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start [2018/01/19 12:45]
Nicolas Schabanel
start [2018/09/23 10:51] (current)
Nicolas Schabanel [Publications]
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-==== Nicolas Schabanel === +==== 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]]**\\
-**Site Monnod - Main Building - 3rd floor South**\\ ​ 
 46 allée d'​Italie\\ 46 allée d'​Italie\\
 69364 Lyon Cedex 07\\ 69364 Lyon Cedex 07\\
 France\\ France\\
-Office: **332 (Site Monnod - Main building - 3rd floor - South)**\\ +Office: **332** //(Site Monnod - Main building - 3rd floor - South)//\\ 
-Phone: +33 4 72 72 80 00+Phone: +33 4 72 72 80 00 / +33 4 26 23 39 67 / +33 4 72 72 87 42
  
 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  ====
-  * **[[http://​www.irif.univ-paris-diderot.fr/​~nschaban/​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+
  
-=== Past Event  === +==== Past Event  ​==== 
-  * **Research school on [[https://​www.irif.fr/​~nschaban/​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 :!:+  * **[[%%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 
 +  * **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!)
   * **Algorithms:​** approximation,​ randomized, online, distributed,​...   * **Algorithms:​** approximation,​ randomized, online, distributed,​...
   * **Complex systems:** such as   * **Complex systems:** such as
-    * **Algorithmic self-assembly,​ Molecular folding** 
     * **Complex networks:** clustering and drawing of dynamical networks     * **Complex networks:** clustering and drawing of dynamical networks
     * **Stochastic cellular automata:** definition, analysis, intrinsic simulations,​ local probabilistic correlations,​...     * **Stochastic cellular automata:** definition, analysis, intrinsic simulations,​ local probabilistic correlations,​...
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     * **Random systems** ​     * **Random systems** ​
  
-My work is currently supported by the **ANR-2010-BLAN-0204 MAGNUM****ANR-12-BS02-005 RDAM** ​and **IXXI-MOLECAL** ​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 ===+==== Students ​====
   * Nicolas **Blanchard** (M2, 2015; PhD advisor 2016-)   * Nicolas **Blanchard** (M2, 2015; PhD advisor 2016-)
   * Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015)   * Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015)
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   * Sandeep **Dey** (Master thesis advisor, 2005)    * Sandeep **Dey** (Master thesis advisor, 2005) 
  
-=== Publications ===+==== Publications ===
 +  *  **2018**  
 +     * **[[%%publiRoot%%/​2018/​2018-ISAAC-OritatamiTuring-GearyMeunierSchabanelSeki.pdf|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]** [ [[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]], 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]],​ 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**
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   *  **2012**   *  **2012**
     * **[[%%publiRoot%%/​2012/​2012-JAC-ArrighiSchabanelTheyssier.pdf|Intrinsic simulations between stochastic cellular automata]]**\\ with Pablo Arrighi and Guillaume Theyssier. //AUTOMATA & JAC, EPTCS,// 90:​208–224,​ 2012.     * **[[%%publiRoot%%/​2012/​2012-JAC-ArrighiSchabanelTheyssier.pdf|Intrinsic simulations between stochastic cellular automata]]**\\ with Pablo Arrighi and Guillaume Theyssier. //AUTOMATA & JAC, EPTCS,// 90:​208–224,​ 2012.
-    * **[[%%publiRoot%%/​2012/​2012-PBMB-Schabanel.pdf|Randomness + Determinism = Progresses: Why random processes could be favored by evolution]]**\\ //Progress in Biophysics and Moleculer ​Biology// (Special edition on the conference ”Chance at the heart of the cell”), 110(1):​129–136,​ 2012.+    * **[[%%publiRoot%%/​2012/​2012-PBMB-Schabanel.pdf|Randomness + Determinism = Progresses: Why random processes could be favored by evolution]]**\\ //Progress in Biophysics and Molecular ​Biology// (Special edition on the conference ”Chance at the heart of the cell”), 110(1):​129–136,​ 2012.
  
   *  **2011**   *  **2011**
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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 ===+==== 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” ​