch/|Automata]]//, Jun. 2016. | * **[[%%publiRoot%%/2016/2016-Automata-Schabanel.pdf|Oritatami systems: a computational model for co-transcriptional folding]]**\\ Nicolas Schabanel. **Invited plenary talk** at //[[http://automata2016.ini.uzh.ch/|Automata]]//, Jun. 2016. | ||
* **[[%%publiRoot%%/2016/2016-MFCS-GearyMeunierSchabanelSeki.pdf|Programming biomolecules that fold greedily during transcription]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //[[http://mfcs.ki.agh.edu.pl|MFCS]]//, LIPIcs 58, 43:1-43:14, Aug. 2016. | * **[[%%publiRoot%%/2016/2016-MFCS-GearyMeunierSchabanelSeki.pdf|Programming biomolecules that fold greedily during transcription]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //[[http://mfcs.ki.agh.edu.pl|MFCS]]//, LIPIcs 58, 43:1-43:14, Aug. 2016. | ||
- | * **[[%%publiRoot%%/2016/2016-HALG-GearyMeunierSchabanelSeki.pdf|Folding Turing is hard but feasible]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki.//[[http://highlightsofalgorithms.org/program/|HALG]]//, Jun. 2016. | + | * **[[https://arxiv.org/abs/1508.00510|Folding Turing is hard but feasible]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki.//[[http://highlightsofalgorithms.org/program/|HALG]]//, Jun. 2016. |
* **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. [[#oritatamituring2018|Full version published at ISAAC 2018]] |
* **2014** | * **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. | ||
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* **2010** | * **2010** | ||
* **[[%%publiRoot%%/2010/2010-WAOA-PruhsRobertSchabanel.pdf|Minimizing Maximum Flowtime of Jobs with Arbitrary Parallelizability]]**\\ with Kirk Pruhs and Julien Robert. //WAOA,// LNCS 6534:237–248, 2010. | * **[[%%publiRoot%%/2010/2010-WAOA-PruhsRobertSchabanel.pdf|Minimizing Maximum Flowtime of Jobs with Arbitrary Parallelizability]]**\\ with Kirk Pruhs and Julien Robert. //WAOA,// LNCS 6534:237–248, 2010. | ||
- | * **[[%%publiRoot%%/2010/HdR-Schabanel.pdf|Systèmes complexes & algorithmes]]** (in French)\\ //Habilitation à diriger des recherches,// Université Paris Diderot, 2010. %%publiRoot%%/2010/HDR-Defense-Schabanel.pdf|Slides}} | + | * **[[%%publiRoot%%/2010/HdR-Schabanel.pdf|Systèmes complexes & algorithmes]]** (in French)\\ //Habilitation à diriger des recherches,// Université Paris Diderot, 2010. [[%%publiRoot%%/2010/HDR-Defense-Schabanel.pdf|Slides]] |
* **[[%%publiRoot%%/2010/2010-DMTCS-RegnaultSchabanelThierry.pdf|On the analysis of “simple” 2D stochastic cellular automata]]**\\ with Damien Regnault and Éric Thierry. //Invited publication to the special issue of DMTCS in honor of Philippe Flajolet,// 12(2):263–294, 2009. | * **[[%%publiRoot%%/2010/2010-DMTCS-RegnaultSchabanelThierry.pdf|On the analysis of “simple” 2D stochastic cellular automata]]**\\ with Damien Regnault and Éric Thierry. //Invited publication to the special issue of DMTCS in honor of Philippe Flajolet,// 12(2):263–294, 2009. | ||
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* **[[%%publiRoot%%/1996/ALST96.ps.gz|Basic linear algebra operations in SLI arithmetic]]**\\ with M. A. Anuta, D. W. Lozier, and Peter R. Turner. //Euro-Par,// LNCS 1124:193-202, Août 1996. | * **[[%%publiRoot%%/1996/ALST96.ps.gz|Basic linear algebra operations in SLI arithmetic]]**\\ with M. A. Anuta, D. W. Lozier, and Peter R. Turner. //Euro-Par,// LNCS 1124:193-202, Août 1996. | ||
- | === Popularization === | + | ==== Popularization ==== |
* 2016 | * 2016 | ||
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* **[[%%publiRoot%%/2003/2003.04-Minotaure-Schabanel.pdf|Thèse idiote: le hasard fabrique des certitudes]]** (in French)\\ //Le minotaure// (trimenstrial journal, 20 000ex), 1:66-69, april-june 2003. | * **[[%%publiRoot%%/2003/2003.04-Minotaure-Schabanel.pdf|Thèse idiote: le hasard fabrique des certitudes]]** (in French)\\ //Le minotaure// (trimenstrial journal, 20 000ex), 1:66-69, april-june 2003. | ||
- | === Teaching === | ||
- | |||
- | * **MPRI 2.11.1 [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1|Approximation Algorithms & Molecular Algorithms]]** | ||
- | |||
- | === Other === | ||
- | * **Algoseum:** “Bringing scientific interactive games and exhibitions to science museum” |