Didier Gonze

Laboratoire de Bioinformatique des Génomes et des Réseaux, CP 263
Université Libre de Bruxelles
Bvd du Triomphe
1050 Bruxelles
Belgium

Phone: +32 2 650 57 30
Fax: +32 2 650 57 67
E-mail: dgonzeulb.ac.be


Education
  • Licence en Sciences Chimiques (ULB, September 1997)
    Thesis: "Etude théorique du couplage entre deux oscillateurs mitotiques".
    Supervisor: A. Goldbeter.

  • DEA inter-universitaire en Bioinformatique (SCMBB, June 2001)
    Training stage: "Prédiction de la réponse transcriptionnelle au phosphate et à la méthionine à l'échelle génomique chez la levure".
    Supervisor: J. van Helden.

  • Doctorat en Sciences (ULB, November 2001)
    Thesis: "Modélisation des rythmes circadiens: mécanismes moléculaires et rôle d'adaptation à l'environnement".
    Supervisor: A. Goldbeter.

Professional experience
  • April 2002 - June 2002: Teacher of mathematics in secondary school (Collège Cardinal Mercier, Braine-l'Alleud, Belgium).

  • July 2002 - September 2003: Researcher in Bioinformatics, Service de Conformation des Macromolécules Biologiques et de Bioinformatique (SCMBB, Prof. S. Wodak, ULB).

  • October 2003 - December 2006: Chargé de Recherche au FNRS, Unité de Chronobiologie Théorique (UTC, Prof. A. Goldbeter, ULB).
    October 2003 - December 2004: Post-doctoral position at the Institute for Theoretical Biology (ITB, Prof. H. Herzel, Humboldt-Universität zu Berlin, Germany).

  • January 2007 - Present: Premier assistant, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe, Prof. J. van Helden, ULB).

Publications
  • Romond P-C, Rustici M, Gonze D, Goldbeter A (1999) Alternating oscillations and chaos in a model of two coupled biochemical oscillators driving successive phases of the cell cycle. Ann. N.Y. Acad. Sci. 30: 180-193. [Abstract]
  • Leloup J-C, Gonze D, Goldbeter A (1999) Limit cycle models based on transcriptional regulation for circadian rhythms in Drosophila and Neurospora. J. Biol. Rhythms. 14: 433-448. [Abstract]
  • Gonze D, Leloup J-C, Goldbeter A (2000) Theoretical models for circadian rhythms in Neurospora and Drosophila. C. R. Acad. Sci. (Paris) Sér. III. 323: 57-67. [Abstract]
  • Roussel MR, Gonze D, Goldbeter A (2000) Modeling the differential fitness of cyanobacterial strains whose circadian oscillators have different free-running periods: Comparing the mutual inhibition and substrate depletion hypotheses. J. Theor. Biol. 205: 321-340. [Abstract]
  • Gonze D, Goldbeter A (2000) Entrainment versus chaos in a model for a circadian oscillator driven by light-dark cycles. J. Stat. Phys. 101: 649-663. [Abstract]
  • Goldbeter A, Gonze D, Houart G, Leloup J-C, Halloy J, Dupont G (2001) From simple to complex oscillatory behavior in metabolic and genetic control networks. Chaos 11: 247-260. [Abstract]
  • Gonze D, Goldbeter A (2001) A model for a network of phosphorylation- dephosphorylation cycles displaying the dynamics of dominoes and clocks. J. Theor. Biol. 210: 167-186. [Abstract]
  • Gonze D, Roussel MR, Goldbeter A (2002) A model for the enhancement of fitness in cyanobacteria based on resonance of a circadian oscillator with the external light-dark cycle. J. Theor. Biol. 214: 577-597. [Abstract]
  • Gonze D, Halloy J, Goldbeter A (2002) Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 99: 673-678. [Abstract] [Suppl. Info.]
  • Gonze D, Halloy J, Gaspard P (2002) Biochemical clocks and molecular noise: Theoretical study of robustness factors. J. Chem. Phys. 116: 10997-11010. [Abstract]
  • Gonze D, Halloy J, Goldbeter A (2002) Deterministic versus stochastic models for circadian rhythms. J. Biol. Phys. 28: 637-653. [Abstract]
  • Gonze D, Halloy J, Leloup J-C, Goldbeter A (2003) Stochastic models for circadian rhythms: effect of molecular noise on periodic and chaotic behavior. C. R. Biologies 326: 189-203. [Abstract]
  • Gonze D, Halloy J, Goldbeter A (2004) Emergence of coherent oscillations in stochastic models for circadian rhythms. Physica A 342: 221-233. [Abstract]
  • Gonze D, Bernard S, Waltermann C, Kramer A, Herzel H (2005) Spontaneous synchronization of coupled circadian oscillators. Biophys. J. 89: 120-129. [PubMed]
  • Gonze D, Pinloche S, Gascuel O, van Helden J (2005) Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs, Bioinformatics 21: 3490-3500. [PubMed] [Suppl. Info.]
  • Kielbasa SM, Gonze D, Herzel H (2005) Measuring similarities between transcription factor binding sites. BMC Bioinformatics 6: 237-247. [PubMed] [Software]
  • Simonis N, Gonze D, Orsi C, van Helden J, Wodak S (2006) Modularity of the transcriptional regulation of protein complexes in yeast, J. Mol. Biol, 363: 589-610 [PubMed].
  • Gonze D, Goldbeter A (2006) Circadian rhythms and molecular noise, Chaos, 16: 026110 [PubMed].
  • Bernard S, Gonze D, Cajavec B, Herzel H, Kramer A (2007) Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus, PLOS Comput. Biol. 3: e68 [PubMed].
  • Forger D, Gonze D, Virshup D, Welsh DK (2007) Beyond intuitive modeling: Coupling biophysical models with careful observation moves the circadian rhythms field forward, J. Biol. Rhythms, 22: 200-210 [PubMed].
  • Goldbeter A, Gonze D, Pourquié O (2007) Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signaling, Dev. Dyn., 236: 1495-1508 [PubMed].
  • Gonze D, Jacquet M, Goldbeter A (2008) Stochastic modelling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast. J. R. Soc. Interface 5:S95-109 [PubMed].
  • Gonze D, Markadieu N, Goldbeter A (2008) Selection of in-phase or out-of-phase synchronization in a model based on global coupling of cells undergoing metabolic oscillations, Chaos 18:037127 [PubMed].
  • Gonze D, Leloup JC (2009) Towards a synthetic circadian clock in mammals, Cell. Sci. 5:45-55.
  • Gérard C, Gonze D, Goldbeter A (2009) Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations, Phil Trans R Soc A, 367:4665-4683 [PubMed].
  • Gonze D (2010) Coupling oscillations and switches in genetic networks, BioSystems 99:60-69. [PubMed].
  • Gonze D, Hafner M (2010) Positive feedbacks contribute to the robustness of the cell cycle with respect to molecular noise, "Advances in the Theory of Control, Signals, and Systems, LNCIS, pp. 283-295 [Editor].
  • Altinok A, Gonze D, Lévi F, Goldbeter A (2011) An automaton model for the cell cycle. Royal Soc J Interface Focus 1:36-47 [Editor].
  • Gonze D, Abou-Jaoudé W, Ouattara A, Halloy J (2011) How molecular should your molecular model be?, Meth. Enzymol. 487:171-215.
  • Gonze D (2011) Modeling circadian clocks: From equations to oscillations, Cent. Eur. J. Biol. 6:699-711.
  • Gonze D (2011) Modeling circadian clocks: Roles, advantages, and limitations, Cent. Eur. J. Biol. 6:712-729.

Book chapters
  • Leloup J-C, Gonze D, Goldbeter A (2005) Computational models for circadian rhythms: deterministic versus stochastic approaches, in Computational Systems Biology, Ed. A. Kriete and R. Eils, pp. 249-291. [Abstract]

Conferences, workshops and schools
  • Participation to the 30ème congrès du Groupe d'Etudes des Rythmes Biologiques (Lyon, France, May 1998). Poster: "Modélisation des rythmes circadiens de la protéine FRQ chez Neurospora et des protéines PER et TIM chez la drosophile".
  • Participation to the conference "Theory and mathematics in biology and medicine" (Amsterdam, The Netherlands, June 1999). Poster: "Theoretical models for circadian rhythms in Drosophila and Neurospora".
  • Participation to the conference "Cellular regulatory mechanisms of circadian clocks" (Tourtour, France, September 1999).
  • Participation to the 20ème séminaire de la Société Française de Biologie Théorique (St Flour, France, June 2000). Talk: "Modélisation du mécanisme moléculaire des rythmes circadiens".
  • Participation to the conference Keystone "Molecular Clocks: Regulation of Circadian Behavioral Rhythms" (Tahoe City, California, USA, March 2001). Poster: "A model for the enhancement of fitness in cyanobacteria based on resonance of a circadian oscillator with the external light-dark cycle".
  • Participation to the 12ème colloque de l'Association de Chronobiologie Médicale (Aussois, France, January 2002). Talk: "Modèles déterministe et stochastique pour les rythmes circadiens".
  • Participation to the workshop "Imaging, modelling and manipulating transcriptional regulatory networks" (Ambleteuse, France, October 2002). Poster: "Deterministic and stochastic models for circadian rhythms" [link].
  • Invitation to the meeting satellite de la "European Conference on Computational Biology" (Paris, France, octobre 2003). Talk: "Deterministic and stochastic models for circadian rhythms" [link].
  • Autumn School and mini-symposium on " Circadian Clocks " (Berlin, Germany, October 2003) [link].
  • Summer School on "Cell Biology and Mathematical Modelling" (Hvar, Croatia, June 2004) [link]. Talk: "Emergence of coherent oscillations in stochastic models for circadian rhythms".
  • Autumn School on " Learning and Memory " (Berlin, Germany, October 2004) [link].
  • Invitation to the workshop "Modélisation des réseaux génétiques: aspects stochastiques de la modélisation des réseaux de régulation" (INLN, Nice, France, January 2005). Talk: "Modélisation stochastique des rythmes circadiens" [link].
  • Participation to the FEBS course "Systems Biology: From Molecules and Modeling To Cells" (Gosau, Austria, March 2005). Poster: "Synchronizing a population of circadian oscillators" [link].
  • Participation to the BBC conference (Gent, Belgium, April 2005).
  • Participation to the workshop "Modélisation dynamique et analyse des réseaux de régulations" (CIRM, Marseille, France, May 2005).
  • Participation to the 6th "European Conference on Mathematical and Theoretical Biology" (Dresden, Germany, July 2005). Talk: "Synchronizing a population of circadian oscillators" [link].
  • Participation to the Interdisciplinary School "Noise and robustness in transcriptional regulatory networks" (Coquelles, France, September 2005). Talk: "Stochastic models for circadian rhythms" [link].
  • Invitation to the 4th workshop on "Computation of biochemical pathways and genetic networks" (Heidelberg, Germany, September 2005). Talk: "Stochastic models for circadian clocks" [link].
  • Participation to the workshop "Abstraction, modularité et compositionalité dans les réseaux géniques et protéiques'' (Institut Poincaré, Paris, France, January 2006).
  • Invitation to the workshop "Complex Systems: New trends and expectations" (Santander, Spain, June 2006). Talk: "Molecular noise and circadian rhythms: factors influencing the robustness of oscillations" [link].
  • Invitation to the workshop "Noise in Life" (Barcelona, Spain, June 2006). Talk: "Circadian rhythms and molecular noise" [link].
  • Invitation to the Conférence Francophone sur la Modélisation Mathématique en Biologie et en Médecine, (Craiova, Romania, July 2006). Talk: "Modélisation des rythmes circadiens: mécanisme moléculaire, couplage et synchronisation" [link].
  • Invitation to the SIAM/SMB conference on "Life Sciences", (Raleigh, North Carolina, USA, July 2006). Talk: "Modeling circadian rhythms: Deterministic and stochastic approaches" [link].
  • Participation to the meeting "Evolving Life Life Evolving" (Namur, Belgium, December, 2006).
  • Spring school "Dynamical Modelling of Biological Regulatory Networks" (Les Houches, France, April, 2007). Lecture: "Stochastic simulation of gene regulatory networks" [link] [summary & slides].
  • Participation to the workshop "Biological switches and clocks" (Santa Barbara, California, USA, July 2007). Talk: "Stochastic models for circadian rhythms" [link].
  • Participation to the BBC conference (Leuven, Belgium, November 2007) [link].
  • Participation to the ECMTB meeting (Edinburgh, UK, July 2008). Talk: "Modeling the nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast" [link].
  • Participation to the second workshop of the European Science Foundation (ESF) on "Functional Dynamics" (FuncDyn) (Rothenburg, Germany, September 2008). Talk: "Circadian rhythms and molecular noise" [link].
  • Invitation to the one-day workshop on "Synchronization in complex networks" (Leuven, Belgium, October 2008). Talk: "Synchronization in a model based on global coupling of cells undergoing metabolic oscillations".
  • Participation to the BBC conference (Maastricht, The Netherlands, December 2008) [link].
  • Invitation to the workshop "Advances in the Theory of Control, Signals, and Systems, with Physical Modeling - Chemical and Life Science" (Lausanne, Switzerland, 3-5 June 2009). Talk: "Modeling circadian rhythms: molecular mechanism, effect of noise, and inter-cellular synchronization" [link].
  • Invitation to the "Third International Conference on Complex Systems and Applications" (ICCSA 2009) (Le Havre, France, 29 June - 2 July 2009). Talk: "Stochastic modeling of the mammalian circadian oscillator" [link].
  • Invitation to the Workshop "Clocks, Switches, and Signals" (Warwick, UK, 14-18 June 2010). Talk: "Modeling the coupling between biological oscillators: application to circadian clocks and to metabolic oscillations" [link].
  • Associate member of the Scientific Commitee for the 9th European Conference on Computational Biology (ECCB, Ghent, Belgium, 26-29 September 2010) [link].
  • Invitation to the Workshop "Timing and Dynamics in Biological Systems" (Dresden, 27 September - 1 October 2010). Talk: "Modeling the mammalian circadian clock: From single cells to cell populations" [link].
  • Invitation to the Workshop "Circadian Clocks in Plants and Fungi" (Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, USA, 25-29 October 2010). Talk: "Modeling the mammalian circadian clock: From single cells to cell populations" [link].

Teaching
  • BMOL-F-413 - Bioinformatique et biomodélisation (Master en biologie moléculaire - MA1).
  • MATH-F-402 - Outils mathématiques pour la biologie (Master en bioinformatique et modélisation - MA1).
  • INFO-F-434 - Bases de données et analyse de séquences macromoléculaires (Master en bioinformatique et modélisation - MA1), with J. Richelle.
  • BIOL-F-525 - Dynamique des systèmes biologiques (Master en bioinformatique et modélisation - MA2), with M. Kaufman.

Didier Gonze - updated: 26/9/2011 - [Home] - [Abstracts] - [Research interests] - [Teaching] - [PDF]