Sabine Peres

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Publications

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Proceedings of the 23rd International Conference on Computational Methods in Systems Biology

François Fages , Sabine Pérès

CMSB 2025, Sep 2025, Lyon, France. Lecture Notes in Computer Science, Lecture Notes in Computer Science (LNCS-15959), Springer Nature Switzerland, 2025, Proceedings of the 23rd International Conference on Computational Methods in Systems Biology, CMSB 2025., ⟨10.1007/978-3-032-01436-8⟩

Proceedings/Recueil des communications hal-05396349v1
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Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections

Maxime Mahout , Ross Carlson , Laurent Simon , Sabine Peres

npj Systems Biology and Applications, 2024, 10 (1), pp.34. ⟨10.1038/s41540-024-00360-6⟩

Article dans une revue hal-04610153v1
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Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma

Maxime Mahout , Laurent Schwartz , Romain Attal , Ashraf Bakkar , Sabine Peres

PLoS ONE, 2024, 19 (12), pp.e0313962. ⟨10.1371/journal.pone.0313962⟩

Article dans une revue hal-04873696v1
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Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy

Camille Siharath , Olivier Biondi , Sabine Peres

Heliyon, 2024, 10 (24), pp.e40918. ⟨10.1016/j.heliyon.2024.e40918⟩

Article dans une revue hal-04845028v1
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Special Issue on “Frontiers in Connecting Steady-State and Dynamic Approaches for Modelling Cell Metabolic Behavior”

Sabine Peres , Mario Jolicoeur

Processes, 2022, Frontiers in Connecting Steady-State and Dynamic Approaches for Modelling Cell Metabolic Behavior), 10 (8), pp.1612. ⟨10.3390/pr10081612⟩

Article dans une revue hal-03903344v1
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Combining Kinetic and Constraint-Based Modelling to Better Understand Metabolism Dynamics

Cecile Moulin , Laurent Tournier , Sabine S. Peres

Processes, 2021, 9 (10), pp.1701. ⟨10.3390/pr9101701⟩

Article dans une revue hal-03592743v1

Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

Jorgelindo da Veiga Moreira , Mario Jolicoeur , Laurent Schwartz , Sabine Peres

Scientific Reports, 2021, 11 (1), pp.878. ⟨10.1038/s41598-020-79577-4⟩

Article dans une revue hal-03209507v1

Cancer and Alzheimer’s disease: intracellular pH scales the metabolic disorders

Laurent Schwartz , Sabine S. Peres , Mario Jolicoeur , Jorgelindo da Veiga Moreira

Biogerontology, 2020, 21 (6), pp.683-694. ⟨10.1007/s10522-020-09888-6⟩

Article dans une revue hal-02968151v1
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Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Maxime Mahout , Ross Carlson , Sabine Peres

Processes, 2020, 8 (12), pp.1649. ⟨10.3390/pr8121649⟩

Article dans une revue hal-03209519v1
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A kinetic metabolic study of lipid production in Chlorella protothecoides under heterotrophic condition

Xiaojie Ren , Jean-Sébastien Deschênes , Réjean Tremblay , Sabine Pérès , Mario Jolicœur

Microbial Cell Factories, 2019, 18 (1), pp.113. ⟨10.1186/s12934-019-1163-4⟩

Article dans une revue hal-02531282v1
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Metabolic therapies inhibit tumor growth in vivo and in silico

Jorgelindo da Veiga Moreira , Minoo Hamraz , Mohammad Abolhassani , Laurent H Schwartz , Mario Jolicœur et al.

Scientific Reports, 2019, 9 (1), pp.3153. ⟨10.1038/s41598-019-39109-1⟩

Article dans une revue hal-02392935v1

Thermodynamic constraints for identifying elementary flux modes

Sabine Pérès , Stefan Schuster , Philippe Dague

Biochemical Society Transactions, 2018, 46 (3), pp.641-647. ⟨10.1042/BST20170260⟩

Article dans une revue hal-01802074v1

Identifying Biomarkers of Wharton’s Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect

Benoît Laflaquière , Gabrielle Leclercq , Chandarong Choey , Jingkui Chen , Sabine Pérès et al.

Metabolites, 2018, 8 (1), pp.18. ⟨10.3390/metabo8010018⟩

Article dans une revue hal-01784012v1
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How important is thermodynamics for identifying elementary flux modes?

Sabine Pérès , Mario Jolicœur , Cecile Moulin , Philippe Dague , Stefan Schuster

PLoS ONE, 2017, 12 (2), pp.e0171440. ⟨10.1371/journal.pone.0171440⟩

Article dans une revue hal-01709642v1

A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Xinhe Zhao , Mayssa Kasbi , Jingkui Chen , Sabine Pérès , Mario Jolicœur

Biotechnology and Bioengineering, 2017, 114 (12), pp.2907 - 2919. ⟨10.1002/bit.26393⟩

Article dans une revue hal-01709638v1
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The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect

Jorgelindo da Veiga Moreira , Minoo Hamraz , Mohammad Abolhassani , Erwan Bigan , Sabine Pérès et al.

Metabolites, 2016, 6 (4), 12 p. ⟨10.3390/metabo6040033⟩

Article dans une revue hal-01417967v1
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Cell cycle progression is regulated by intertwined redox oscillators

Jorgelindo da Veiga Moreira , Sabine Pérès , Jean-Marc Steyaert , Erwan Bigan , Loïc Paulevé et al.

Theoretical Biology and Medical Modelling, 2015, 12 (1), pp.10. ⟨10.1186/s12976-015-0005-2⟩

Article dans une revue hal-01158514v1

Elementary Flux Modes Analysis of Functional Domain Networks Allows a Better Metabolic Pathway Interpretation

Sabine Pérès , Liza L. Felicori , Franck Molina

PLoS ONE, 2013, 8 (10), ⟨10.1371/journal.pone.0076143⟩

Article dans une revue hal-01709661v1

ACoM: A classification method for elementary flux modes based on motif finding

Sabine Pérès , Francois Vallee , Marie M. Beurton-Aimar , Jean-Pierre Mazat

BioSystems, 2011, 103 (3), pp.410-419

Article dans une revue hal-00629161v1

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome

Laurence Molina , Nicolas Salvetat , Randa Ben Ameur , Sabine Pérès , Nicolas Sommerer et al.

Journal of Proteomics, 2011, 75 (1), pp.70 - 80. ⟨10.1016/j.jprot.2011.06.031⟩

Article dans une revue istex hal-02652376v1

Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

Sabine Peres , Liza Felicori , Stéphanie Rialle , Elodie Jobard , Franck Molina

Bioinformatics, 2010, 26 (12), pp.1542-1547. ⟨10.1093/bioinformatics/btq169⟩

Article dans une revue hal-04814816v1

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

Stéphanie Rialle , Liza Felicori , Camila Dias-Lopes , Sabine Peres , Sanaâ El Atia et al.

Bioinformatics, 2010, 26 (18), pp.2298-2304. ⟨10.1093/bioinformatics/btq409⟩

Article dans une revue hal-04814810v1

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

Sabine Peres , Laurence Molina , Nicolas Salvetat , Claude Granier , Franck Molina

BMC Bioinformatics, 2008, 9 (1), pp.460. ⟨10.1186/1471-2105-9-460⟩

Article dans une revue hal-04814821v1

Structure et modélisation des réseaux métaboliques

Jean-Pierre Mazat , Christine Nazaret , Sabine Pérès

Biofutur, 2007, 275, pp.29-33

Article dans une revue hal-00282723v1

Mycotoxin fumonisin B-1 selectively down-regulates the basal IL-8 expression in pig intestine: in vivo and in vitro studies

S Bouhet , E Le Dorze , Sabine Pérès , Jm Fairbrother , Isabelle P. Oswald

Food and Chemical Toxicology, 2006, 44 (10), pp.1768-1773

Article dans une revue hal-02665625v1

Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa

Sabine Peres , Comet Jean-Paul

Lecture Notes in Computer Science, 2003, Lecture Notes in Computer Science, 2602, pp.47-56. ⟨10.1007/3-540-36481-1_5⟩

Article dans une revue hal-04814744v1
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Computing Thermodynamically Consistent Elementary Flux Modes with Answer Set Programming

Emma Crisci , Maxime Mahout , Sabine Peres

CMSB 2024 - 22nd International Conference Computational Methods in Systems Biology, Sep 2024, Pise, Italy. pp.80-88, ⟨10.1007/978-3-031-71671-3_7⟩

Communication dans un congrès hal-04707880v1

Hybrid modelling to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres

BIOSTEC 2023, Feb 2023, Lisbon (Portugal), Portugal

Communication dans un congrès hal-04036239v1

Minimal Cut Sets of a Consortium Model of P. aeruginosa and S. aureus Reveal New Cross-Feeding Interactions

Maxime Mahout , Sabine Peres

Metabolic Pathway Analysis 2023, Jul 2023, Séoul [en ligne], South Korea

Communication dans un congrès hal-04392553v1

Mod ́elisation m ́etabolique pour identifier de nouvelles strat ́egies de contrˆole des organismes vivants

Sabine Peres

Meetochondrie, May 2022, Lège-Cap-Ferret, France

Communication dans un congrès hal-03903355v1

Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres , Marc Dinh , Vincent Fromion

International Conference on System Biology, Oct 2022, Berlin, Germany

Communication dans un congrès hal-03903360v1

Hybrid metabolic modeling to identify new control strategies of living organisms

Sabine Peres

Hybrid models and methods in systems medicine, Jul 2022, Paris, France

Communication dans un congrès hal-03903353v1

Answer set programming to compute constraint elementary flux modes

Maxime Mahout , Laurent Simon , Sabine Peres

Metabolic Pathway Analysis, Aug 2021, Knoxville, United States

Communication dans un congrès hal-03903367v1

Answer set programming to compute constraint elementary flux modes

Maxime Mahout , Laurent Simon , Sabine Peres

Computational Methods in System Biology, Sep 2021, Bordeaux, France

Communication dans un congrès hal-03903363v1

Using a hybrid approach to model central carbon metabolism across the cell cycle

Cecile Moulin , Laurent Tournier , Sabine Pérès

International Workshop on Hybrid Systems Biology, Apr 2019, Prague, Czech Republic. ⟨10.1007/978-3-030-28042-0_9⟩

Communication dans un congrès hal-02791386v1

Modulating mitochondria horsepower for biotechnological applications

Jorgelindo da Veiga Moreira , Laurent Schwartz , Sabine S. Peres

Metabolic Pathway Analysis 2019, Aug 2019, Riga, Latvia

Communication dans un congrès hal-03230443v1

Metabolic view of tumor growth: a kinetic model to screen potential therapeutic targets

Sabine Pérès

Computational systems biology for cancer, Jan 2018, Paris, France

Communication dans un congrès hal-01802079v1

HSM a reduced model of Central Carbon Metabolism: a dynamical approach

Bertrand Beauvoit , Sophie Colombie , Razanne Issa , Jean-Pierre Mazat , Christine Nazaret et al.

advances in Systems and Synthetic Biology, Mar 2017, Lyon, France

Communication dans un congrès hal-01709748v1

Computing EFMs consistent with equilibrium constants

Sabine Pérès , Philippe Dague , Mario Jolicœur , Stefan Schuster

Metabolic Pathway Analysis MPA 2017, Jul 2017, Bozeman, United States

Communication dans un congrès hal-01676892v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent Fromion et al.

IC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France

Communication dans un congrès hal-02741418v1

Minimality of Metabolic Flux Modes under Boolean Regulation Constraints

Morterol Martin , Philippe Dague , Sabine Pérès , Laurent Simon

12th International Workshop on Constraint-Based Methods for Bioinformatics WCB’16, Sep 2016, Toulouse, France

Communication dans un congrès hal-01483433v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent J. Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent V. Fromion et al.

IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France

Communication dans un congrès hal-01442727v1

Human-Scale Metabolic Network of Central Carbon Metabolism: application to serine metabolism from glutamine in Cancer Cells

Bertrand Beauvoit , Sophie Colombie , Razanne Issa , Jean-Pierre Mazat , Christine Nazaret et al.

advances in Systems and Synthetic Biology, Mar 2016, Evry, France

Communication dans un congrès hal-01709760v1

Systematic study of a metabolic network

Bertrand P Beauvoit , Sophie Colombié , Jean-Pierre Mazat , Christine Nazaret , Sabine Pérès

advances in Systems and Synthetic Biology, Mar 2014, Evry, France. 173 p

Communication dans un congrès hal-01108859v1

SAT-Based Metabolics Pathways Analysis without Compilation

Sabine Pérès , Morterol Martin , Laurent Simon

CMSB 2014, Nov 2014, Manchester, United Kingdom

Communication dans un congrès hal-01108840v1

Analysis of metabolic networks using elementary flux modes

Sabine Pérès

Advances in systems and synthetic biology, Mar 2013, La Colle-sur-Loup, France. pp.165--170

Communication dans un congrès hal-00946692v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.

JOBIM2010, Sep 2010, Montpellier, France

Communication dans un congrès hal-02753839v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.

Séminaire Génomique Végétale, Mar 2010, Pont-Royal en Provence, France

Communication dans un congrès hal-02752562v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.

18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Jul 2010, Boston, United States

Communication dans un congrès hal-02753301v1

Thermodynamic Approaches in Flux Analysis

Sabine S. Peres , Vincent Fromion

Metabolic Flux Analysis in Eukaryotic Cells, Humana, pp.359-367, 2020, Methods in Molecular Biology, ⟨10.1007/978-1-0716-0159-4_17⟩

Chapitre d'ouvrage hal-02968157v1