- Linear modes of gene expression determined by independent component analysis
Theoretische Biophysik, Institut fur Biologie, Humboldt Universitat zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
Bioinformatics 18:51-60. 2002
..A projection to expression modes helps to highlight particular biological functions, to reduce noise, and to compress the data in a biologically sensible way...
- Structural analysis of expressed metabolic subnetworks
Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
Genome Inform 17:163-72. 2006
..These findings indicate that gene regulation increases the range of essential compounds that can be obtained from the available nutrients, while minimising the number of expressed enzymes and therefore the burden of protein synthesis...
- Annotation and merging of SBML models with semanticSBML
Theoretische Biophysik, Humboldt Universitat zu Berlin, Invalidenstrasse 42, D 10115 Berlin, Germany
Bioinformatics 26:421-2. 2010
..Conflicts can then be resolved automatically or manually, allowing the user to control the merging process in detail...
- Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Institut fur Biologie, Theoretische Biophysik, Humboldt Universitat zu Berlin, Berlin, Germany
Bioinformatics 26:1528-34. 2010
..At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations...
- Does mapping reveal correlation between gene expression and protein-protein interaction?
Nat Genet 33:15-6; author reply 16-7. 2003
- A theory of optimal differential gene expression
Berlin Center for Genome Based Bioinformatics, Max Planck Institute for Molecular Genetics, Berlin, Germany
Biosystems 76:261-78. 2004
..Where the optimality assumption is valid, our results justify the use of expression data for functional annotation and for pathway reconstruction and suggest the use of linear factor models for the analysis of gene expression data...
- Inferring dynamic properties of biochemical reaction networks from structural knowledge
Berlin Center for Genome Based Bioinformatics BCB, Max Planck Institute for Molecular Genetics, Dept Vertebrate Genomics, Ihnestr 73, Berlin 14195, Germany
Genome Inform 15:125-37. 2004
..This analysis reveals how much information about dynamic behavior can be drawn from structural knowledge...
- Predicting physiological concentrations of metabolites from their molecular structure
Max Planck Institute for Molecular Genetics, Kinetic Modelling Group, Berlin, Germany
J Comput Biol 12:1307-15. 2005
..The model explains about 22% of the variance of the logarithmic mean concentrations...
- A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Israel
Nat Methods 3:623-8. 2006
..coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells...