Wolfram Liebermeister

Wolfram Liebermeister
wolfram.liebermeister@gmail.com



INRAE - Unité MaIAGE
Domaine de Vilvert
78352 Jouy-en-Josas, France
Website   |   Projects   |   Publications   |   Presentations   |   Teaching   |   Textbook   |   Personal

All publications / Selected publications

Preprints

  1. A compact model of Escherichia coli core and biosynthetic metabolism
    Corrao M., He H., Liebermeister W., Noor E., Bar-Even A. (2024)
    arXiv:2406.16596
  2. Fibration symmetry uncovers minimal regulatory networks for logical computation in bacteria
    Álvarez-García L.A., Liebermeister W., Leifer I., Makse H.A. (2023)
    arXiv:2310.10895
  3. ObjTables: structured spreadsheets that promote data quality, reuse, and integration
    Karr J.R., Liebermeister W., Goldberg A.P., Sekar J.A.P., Shaikh B. (2020)
    arXiv:2005.05227
  4. Optimal metabolic states in cells
    Liebermeister W. (2018/2022)
    bioRxiv doi:10.1101/483867
  5. The value structure of metabolic states
    Liebermeister W. (2018/2022)
    bioRxiv doi:10.1101/483891
  6. Flux cost functions and optimal metabolic states
    Liebermeister W. (2018/2022)
    arXiv:1801.05742
  7. Optimal enzyme rhythms in cells
    Liebermeister W. (2016/2022)
    arXiv:1602.05167
  8. Enzyme economy and metabolic control
    Liebermeister W. (2014/2022)
    arXiv:1404.5252
  9. Metabolic fluxes and value production
    Liebermeister W. (2014/2022)
    arXiv:1404.5072

Commentaries

  1. How mammals adapt their breath to body activity – and how this depends on body size.
    Recommendation for PCI Math Comp Biol (2021)
    doi.org/10.24072/pci.mcb.100005

Journal articles

  1. Optimal enzyme profiles in unbranched metabolic pathways
    Noor E. and Liebermeister W. (2024)
    Interface Focus 14 (1), Special Issue "50 Years of metabolic control analysis"
  2. A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
    Faure L., Mollet B., Liebermeister W., Faulon J.-L. (2023)
    Nature Communications 14, 4669
  3. Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth
    Dourado H., Liebermeister W., Ebenhöh O., Lercher M.J. (2023)
    PLoS Computational Biology, doi 10.1371/journal.pcbi.1011156
  4. RBAtools: a programming interface for Resource Balance Analysis models
    Bodeit O., Ben Samir I., Karr J.R., Goelzer A., Liebermeister W. (2023)
    Bioinformatics Advances, vbad056
  5. Structural thermokinetic modelling
    Liebermeister W. (2022)
    Metabolites 12(5), 434
  6. BioSimulators: a central registry of simulation engines and services for recommending specific tools
    Shaikh B., Smith L.P., Vasilescu D., Marupilla G., et al. (2022)
    Nucleic Acids Research, gkac331
  7. Model Balancing: a search for in-vivo kinetic constants and consistent metabolic states
    Liebermeister W. and Noor E. (2021)
    Metabolites 11(11), 749
  8. SBML Level 3: an extensible format for the exchange and reuse of biological models
    Keating S.M. et al. (2020)
    Molecular Systems Biology (2020)16:e9110
  9. Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs
    Mondeel T.D.G.A., Ivanov O., Westerhoff H.V., Liebermeister W., Barberis M. (2020)
    npj Systems Biology and Applications 6, Article number: 8
  10. Automated generation of bacterial resource allocation models
    Bulović A., Fischer S., Dinh M., Golib F., Liebermeister W., Poirier C., Tournier L., Klipp E., Fromion V., Goelzer A. (2019),
    Metabolic Engineering 55 (2019) 12–22
  11. Parameter balancing: consistent parameter sets for kinetic metabolic models
    Lubitz T. and Liebermeister W. (2019),
    Bioinformatics 35 (19) 3857
  12. Metabolite–enzyme coevolution: from single enzymes to metabolic pathways and networks
    Noda-Garcia L., Liebermeister W., and Tawfik D.S. (2018),
    Annual Review of Biochemistry (87): 187-216 [pdf]
  13. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield
    Wortel M.T., Noor E., Ferris M., Bruggeman F.J., Liebermeister W. (2018),
    PLoS Computational Biology 14(2): e1006010.
  14. The protein cost of metabolic fluxes: prediction from enzymatic rate laws and cost minimization
    Noor E., Flamholz A., Bar-Even A., Davidi D., Milo R., Liebermeister W. (2016),
    PLoS Computational Biology 12 (10): e1005167. [convexity proof on arXiv]
  15. Notions of similarity for systems biology models
    Henkel R., Hoehndorf R., Kacprowski T., Knüpfer C., Liebermeister W., Waltemath D. (2016),
    Briefings in Bioinformatics, doi 10.1093/bib/bbw090 [preprint on bioRxiv]
  16. Toward community standards and software for whole-cell modeling
    Waltemath D. , Karr J. , Bergmann F. , Chelliah V. , Hucka M. , Krantz M., Liebermeister W., Mendes P., Myers C., Pir P., Alaybeyoglu B., Aranganathan N., Baghalian K., Bittig A., Burke P., Cantarelli M., Chew Y., Costa R., Cursons J., Czauderna T., Goldberg A., Gomez H., Hahn J., Hameri T., Gardiol D., Kazakiewicz D., Kiselev I., Knight-Schrijver V., Knüpfer C., König M., Lee D., Lloret-Villas A., Mandrik N., Medley J., Moreau B., Naderi-Meshkin H., Palaniappan S., Priego-Espinosa D., Scharm M., Sharma M., Smallbone K., Stanford N., Song J. H., Theile T., Tokic M., Tomar N., Toure V., Uhlendorf J., Varusai T., Watanabe L., Wendland F., Wolfien M., Yurkovich J., Zhu Y., Zardilis A., Zhukova A., Schreiber F. (2016)
    IEEE Transactions on Biomedical Engineering
  17. SBtab: A flexible table format for data exchange in systems biology
    Lubitz T., Hahn J., Bergmann F.T., Noor E., Klipp E., Liebermeister W. (2016)
    Bioinformatics 32 (16) 2559–2561
  18. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
    Davidi D., Noor E., Liebermeister W., Bar-Even A., Flamholz A., Tummler K., Barenholz U., Goldenfeld M., Shlomi T., Milo R. (2016)
    PNAS 113 (12) 3401-3406
  19. Visual account of protein investment in cellular functions
    Liebermeister W., Noor E., Flamholz A., Davidi D., Bernhardt J., Milo R. (2014)
    PNAS 111 (23), 8488-8493
  20. Pathway thermodynamics highlights kinetic obstacles in central metabolism
    Noor E., Bar-Even A., Flamholz A., Reznik E., Liebermeister W., Milo R. (2014)
    PLoS Computational Biology 10 (2) e1003483
  21. Systematic construction of kinetic models from genome-scale metabolic networks
    Stanford N.J., Lubitz T., Smallbone K., Klipp E., Mendes P., Liebermeister W. (2013)
    PLoS ONE 8(11): E79195
  22. Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load
    Tepper N., Noor E., Amador-Noguez D., Haraldsdóttir H.S., Milo R., Rabinowitz J., Liebermeister W., Shlomi T. (2013)
    PLoS ONE 8(9): e75370
  23. A note on the kinetics of enzyme action: a decomposition that highlights thermodynamic effects
    Noor E., Flamholz A., Liebermeister W., Bar-Even A., Milo R. (2013)
    FEBS Letters 587(17): 2772-2777.
  24. Glycolytic strategy as a tradeoff between energy yield and protein cost
    Flamholz A., Noor E., Bar-Even A., Liebermeister W., Milo R. (2013)
    PNAS 110(24): 10039-10044.
  25. Spanning high-dimensional expression space using ribosome-binding site combinatorics
    Zelcbuch L., Antonovsky N., Bar-Even A., Levin-Karp A., Barenholz U., Dayagi M., Liebermeister W., Flamholz A., Noor E., Amram S., Brandis A., Bareia T., Yofe I., Jubran H., Milo R. (2013)
    Nucleic Acids Res. 41(9):e98.
  26. Shapes and deformations of polyhedral rings formed by corpuscle elements
    Wohlleben E. and Liebermeister W. (2012)
    Journal for Geometry and Graphics 16 (1), 59-67.
    [Preprint pdf]
  27. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
    Buescher J.M., Liebermeister W. , Jules M., Uhr M., Muntel J., Botella E. , Hessling B. , Kleijn R.J., Le Chat L., Lecointe F., Mäder U., Nicolas P., Piersma S., Rügheimer F., Becher D., Bessieres P., Bidnenko E., Denham E.L., Dervyn E., Devine K.M., Doherty G., Drulhe S., Felicori L., Fogg M.J., Goelzer A., Hansen A., Harwood C.R., Hecker M., Hubner S., Hultschig C., Jarmer H., Klipp E., Leduc A., Lewis P., Molina F., Noirot P., Peres S. , Pigeonneau N., Pohl S., Rasmussen S., Rinn B., Schaffer M., Schnidder J., Schwikowski B., van Dijl J.M., Veiga P., Walsh S., Wilkinson A.J., Stelling J., Aymerich S., Sauer U. (2012)
    Science 335 (6072), 1099-1103.
    [Abstract]
  28. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
    Nicolas P., Mäder U., Dervyn E., Rochat T., Leduc A., Pigeonneau N., Bidnenko E., Marchadier E., Hoebeke M., Aymerich S., Becher D., Bisicchia P., Botella E., Delumeau O., Doherty G., Denham E.L., Fogg M.J., Fromion V., Goelzer A., Hansen A., Härtig E., Harwood C.R., Homuth G., Jarmer H., Jules M., Klipp E., Le Chat L., Lecointe F., Lewis P., Liebermeister W., March A., Mars R.A.T., Nannapaneni P., Noone D., Pohl S., Rinn B., Rügheimer F., Sappa P.K., Samson F., Schaffer M., Schwikowski B., Steil L., Stülke J., Wiegert T., Devine K.M., Wilkinson A.J., van Dijl J.M., Hecker M., Völker U., Bessieres P., Noirot P. (2012)
    Science 335 (6072), 1103-1106.
    [Abstract]
  29. Propagating semantic information in biochemical network models
    Schulz M., Klipp E., Liebermeister W. (2012)
    BMC Bioinformatics 13:18.
  30. Retrieval, alignment, and clustering of computational models based on semantic annotations
    Schulz M., Krause F., Le Novère N., Klipp E., Liebermeister W. (2011)
    Molecular Systems Biology 7, Article number: 512.
  31. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters
    Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik DS., Milo R. (2011)
    Biochemistry 50 (21): 4402-4410.
    [Abstract]
  32. Parameter balancing in kinetic models of cell metabolism
    Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010)
    Journal of Physical Chemistry B 114(49):16298-16303.
  33. Integrating quantitative proteomics and metabolomics with a genome-scale metabolic model
    Yizhak K., Benyamini T., Liebermeister W., Ruppin E., Shlomi T. (2010)
    ISMB 2010. Bioinformatics 26 (12) Pp. i255-i260. [pdf]
  34. Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation
    Liebermeister W., Uhlendorf J., Klipp E. (2010)
    Bioinformatics 26(12):1528-1534. [pdf]
  35. A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae
    Zhi Z., Liebermeister W., Klipp E. (2010)
    PLoS One 5 (3), e9522. [pdf]
  36. Annotation and merging of SBML models with semanticSBML
    Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010)
    Bioinformatics 26 (3), 421-422. [pdf] [semanticSBML website]
  37. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    Herrgard M. J., Swainston N., Dobson P., Dunn W. B., Arga K. Y., Arvas M., Blüthgen N., Borger S., Costenoble R., Heinemann M., Hucka M., Le Novere N., Li P., Liebermeister W., Mo M. L., Oliveira A. P., Petranovic D., Pettifer S., Simeonidis E., Smallbone K., Spasie I., Weichart D., Brent R., Broomhead D. S., Westerhoff H. V., Kürdar B., Penttilä M., Klipp E., Palsson B. O., Sauer U., Oliver S. G., Mendes P., Nielsen J., Kell D. B. (2008)
    Nature Biotechnology 26, 1155-1160. [pdf]
  38. Systems biology standards - the community speaks
    Klipp E., Liebermeister W., Helbig A., Kowald A., Schaber J. (2007)
    Nature Biotechnology 25, 390 - 391. [pdf] [supplement]
  39. Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data
    Liebermeister W. and Klipp E. (2006)
    Theoretical Biology and Medical Modelling 3:42. [pdf]
  40. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
    Liebermeister W. and Klipp E. (2006)
    Theoretical Biology and Medical Modelling 3:41. [pdf] [correction]
  41. Mathematical modeling of intracellular signaling pathways
    Klipp E. and Liebermeister W. (2006)
    BMC Neuroscience 2006, 7 (Suppl 1):S10. [pdf]
  42. A comprehensive library of fluorescent transcriptional reporters for Escherichia Coli
    Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette M. G., Alon U., (2006)
    Nature Methods 3, 623 - 628. [pdf]
  43. Predicting physiological concentrations of metabolites from their molecular structure
    Liebermeister W. (2005)
    Journal of Computational Biology 12 (10), 1307-1315.
    [Abstract] [pdf]
  44. Biochemical networks with uncertain parameters
    Liebermeister W., Klipp E. (2005)
    IEE Proceedings - Systems Biology 152 (3) 97-107.
    [Abstract] [pdf]
  45. Biochemical network models simplified by balanced truncation
    Liebermeister W., Baur U., Klipp E. (2005)
    FEBS Journal, 272 (16) 4034 - 4043.
  46. Response to temporal parameter fluctuations in biochemical networks
    Liebermeister W. (2005)
    Journal of Theoretical Biology 234 (3), 423-438. [pdf]
  47. A theory of optimal differential gene expression
    Liebermeister W., Klipp E., Schuster S., Heinrich R. (2004)
    BioSystems 76, 261-278. [pdf]
  48. Does mapping reveal correlation between gene expression and protein-protein interaction?
    Mrowka R., Liebermeister W., Holste D. (2003)
    Nature Genetics 33 (1), 15-16. [pdf]
  49. Linear modes of gene expression determined by independent component analysis
    Liebermeister W. (2002)
    Bioinformatics 18, 51-60. [supplement]
  50. Ratcheting in post-translational protein translocation: a mathematical model
    Liebermeister W., Rapoport T. A., Heinrich R. (2001)
    Journal of Molecular Biology 305, 643-656. [Abstract] [pdf]

Textbooks

  1. Economic Principles in Cell Biology
    zenodo.org/record/8156387 (2023): The Economic Cell Collective.
  2. Systems Biology - A Textbook
    First Edition (2009): Klipp E., Liebermeister W., Wierling C., Kowald A., Lehrach H., Herwig R.
  3. Systems Biology - A Textbook
    Second Edition (2016): Klipp E., Liebermeister W., Wierling C., Kowald A.

Book chapters

  1. The enzyme cost of metabolic fluxes
    Liebermeister, W. and Noor, E. (2023) [pdf on zenodo]
    The Economic Cell Collective: Economic Principles in Cell Biology
  2. Optimization of metabolic states
    Kremling A., Liebermeister W., Noor E. and Wortel M.T.(2023) [pdf on zenodo]
    The Economic Cell Collective: Economic Principles in Cell Biology
  3. Resource allocation in complex cell models
    Dourado H., Goelzer A., Grigaitis P., Liebermeister W. and Noor, E. (2023) [pdf on zenodo]
    The Economic Cell Collective: Economic Principles in Cell Biology
  4. Traces and Frames
    Liebermeister, W. and Pollman T.C. (2017)
    In Pollman T.C.: tracelation. [pdf]
  5. Knowledge Management for Systems Biology
    Leser, U. and Liebermeister, W. (2013)
    In Dubitzky, W., Wolkenhauer, O., Cho, K.-H. and Yokota, H. (ed):
    Encyclopedia of Systems Biology.
  6. Sustainable model building: the role of standards and biological semantics
    Krause F., Schulz M., Swainston N., Liebermeister W. (2011)
    In Jameson D., Verma M., and Westerhoff H.V. (ed): Methods in Enzymology, Vol. 500, 371-395. [Science direct]

Theses

  1. Construction and control analysis of biochemical network models
    Habilitation treatise (2012)
    [pdf]
  2. Analysis of optimal gene expression
    PhD thesis (2004)
    [pdf]
  3. Geometrie und Elektronenstruktur der Quasikristalle i-AlCuFe und i-AlPdMn
    Diploma thesis (1998)
    [pdf] [html]

Conference articles

  1. Deciphering the design principles of dynamic cell cycle control
    Barberis M., Mondeel T.D.G.A., Linke C., Supady A., Chasapi A., Liebermeister W., Loog M., Xenarios I., and Kitano H. (2015)
    27th International Conference on Yeast Genetics and Molecular Biology
    Yeast 32 (S1), S1-S292
  2. Periodic corpuscle structures and the spaces in between
    Wohlleben E. and Liebermeister W. (2012)
    15th International Conference on Geometry and Graphics [pdf]
  3. semanticsSBML 2.0 - A Collection of Online Services for SBML Models
    Krause F., Schulz M., Lubitz T., Liebermeister W. (2010)
    Workshop on Semantic Web Applications and Tools for Life Sciences
  4. Tension and deformations in elastic polyhedral rings made of corpuscle elements
    Wohlleben E. and Liebermeister W. (2010)
    14th International Conference on Geometry and Graphics [pdf]
  5. Nested uncertainty in biochemical models
    Schaber J., Liebermeister W., Klipp E. (2009)
    IET Systems Biology 3 (1), 1-9. [pdf]
  6. Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis
    Bruck J., Liebermeister W., Klipp E. (2008)
    Genome Informatics Series 20. [pdf]
  7. Merging of systems biology models with semanticSBML
    Liebermeister W., Krause F., Klipp E. (2008)
    5th Workshop on Computation of Biochemical Pathways and Genetic Networks. [pdf]
  8. The corpuscle - a simple building block for polyhedra networks
    Wohlleben E. and Liebermeister W. (2008)
    13th International Conference on Geometry and Graphics. [pdf]
  9. Validity and combination of biochemical models
    Liebermeister W. (2008)
    Proceedings of 3rd International ESCEC Workshop on Experimental Standard Conditions on Enzyme Characterizations.
    [proceedings] [pdf]
  10. Automatically generated model of a metabolic network
    Borger S., Liebermeister W., Uhlendorf J., Klipp E. (2007)
    Genome Informatics Series 18 (1), 215-224. [pdf]
  11. Integration of enzyme kinetic data from various sources
    Borger S., Uhlendorf J., Helbig A., Liebermeister W. (2007)
    In Silico Biology 7 S1, 09. [pdf]
  12. Structural analysis of expressed metabolic subnetworks
    Ebenhöh O. and Liebermeister W. (2006)
    Genome Informatics Series 17 (1).
    [Abstract] [pdf]
  13. Prediction of enzyme kinetic parameters based on statistical learning
    Borger S., Liebermeister W., Klipp E. (2006)
    Genome Informatics Series 17 (1).
    [Abstract] [pdf]
  14. SBMLmerge, a system for combining biochemical network models
    Schulz M., Uhlendorf J., Klipp E., Liebermeister W. (2006)
    Genome Informatics Series 17 (1). [pdf]
  15. Dimension reduction by balanced truncation applied to a model of glycolysis
    Liebermeister W. (2005)
    Proceedings of the 4th workshop on computation of biochemical pathways and genetic networks
    Logos-Verlag, Berlin, 21-28. [pdf]
  16. Distribution of a bifurcation parameter in a genetic network with uncertain parameters
    Borger S., Liebermeister W., Klipp E. (2005)
    Proceedings of the 4th workshop on computation of biochemical pathways and genetic networks
    Logos-Verlag, Berlin, 95-101. [pdf]
  17. Inferring dynamic properties of biochemical reaction networks from structural knowledge
    Klipp E., Liebermeister W., Wierling C. (2004)
    Genome Informatics Series 15 (1), 125-137. [pdf]
  18. Independent component analysis of gene expression data
    Liebermeister W. (2001)
    Proceedings of the 2nd workshop on computation of biochemical pathways and genetic networks
    Logos-Verlag, Berlin, 39-44.
  19. Mathematical modelling of posttranslational protein translocation
    Heinrich R., Liebermeister W., Rapoport T.A. (2000)
    9th International BioThermoKinetics Meeting (BTK 2000), 237-241.
  20. Mutual information analysis of surrogate gene expression data
    Holste D., Beule D., Liebermeister W., Schuchhardt J., Herzel H. (1999)
    German Conference on Bioinformatics, 201-204.
  21. Atomic positions in icosahedral quasicrystals
    Kramer P., Papadopolos Z., Liebermeister W. (1998)
    Proceedings of the 6th International Conference on Quasicrystals, Yamada Conference XLVII, World Scientific, Singapore, 71-76.
  22. Atomic positions for the icosahedral F-Phase tiling
    Papadopolos Z., Kramer P., Liebermeister W. (1998)
    Proceedings of the International Conference on Aperiodic Crystals, Aperiodic 1997, World Scientific, Singapore, 173-81.

Documents on model formats and standards

  1. SBtab - Conventions for structured data tables in Systems Biology
    Liebermeister W., Lubitz T., and Hahn J. (2015),
    arXiv:1502.01463
  2. SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
    Smith L.P., Hucka M., Hoops S., Finney A., Ginkel M., Myers C.J., Moraru I., Liebermeister W. (2015)
    Journal of Integrative Bioinformatics, 12(2):268
  3. SBML Level 3 Package Proposal: Annotation
    Waltemath D., Swainston N., Lister AL., Bergmann F., Henkel R., Hoops S., Hucka M., Juty N., Keating S., Knüpfer C., Krause F., Laibe C., Liebermeister W., Lloyd C., Misirli G., Schulz M., Taschuk M., Le Novere N. (2011), Nature Precedings
  4. A simple clustering of the BioModels database using semanticSBML
    Krause F., Liebermeister W. (2009)
    BioModels Meeting 2009, March 2009, Nature Precedings
  5. SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format
    Liebermeister W., Krause F., Uhlendorf J., Lubitz T., Klipp E. (2009)
    3rd International Biocuration Conference, 2009, Nature Precedings