GECO Evolutionary and Computational Genomics

Baobab Group

Peres Sabine

Professeur des universités

UCBL

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 04 72 44 81 42

Email

Systems biology - Biological networks modelling

Metabolic Pathway Analysis

  • Constraint-based modelling
  • Logic programming
  • Thermodynamics

Cancer metabolism

  • Metabolic rerouting
  • Dynamic modelling
  • Metabolic therapies

Publications

Display of 1 to 30 publications on 49 in total

Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy

Camille Siharath, Olivier Biondi, Sabine Peres

Heliyon . 10 ( 24 ) : e40918

DOI: 10.1016/j.heliyon.2024.e40918

Journal article

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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 . LNCS-14971 : 80-88

DOI: 10.1007/978-3-031-71671-3_7

Conference paper

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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 . 10 ( 1 ) : 34

DOI: 10.1038/s41540-024-00360-6

Journal article

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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 .

Conference paper

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

Sabine Peres

BIOSTEC 2023 .

Conference paper

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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 .

Conference paper

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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 . 10 ( 8 ) : 1612

DOI: 10.3390/pr10081612

Journal article

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Hybrid metabolic modeling to identify new control strategies of living organisms

Sabine Peres

Hybrid models and methods in systems medicine .

Conference paper

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

Sabine Peres

Meetochondrie .

Conference paper

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Answer set programming to compute constraint elementary flux modes

Maxime Mahout, Laurent Simon, Sabine Peres

Computational Methods in System Biology .

Conference paper

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Answer set programming to compute constraint elementary flux modes.

Maxime Mahout, Laurent Simon, Sabine Peres

Metabolic Pathway Analysis .

Conference paper

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Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

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

Scientific Reports . 11 ( 1 ) : 878

DOI: 10.1038/s41598-020-79577-4

Journal article

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Combining Kinetic and Constraint-Based Modelling to Better Understand Metabolism Dynamics

Cecile Moulin, Laurent Tournier, Sabine S. Peres

Processes . 9 ( 10 ) : 1701

DOI: 10.3390/pr9101701

Journal article

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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 . 8 ( 12 ) : 1649

DOI: 10.3390/pr8121649

Journal article

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

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

Biogerontology . 21 ( 6 ) : 683-694

DOI: 10.1007/s10522-020-09888-6

Journal article

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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 . 18 ( 1 ) : 113

DOI: 10.1186/s12934-019-1163-4

Journal article

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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, Sabine Pérès

Scientific Reports . 9 ( 1 ) : 3153

DOI: 10.1038/s41598-019-39109-1

Journal article

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Modulating mitochondria horsepower for biotechnological applications

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

Metabolic Pathway Analysis 2019 .

Conference paper

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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 . 11705

DOI: 10.1007/978-3-030-28042-0_9

Conference paper

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Thermodynamic constraints for identifying elementary flux modes

Sabine Pérès, Stefan Schuster, Philippe Dague

Biochemical Society Transactions . 46 ( 3 ) : 641-647

DOI: 10.1042/BST20170260

Journal article

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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, Caryn Ito...

Metabolites . 8 ( 1 ) : 18

DOI: 10.3390/metabo8010018

Journal article

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

Sabine Pérès

Computational systems biology for cancer .

Conference paper

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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 . 114 ( 12 ) : 2907 - 2919

DOI: 10.1002/bit.26393

Journal article

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Computing EFMs consistent with equilibrium constants

Sabine Pérès, Philippe Dague, Mario Jolicœur, Stefan Schuster

Metabolic Pathway Analysis MPA 2017 .

Conference paper

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

Bertrand Beauvoit, Sophie Colombie, Razanne Issa, Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

advances in Systems and Synthetic Biology .

Conference paper

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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 . 12 ( 2 ) : e0171440

DOI: 10.1371/journal.pone.0171440

Journal article

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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 .

Conference paper

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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, Sarah Cohen-Boulakia...

IC2016 - Ingénierie des Connaissances .

Conference paper

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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent Fromion, Sarah Cohen-Boulakia...

IC201: 27es Journées francophones d'Ingénierie des Connaissances .

Conference paper

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