Current Position

Rockefeller University New York, NY, USA

Post doctoral fellow with Prof Eric Siggia

Current research interests :

• models of genetic networks : adaptive networks, circadian clocks,
• computational evolution : development of software and methods to study evolution in silico,
• modeling of genetic expressions during developmental processes : somitogenesis, gastrulation.

Academic Degrees

• École Normale Supérieure Paris, France
  • 2005 PhD, Theoretical Physics, “summa cum laude”, University Paris VII, supervisor Vincent Hakim
  • 2002 M.S. Degree, Theoretical Physics, “magna cum laude”, ranking 3rd of 25 students
• École Polytechnique Palaiseau, France
  • 2001 Engineer, Bachelor, Degree of Science : Major of Physics, ranking: 4th of 400 students
• Lycée Corneille Rouen, France
  • 1996-1998 Preparatory Classes (Mathematics, Physics, MP*)
  • 1996 French Baccalauréat, scientific series, “summa cum laude” (1st in Normandy region)

Teaching Positions Held

Université Paris VII Denis-Diderot, Paris, France.

• 2003-2005 Teaching assistant in a Physics Undergraduate Course (Optics, Fluid mechanics and Classical Mechanics)
• 2002-2003 Teaching assistant in a Mathematics Undergraduate Course (Mathematics for Biologists)

Inspection Académique, Seine St-Denis, Bobigny, France

• 1998-1999 Scientific advisor in the program “La Main à la pâte” aiming at teaching science in Elementary School with a “Hands-On” method.

Honors and Awards

• 2007 Lavoisier Post-doctoral Fellowship ( French Ministry of Foreign Affairs).
• 2007 “Le Monde” award for scientific research. “Le Monde” is the biggest and most famous French Newspaper. Every two years, “Le Monde” attributes 10 to 15 awards to young scientists having recently defended their phD. All French phD with “Summa cum Laude” can apply.
• 2005 Award for the Best Poster at the Société Française de Physique and Belgian Physical Society general congress
• 2002-2005 École Polytechnique doctoral AMX Fellowship
• 2002 Julia Award - promotion X98 : attributed to the best student of the Ecole Polytechnique who chooses graduate studies.
• 2001-2002 École Polytechnique Master's Fellowship
• 2001 École Polytechnique Best Senior Thesis Award in Physics (out of around 60 students from Ecole Polytechnique performing a traineeship in physics ).

Work and Other Research Experience

• 2002 Six weeks experimental Traineeship in CEA Saclay studying dynamics of granular materials, team of Olivier Dauchot, Saclay, France
• 2001 Three months research Traineeship in CEA Saclay (SPHT) studying asymmetric exclusion process, supervisor Kirone Mallick, Saclay, France
• 2001 Freelance Journalist for “Science et Vie”, working on an article about “global warming”, Paris, France
• 2000 One month Traineeship as a blue-collar worker in a Japanese Factory, Harima, Japan

Aptitude and Skills

• PhD in Theoretical Physics applied to Biology : computational evolution, models and analytical studies of biological non-linear systems such as circadian clocks
• Master in Theoretical Physics : quantum mechanics, statistical physics, quantum and statistical field theory, special and general relativity.
• Undergraduate research in Out of Equilibrium Statistical Physics : Exclusion Process and related systems.
• Very good knowledge of many computational languages and operating systems : C/C++, Perl, MATLAB, Python, Unix/Linux, Mac OS X, Windows. First implementation of evolutionary codes written in C++, current version developed in C and Python.
• Languages: Native French; Fluent English; Basic German ; Basic Japanese (Yon-kyû).

Scientific Publications

• “A case study of evolutionary computation of biochemical adaptation”, François P, Siggia E, submitted, (2008)
  
• “Deriving structure from evolution : metazoan segmentation”, François P, Hakim V, Siggia E, Mol. Syst. Biol., 3:154 (2007)
  
• “ Core genetic module: the Mixed Feedback Loop ”, François P, Hakim V, Phys. Rev. E., 72: 031908 (2005)
• “ A model for the Neurospora circadian clock ”, François P, Biophys. J., 88 (4): 2369-2383 (2005)
• “ Design of genetic networks with specified functions by evolution in silico ”, François P, Hakim V, Proc. Natl. Acad. Sci. U S A, 101(2):580-5 (2004)
• “A matrix ansatz for the diffusion of an impurity in the asymmetric exclusion process”, Boutillier C, François P, Mallick K, Mallick S, J. Phys. A, Math. Gen, 35 (46): 9703-9730 (2002)

Popular science Publications

• “ Genetic networks: design in silico and applications”, François P, Physicalia Magazine (journal of the Belgian Physical Society) (2005)
• “Ces gaz qui soufflent le chaud”, François P, Science et vie hors série Énergie (2001)

Conferences and Invited Oral presentations

• 2008 :"Deriving structure from computational evolution"
  April : Seminar at Université de Montreal (Montreal,Canada)
  April : Seminar at McGill University (Montreal,Canada)
  February : Seminar at Rutgers University (New Brunswick, USA)
  February : Seminar at Toronto University (Toronto, Canada)
  
• 2007: "Deriving structure from computational evolution"
  November : Biophysical Seminar at Princeton University (Princeton, USA)
  September : Seminar at Physics Department in McGill university (Montreal, Canada)
  August : Seminar at Stowers Institute (Kansas City,USA)
  April : Seminar at Laboratoire de Physique Théorique de l'Ecole Normale Supérieure (Paris, France)
  February : Seminar at Center for Nonlinear Dynamics in Physiology and Medecine (McGill University, Montreal, Canada)
  
• 2006 : "Design of genetic networks and applications"
  November : Seminar at Service de Physique Théorique (Saclay, France)
  
• 2005 : "Design of genetic networks in silico and applications to circadian clocks"
  September : Seminar in the Institute for Scientific Interchange Foundation (Torino, Italy)
  March : Short Presentation, Rencontres du non linéaire (Paris, France)
  January : Short Presentation Journées de physique statistique (Paris, France)
  
• 2004: "Design of genetic networks in silico "
  

  November : Seminar in Dartmouth Medical School (Dunlap's lab) (Hanover, USA)
  November : Seminar in Rockefeller University (Siggia's lab) (New York, USA)
  November : Seminar in New York University (Rajewski's lab) (New York, USA)
  November : Seminar in Princeton Molecular Cell biology lab (Wingreen's lab) (Princeton, USA)
  October : ENS Biophysical seminar (Paris, France)
  September : Seminar at IBL (Lille, France) "Models of circadian clocks"
  September : Presentation at Journées du LPS (Paris, France)
  August : Presentation at the summer school “Advanced Modelling of Biological Function, Expression, Networks and Structure” (International University of Bremen, Germany)
  March: Presentation at the spring school “Modélisation de processus biologiques dans le contexte de la génomique” (Evry, France)
  March : Long Presentation, Rencontres du non linéaire (Paris, France)
  January : Short Presentation Journées de physique statistique (Paris, France)
  

• 2003: "Design of genetic networks in silico "
  November : Seminar Institut Cochin (Paris, France)
  

Schools ans Workshops

• 2008 :
  Sackler colloquium : Gene Networks in Animal Development and Evolution (Santa Ana,USA)
  
• 2007 :
  Deconstructing Biochemical Network (Montreal, Canada)
  Computational Cell Biology meeting (Cold Spring Harbour, USA), 1 poster : "Deriving structure from evolution : segmentation in silico"
  Workshop on the Evolution of Molecular Networks (KITP, Santa Barbara, USA)
• 2006 :
  First and Founding meeting of the European society for Evolutionary Developmental biology (Prag, Czech Republic), 1 poster : "Evolution in silico of segmentation gene networks"
  
• 2005:
  Thematic Institute “Complex Biological Networks: Gene Regulation and Protein Interaction” (ISI, Torino, Italy)
  Société Française de Physique and Belgian Physical Society Meeting (Lille, France), 1 poster, "Design of genetic networks in silico and applications", 1 award
  
• 2004:
  Summer school “Advanced Modelling of Biological Function, Expression, Networks and Structure” (International University of Bremen, Germany), 2 posters "Design of genetic networks in silico" and "Models of circadian clocks"
  Workshop: “ Oscillations ans Waves in Cells and Cell Networks” (Cargèse, France), 1 poster "Models of circadian clocks"
  2004 Spring school: “Modélisation de processus biologiques dans le contexte de la génomique” (Evry, France), 1 poster, "Design of genetic networks in silico"
  
• 2003:
  Summer school: Experimental Biology for Theoreticians (Harvard University, Boston, USA)
  Spring school “Modélisation et simulation de processus biologiques dans le contexte de la génomique” (Dieppe, France), 1 poster, "Circadian clocks"
  
• 2002 :
  Imaging, modelling and manipulating transcriptional regulatory networks (Ambleteuse, France)
  2002 Dynamics of Biological Systems, From Molecules to Networks (Krogerup, Denmark)
  2002 Workshop on Regulatory proteins interplay and traffic on DNA (Evry, France)
  2002 Symposium on Macromolecular Networks (Paris, France)
  

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