Wolfram Liebermeister

52
Documents

Publications

Publications

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Balancing Metabolic Homeostasis and Enzyme Cost with Multi-Objective Evolutionary Algorithms

Arthur Lequertier , Wolfram Liebermeister , Alberto Tonda
GECCO 2025, Jul 2025, Malaga, Espagne, Spain. pp.1
Poster de conférence hal-05195025 v1
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Inferring Reaction Elasticities from Metabolic Correlations in Cells through Multi-objective Evolutionary Optimization

Arthur Lequertier , Wolfram Liebermeister , Alberto Tonda
EvoStar 2025, Apr 2025, Trieste, Italy
Poster de conférence hal-05085279 v1
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Information Transmission Through State Perturbations in Metabolic Networks

Arthur Lequertier , Wolfram Liebermeister
ECMTB 2024, Jul 2024, Toledo (ESP), Spain
Poster de conférence hal-05085176 v1
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Complexity Reduction by Symmetry: Uncovering the minimal regulatory network for logical computation in bacteria

Luis A Álvarez-García , Wolfram Liebermeister , Ian Leifer , Hernán A. Makse
NetSci 2024, Jun 2024, Québec City, France
Poster de conférence hal-05195042 v1
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Information transmission through state perturbations in metabolic networks

Arthur Lequertier , Wolfram Liebermeister
ISMB-ECCB 2023, Jul 2023, Lyon, France.
Poster de conférence hal-04379407 v1
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rbatools -a programming interface to cellular resource allocation modelling with Resource Balance Analysis

Oliver Bodeit , Wolfram Liebermeister , Anne Goelzer
Metabolic Pathway Analysis, Aug 2021, Knoxville, United States
Poster de conférence hal-04426315 v1

Enzyme economy in metabolic networks

Wolfram Liebermeister
ICSB 2018, Oct 2018, Lyon, France. , 2018
Poster de conférence hal-02786771 v1
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Growth Mechanics and the emergence of metabolic oscillations in growing cells

Hugo Dourado , Chilperic Armel Foko Kuate , Wolfram Liebermeister , Martin Lercher
2025
Pré-publication, Document de travail hal-05134103 v1
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Optimal enzyme profiles in unbranched metabolic pathways

Elad Noor , Wolfram Liebermeister
2023
Pré-publication, Document de travail hal-04149785 v1
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Fibration symmetry uncovers minimal regulatory networks for logical computation in bacteria

Luis A. Álvarez-García , Wolfram Liebermeister , Ian Leifer , Hernán A. Makse
2023
Pré-publication, Document de travail hal-04247231 v1
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BioSimulators: a central registry of simulation engines and services for recommending specific tools

Bilal Shaikh , Lucian Smith , Dan Vasilescu , Gnaneswara Marupilla , Michael Wilson et al.
2022
Pré-publication, Document de travail hal-03613651 v1
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Artificial Metabolic Networks: enabling neural computation with metabolic networks

Léon Faure , Bastien Mollet , Wolfram Liebermeister , Jean-Loup Faulon
2022
Pré-publication, Document de travail hal-03613655 v2

Structural thermokinetic modelling

Wolfram Liebermeister
2022
Pré-publication, Document de travail hal-03613706 v1

Growth Mechanics: General principles of optimal cellular resource allocation in balanced growth

Hugo Dourado , Wolfram Liebermeister , Oliver Ebenhoeh , Martin Lercher
2022
Pré-publication, Document de travail hal-03834977 v1
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ObjTables: structured spreadsheets that promote data quality, reuse, and integration

Jonathan R Karr , Wolfram Liebermeister , Arthur P Goldberg , John a P Sekar , Bilal Shaikh
2021
Pré-publication, Document de travail hal-03337093 v1
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Model balancing: consistent in-vivo kinetic constants and metabolic states obtained by convex optimisation

Wolfram Liebermeister
2019
Pré-publication, Document de travail (preprint/prepublication) hal-02437604 v1

Flux cost functions and the choice of metabolic fluxes

Wolfram Liebermeister
2018
Pré-publication, Document de travail (preprint/prepublication) hal-02790668 v1
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Optimal metabolic states in cells

Wolfram Liebermeister
2018
Pré-publication, Document de travail (preprint/prepublication) hal-02790125 v1
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The value structure of metabolic states

Wolfram Liebermeister
2018
Pré-publication, Document de travail (preprint/prepublication) hal-02791023 v1
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Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria

Luis A Álvarez-García , Wolfram Liebermeister , Ian Leifer , Hernán A Makse
PLoS Computational Biology, 2025, 21 (4), pp.e1013005. ⟨10.1371/journal.pcbi.1013005⟩
Article dans une revue hal-05056721 v1
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A compact model of Escherichia coli core and biosynthetic metabolism

Marco Corrao , Hai He , Wolfram Liebermeister , Elad Noor , Arren Bar-Even
PLoS Computational Biology, 2025, 21 (10), pp.e1013564. ⟨10.1371/journal.pcbi.1013564⟩
Article dans une revue hal-05056734 v2
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Optimal enzyme profiles in unbranched metabolic pathways

Elad Noor , Wolfram Liebermeister
Interface Focus, 2024, 14, pp.20230029. ⟨10.1098/rsfs.2023.0029⟩
Article dans une revue hal-04448194 v1
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A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Léon Faure , Bastien Mollet , Wolfram Liebermeister , Jean-Loup Faulon
Nature Communications, 2023, 14, pp.4669. ⟨10.1038/s41467-023-40380-0⟩
Article dans une revue hal-04178761 v1
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Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

Hugo Dourado , Wolfram Liebermeister , Oliver Ebenhöh , Martin J Lercher
PLoS Computational Biology, 2023, 19 (6), pp.e1011156. ⟨10.1371/journal.pcbi.1011156⟩
Article dans une revue hal-04131693 v1
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RBAtools: a programming interface for Resource Balance Analysis models

Oliver Bodeit , Inès Ben Samir , Jonathan R Karr , Anne Goelzer , Wolfram Liebermeister
Bioinformatics Advances, 2023, pp.1-4. ⟨10.1093/bioadv/vbad056⟩
Article dans une revue hal-04093676 v1
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Structural thermokinetic modelling

Wolfram Liebermeister
Metabolites, 2022, 12 (5), pp.1-53. ⟨10.3390/metabo12050434⟩
Article dans une revue hal-03666375 v1
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Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States

Wolfram Liebermeister , Elad Noor
Metabolites, 2021, 11 (749), pp.1-19. ⟨10.3390/metabo11110749⟩
Article dans une revue hal-03410872 v1
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SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah Keating , Frank Bergmann , Tomáš Helikar , Rahuman Malik‐sheriff , Ion Moraru et al.
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Article dans une revue (article de synthèse) hal-02924909 v1
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Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs

Thierry D G A Mondeel , Oleksandr Ivanov , Hans V Westerhoff , Wolfram Liebermeister , Matteo Barberis
npj Systems Biology and Applications, 2020, ⟨10.1038/s41540-020-0125-0⟩
Article dans une revue hal-02538622 v1
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Automated generation of bacterial resource allocation models

Ana Bulovic , Stéphan Fischer , Marc Dinh , Felipe Golib , Wolfram Liebermeister et al.
Metabolic Engineering, 2019, 55, pp.12-22. ⟨10.1016/j.ymben.2019.06.001⟩
Article dans une revue hal-02623933 v1

Parameter balancing: consistent parameter sets for kinetic metabolic models

Timo Lubitz , Wolfram Liebermeister
Bioinformatics, 2019, 35 (19), pp.1-2. ⟨10.1093/bioinformatics/btz129⟩
Article dans une revue hal-02273374 v1

Metabolite–Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks

Lianet Noda-Garcia , Dan S. Tawfik , Wolfram Liebermeister
Annual Review of Biochemistry, 2018, 87 (1), pp.187-216. ⟨10.1146/annurev-biochem-062917-012023⟩
Article dans une revue (article de synthèse) hal-02020715 v1
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Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Meike T. Wortel , Elad Noor , Michael Ferris , Frank J. Bruggeman , Wolfram Liebermeister
PLoS Computational Biology, 2018, 14 (2), 21 p. ⟨10.1371/journal.pcbi.1006010⟩
Article dans une revue hal-02625591 v1
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Toward Community Standards and Software for Whole-Cell Modeling

Dagmar Waltemath , Jonathan Karr , Frank Bergmann , Vijayalakshmi Chelliah , Michael Hucka et al.
IEEE Transactions on Biomedical Engineering, 2016, 63 (10), pp.2007-2014. ⟨10.1109/TBME.2016.2560762⟩
Article dans une revue hal-04361601 v1

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

Pierre P. Nicolas , Ulrike U. Mäder , Etienne Dervyn , Tatiana Rochat , Aurelie A. Leduc et al.
Science, 2012, 335 (6072), pp.1103-1106. ⟨10.1126/science.1206848⟩
Article dans une revue hal-01000245 v1

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

P. Nicolas , U. Mader , Etienne Dervyn , T. Rochat , A. Leduc et al.
Science, 2012, 335 (6072), pp.1103-1106. ⟨10.1126/science.1206848⟩
Article dans une revue hal-03343060 v1
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Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

Joerg Martin Buescher , Wolfram Liebermeister , Matthieu Jules , Markus Uhr , Jan Muntel et al.
Science, 2012, 335 (6072), pp. 1099-1103. ⟨10.1126/science.1206871⟩
Article dans une revue hal-03968015 v1

Hybrid models for neural computations with metabolism

Léon Faure , Bastien Mollet , Wolfram Liebermeister , Jean-Loup Faulon
University of Stuttgart seminatr series, University of Stuttgart, Jun 2022, Stuttgart, Germany
Communication dans un congrès hal-04275845 v1

A simple thermodynamic relation, very useful for metabolic modelling

Wolfram Liebermeister
Workshop "Principles of Microbial Adaptation", Mar 2018, Leiden, Netherlands
Communication dans un congrès hal-02786772 v1