Wolfram Liebermeister wolfram.liebermeister@gmail.com INRAE - Unité MaIAGE Domaine de Vilvert 78352 Jouy-en-Josas, France

All publications / Selected publications

Protein economy in metabolism

1. 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
2. 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 Comp. Biol. 12 (10): e1005167
3. 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
4. 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
5. A theory of optimal differential gene expression
   Liebermeister W., Klipp E., Schuster S., Heinrich R. (2004)
   BioSystems 76, 261-278

Metabolic dynamics and control

1. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
   Buescher J.M. et al (2012)
   Science 335 (6072), 1099-1103
2. Response to temporal parameter fluctuations in biochemical networks
   Liebermeister W. (2005)
   Journal of Theoretical Biology 234 (3), 423-438 - [pdf]
3. Biochemical network models simplified by balanced truncation
   Liebermeister W., Baur U., Klipp E. (2005)
   FEBS Journal, 272 (16) 4034 - 4043 - [pdf]

Model building and analysis

1. Systematic construction of kinetic models from genome-scale metabolic networks
   Natalie J. Stanford, Lubitz T., Smallbone K., Klipp E., Mendes P., Liebermeister W. (2013)
   PLoS ONE 8(11): E79195
2. 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 - [pdf]
3. Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation
   Liebermeister W., Uhlendorf J., Klipp E. (2010)
   Bioinformatics 26(12):1528-1534
4. Biochemical networks with uncertain parameters
   Liebermeister W., Klipp E. (2005)
   IEE Proceedings - Systems Biology 152 (3) 97-107 - [pdf]

Model semantics and model combination

1. 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
2. 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
3. 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]
4. Validity and combination of biochemical models
   Liebermeister W. (2008)
   3rd International ESCEC Workshop on Experimental Standard Conditions
   on Enzyme Characterizations. - [pdf]