Sabine Peres

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Publications

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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-04845028 v1
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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-04610153 v1
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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-04873696 v1
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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-03903344 v1
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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-03592743 v1

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-03209507 v1

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-02968151 v1
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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-03209519 v1
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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-02531282 v1
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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-02392935 v1

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-01784012 v1

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-01802074 v1
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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-01709642 v1

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-01709638 v1
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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-01417967 v1
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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-01158514 v1

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-01709661 v1

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-02652376 v1

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-00629161 v1

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-04814816 v1

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-04814810 v1

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-04814821 v1

Structure et modélisation des réseaux métaboliques

Jean-Pierre Mazat , Christine Nazaret , Sabine Pérès
Biofutur, 2007, 275, pp.29-33
Article dans une revue hal-00282723 v1

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-02665625 v1

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

Sabine Peres , Comet Jean-Paul
Lecture Notes in Computer Sciences, 2003, Lecture Notes in Computer Science, 2602, pp.47-56. ⟨10.1007/3-540-36481-1_5⟩
Article dans une revue hal-04814744 v1
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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-04707880 v1

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-04036239 v1

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-04392553 v1

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-03903353 v1

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-03903355 v1

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-03903360 v1

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-03903367 v1

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-03903363 v1

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-02791386 v1

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-03230443 v1

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-01802079 v1

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-01709748 v1

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-01676892 v1

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-01709760 v1

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-01483433 v1
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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-01442727 v1
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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-02741418 v1

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-01108859 v1

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-01108840 v1

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-00946692 v1

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-02753839 v1

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-02752562 v1

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-02753301 v1

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-02968157 v1