D. Gonze

发表

Robustness of circadian rhythms with respect to molecular noise

A. Goldbeter, D. Gonze, J. Halloy, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Limit Cycle Models for Circadian Rhythms Based on Transcriptional Regulation in Drosophila and Neurospora

A. Goldbeter, J. Leloup, D. Gonze, 1999, Journal of biological rhythms.

Spontaneous synchronization of coupled circadian oscillators.

S. Bernard, H. Herzel, D. Gonze, 2005, Biophysical journal.

Biochemical Clocks and Molecular Noise: Theoretical Study of Robustness Factors

P. Gaspard, D. Gonze, J. Halloy, 2002 .

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

Daniela Besozzi, Marija Cvijovic, Anders Blomberg, 2016, npj Systems Biology and Applications.

From simple to complex oscillatory behavior in metabolic and genetic control networks.

A. Goldbeter, J. Leloup, D. Gonze, 2001, Chaos.

Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations

Albert Goldbeter, Didier Gonze, Claude Gérard, 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Circadian Clock Field Forward Beyond Intuitive Modeling : Combining Biophysical Models with Innovative Experiments to Move the

Daniel B. Forger, D. Welsh, D. Forger, 2007 .

Circadian rhythms and molecular noise.

Albert Goldbeter, Didier Gonze, A. Goldbeter, 2006, Chaos.

Stochastic models for circadian oscillations: Emergence of a biological rhythm

José Halloy, Albert Goldbeter, Didier Gonze, 2004 .

Emergence of coherent oscillations in stochastic models for circadian rhythms

José Halloy, Albert Goldbeter, Didier Gonze, 2004 .

Stochastic models for circadian rhythms: effect of molecular noise on periodic and chaotic behaviour.

José Halloy, Albert Goldbeter, Didier Gonze, 2003, Comptes rendus biologies.

[Deterministic and stochastic models for circadian rhythms].

D Gonze, A Goldbeter, A. Goldbeter, 2003, Pathologie-biologie.

A model for the enhancement of fitness in cyanobacteria based on resonance of a circadian oscillator with the external light-dark cycle.

Albert Goldbeter, Didier Gonze, Marc R Roussel, 2002, Journal of theoretical biology.

Theoretical models for circadian rhythms in Neurospora and Drosophila.

D Gonze, A Goldbeter, A. Goldbeter, 2000, Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie.

Modeling the differential fitness of cyanobacterial strains whose circadian oscillators have different free-running periods: comparing the mutual inhibition and substrate depletion hypotheses.

D Gonze, A Goldbeter, A. Goldbeter, 2000, Journal of theoretical biology.

Entrainment Versus Chaos in a Model for a Circadian Oscillator Driven by Light-Dark Cycles

Albert Goldbeter, Didier Gonze, A. Goldbeter, 2000 .

Modularity of the transcriptional response of protein complexes in yeast.

Didier Gonze, Shoshana J Wodak, Chris Orsi, 2006, Journal of molecular biology.

Systems biology of cellular rhythms

A. Goldbeter, J. Leloup, D. Gonze, 2012, FEBS letters.

Modeling clock-related metabolic syndrome due to conflicting light and food cues

D. Gonze, Aurore Woller, 2018, Scientific Reports.

Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

A. Goldbeter, D. Gonze, C. Chazaud, 2014, Development.

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

J. Raes, G. Falony, J. Danckaert, 2018, eLife.

A Compact Model for the Complex Plant Circadian Clock

Didier Gonze, Christian Hermans, Nathalie Verbruggen, 2016, Front. Plant Sci..

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a synthetic gut community

J. Raes, G. Falony, J. Danckaert, 2018, bioRxiv.

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations

J. Danckaert, D. Gonze, Karoline Faust, 2018, PloS one.

Effect of positive feedback loops on the robustness of oscillations in the network of cyclin‐dependent kinases driving the mammalian cell cycle

Albert Goldbeter, Didier Gonze, Claude Gérard, 2012, The FEBS journal.

Positive Feedbacks Contribute to the Robustness of the Cell Cycle with Respect to Molecular Noise

Marc Hafner, Didier Gonze, D. Gonze, 2010 .

Metagenomics meets time series analysis: unraveling microbial community dynamics.

Karoline Faust, Didier Gonze, Leo Lahti, 2015, Current opinion in microbiology.

Revisiting a skeleton model for the mammalian cell cycle: From bistability to Cdk oscillations and cellular heterogeneity.

A. Goldbeter, D. Gonze, C. Gérard, 2019, Journal of theoretical biology.

Alternating Oscillations and Chaos in a Model of Two Coupled Biochemical Oscillators Driving Successive Phases of the Cell Cycle

A. Goldbeter, D. Gonze, M. Rustici, 1999, Annals of the New York Academy of Sciences.

Computational models for the dynamics of early mouse embryogenesis.

D. Gonze, C. Chazaud, G. Dupont, 2019, The International journal of developmental biology.

Signalling-modulated gene regulatory networks in early mammalian development.

D. Gonze, G. Dupont, Joëlle De Caluwé, 2019, Journal of theoretical biology.

Cell Fate Specification Based on Tristability in the Inner Cell Mass of Mouse Blastocysts.

A. Goldbeter, D. Gonze, C. Chazaud, 2016, Biophysical journal.

Strong feedback limit of the Goodwin circadian oscillator

D. Gonze, T. Erneux, Aurore Woller, 2013 .

Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO.

J. Leloup, D. Gonze, Christoph Schmal, 2014, Methods in molecular biology.

Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

B. Teusink, D. Gonze, L. De Vuyst, 2019, Front. Microbiol..

Time-keeping and decision-making in living cells: Part II

J. Tyson, A. Csikász-Nagy, J. Wolf, 2022, Interface Focus.

Multi-stability and the origin of microbial community types

Karoline Faust, Didier Gonze, Leo Lahti, 2017, The ISME Journal.

Modeling the Dynamics of Let-7-Coupled Gene Regulatory Networks Linking Cell Proliferation to Malignant Transformation

D. Gonze, C. Gérard, F. Lemaigre, 2019, Frontiers in physiology.

Modeling the dynamics of Let-7-coupled gene regulatory networks linking cell proliferation to malignant transformation

D. Gonze, C. Gérard, F. Lemaigre, 2019, bioRxiv.

Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo

D. Gonze, G. Dupont, Y. De Decker, 2022, Interface Focus.

Beyond Intuitive Modeling: Combining Biophysical Models with Innovative Experiments to Move the Circadian Clock Field Forward

Daniel B. Forger, D. Welsh, D. Forger, 2007, Journal of biological rhythms.

Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848T and Acetobacter senegalensis 108B cocoa strains

D. Gonze, L. De Vuyst, S. Weckx, 2022, Frontiers in Microbiology.

The Goodwin Oscillator and its Legacy

P. Ruoff, D. Gonze, 2020, Acta Biotheoretica.

Magnesium maintains the length of the circadian period in Arabidopsis.

J. Leloup, D. Gonze, C. Hermans, 2021, Plant physiology.

Magnesium maintains length of circadian period in Arabidopsis thaliana

J. Leloup, D. Gonze, Joëlle De Caluwé, 2020, bioRxiv.

Modeling circadian clocks: Roles, advantages, and limitations

Didier Gonze, D. Gonze, 2011, Central European Journal of Biology.

Modeling circadian clocks: From equations to oscillations

Didier Gonze, D. Gonze, 2011, Central European Journal of Biology.

The Bird Circadian Clock: Insights from a Computational Model

D. Gonze, Aurore Woller, 2013, Journal of biological rhythms.

Chemical and enzyme kinetics

D. Gonze, M. Kaufman, 2010 .

Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signaling

Albert Goldbeter, Didier Gonze, Olivier Pourquié, 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

DEV109678 3637..3648

A. Goldbeter, D. Gonze, C. Chazaud, 2014 .

STEM CELLS AND REGENERATION Gata 6 , Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

Albert Goldbeter, Didier Gonze, A. Goldbeter, 2014 .

Starvation response strategies impact the interaction dynamics of human gut bacteria: a study of Bacteroides thetaiotaomicron and Roseburia intestinalis

D. Gonze, Karoline Faust, K. Bernaerts, 2023, bioRxiv.

Metabolic models of human gut microbiota: Advances and challenges.

D. Gonze, Karoline Faust, Bin Liu, 2023, Cell systems.

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Olivier Gascuel, Jacques van Helden, Didier Gonze, 2005, Bioinform..

Stochastic modelling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast

Albert Goldbeter, Didier Gonze, M. Jacquet, 2008, Journal of The Royal Society Interface.

An automaton model for the cell cycle

Albert Goldbeter, Didier Gonze, Francis Lévi, 2011, Interface Focus.

A Computational Model for the Cold Response Pathway in Plants

A. Goldbeter, D. Gonze, X. Hou, 2020, Frontiers in Physiology.

Szymon M. Kielbasa, Hanspeter Herzel, Didier Gonze, 2005, BMC Bioinformatics.

Microbial communities as dynamical systems.

Karoline Faust, Didier Gonze, Leo Lahti, 2018, Current opinion in microbiology.

Signatures of ecological processes in microbial community time series

Stefanie Widder, Karoline Faust, Didier Gonze, 2018, Microbiome.

The Goodwin Oscillator and its Legacy

Peter Ruoff, Didier Gonze, P. Ruoff, 2020, Acta Biotheoretica.

Coupling oscillations and switches in genetic networks

Didier Gonze, D. Gonze, 2010, Biosyst..

Single-Molecule Stochastic Analysis of Channeling Enzyme Tryptophan Synthase.

A. Mikhailov, D. Gonze, Dimitri Loutchko, 2016, The journal of physical chemistry. B.

Genome-scale metabolic modeling of Acetobacter pasteurianus 386B reveals its metabolic adaptation to cocoa fermentation conditions.

D. Gonze, L. De Vuyst, S. Weckx, 2020, Food microbiology.

A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches

Didier Gonze, Claude Gérard, Béla Novák, 2014, PLoS Comput. Biol..

Modeling the effect of cell division on genetic oscillators.

D. Gonze, 2013, Journal of theoretical biology.

How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

José Halloy, Didier Gonze, Djomangan Adama Ouattara, 2011, Methods in enzymology.

A multiscale model of early cell lineage specification including cell division

D. Gonze, C. Chazaud, G. Dupont, 2017, npj Systems Biology and Applications.

Stochastic simulations Application to molecular networks

Didier Gonze, D. Gonze, 2007 .

Mutualistic cross-feeding in microbial systems generates bistability via an Allee effect

D. Gonze, L. Gelens, Stefan Vet, 2019, Scientific Reports.

The Goodwin Model: Behind the Hill Function

Didier Gonze, Wassim Abou-Jaoudé, D. Gonze, 2013, PloS one.

Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus

Heinz Koeppl, Marc Hafner, Didier Gonze, 2012, PLoS Comput. Biol..

Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus

Achim Kramer, Samuel Bernard, Hanspeter Herzel, 2007, PLoS Comput. Biol..

Computational Models for Circadian Rhythms: Deterministic versus Stochastic Approaches

Roland Eils, Albert Goldbeter, Didier Gonze, 2006 .

Chapter 13 – Computational Models for Circadian Rhythms: Deterministic Versus Stochastic Approaches

Albert Goldbeter, Didier Gonze, Jean-Christophe Leloup, 2006 .

Do ircadian rhythms and molecular noise

A. Goldbeter, D. Gonze, 2006 .

Signatures of ecological processes in microbial community time series

D. Gonze, B. Laroche, Karoline Faust, 2018, Microbiome.

Deterministic Versus Stochastic Models for Circadian Rhythms

J Halloy, D Gonze, A Goldbeter, 2002, Journal of biological physics.

Modeling-Based Investigation of the Effect of Noise in Cellular Systems

Albert Goldbeter, Didier Gonze, Claude Gérard, 2018, Front. Mol. Biosci..

Circadian Misalignment and Metabolic Disorders: A Story of Twisted Clocks

D. Gonze, Aurore Woller, 2021, Biology.

The Goodwin model revisited: Hopf bifurcation, limit-cycle, and periodic entrainment

Thomas Erneux, Didier Gonze, Aurore Woller, 2014, Physical biology.

Modeling the Circadian Control of the Cell Cycle and Its Consequences for Cancer Chronotherapy

D. Gonze, C. Gérard, Courtney Leung, 2023, Biology.

Theory of non-linear dynamical systems

D. Gonze, M. Kaufman, 2009 .

Time-keeping and decision-making in living cells: Part I

Jae Kyoung Kim, J. Tyson, A. Csikász-Nagy, 2022, Interface Focus.

Quantifying the impact of ecological memory on the dynamics of interacting communities

D. Gonze, Karoline Faust, L. Lahti, 2021, bioRxiv.

Selection of in-phase or out-of-phase synchronization in a model based on global coupling of cells undergoing metabolic oscillations.

Albert Goldbeter, Didier Gonze, A. Goldbeter, 2008, Chaos.

Modeling the photoperiodic entrainment of the plant circadian clock.

J. Leloup, D. Gonze, Joëlle De Caluwé, 2017, Journal of theoretical biology.

Exploring chronomodulated radiotherapy strategies in a chaotic population model

D. Gonze, G. Dupont, G. Ramírez-Ávila, 2023, Chaos, Solitons & Fractals.

Towards a synthetic circadian clock in mammals

J. Leloup, D. Gonze, 2009 .

A model for a network of phosphorylation-dephosphorylation cycles displaying the dynamics of dominoes and clocks.

D Gonze, A Goldbeter, A. Goldbeter, 2001, Journal of theoretical biology.

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

D. Gonze, Karoline Faust, K. Bernaerts, 2023, bioRxiv.

Deciphering Interactions Within a 4-Strain Riverine Bacterial Community

D. Gonze, Karoline Faust, I. George, 2023, Current Microbiology.

Modeling the effect of cell division on genetic oscillators.

D. Gonze, 2013, Journal of Theoretical Biology.