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Didier Gonze
Laboratoire de Bioinformatique des
G´enomes et des R´eseaux,CP 263
Universit´e Libre de Bruxelles
Bvd.du Triomphe
1050 Bruxelles
Belgium
Education
• Licence en Sciences Chimiques (Universit´e Libre de Bruxelles,September 1997)
Thesis:“Etude th´eorique du couplage entre deux oscillateurs mitotiques”.
Supervisor:Prof.A.Goldbeter.
• DEA en Bioinformatique (Universit´e Libre de Bruxelles,June 2001)
Training stage:“Pr´ediction de la r´eponse transcriptionnelle au phosphate et`a la
m´ethionine`a l’´echelle g´enomique chez la levure”.
Supervisor:Dr.J.van Helden.
• Doctorat en Sciences (Universit´e Libre de Bruxelles,November 2001)
Thesis:“Mod´elisation des rythmes circadiens:m´ecanismes mol´eculaires et rˆole
d’adaptation`a l’environnement”.
Supervisor:Prof.A.Goldbeter.
Professional experience
• April 2002 - June 2002:Teacher of mathematics in secondary school (Coll`ege Car-
dinal Mercier,Braine-l’Alleud,Belgium).
• July 2002 - September 2003:Researcher in Bioinformatics,Service de Conformation
des Macromol´ecules Biologiques et de Bioinformatique (Prof.S.Wodak,Universit´e
Libre de Bruxelles,Belgium).
• October 2003 - December 2006:Charg´e de Recherches du FNRS (Fonds National de
la Recherche Scientifique,Belgium),Unit´e de Chronobiologie Th´eorique (Prof.A.
Goldbeter,Universit´e Libre de Bruxelles,Belgium).
October 2003 - December 2004:Post-doctoral fellow at the Institute for Theoretical
Biology (Prof.H.Herzel,Humboldt-Universit¨at zu Berlin,Germany).
• January 2007 - Present:Premier Assistant ULB,Laboratoire de Bioinformatique
des G´enomes et des R´eseaux (Prof.J.van Helden,Universit´e Libre de Bruxelles,
Belgium).
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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.
• Leloup J-C,Gonze D,Goldbeter A (1999) Limit cycle models based on transcrip-
tional regulation for circadian rhythms in Drosophila and Neurospora.J.Biol.
Rhythms.14:433-448.
• Gonze D,Leloup J-C,Goldbeter A (2000) Theoretical models for circadian rhythms
in Neurospora and Drosophila.C.R.Acad.Sci.(Paris) S´er.III.323:57-67.
• Roussel MR,Gonze D,Goldbeter A (2000) Modeling the differential fitness of
cyanobacterial strains whose circadian oscillators have different free-running pe-
riods:Comparing the mutual inhibition and substrate depletion hypotheses.J.
Theor.Biol.205:321-340.
• 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.
• 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.
• Gonze D,Goldbeter A (2001) A model for a network of phosphorylation-dephospho-
rylation cycles displaying the dynamics of dominoes and clocks.J.Theor.Biol.210:
167-186.
• 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.
• Gonze D,Halloy J,Goldbeter A (2002) Robustness of circadian rhythms with re-
spect to molecular noise.Proc.Natl.Acad.Sci.USA 99:673-678.
• Gonze D,Halloy J,Gaspard P (2002) Biochemical clocks and molecular noise:The-
oretical study of robustness factors.J.Chem.Phys.116:10997-11010.
• Gonze D,Halloy J,Goldbeter A (2002) Deterministic versus stochastic models for
circadian rhythms.J.Biol.Phys.28:637-653.
• Gonze D,Halloy J,Goldbeter A (2003) Mod`eles deterministe et stochastique pour
les rythmes circadiens.Pathol Biol.51:227-230.[Article in French].
• 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.
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• Gonze D,Halloy J,Goldbeter A (2004) Stochastic models for circadian oscillations:
Emergence of a biological rhythm.Int.J.Quant.Chem.98:228-238.
• Gonze D,Halloy J,Goldbeter A(2004) Emergence of coherent oscillations in stochas-
tic models for circadian rhythms.Physica A 342:221-233.
• Gonze D,Bernard S,Waltermann C,Kramer A,Herzel H (2005) Spontaneous syn-
chronization of coupled circadian oscillators.Biophys.J.89:120-129.
• 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 6:237-247.
• 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.
• Gonze D,Goldbeter A(2006) Circadian rhythms and molecular noise,Chaos 16:026110.
• 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.
• Forger D,Gonze D,Virshup D,Welsh DK (2007) Beyond intuitive modeling:Cou-
pling biophysical models with careful observation moves the circadian rhythms field
forward,J.Biol.Rhythms.22:200-210.
• Goldbeter A,Gonze D,Pourqui´e O (2007) Sharp developmental thresholds defined
through bistability by antagonistic gradients of retinoic acid and FGF signaling,
Dev.Dyn.236:1495-1508.
• 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.
• 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.
• Gonze D,Leloup JC (2009) Towards a synthetic circadian clock in mammals,Cell.
Sci.5:45-55 [Invited Commentary].
• Gonze D (2009) Stochastic modeling of the mammalian circadian oscillator,Pro-
ceedings of the ICCSA 2009 Conference,pp.8-12.
• G´erard 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.
• Gonze D (2010) Coupling oscillations and switches in genetic networks,BioSystems
99:60-69.
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• 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.
• Altinok A,Gonze D,L´evi F,Goldbeter A (2011) An automaton model for the cell
cycle.Royal Soc.J.Interface Focus,1:36-47.
• Gonze D,Abou-Jaoud´e 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.
• Hafner M,Koeppl H,Gonze D (2012) Effect of network architecture on synchroniza-
tion and entrainment properties of the circadian oscillations in the suprachiasmatic
nucleus,PLOS Comput.Biol.,8:e1002419.
• G´erard 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 J,279:3411-31.
• Goldbeter A,G´erard C,Gonze D,Leloup JC,Dupont G (2012) Systems biology of
cellular rhythms,FEBS Lett.586:2955-65
Book chapter
• Leloup J-C,Gonze D,Goldbeter A (2006) Computational models for circadian
rhythms:deterministic versus stochastic approaches,in Computational Systems
Biology.,Ed.A.Kriete and R.Eils,pp.249-291,Elsevier,Burlington-San Diego,
USA.
Conferences,workshops,and schools
• Participation to the 30th congress of the Groupe d’Etudes des Rythmes Biologiques
(Lyon,France,May 1998).Poster:“Mod´elisation des rythmes circadiens de la
prot´eine FRQ chez Neurospora et des prot´eines PER et TIM chez la drosophile”.
• Participation to the conference “Theory and mathematics in biology and medicine”
(Amsterdam,Netherlands,June 1999).Poster:“Theoretical models for circadian
rhythms in Drosophila and Neurospora”.
• Participation to the Assembl´ee G´en´erale Annuelle de la Soci´et´e Royale de Chimie
(Li`ege,Belgium,October 1999).Poster:“Theoretical models for circadian rhythms
in Drosophila and Neurospora”.
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• Participation to the conference “Cellular regulatory mechanisms of circadian clocks”
(Tourtour,France,September 1999).
• Participation to the 20th seminar of the Soci´et´e Fran¸caise de Biologie Th´eorique
(St Flour,France,June 2000).Talk:“Mod´elisation du m´ecanisme mol´eculaire des
rythmes circadiens”.
• Participation to the conference Keystone “Molecular Clocks:Regulation of Cir-
cadian 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 12th colloquium of the Association de Chronobiologie M´edicale
(Aussois,France,January 2002).Talk:“Mod`eles d´eterministe 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”.
• Participation to the meeting CYGD(Comprehensive Yeast Genome Database) (Grignon,
France,December 2002).Report:“Annotation of S.cerevisiae metabolic pathway”.
• Invitation to the satellite meeting of the “European Conference on Computational
Biology” (ENS,Paris,France,October 2003).Talk:“Deterministic and stochastic
models for circadian rhythms”.
• Participation to the autumn school on “Circadian Clocks” (Berlin,Germany,Octo-
ber 2003).
• Participation to the summer school on “Cell Biology and Mathematical Modelling”
(Hvar,Croatia,June 2004).Talk:“Emergence of coherent oscillations in stochastic
models for circadian rhythms”.
• Participation to the workshop “Synchronization and high-dimensional chaos in cou-
pled systems” (Berlin,Germany,November 2004).
• Invitation to the workshop “Mod´elisation des r´eseaux g´en´etiques:aspects stochas-
tiques de la mod´elisation des r´eseaux de r´egulation” (INLN,Nice,France,January
2005).Talk:“Mod´elisation stochastique des rythmes circadiens”.
• Participation to the FEBS course “Systems Biology:From Molecules and Modeling
To Cells” (Gosau,Austria,March 2005).Poster:“Synchronizing a population of
circadian oscillators”.
• Participation to the Benelux Bioinformatics Conference (Gent,Belgium,April 2005).
• Participation to the workshop “Mod´elisation dynamique et analyse des r´eseaux de
r´egulations” (CIRM,Marseille,France,May 2005).
• Participation to the 6th ECMTB meeting (Dresden,Germany,July 2005).Talk:
“Synchronizing a population of circadian oscillators”.
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• Participation to the interdisciplinary school “Noise and robustness in transcriptional
regulatory networks” (Coquelles,France,September 2005).Talk:“Stochastic mod-
els for circadian rhythms”.
• Invitation to the 4th workshop on “Computation of biochemical pathways and ge-
netic networks” (Heidelberg,Germany,September 2005).Talk:“Stochastic models
for circadian clocks”.
• Participation to the workshop “Abstraction,modularit´e et compositionalit´e dans les
r´eseaux g´eniques et prot´eiques” (Institut Poincar´e,Paris,France,January 2006).
• Invitation to the workshop “Complex Systems:New trends and expectations” (San-
tander,Spain,June 2006).Talk:“Molecular noise and circadian rhythms:factors
influencing the robustness of oscillations”.
• Invitation to the workshop “Noise in Life” (Barcelona,Spain,June 2006).Talk:
“Circadian rhythms and molecular noise”.
• Invitation to the Conf´erence Francophone sur la Mod´elisation Math´ematique en
Biologie et en M´edecine,(Craiova,Romania,July 2006).Talk:“Mod´elisation des
rythmes circadiens:m´ecanisme mol´eculaire,couplage et synchronisation”.
• Invitation to the SIAM/SMB conference on “Life Sciences” (Raleigh,North Car-
olina,USA,August 2006).Talk:“Modeling circadian rhythms:Deterministic and
stochastic approaches”.
• Participation to the meeting “Evolving Life Life Evolving” (Namur,Belgium,De-
cember,2006).
• Invitation to the spring school “Dynamical Modelling of Biological Regulatory Net-
works” (Les Houches,France,April 2007).Lecture:“Stochastic simulation of gene
regulatory networks”.
• Participation to the workshop “Biological Switches and Clocks” (Santa Barbara,
California,USA,July 2007).Talk:“Stochastic models for circadian rhythms”.
• Participation to the Benelux Bioinformatics Conference (Leuven,Belgium,Novem-
ber 2007).
• Participation to the Workshop in honor of Prof.Ren´e Thomas “The logic of gene
regulatory networks” (Brussles,Belgium,May 2008).
• Participation to the 7th ECMTB meeting (Edinburgh,UK,July 2008).Talk:“Mod-
eling the nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast”.
• 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”.
• Invitation to the one-day workshop on “Synchronization in complex networks” (Leu-
ven,Belgium,October 2008).Talk:“Synchronization in a model based on global
coupling of cells undergoing metabolic oscillations”.
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• Participation to the Benelux Bioinformatics Conference (Maastricht,The Nether-
lands,December 2008).
• Invitation to the workshop “Advances in the Theory of Control,Signals,and Sys-
tems,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”.
• Invitation to the “Third International Conference on Complex Systems and Appli-
cations” (ICCSA 2009) (Le Havre,France,29 June - 2 July 2009).Talk:“Stochastic
modeling of the mammalian circadian oscillator”.
• 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”.
• Associate member of the Scientific Commitee for the 9th European Conference on
Computational Biology (ECCB,Ghent,Belgium,26-29 September 2010).
• Invitation to the Workshop “Timing and Dynamics in Biological Systems” (Dres-
den,Germany,27 September - 1 October 2010).Talk:“Modeling the mammalian
circadian clock:From single cells to cell populations”.
• Invitation to the Workshop “Circadian Clocks in Plants and Fungi” (Mathematical
Biosciences Institute,The Ohio State University,Columbus,Ohio,USA,25-29 Oc-
tober 2010).Talk:“Modeling the mammalian circadian clock:From single cells to
cell populations”.
• Participation to the 8th ECMTB meeting (Krakow,Poland,27 June - 2 July 2011).
Poster:“Synchronizing a population of circadian clocks”.
• Participation to the Benelux Bioinformatics Conference (Luxembourg,12-13 De-
cember 2011).
• Participation to the Solvay Workshop “Design principles and hardware of biological
circuits” (Brussels,15-17 February 2012).
• Participation to the European Conference on Complex Systems (ECCS’12,Brussels,
3-7 September 2012).Co-organization (with J.-C.Leloup and G.Dupont) of the
satellite meeting ”Complex Dynamics in Cellular Systems”.
Seminars
• Seminar given at the Institute for Theoretical Biology (Prof.H.Herzel,Humboldt-
Universit¨at zu Berlin,Germany,February 14,2003):“Deterministic versus stochas-
tic models for circadian rhythms”.
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• Seminar given at the Institute of Biology and Theoretical Biophysics (Prof.T.
H¨ofer,Humboldt-Universit¨at zu Berlin,Germany,July 1,2004):“Deterministic
and stochastic models for circadian rhythms”.
• Seminar given at the Service des Macromol´ecules biologiques et de Bioinformatique
(Prof.J.van Helden,Universit´e Libre de Bruxelles,March 25,2005):“Modeling
circadian clocks”.
• Seminar given at the Physics Institute (Prof.J.Timmer,Freiburg University,Ger-
many,May 3,2006):“Modeling circadian clocks:molecular mechanism,synchro-
nization and effect of noise”.
• Seminar given at the Biochemiezentrum (Prof.M.Brunner,Heidelberg University,
Germany,May 18,2006):“Modeling circadian clocks with differential equations”.
• Seminar given at the D´epartement de Biologie Mol´eculaire (Universit´e Libre de
Bruxelles,Belgium,June 7,2007):“Mod´elisation des rythmes circadiens”.
• Seminar given at the meeting ”Mod´elisation du rythme circannuel de reproduc-
tion des mammif`eres d’´elevage” (Prof.P.Chemineau,Paris,November 6,2007):
“Mod´elisation des rythmes circadiens et du rythme annuel de floraison chez Ara-
bidopsis”.
• Seminar given at the Institute for Theoretical Biology (Prof.H.Herzel,Humboldt-
Universit¨at zu Berlin,Germany,July 24,2009):“Stochastic modeling of circadian
clocks”.
• Seminar given at the Service de Biosyst`emes,Biomod´elisation et Bioproc´ed´es (Uni-
versit´e Libre de Bruxelles,Belgium,February 22,2011):“Motifs and noise in genetic
networks”.
• Seminar given (with A.Goldbeter and C.G´erard) for the C5Sys meeting (EU
project) at the Institut Henri Poincar´e (Paris,France,September 17,2011):“Posi-
tive feedback loops and robustness of the cell cycle”.
• Seminar given for the C5Sys meeting (EU project) at Rotterdam(Netherlands,May
14,2012):“Entrainment properties of the cell cycle automaton”.
Lectures
• Lecture given at the doctoral school “Innovations th´erapeutiques:du fondamental
`a l’appliqu´e” (Prof.F.L´evi,Paris-Villejuif,France,May 13,2007):“Mod´elisation
du m´ecanisme mol´eculaire de l’horloge circadienne”.
• Lecture given for the Master in Molecular Biology for a course entitled “System
Biology” (Prof.P.Hilson,Gent,Belgium,December 13,2009):“Modeling the
molecular mechanism of circadian rhythms”.
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• Lecture given at the doctoral school “Innovations th´erapeutiques:du fondamental
`a l’appliqu´e” (Prof.F.L´evi,Paris-Villejuif,France,May 17,2010):“Mod´elisation
de l’horloge circadienne mol´eculaire”.
• Lecture given at the doctoral school “Innovations th´erapeutiques:du fondamental
`a l’appliqu´e” (Prof.F.L´evi,Paris-Villejuif,France,May 26,2011):“Mod´elisation
des horloges circadiennes et application`a la chronopharmacologie”.
• Lecture given at the doctoral school “Innovations th´erapeutiques:du fondamental
`a l’appliqu´e” (Prof.F.L´evi,Paris-Villejuif,France,June 18,2012):“Mod´elisation
du cycle cellulaire et application`a la chronopharmacologie”.
Teaching
Courses taught since September 2007:
• BIOL-F-451 - Mod´elisation des Syst`emes Biologiques (Master en bioinformatique et
mod´elisation - MA1),with Prof.A.Goldbeter and Prof.J.-L.Deneubourg.
• BIOL-F-460 - Dynamique des Syst`emes Biologiques (Master en bioinformatique et
mod´elisation - MA2),with Prof.M.Kaufman.
• BMOL-F-413 - Bioinformatique et Biomod´elisation (Master en biochimie et biologie
mol´eculaire et cellulaire - MA1).
• INFO-F-434 - Bases de Donn´ees et Analyse de S´equences Macromol´eculaires (Master
en bioinformatique et mod´elisation - MA1),with Prof.J.Richelle.
• MATH-F-402 - Math´ematiques et Statistique pour la Bioinformatique (Master en
bioinformatique et mod´elisation - MA1),with Prof.J.van Helden.
Supervision of master theses
• Co-supervision (with Prof.Thomas Erneux) of the Master thesis of Aurore Woller
(Master in Physics,May 2011):“Modeling circadian clocks:Goodwin model revis-
ited”.
Member of PhD theses juries
• Member of the jury of the PhD thesis of Constant Vandermo¨ere (Universit´e de Lille,
Supervisor:Prof.M.Lefranc,defended in Lille,France,on December 15,2011).
• Member of the jury of the PhD thesis of Xio Yu Ni (University of Stavanger,Su-
pervisor:Prof.P.Ruoff,defended in Stavanger,Norway,on June 4,2012).
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