Wolfram Liebermeister Institut für Biochemie Charité - Universitätsmedizin Berlin Seestraße 73 13347 Berlin Tel. +49 30 450 528022 wolfram.liebermeister AT charite.de

Journal publications
(see selected publications)

• 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.
  [Abstract]
• 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]
• 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.
  [Abstract] [html] [pdf]
• Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation
  Liebermeister W., Uhlendorf J., Klipp E. (2010)
  Bioinformatics 26(12):1528-1534.
  [Abstract] [pdf]
• 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.
  [html] [pdf]
• 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. [html] [pdf] [semanticSBML website]
• 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.
  [html] [pdf]
• Systems biology standards - the community speaks
  Klipp E., Liebermeister W., Helbig A., Kowald A., Schaber J. (2007)
  Nature Biotechnology 25, 390 - 391.
  [html] [pdf] [supplement]
• 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.
  [html] [pdf]
• Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
  Liebermeister W. and Klipp E. (2006)
  Theoretical Biology and Medical Modelling 3:41.
  [html] [pdf] [correction]
• Mathematical modeling of intracellular signaling pathways
  Klipp E. and Liebermeister W. (2006)
  BMC Neuroscience 2006, 7 (Suppl 1):S10.
  [html] - [pdf]
• 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.
  [html] - [pdf]
• Predicting physiological concentrations of metabolites from their molecular structure
  Liebermeister W. (2005)
  Journal of Computational Biology 12 (10), 1307-1315.
  [Abstract] - [pdf]
• Biochemical networks with uncertain parameters
  Liebermeister W., Klipp E. (2005)
  IEE Proceedings - Systems Biology 152 (3) 97-107.
  [Abstract] - [pdf]
• Biochemical network models simplified by balanced truncation
  Liebermeister W., Baur U., Klipp E. (2005)
  FEBS Journal, 272 (16) 4034 - 4043.
  [Abstract] [pdf]
• Response to temporal parameter fluctuations in biochemical networks
  Liebermeister W. (2005)
  Journal of Theoretical Biology 234 (3), 423-438.
  [html] - [pdf]
• A theory of optimal differential gene expression
  Liebermeister W., Klipp E., Schuster S., Heinrich R. (2004)
  BioSystems 76, 261-278.
  [html] - [pdf]
• Does mapping reveal correlation between gene expression and protein-protein interaction?
  Mrowka R., Liebermeister W., Holste D. (2003)
  Nature Genetics 33 (1), 15-16.
  [html] - [pdf]
• Linear modes of gene expression determined by independent component analysis
  Liebermeister W. (2002)
  Bioinformatics 18, 51-60.
  [Abstract] - [pdf] - [supplement]
• Ratcheting in post-translational protein translocation: a mathematical model
  Liebermeister W., Rapoport T. A., Heinrich R. (2001)
  Journal of Molecular Biology 305, 643-656.
  [html] - [Abstract] - [pdf]

Textbook

• Systems Biology
  Klipp E., Liebermeister W., Wierling C., Kowald A., Lehrach H., Herwig R.

Book chapters

• 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., editors: Methods in Enzymology, Vol. 500, 371-395.
  [Science direct]

Conference articles

• 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]
• 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.
  [html] [pdf]
• Nested uncertainty in biochemical models
  Schaber J., Liebermeister W., Klipp E. (2009)
  IET Systems Biology 3 (1), 1-9.
  [pdf]
• 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]
• 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]
• The corpuscle - a simple building block for polyhedra networks
  Wohlleben E. and Liebermeister W. (2008)
  Proceedings of the 13th International Conference on Geometry and Graphics.
  [pdf]
• Validity and combination of biochemical models
  Liebermeister W. (2008)
  Proceedings of 3rd International ESCEC Workshop on Experimental Standard Conditions on Enzyme Characterizations.
  [proceedings] [pdf]
• Automatically generated model of a metabolic network
  Borger S., Liebermeister W., Uhlendorf J., Klipp E. (2007)
  Genome Informatics Series 18 (1), 215-224.
  [pdf]
• Integration of enzyme kinetic data from various sources
  Borger S., Uhlendorf J., Helbig A., Liebermeister W. (2007)
  In Silico Biology 7 S1, 09.
  [html] [pdf]
• Structural analysis of expressed metabolic subnetworks
  Ebenhöh O. and Liebermeister W. (2006)
  Genome Informatics Series 17 (1).
  [Abstract] - [pdf]
• Prediction of enzyme kinetic parameters based on statistical learning
  Borger S., Liebermeister W., Klipp E. (2006)
  Genome Informatics Series 17 (1).
  [Abstract] - [pdf]
• SBMLmerge, a system for combining biochemical network models
  Schulz M., Uhlendorf J., Klipp E., Liebermeister W. (2006)
  Genome Informatics Series 17 (1).
  [Abstract] - [pdf]
• 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]
• 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]
• 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]
• 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.
  
• 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.
  
• 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.
  
• 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 Nature Precedings

• SBML Level 3 Package Proposal: Annotation
  Waltemath D., Swainston N., Lister AL., Bergmann F., Henkel R., Hoops S., Hucka M., Juty N., Keating S., Knuepfer C., Krause F., Laibe C., Liebermeister W., Lloyd C., Misirli G., Schulz M., Taschuk M., Le Novere N. (2011)
  [html]
• A simple clustering of the BioModels database using semanticSBML
  Krause F., Liebermeister W. (2009)
  BioModels Meeting 2009, March 2009
  [html]
• 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
  [html]

Theses

• Analysis of optimal gene expression
  PhD thesis, 2004.
  [pdf]
• Geometrie und Elektronenstruktur der Quasikristalle i-AlCuFe und i-AlPdMn
  Diploma thesis, 1998.
  [pdf] [html]