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 50 in total

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 . 19 ( 12 ) : e0313962

DOI: 10.1371/journal.pone.0313962

Journal article

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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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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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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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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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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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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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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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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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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, Sabine Pérès

advances in Systems and Synthetic Biology .

Conference paper

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