Dr Didier Gonze

Chargé de cours

Unité de Chronobiologie Théorique
Faculté des Sciences
Campus Plaine, C.P. 231
Université Libre de Bruxelles
1050 Brussels, Belgium

email: dgonzeulb.ac.be
Phone: (32) 02 6505730
Fax: (32) 02 6505767

Picture of D. Gonze



Education

  • Licence en Chimie, Université Libre de Bruxelles, 1997
  • PhD, Université Libre de Bruxelles, 2001


    Research Interests


    List of publications

    2016

  • Bessonnard S, Gonze D et Dupont G (2016) Spécification de l'Epiblaste et de l'Endoderme Primitif au cours du développement préimplantatoire murin : combinaison de la biologie et de la modélisation mathématique. Médecine/Sciences 32: 192-197.
  • Cvijovic M et al (2016) Strategies for structuring interdisciplinary education, in Systems Biology: A European perspective, npj Systems Biology and Applications 2: 16011.
  • De Mot L, Gonze D, Bessonnard S, Chazaud C, Goldbeter A and Dupont G (2016) Cell fate specification based on tristability in the inner cell mass of mouse blastocysts. Biophys. J. 110, pp. 710-722. [pdf file]
  • Loutchko D, Gonze D, Mikhailov A S (2016) Single-molecule stochastic analysis of channeling enzyme tryptophan synthase. J. Phys. Chem. 120: 2179-2186.

    2015

  • Faust K, Lahti L, Gonze D, de Vos W M, Raes J (2015) Metagenomics meets time series analysis: Unraveling microbial community dynamics. Curr. Op. Microbiol. 25: 56-66.

    2014

  • Bessonnard S, De Mot L, Gonze D, Barriol M, Dennis C, Goldbeter A, Dupont G and Chazaud C (2014) Gata6, Nanog, and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network. Development. 141: 3637-48. doi: 10.1242/dev.109678. Epub 2014 Sep 10
  • Gérard C, Gonze D, Lemaigre F, Novak B (2014) A model for the epigenetic switch linking inflammation to cell transformation: deterministic and stochastic approaches. PLoS Comput. Biol. 10: e1003455.
  • Schmal C, Leloup J-C, and Gonze D (2014) Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. Met. Mol. Biol. 1158, 337-58.
  • Woller A, Gonze D, Erneux T (2014) The Goodwin model revisited: Hopf bifurcation, limit-cycle, and periodic entrainment. Phys. Biol. 11: 045002.

    2013

  • Gonze D (2013) Modeling the effect of cell division on genetic oscillators. J. Theor. Biol. 325, 22-33.
  • Gonze D, Abou-Jaoudé W (2013) The Goodwin model: Behind the Hill function. PLoS One 8, e69573.
  • Woller A, Gonze D (2013) The bird circadian clock: Insights from a computational model. J. Biol. Rhythms 28, 390-402.
  • Woller A, Gonze D, Erneux T (2013) Strong feedback limit of the Goodwin circadian oscillators. Phys. Rev. E 87, 032722.

    2012

  • Gérard C, Gonze D, Goldbeter A (2012) Effect of positive feedback loops on the robustness of oscillations in the network of cyclin-dependent kinases driving the mammalian cell cycle. FEBS Journal 279: 3411-3431. doi: 10.111/j.1742-4658.2012.08585.x.
  • Hafner M, Koeppl H, Gonze D (2012) Effect of network architecture on synchronization and entrainment properties of the circadian oscillations in the suprachiasmatic nucleus. Plos Comput. Biol. 8, e1002419.
  • Goldbeter A, Gérard C, Gonze D, Leloup J-C, Dupont G (2012) Systems biology of cellular rhythms. FEBS Lett. (in press).

    2011

  • Altinok A, Gonze D, Lévi F, Goldbeter A (2011) An automaton model for the cell cycle. Royal Soc J Interface Focus 1, 36-47.
  • 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.
  • Gonze D, Abou-Jaoudé W, Ouattara A, Halloy J (2011) How molecular should your molecular model be?. Meth. Enzymol. 487, 171-215.

    2010

  • Gonze D (2010) Coupling oscillations and switches in genetic networks. Biosystems 99, 60-69. [Abstract] [Request a pdf file]

    2009

  • Gonze D, and Leloup J-C (2009) Towards a synthetic circadian clock in mammals. Cell Sci Rev 5, 45-55. [Abstract] [Request a pdf file]
  • Gérard C, Goldbeter A (2009) Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations. Phil Tran Royal Soc A 367, 4665-4683. [Abstract] [Request a pdf file]

    2008

  • 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. [Abstract] [pdf file]
  • Gonze D, Jacquet M, Goldbeter A (2008) Stochastic modeling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast. J R Soc Interface 5 Suppl 1, S95-109. [Abstract] [pdf file]

    2007

  • 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. [pdf file]
  • 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.
  • 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. [Abstract] [pdf file]

    2006

  • Gonze D and Goldbeter A (2006) Circadian rhythms and molecular noise. Chaos 16(2), 26110. [Abstract] [pdf file]
  • Leloup J-C, Gonze D, and Goldbeter A (2006) Computational models for circadian rhythms : Deterministic versus stochastic approaches. In : "Computational Systems Biology", A Kriete and R Eils eds, pp. 249-291 (Elsevier Academic Press, Burlington-San Diego, USA). [Abstract] [pdf file]
  • 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. [Abstract] [pdf file]

    2005

  • Gonze D, Bernard S, Waltermann C, Kramer A, Herzel H (2005) Spontaneous synchronization of coupled circadian oscillators. Biophys J, 89, 120-129. [Abstract] [pdf file]
  • 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.
  • Kielbasa SM, Gonze D, Herzel H (2005) Measuring similarities between transcription factor binding sites. BMC Bioinformatics 6(1), 237. [Abstract] [pdf file]

    2004

  • Gonze D, Halloy J, and Goldbeter A (2004) Stochastic models for circadian oscillations : Emergence of a biological rhythm. Int J Quantum Chem 98, 228-238. [Abstract] [pdf file]
  • Gonze D, Halloy J, and Goldbeter A (2004) Emergence of coherent oscillations in stochastic models for circadian rhythms. Physica A: Statistical Mechanics and its Applications 342, 221-233. [Abstract] [pdf file]

    2003

  • Gonze D, Halloy J, and Goldbeter A (2003) Deterministic and stochastic models for circadian rhythms. Pathol Biol (Paris) 51, 227-230. [Abstract] [pdf file]
  • Gonze D, Halloy J, Leloup J-C, and Goldbeter A (2003) Stochastic models for circadian rhythms: Effect of molecular noise on periodic and chaotic behaviour. C R Biologies 326, 189-203. [Abstract] [pdf file]

    2002

  • Gonze D, Halloy J, and Goldbeter A (2002) Robustness of circadian rhythms with respect to molecular noise. Proc Natl Acad Sci USA 99, 673-678. [Abstract] [pdf file] [Supporting Information]
  • Gonze D, Halloy J, and Goldbeter A (2002) Deterministic versus stochastic models for circadian rhythms. J Biol Phys 28, 637-653. [Abstract] [pdf file]
  • Gonze D, Halloy J, and Gaspard P (2002) Biochemical clocks and molecular noise: Theoretical study of robustness factors. J Chem Phys 116, 10997-11010. [Abstract] [pdf file]
  • Gonze D, Roussel M, and 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] [pdf file]

    2001

  • Goldbeter A, Gonze D, Houart G, Leloup J-C, Halloy J, and Dupont G (2001) From simple to complex oscillatory behavior in metabolic and genetic control network. Chaos 11, 247-260. [Abstract] [pdf file]
  • Gonze D and Goldbeter A (2001) A model for a network of phosphorylation-dephosphorylation cycles displaying the dynamics of dominoes and clocks. J Theor Biol 210, 167-86. [Abstract] [ pdf file & erratum]

    2000

  • Gonze D and Goldbeter A (2000) Entrainment versus chaos in a model for a circadian oscillator driven by light-dark cycles. J Stat Phys 101, 649-663.
  • Gonze D, Leloup J-C, and Goldbeter A (2000) Theoretical models for circadian rhythms in Neurospora and Drosophila. Comptes Rendus Hebd Acad Sci (Paris) Ser III 323, 57-67. [Abstract] [pdf file]
  • Roussel MR, Gonze D, and 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] [pdf file]

    1999

  • Leloup J-C, Gonze D, and Goldbeter A (1999) Limit cycle models for circadian rhythms based on transcriptional regulation in Neurospora and Drosophila. J Biol Rhythms 14, 433-448. [Abstract] [pdf file]
  • Romond P-C, Rustici M, Gonze D, and Goldbeter A (1999) Alternating oscillations and chaos in a model of two coupled biochemical oscillators driving successive phases of the cell cycle. Ann NY Acad Sci 879, 180-193. [Abstract] [pdf file]

    Interesting links

  • My personal homepage



    ULB - UTC: D. Gonze / Revised :