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]
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]