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Ovidiu Radulescu

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**EDUCATION Habilitation in Applied Mathematics (University of Rennes 1, 11/12/2006) Master degree in Probability theory and analysis (University of Marne-la-Vallée, 1996) PhD in Theoretical Solid State Physics (Orsay, University of Paris 11, 1994) Engineering degree in Solid State Physics (University of Bucharest, 1989) PROFESSIONAL CAREER ==================== **Current position :** Full Professor (Professeur classe exceptionnelle), Team leader in the Laboratory of Pathogen Host Interactions (LPHI) UMR 5235, University of Montpellier, since 2009. **Other positions** 01/09/1999-31/08/2009, Institute for Mathematical Research (IRMAR), University of Rennes 1, Rennes, France, Associate Professor in mathematics (MCF classe normale, CNU26) 01/09/2005-31/08/2007, National Institute for Computer Science and Applied Mathematics (INRIA), team SYMBIOSE, Rennes, France, Visiting professor (secondment, délégation). 01/03/1998-31/08/2009, IRC in Polymer Physics and Department of Physics, University of Leeds, Leeds, UK, Post-doc in theoretical polymer physics. 01/03/1996-28/02/1998 Institute of Theoretical Physics, Raadboud University, Nijmegen, The Netherlands, HCM EU fellow in theoretical condensed matter physics. 01/09/1993-28/02/1996, University of Marne-la-Vallée, Noisy le Grand, France, Assistant Professor (untenured teaching and research position, ATER) in theoretical condensed matter physics. 01/09/1990-31/08/1993, University of Paris 11, Orsay, France, Teaching assistant (Moniteur). 01/01/1990-31/08/1990, Institute of Research on Materials, Bucharest, Romania, Researcher in theoretical condensed matter theory. **Recent Management Activities:** Member of the Councils of University of Rennes 1 (2008-2009) and University of Montpellier (2011-2015); Adjoint chief of the BioHealth Department at University of Montpellier (2013-2014) **Participation to National and International Scientific Networks Management** Coordinator of the Interdisciplinary axis of Pole Rabelais; Member of Labex Epigenmed; Member of the international network IPols (International Physics of Living Systems Program). **Participation to National and International Expert Committees** Expert for ERC (European Research Council), ANR (French National Research Agency), HCERES (High Council for the Evaluation of Research and Higher Education), NW0 (Netherlands Organisation for Scientific Research) Member of the interdisciplinary committee CID51 of CNRS (2013-2016). **Editorial activity:** Associated Editor of Frontiers in Bioinformatics and Computational Biology. **Participation to program committees (PC) of international conferences:** Member of the PC of the International Workshop on Static Analysis and Systems Biology SASB (2011-12) Member of the PC of the International Conference on Computational Methods in Systems Biology CMSB (2011-12, 2015-20) Member of the PC of the Workshop on Interactions between Computer Science and Biology CS2BIO (2014) Member of the PC of the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology CIBCB (2019-20) **Supervision:** Supervision of 10 phD students, 31 master students, 5 post-docs Direction of the master program “Biophysics Structure and Systems” **Recent invited international conferences:** 1\) **Keynote talk**, CASC 2020 (Computer Algebra in Scientific Computing), Linz, Austria, Sept 14-18, 2020. 2\) **Plenary invited talk**, Workshop on Robustness, Heterogeneity and Adaptation, Gordon Center for Integrative Sciences, University of Chicago, June 20-21, 2016. 3\) **Plenary invited talk**, Symmetry and Dynamics in Biology, Paulista Medical School, (EPM – Unifesp), São Paulo -SP-Brazil, April 17, 2015. 4\) **Plenary invited talk**, workshop Mathematical Trends in Reaction Network Theory, Copenhagen, July 1-3, 2015. 5\) **Plenary invited talk**, Applications of statistical physics in quantitative biology mini-symposium, 9th European Conference on Mathematical and Theoretical Biology, Gothenburg, Sweden, 2014. 6\) **Invited talk**, Franco-Indian Technology Summit, IT & Health, 24 Octobre 2013, New Delhi, India. 7\) **Keynote talk**, 9th BioMalPar - Evimalar Conference, 13-15 Octobre 2013, EMBL Heidelberg, Germany. HONORSANDAWARDS ================ Medals at International Physics Olympiads (1981 bronze, 1982 silver); BGF (French government) fellow (1990-94); DAAD fellow (1995); HCM EU fellow (1996-98); bonus for scientific excellence (PES, PEDR) since 2009.

Publications

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A Skin Microbiome Model with AMP interactions and Analysis of Quasi-Stability vs Stability in Population Dynamics

Eléa Thibault Greugny , François Fages , Ovidiu Radulescu , Peter Szmolyan , Georgios Stamatas
Theoretical Computer Science, 2023, pp.114294. ⟨10.1016/j.tcs.2023.114294⟩
Journal articles hal-04253028v1
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Transcriptional Stochasticity as a Key Aspect of HIV-1 Latency

Alexia Damour , Vera Slaninova , Ovidiu Radulescu , Edouard Bertrand , Eugenia Basyuk
Viruses, 2023, 15 (9), pp.1969. ⟨10.3390/v15091969⟩
Journal articles hal-04235056v1
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BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells

Maria Douaihy , Rachel Topno , Mounia Lagha , Edouard Bertrand , Ovidiu Radulescu
Nucleic Acids Research, 2023, 51 (16), pp.e88-e88. ⟨10.1093/nar/gkad629⟩
Journal articles hal-04286170v1

ODEbase: A Repository of ODE Systems for Systems Biology

Christoph Lüders , Thomas Sturm , Ovidiu Radulescu
Bioinformatics Advances, 2022, 2 (1), ⟨10.1093/bioadv/vbac027⟩
Journal articles hal-03651751v1
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La résistance aux inhibiteurs de BRAF, les leçons de la clinique

Cylia Dahmani , Eulalie Corre , Sarah Dandou , Alain Mangé , Ovidiu Radulescu
Médecine/Sciences, 2022, 38 (6-7), pp.570-578. ⟨10.1051/medsci/2022083⟩
Journal articles hal-03805000v1
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The control of transcriptional memory by stable mitotic bookmarking

Maëlle Bellec , Jérémy Dufourt , George Hunt , Hélène Lenden-Hasse , Antonio Trullo
Nature Communications, 2022, 13 (1), pp.1176. ⟨10.1038/s41467-022-28855-y⟩
Journal articles hal-03858303v1
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Computational Model of Heterogeneity in Melanoma: Designing Therapies and Predicting Outcomes

Arran Hodgkinson , Dumitru Trucu , Matthieu Lacroix , Laurent Le Cam , Ovidiu Radulescu
Frontiers in Oncology, 2022, 12, pp.857572. ⟨10.3389/fonc.2022.857572⟩
Journal articles hal-03644347v1
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Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions

Marion Buffard , Aurélien Naldi , Gilles Gf Freiss , Marcel Deckert , Ovidiu Radulescu
Biomolecules, 2021, 11 (2), pp.308. ⟨10.3390/biom11020308⟩
Journal articles hal-03160560v1
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Algorithmic Reduction of Biological Networks with Multiple Time Scales

Niclas Kruff , Christoph Lüders , Ovidiu Radulescu , Thomas Sturm , Sebastian Walcher
Mathematics in Computer Science, 2021, 15 (3), pp.499 - 534. ⟨10.1007/s11786-021-00515-2⟩
Journal articles hal-03438176v1
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Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Katjana Tantale , Encar Garcia-Oliver , Marie-Cécile Robert , Adèle L’hostis , Yueyuxiao Yang
Nature Communications, 2021, 12 (1), pp.4503. ⟨10.1038/s41467-021-24462-5⟩
Journal articles hal-03382893v1
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Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics

Virginia L Pimmett , Matthieu Dejean , Carola Fernandez , Antonio Trullo , Edouard Bertrand
Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-24461-6⟩
Journal articles hal-03382887v1
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Push-forward method for piecewise deterministic biochemical simulations

Guilherme C.P. Innocentini , Arran Hodgkinson , Fernando Antoneli , Arnaud Debussche , Ovidiu Radulescu
Theoretical Computer Science, 2021, 893, pp.17-40. ⟨10.1016/j.tcs.2021.05.025⟩
Journal articles hal-03644175v1
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Push-forward method for piecewise deterministic biochemical simulations

Guilherme C. P. Innocentini , Arran Hodgkinson , Fernando Antoneli , Arnaud Debussche , Ovidiu Radulescu
Theoretical Computer Science, 2021, 893, pp.17-40. ⟨10.1016/j.tcs.2021.05.025⟩
Journal articles hal-03137189v1
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Identifying the parametric occurrence of multiple steady states for some biological networks

Russell Bradford , James Harold Davenport , Matthew England , Hassan Errami , Vladimir Gerdt
Journal of Symbolic Computation, 2020, 98, pp.84-119. ⟨10.1016/j.jsc.2019.07.008⟩
Journal articles hal-02397154v1
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Is biological randomness a statistical physics concept?

Ovidiu Radulescu , Adrian Devenyi
LINKs series, 2019, pp.120-123
Journal articles hal-02532029v1
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An in silico analysis of robust but fragile gene regulation links enhancer length to robustness

Kenneth Barr , John Reinitz , Ovidiu Radulescu
PLoS Computational Biology, 2019, 15 (11), pp.e1007497. ⟨10.1371/journal.pcbi.1007497⟩
Journal articles hal-03644267v1
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Zelda, le maestro du réveil du génome zygotique

Jeremy Dufourt , Maëlle Bellec , Olivier Messina , Antonio Trullo , Cyril Favard
Médecine/Sciences, 2019, 35 (11), pp.821-841. ⟨10.1051/medsci/2019160⟩
Journal articles hal-03644266v1
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Spatio-Genetic and phenotypic modelling elucidates resistance and re-sensitisation to treatment in heterogeneous melanoma

Arran Hodgkinson , Laurent Le Cam , Dumitru Trucu , Ovidiu Radulescu
Journal of Theoretical Biology, 2019, 466, pp.84 - 105. ⟨10.1016/j.jtbi.2018.11.037⟩
Journal articles hal-03486027v1
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Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells

Marion Buffard , Aurélien Naldi , Ovidiu Radulescu , Peter Coopman , Romain Larive
Proteomics, 2019, 19 (21-22), pp.1800450. ⟨10.1002/pmic.201800450⟩
Journal articles hal-03049205v1
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Signal Propagation in Sensing and Reciprocating Cellular Systems with Spatial and Structural Heterogeneity

Arran Hodgkinson , Ovidiu Radulescu , · Gilles Uzé , Dumitru Trucu
Bulletin of Mathematical Biology, 2018, 80 (7), pp.1900-1936. ⟨10.1007/s11538-018-0439-x⟩
Journal articles hal-02322020v1
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Remembering the past: Mitotic bookmarking in a developing embryo

Maëlle Bellec , Ovidiu Radulescu , Mounia Lagha
Current Opinion in Systems Biology, 2018, 11, pp.41-49. ⟨10.1016/j.coisb.2018.08.003⟩
Journal articles hal-02323370v1

The SYMBIONT project: symbolic methods for biological networks

François Boulier , François Fages , Ovidiu Radulescu , Satya Swarup Samal , Andreas Schuppert
ACM Communications in Computer Algebra, 2018, 52 (3), pp.67-70. ⟨10.1145/3313880.3313885⟩
Journal articles hal-02061018v1
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Cyclin A-cdk1-Dependent Phosphorylation of Bora Is the Triggering Factor Promoting Mitotic Entry

Suzanne Vigneron , Lena Sundermann , Jean-Claude Labbé , Lionel Pintard , Ovidiu Radulescu
Developmental Cell, 2018, 45 (5), pp.637--650.e7. ⟨10.1016/j.devcel.2018.05.005⟩
Journal articles hal-01872979v1
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Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

Jeremy Dufourt , Antonio Trullo , Jennifer Hunter , Carola Fernandez , Jorge Lazaro
Nature Communications, 2018, 9 (1), pp.821 - 841. ⟨10.1038/s41467-018-07613-z⟩
Journal articles hal-02323402v1
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Time Dependent Stochastic mRNA and Protein Synthesis in Piecewise-Deterministic Models of Gene Networks

Guilherme Innocentini , Arran Hodgkinson , Ovidiu Radulescu
Frontiers in Physics, 2018, 6, pp.46. ⟨10.3389/fphy.2018.00046⟩
Journal articles hal-03644316v1
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Centralized Networks to Generate Human Body Motions

Sergei Vakulenko , Ovidiu Radulescu , Ivan Morozov , Andres Weber
Sensors, 2017, 17 (12), pp.2907. ⟨10.3390/s17122907⟩
Journal articles hal-03644285v1
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Far-From-Equilibrium Time Evolution between Two Gamma Distributions

Eun-Jin Kim , Lucille-Marie Tenkès , Rainer Hollerbach , Ovidiu Radulescu
Entropy, 2017, 19 (10), pp.511. ⟨10.3390/e19100511⟩
Journal articles hal-03644310v1

Transcriptional Memory in the Drosophila Embryo

Mounia Lagha , Teresa Ferraro , Jeremy Dufourt , Ovidiu Radulescu , Matilde Mantovani
Mechanisms of Development, 2017, 145, pp.S137. ⟨10.1016/j.mod.2017.04.382⟩
Journal articles hal-03644293v1
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Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

Aurélien Naldi , Romain Larive , Urszula Czerwinska , Serge Urbach , Philippe Montcourrier
PLoS Computational Biology, 2017, 13 (3), pp.e1005432. ⟨10.1371/journal.pcbi.1005432⟩
Journal articles hal-02073659v1

Linking metabolic network features to phenotypes using sparse group lasso

Satya Swarup Samal , Ovidiu Radulescu , Andreas Weber , Holger Fröhlich
Bioinformatics, 2017, 33 (21), pp.3445-3453. ⟨10.1093/bioinformatics/btx427⟩
Journal articles hal-03644287v1

Protein Synthesis Driven by Dynamical Stochastic Transcription

Guilherme Innocentini , Michael Forger , Ovidiu Radulescu , Fernando Antoneli
Bulletin of Mathematical Biology, 2016, 78 (1), pp.110-131. ⟨10.1007/s11538-015-0131-3⟩
Journal articles hal-03644309v1
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Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors

Satya Swarup Samal , Aurélien Naldi , Dima Grigoriev , Andreas Weber , Nathalie Théret
BioSystems, 2016, 149, pp.3-14. ⟨10.1016/j.biosystems.2016.07.004⟩
Journal articles hal-01379033v1

Analytic framework for a stochastic binary biological switch

Guilherme Innocentini , Sarah Guiziou , Jerome Bonnet , Ovidiu Radulescu
Physical Review E , 2016, 94 (6), pp.062413. ⟨10.1103/PhysRevE.94.062413⟩
Journal articles hal-03644297v1

Maximal switchability of centralized networks

Sergei Vakulenko , Ivan Morozov , Ovidiu Radulescu
Nonlinearity, 2016, 29 (8), pp.2327-2354. ⟨10.1088/0951-7715/29/8/2327⟩
Journal articles hal-03644308v1

Stress diffusion in shear banding wormlike micelles

Marc-Antoine Fardin , Ovidiu Radulescu , Alexander Morozov , Olivier Cardoso , Julien Browaeys
Journal of Rheology, 2015, 59 (6), pp.1335-1362. ⟨10.1122/1.4930858⟩
Journal articles hal-03195234v1
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A constraint solving approach to model reduction by tropical equilibration

Sylvain Soliman , François Fages , Ovidiu Radulescu
Algorithms for Molecular Biology, 2014, 9 (1), pp.24. ⟨10.1186/s13015-014-0024-2⟩
Journal articles hal-01098530v1
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Reduction of dynamical biochemical reaction networks in computational biology

Ovidiu Radulescu , Alexander N. Gorban , Andrei Zinovyev , Vincent Noël
Frontiers in Genetics, 2012, 131 (2), ⟨10.3389/fgene.2012.00131⟩
Journal articles hal-00770213v1

Tropical Geometries and Dynamics of Biochemical Networks Application to Hybrid Cell Cycle Models

Vincent Noël , Dima Grigoriev , Sergey A. Vakulenko , Ovidiu Radulescu
Electronic Notes in Theoretical Computer Science, 2012, 284, pp.75-91. ⟨10.1016/j.entcs.2012.05.016⟩
Journal articles hal-00714358v1
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Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states

Matthew L. M. L. Ferguson , Dominique D. Le Coq , Matthieu M. Jules , Stephane S. Aymerich , Ovidiu O. Radulescu
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (1), pp.155 - 160. ⟨10.1073/pnas.1110541108⟩
Journal articles hal-01004232v1
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Convergence of stochastic gene networks to hybrid piecewise deterministic processes

Alina Crudu , Arnaud Debussche , Aurélie Muller , Ovidiu Radulescu
The Annals of Applied Probability, 2012, 22 (5), pp.1822-1859. ⟨10.1214/11-AAP814⟩
Journal articles hal-00553482v1

Genetically regulated metabolic networks: Gale-Nikaido modules and differential inequalities

Ovidiu Radulescu , Anne Siegel , Elisabeth Pecou , Clément Chatelain , Sandrine Lagarrigue
Transactions on Computational Systems Biology, 2011, Transactions on Computational Systems Biology XIII, 6575 (Lecture Notes in Computer Science 6575), pp.110-130. ⟨10.1007/978-3-642-19748-2_6⟩
Journal articles inria-00538136v1

Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling.

Carito Guziolowski , Sylvain Blachon , Tatiana Baumuratova , Gautier Stoll , Ovidiu Radulescu
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8 (5), pp.1223-1234. ⟨10.1109/TCBB.2010.71⟩
Journal articles inria-00538134v1

Asymptotology of Chemical Reaction Networks

Alexander N. Gorban , Ovidiu Radulescu , Andrei Zinovyev
Chemical Engineering Science, 2010, 65 (7), pp.2310-2324. ⟨10.1016/j.ces.2009.09.005⟩
Journal articles inria-00431225v1
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Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.

Tatiana Baumuratova , Didier Surdez , Bernard Delyon , Gautier Stoll , Olivier Delattre
BMC Systems Biology, 2010, 4 (1), pp.146. ⟨10.1186/1752-0509-4-146⟩
Journal articles inserm-00984711v1

Size Regulation in the Segmentation of Drosophila: Interacting Interfaces between Localized Domains of Gene Expression Ensure Robust Spatial Patterning

S.A. Vakulenko , Manu Manu , John Reinitz , Ovidiu Radulescu
Physical Review Letters, 2009, 103, pp.168102
Journal articles inria-00431224v1

Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors

Manu Manu , Svetlana Surkova , Alexander V. Spirov , Vitaly Gursky , Hilde Janssens
PLoS Computational Biology, 2009, 5, pp.3
Journal articles inria-00431228v1

Canalization of gene expression in the Drosophila blastoderm by gap genes cross regulation

Manu Manu , Svetlana Surkova , Alexander V. Spirov , Vitaly Gursky , Hilde Janssens
PLoS Biology, 2009, 7, pp.3
Journal articles inria-00431229v1
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Hybrid stochastic simplifications for multiscale gene networks

Alina Crudu , Arnaud Debussche , Ovidiu Radulescu
BMC Systems Biology, 2009, 3 (1), pp.89. ⟨10.1186/1752-0509-3-89⟩
Journal articles hal-00784449v1
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A minimal model for hepatic fatty acid balance during fasting: Application to PPAR alpha-deficient mice

Pierre Blavy , Florence Gondret , Hervé Guillou , Sandrine Lagarrigue , P.G.P. Martin
Journal of Theoretical Biology, 2009, 261 (2), pp.266. ⟨10.1016/j.jtbi.2009.07.025⟩
Journal articles hal-00559147v1

Inferring the role of transcription factors in regulatory networks

Philippe Veber , Carito Guziolowski , Michel Le Borgne , Ovidiu Radulescu , Anne Siegel
BMC Bioinformatics, 2008, 9, ⟨10.1186/1471-2105-9-228⟩
Journal articles inria-00330578v1

Dynamic and static limitation in multiscale reaction networks, revisited

Alexander N. Gorban , Ovidiu Radulescu
Chemical Engineering Science, 2008, Advances in Chemical Engineering, 34, pp.103-173
Journal articles inria-00184976v1

From Molecules to Organisms: Towards Multiscale Integrated Models of Biological Systems

Christophe Lavelle , Hugues Berry , Guillaume Beslon , Francisco Ginelli , Jean-Louis Giavitto
Theoretical Biology Insights, 2008, 1, pp.13-22
Journal articles inria-00331281v1

Robust simplifications of multiscale biochemical networks

Ovidiu Radulescu , Alexander N. Gorban , Andrei Zinovyev , Alain Lilienbaum
BMC Systems Biology, 2008, 2:86
Journal articles inria-00331212v1

Théorèmes limites pour des processus de Markov à sauts. Synthèse des résultats et applications en biologie moleculaire

Ovidiu Radulescu , Aurélie Muller , Alina Crudu
Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2007, 26 (3-4), pp.443-469. ⟨10.3166/tsi.26.443-469⟩
Journal articles inria-00181451v1

Dynamical robustness of biological networks with hierarchical distribution of time scales

Alexander N. Gorban , Ovidiu Radulescu
IET Systems Biology, 2007
Journal articles inria-00181450v1
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Optimiser un plan d'expérience à partir de modèles qualitatifs?

Anne Siegel , Carito Guziolowski , Philippe Veber , Ovidiu Radulescu , Michel Le Borgne
Biofutur, 2007, 275, pp.27-31
Journal articles inria-00178791v1
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Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study

Carito Guziolowski , Philippe Veber , Michel Le Borgne , Ovidiu Radulescu , Anne Siegel
Journal of Biological Physics and Chemistry, 2007, 7, pp.37-43
Journal articles inria-00178914v1
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Topology and static response of interaction networks in molecular biology

Ovidiu Radulescu , Sandrine Lagarrigue , Anne Siegel , Philippe Veber , Michel Le Borgne
Journal of the Royal Society Interface, 2006, 3 (6), pp.185 - 196. ⟨10.1098/rsif.2005.0092⟩
Journal articles inria-00178842v1
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Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks

Anne Siegel , Ovidiu Radulescu , Michel Le Borgne , Philippe Veber , Julien Ouy
BioSystems, 2006, 84, pp.153-174
Journal articles inria-00178809v1

Complex Qualitative Models in Biology: a new approach

Philippe Veber , Michel Le Borgne , Anne Siegel , Sandrine Lagarrigue , Ovidiu Radulescu
Complexus, 2005, 2, pp.140-151
Journal articles inria-00178819v1

Timescales in shear banding of wormlike micelles

Ovidiu Radulescu , Peter D. Olmsted , Jean-Paul Decruppe , Sandra Lerouge , Jean-François Berret
EPL - Europhysics Letters, 2003, 62 (2), pp.230-236. ⟨10.1209/epl/i2003-00351-x⟩
Journal articles hal-00136480v1

Dynamics of modulated and composite aperiodic crystals: the signature of the inner polarization in the neutron coherent inelastic scattering

Ovidiu Radulescu , T. Janssen , J. Etrillard
The European Physical Journal B: Condensed Matter and Complex Systems, 2002, 29, pp.385-398
Journal articles hal-00122070v1
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A classification of the periodic directions in the rational approximants of icosahedral quasicrystals

Ovidiu Radulescu
Journal de Physique I, 1993, 3 (10), pp.2099-2113. ⟨10.1051/jp1:1993234⟩
Journal articles jpa-00246854v1
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Reconstruction vasculaire 3D et analyse de lames virtuelles H&E dans l'étude du mélanome

Janan Arslan , Haocheng Luo , Pawan Kumar , Matthieu Lacroix , Pierrick Dupré
IABM2023 : Colloque Français d'Intelligence Artificielle en Imagerie Biomédicale, Mar 2023, Paris, France
Conference papers hal-03928851v1
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Efficient 3D Reconstruction of H&E Whole Slide Images in Melanoma

Janan Arslan , Mehdi Ounissi , Haocheng Luo , Matthieu Lacroix , Pierrick Dupré
SPIE Medical Imaging 2023, Feb 2023, San Diego, California, United States
Conference papers hal-03834014v2

Mitotic Memory as Spontaneous Symmetry Breaking in the Cell

Arran Hodgkinson , Maelle Bellec , Maria Douaihy , Adrian Devenyi , Mounia Lagha
International Conference in Systems Biology, Oct 2022, Berlin, Germany
Conference papers hal-03814916v1
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Introducing [MALMO]: Mathematical approaches to modelling metabolic plasticity and heterogeneity in Melanoma

Janan Arslan , Laurent Le Cam , Matthieu Lacroix , Emmanuel Faure , Pierrick Dupré
RITS 2022 - Recherche en Imagerie et Technologie pour la Santé, May 2022, Brest, France
Conference papers hal-03834055v1

3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma

Janan Arslan , Pawan Kumar , Arran Hodgkinson , Haocheng Luo , Pierrick Dupré
International Conference in Systems Biology, Oct 2022, Berlin, Germany
Conference papers hal-03814995v1

Data driven mechanistic modeling of oxygen distribution and hypoxia profile in tumor microenvironment

Pawan Kumar , Janan Arslan , Arran Hodgkinson , Haocheng Luo , Sarah Dandou
COMPSYSCAN2022: A complex systems approach to cancer understanding, Oct 2022, Lyon, France
Conference papers hal-03834400v1

Stochasticity of Meiotic Entry in Xenopus Oocytes

Deniz Fettahoglu , Charbel Choufani , Pawan Kumar , Anna Castro , Thierry Lorca
International Conference in Systems Biology, Oct 2022, Berlin, Germany
Conference papers hal-03814944v1
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LNetReduce: tool for reducing linear dynamic networks with separated time scales

Marion Buffard , Aurélien Desoeuvres , Aurélien Naldi , Clément Requilé , Andrei Zinovyev
Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. ⟨10.1007/978-3-030-85633-5_15⟩
Conference papers hal-03226633v1
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Tropical Geometry of Biological Systems

Ovidiu Radulescu
CASC 2020, Sep 2020, Linz, Austria
Conference papers hal-02949563v1
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Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity

Aurélien Desoeuvres , Gilles Trombettoni , Ovidiu Radulescu
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, Sep 2020, Konstanz, Germany. pp.79-101, ⟨10.1007/978-3-030-60327-4_5⟩
Conference papers hal-03644249v1
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Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

Matthew England , Hassan Errami , Dima Grigoriev , Ovidiu Radulescu , Thomas Sturm
CASC 2017 - 19th International Workshop on Computer Algebra in Scientific Computing, Sep 2017, Beijing, China. ⟨10.1007/978-3-319-66320-3⟩
Conference papers hal-01648691v1

A Case Study on the Parametric Occurrence of Multiple Steady States

Russell Bradford , James H. Davenport , Matthew England , Hassan Errami , Vladimir Gerdt
ISSAC 2017 - International Symposium on Symbolic and Algebraic Computation, Jul 2017, Kaiserslautern, Germany. pp.45-52, ⟨10.1145/3087604.3087622⟩
Conference papers hal-01648694v1
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A Constraint Solving Approach to Tropical Equilibration and Model Reduction

Sylvain Soliman , François Fages , Ovidiu Radulescu
WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013, Sep 2013, Uppsala, Sweden. pp.27--36
Conference papers hal-00906419v1

Tropicalization and tropical equilibration of chemical reactions

Vincent Noël , Dima Grigoriev , Sergey A. Vakulenko , Ovidiu Radulescu
International Workshop on Tropical and Idempotent Mathematics, Independent University of Moscow, Aug 2012, Moscow, Russia. pp.261-275, ⟨10.1090/conm/616/12316⟩
Conference papers hal-00812614v1

Hybrid models of the cell cycle molecular machinery

Vincent Noël , Dima Grigoriev , Sergey A. Vakulenko , Ovidiu Radulescu
Hybrid Systems and Biology (HSB 2012), Sep 2012, Newcastle, United States. pp.88-105, ⟨10.4204/EPTCS.92⟩
Conference papers hal-00770222v1
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Two types of transcriptional repression in living cells of [i]Bacillus subtilis[/i] characterized by number and brightness analysis

Matthew L. Ferguson , Dominique Le Coq , Matthieu Jules , Bryan Chun , Stephane Aymerich
55. Annual Meeting of the Biophysical-Society, Mar 2011, Baltimore, Maryland, United States. ⟨10.1016/j.bpj.2010.12.1179⟩
Conference papers hal-01190611v1

Asymptotology of Chemical Reaction Networks

Alexander N. Gorban , Ovidiu Radulescu , Andrei Zinovyev
International Symposium on Mathematics in Chemical Kinetics and Engineering (MACKIE-2009), Nov 2009, Ghent, Belgium
Conference papers inria-00599258v1

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks

Sylvain Blachon , Gautier Stoll , Carito Guziolowski , Andrei Zinovyev , Emmanuel Barillot
AIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87
Conference papers inria-00429801v1
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CURATING A LARGE-SCALE REGULATORY NETWORK BY EVALUATING ITS CONSISTENCY WITH EXPRESSION DATASETS

Carito Guziolowski , Jérémy Gruel , Ovidiu Radulescu , Anne Siegel
CIBB 2008: COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, Oct 2008, Salerno, Italy. pp.144-155
Conference papers inria-00331385v1

Timescales and instabilities of shear thinning solutions of wormlike micelles

Ovidiu Radulescu , Sandra Lerouge , Benoit Lasne
15th International Congress on Rheology 2008, Aug 2008, Monterey, United States. pp.CF36
Conference papers inria-00331217v1
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A minimal and dynamic model for fatty acid metabolism in mouse liver

Pierre Blavy , Florence Gondret , Hervé Guillou , Sandrine Lagarrigue , Pascal G.P. Martin
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2008, Lille (FR), France
Conference papers hal-00729742v1

A minimal and dynamic model for fatty acid metabolism in mouse liver

Pierre Blavy , Florence Gondret , Hervé Guillou , Sandrine Lagarrigue , Pascal G.P. Martin
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2008, Lille, France
Conference papers hal-02756716v1

Modélisation multi-organes et multi-espèces du métabolisme des lipides

Pierre Blavy , Anne Siegel , Ovidiu Radulescu , Florence Gondret , Jaap J. van Milgen
2. Journées d'Animation Scientifique du Département PHASE, Oct 2007, Tours, France
Conference papers hal-02756643v1
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Qualitative response of interaction networks: application to the validation of biological models

Anne Siegel , Carito Guziolowski , Philippe Veber , Ovidiu Radulescu , Michel Le Borgne
6th International Congress on Industrial and Applied Mathematics. ICIAM 07, Jul 2007, Zurich, Switzerland
Conference papers inria-00178854v1

A Linear Algebra Approach for Detecting Binomiality of Steady State Ideals of Reversible Chemical Reaction Networks

Hamid Rahkooy , Ovidiu Radulescu , Thomas Sturm
Computer Algebra in Scientific Computing: 22nd International Workshop - CASC 2020, pp.492-509, 2020, ⟨10.1007/978-3-030-60026-6_29⟩
Book sections hal-02977486v1

Tropical Geometry of Biological Systems (Invited Talk)

Ovidiu Radulescu
Computer Algebra in Scientific Computing, 12291, Springer International Publishing, pp.1-13, 2020, Lecture Notes in Computer Science, ⟨10.1007/978-3-030-60026-6_1⟩
Book sections hal-03644251v1
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Integrative models for TGF-$\beta$ signaling and extracellular matrix

Nathalie Theret , Jérôme Feret , Arran Hodgkinson , Pierre Boutillier , Pierre Vignet
Sylvie Ricard-Blum. Extracellular Matrix Omics, 7, Springer, pp.17, 2020, Biology of Extracellular Matrix, 978-3-030-58329-3. ⟨10.1007/978-3-030-58330-9_10⟩
Book sections hal-02458073v1

Effective Computational Methods for Hybrid Stochastic Gene Networks

Ovidiu Radulescu , Guilherme Innocentini , Fernando Antoneli , Arran Hodgkinson
Computational Methods in Systems Biology, 11773 (21-22), Springer International Publishing, pp.60-77, 2019, Lecture Notes in Computer Science, ⟨10.1007/978-3-030-31304-3_4⟩
Book sections hal-03644270v1

Metastable Regimes and Tipping Points of Biochemical Networks with Potential Applications in Precision Medicine

Satya Swarup Samal , Jeyashree Krishnan , Ali Hadizadeh Esfahani , Christoph Lüders , Andreas Weber
Automated Reasoning for Systems Biology and Medicine, 30, Springer International Publishing, pp.269-295, 2019, Computational Biology, ⟨10.1007/978-3-030-17297-8_10⟩
Book sections hal-03644180v1

Mathematical Modeling and Omic Data Integration to Understand Dynamic Adaptation of Apicomplexan Parasites and Identify Pharmaceutical Targets

Partho Sen , Henri Vial , Ovidiu Radulescu
Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery, Wiley-VCH Verlag GmbH & Co. KGaA, pp.455-486, 2016, ⟨10.1002/9783527694082.ch20⟩
Book sections hal-03644305v1

Hybrid Reductions of Computational Models of Ion Channels Coupled to Cellular Biochemistry

Jasha Sommer-Simpson , John Reinitz , Leonid Fridlyand , Louis Philipson , Ovidiu Radulescu
Computational Methods in Systems Biology, 9859, Springer International Publishing, pp.273-288, 2016, Lecture Notes in Computer Science, ⟨10.1007/978-3-319-45177-0_17⟩
Book sections hal-03644304v1

Algorithm for identification of piecewise smooth hybrid systems: application to Eukaryotic Cell Cycle regulation

Vincent Noël , Sergey A. Vakulenko , Ovidiu Radulescu
Teresa Przytycka, Marie-France Sagot. Algorithms in Bioinformatics, Springer, pp.225-236, 2011, Lecture Notes in Computer Science, vol. 6833, 9783642230370. ⟨10.1007/978-3-642-23038-7_20⟩
Book sections hal-00725282v1