Caroline Baroukh

46
Documents
Affiliation actuelle
  • Laboratoire des Interactions Plantes Microbes Environnement (LIPME)
Contact

Domaines de recherche

Bio-Informatique, Biologie Systémique [q-bio.QM] Phytopathologie et phytopharmacie Biologie végétale

Publications

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Publications

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Putrescine, a double-edged molecule in plant-bacteria interactions

Stephane Genin , Caroline Baroukh

Molecular Plant, 2026, ⟨10.1016/j.molp.2026.02.010⟩

Article dans une revue hal-05549247v1
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Disruption of putrescine export in experimentally evolved <i>Ralstonia pseudosolanacearum</i> enhances symbiosis with <i>Mimosa pudica</i>

Anne-Claire Cazalé , Marvin Navarro , Ginaini Grazielli Doin de Moura , Sophie Valière , Floriant Bellvert et al.

mBio, 2026, 17 (1), pp.e01225-25. ⟨10.1128/mbio.01225-25⟩

Article dans une revue hal-05344083v2
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Unraveling the in planta population dynamics of the plant pathogen Ralstonia pseudosolanacearum by mathematical modeling

Caroline Baroukh , Léo Gerlin , Antoine Escourrou , Stéphane Genin

New Phytologist, 2025, 246, pp.251-261. ⟨10.1111/nph.20216⟩

Article dans une revue hal-04782291v1
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Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex

Caroline Baroukh , Ludovic Cottret , Emma Pires , Rémi Peyraud , Alice Guidot et al.

mSystems, 2023, 18 p. ⟨10.1128/msystems.00083-23⟩

Article dans une revue hal-04172034v1
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Letter to the Editor: The Ralstonia research community rejects the proposal to classify phylotype I Ralstonia into the new species Ralstonia nicotianae

Tiffany Lowe-Power , Parul Sharma , Poliane Alfenas-Zerbini , Belén Álvarez , Mohammad Arif et al.

PhytoFrontiers, 2023, ⟨10.1094/PHYTOFR-06-23-0071-LE⟩

Article dans une revue hal-04188467v1
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A universal dynamical metabolic model representing mixotrophic growth of Chlorella sp. on wastes

Bruno Assis Pessi , Caroline Baroukh , Anais Bacquet , Olivier Bernard

Water Research, 2023, 229, pp.119388. ⟨10.1016/j.watres.2022.119388⟩

Article dans une revue hal-03920752v1
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MERRIN: MEtabolic Regulation Rule INference from time series data

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.

Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩

Article dans une revue hal-03701755v2
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The paradoxes hidden behind the Droop model highlighted by a metabolic approach

Caroline Baroukh , Francis Mairet , Olivier Bernard

Frontiers in Plant Science, 2022, 13, 16 p. ⟨10.3389/fpls.2022.941230⟩

Article dans une revue hal-03781716v1
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The Fucoxanthin Chlorophyll a/c-Binding Protein in Tisochrysis lutea: Influence of Nitrogen and Light on Fucoxanthin and Chlorophyll a/c-Binding Protein Gene Expression and Fucoxanthin Synthesis

Anne Pajot , Johann Lavaud , Gregory Carrier , Matthieu Garnier , Bruno Saint-Jean et al.

Frontiers in Plant Science, 2022, 13, pp.830069. ⟨10.3389/fpls.2022.830069⟩

Article dans une revue hal-03587582v1
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Trophic preferences of the pathogen Ralstonia solanacearum and consequences on its growth in xylem sap

Caroline Baroukh , Meriem Zemouri , Stéphane Genin

MicrobiologyOpen, 2022, 11 (1), 14 p. ⟨10.1002/mbo3.1240⟩

Article dans une revue hal-03745744v1
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A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations

Léo Gerlin , Ludovic Cottret , Antoine Escourrou , Stéphane Genin , Caroline Baroukh

Plant Physiology, 2022, 188 (3), pp.1709-1723. ⟨10.1093/plphys/kiab548⟩

Article dans une revue hal-03727243v1
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Unravelling physiological signatures of tomato bacterial wilt and xylem metabolites exploited by Ralstonia solanacearum

Léo Gerlin , Antoine Escourrou , Cédric Cassan , Felicià Maviane Macia , Nemo Peeters et al.

Environmental Microbiology, 2021, 23 (10), pp.5962-5978. ⟨10.1111/1462-2920.15535⟩

Article dans une revue hal-03211148v1
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Polyamines: double agents in disease and plant immunity

Léo Gerlin , Caroline Baroukh , Stéphane Genin

Trends in Plant Science, 2021, 26 (10), pp.1061-1071. ⟨10.1016/j.tplants.2021.05.007⟩

Article dans une revue hal-03259585v1
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Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth

Léo Gerlin , Ludovic Cottret , Sophie Cesbron , Geraldine G. Taghouti , Marie-Agnès Jacques et al.

mSystems, 2020, 5 (2), 15 p. ⟨10.1128/mSystems.00698-19⟩

Article dans une revue hal-02901652v1
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Draft genomes and phenotypic characterization of Tisochrysis lutea strains. Toward the production of domesticated strains with high added value

Gregory Carrier , Caroline Baroukh , Catherine Rouxel , Laetitia Duboscq-Bidot , Nathalie Schreiber et al.

Algal Research - Biomass, Biofuels and Bioproducts, 2018, 29 (Supplement C), pp.1-11. ⟨10.1016/j.algal.2017.10.017⟩

Article dans une revue hal-02627937v1
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Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés et al.

PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩

Article dans une revue hal-01635688v1
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Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes

Caroline Baroukh , Violette Turon , Olivier Bernard

PLoS Computational Biology, 2017, 13 (6), pp.e1005590. ⟨10.1371/journal.pcbi.1005590⟩

Article dans une revue hal-01576858v1
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Reply to the Comment on “Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production” by Baroukh et al. [Curr. Opin. Biotechnol. 2015, 33:198–205]

Caroline Baroukh , Rafael Munoz Tamayo , Olivier A. Bernard , Jean-Philippe Steyer

Current Opinion in Biotechnology, 2016, 38, pp.200 - 202. ⟨10.1016/j.copbio.2016.02.018⟩

Article dans une revue istex hal-01410975v1
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Use of fermentative metabolites for heterotrophic microalgae growth: Yields and kinetics

Violette Turon , Caroline Baroukh , Eric Trably , Eric Latrille , Eric Fouilland et al.

Bioresource Technology, 2015, 175, pp.342-349. ⟨10.1016/j.biortech.2014.10.114⟩

Article dans une revue hal-01165732v1
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A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production

Caroline Baroukh , Rafael Munoz Tamayo , Jean-Philippe Steyer , Olivier Bernard

Metabolic Engineering, 2015, 30, pp.49-60. ⟨10.1016/j.ymben.2015.03.019⟩

Article dans une revue (article de synthèse) istex hal-01163453v1
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Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production

Caroline Baroukh , Rafael Munoz Tamayo , Olivier Bernard , Jean-Philippe Steyer

Current Opinion in Biotechnology, 2015, 33, pp.198-205. ⟨10.1016/j.copbio.2015.03.002⟩

Article dans une revue (article de synthèse) istex hal-01163456v1
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DRUM: A new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae

Caroline Baroukh , Rafael Munoz Tamayo , Jean-Philippe Steyer , Olivier Bernard

PLoS ONE, 2014, 9 (8), pp.e104499. ⟨10.1371/journal.pone.0104499⟩

Article dans une revue hal-01123224v1

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

H. Xu , Caroline Baroukh , R. Dannenfelser , E. Y. Chen , C. M. Tan et al.

Database - The journal of Biological Databases and Curation, 2013, 2013 (bat045), pp.1-12. ⟨10.1093/database/bat045⟩

Article dans une revue hal-02644065v1

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

Caroline Baroukh , Sherry Jenkins , Ruth Dannenfelser , Avi Ma'Ayan

Source Code for Biology and Medicine, 2011, 6 (15), pp.1-15. ⟨10.1186/1751-0473-6-15⟩

Article dans une revue hal-02646115v1
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MULTI-ORGAN GENOME-SCALE METABOLIC MODELING OF A TOMATO PLANT AT VEGETATIVE GROWTH STAGE

Léo Gerlin , Antoine Escourrou , Ludovic Cottret , Stéphane Genin , Caroline Baroukh

13ème Congrès international de la SFBV, Société Française de la Biologie Végétale, Aug 2022, Montpellier, France

Communication dans un congrès hal-04718279v1
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Multi-organ genome-scale metabolic modeling of tomato plant

Leo Gerlin , Antoine Escourrou , Ludovic Cottret , Stephane Genin , Caroline Baroukh

7th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), Mar 2021, Virtual, France

Communication dans un congrès hal-03350567v1

Investigation of the metabolic network of Xylella fastidiosa responsible of its fastidious growth

Leo Gerlin , Ludovic Cottret , Sophie Cesbron , Geraldine G. Taghouti , Marie-Agnès Jacques et al.

3rd European Conference on Xylella fastidiosa and the final meeting of the XF-ACTORS project, Apr 2021, Virtual, France

Communication dans un congrès hal-03350588v1
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Learning Boolean controls in regulated metabolic networks: a case-study

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.

CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩

Communication dans un congrès hal-03207589v3
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Modélisation métabolique et interaction plante-pathogènes

Caroline Baroukh

Séminaire INRA SPE, Dec 2018, Lyon, France

Communication dans un congrès hal-02787691v1
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Exploration of the growth-virulence trade-off in the plant pathogen Ralstonia solanacearum species complex

Caroline Baroukh , Emma Pires , Ludovic Cottret , Remi Peyraud , Stéphane Genin

MicrobiOccitanie 2019 - Rencontre des Microbiologistes Région Occitanie, Feb 2019, Montpellier, France

Communication dans un congrès hal-02786961v1
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Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth

Leo Gerlin , Ludovic Cottret , Sophie Cesbron , Géraldine Taghouti , Marie-Agnès Jacques et al.

Symposium on Synthetic and Systemic Biology, Nov 2019, Bordeaux, France

Communication dans un congrès hal-03350558v1

Metabolic modeling of C. sorokiniana diauxic heterotrophic growth

Caroline Baroukh , Olivier Bernard

6. IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Oct 2016, Magdeburg, Germany. pp.330-335, ⟨10.1016/j.ifaco1.2016.12.148⟩

Communication dans un congrès hal-01602803v1
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Dynamic Flux Balance Analysis of the Metabolism of Microalgae under a Diurnal Light Cycle

Caroline Baroukh , Jean Philippe Steyer , Olvier Bernard , Benoit Chachuat

DYCOPS-CAB 2016 - 11th IFAC Symposium on Dynamics and Control of Process Systems, Including Biosystems DYCOPS-CAB 2016, International Federation of Automatic Control (IFAC). AUT., Jun 2016, Trondheim, Norway. pp.791 - 796, ⟨10.1016/j.ifacol.2016.07.285⟩

Communication dans un congrès hal-01413531v1
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Bayesian optimization with dimension scheduling: application to biological systems

Doniyor Ulmasov , Caroline Baroukh , Benoit Chachuat , Marc Peter Deisenroth , Ruth Misener

26. European Symposium on Computer Aided Process Engineering. ESCAPE 26, Jun 2016, Portorož, Slovenia. 2423 p., ⟨10.1016/B978-0-444-63428-3.50180-6⟩

Communication dans un congrès hal-01602485v1
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A new approach to unravel metabolic regulations. Application to microalgae growth and lipid production under day/night cycles and nitrogen starvation

Caroline Baroukh , Olivier Bernard , Jean-Philippe Steyer , Rafael Munoz Tamayo , Benoit Chachuat

BioSynSys 2015 : 1er colloque du GDR "Biologie de Synthèse et des Systèmes", Sep 2015, Paris, France

Communication dans un congrès hal-01601441v1

Metabolic modeling of microalgae growth and lipids production during day/night cycles and nitrogen starvation

Caroline Baroukh , Rafael Munoz Tamayo , Jean-Philippe Steyer , Olivier Bernard

Metabolic Pathway Analysis 2015, Jun 2015, Braga, Portugal

Communication dans un congrès hal-01603450v1
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A new framework for metabolic modeling under non-balanced growth. Application to carbon metabolism of unicellular microalgae

Caroline Baroukh , Rafael Munoz Tamayo , Jean-Philippe Steyer , Olivier Bernard

CAB 2013 - International on Computer Applications to Biotechnology, Dec 2013, Mumbai, India

Communication dans un congrès hal-00856042v2

A new framework for metabolic modelling under non-balanced growth. Application to photoautotrophic microalgae in day/night cycle.

Caroline Baroukh , Rafael Munoz Tamayo , Jean-Philippe Steyer , Olivier Bernard

Metabolic Pathway Analysis 2013, Sep 2013, Oxford, United Kingdom

Communication dans un congrès hal-01601779v1

A new modelling framework: application to microalgae growth

Caroline Baroukh

Young Algaeneers Symposium (YAS2012), 2012, Wageningen, Netherlands

Communication dans un congrès hal-00848381v1

Process calculi for systems biology

Caroline Baroukh , Anthony Rowe , Yike Guo

ACM International Conference on Bioinformatics and Computational Biology, 2010, Niagara Falls, United States. ⟨10.1145/1854776.1854869⟩

Communication dans un congrès hal-02751394v1

Process Calculi for Systems Biology and applications in severe asthma

Caroline Baroukh , Anthony Rowe , Yike Guo

2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), Dec 2010, Hong-Kong, Hong Kong SAR China. ⟨10.1109/BIBMW.2010.5703802⟩

Communication dans un congrès hal-02752857v1

Plant genome-scale metabolic networks

Léo Gerlin , Clément Frainay , Fabien Jourdan , Caroline Baroukh , Sylvain Prigent

Science Direct. Plant Metabolomics in full swing, 98, 2021, Advances in Botanical Research, ⟨10.1016/bs.abr.2020.09.021⟩

Chapitre d'ouvrage hal-03149497v1
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Metabolic modeling under non-balanced growth. Application to microalgae for biofuels production

Caroline Baroukh

Life Sciences [q-bio]. Université Montpellier 2 (Sciences et Techniques), 2014. English. ⟨NNT : ⟩

Thèse tel-02794871v2