Journal Article (145)
2013
Journal Article
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 9 (7), pp. 1576 - 1583 (2013)
Journal Article
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 12, 84 (2013)
Journal Article
Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 110 (10), pp. 2633 - 2642 (2013)
Journal Article
Multistationarity in Sequential Distributed Multisite Phosphorylation Networks. Bulletin of mathematical biology 75 (11), pp. 2028 - 2058 (2013)
Journal Article
A role for EIIANtr in controlling fluxes in the central metabolism of E. coli K12. Biochimica et Biophysica Acta-Molecular Cell Research 1833 (12), pp. 2879 - 2889 (2013)
Journal Article
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14 (1), p. 318 (2013)
Journal Article
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 9 (9), p. e1003204 (2013)
Journal Article
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 7, p. 73 (2013)
Journal Article
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11 (1), p. 43 (2013)
Journal Article
Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS One 8 (10), p. e7541 (2013)
Journal Article
Sensitivity and Robustness in Covalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105 (8), pp. 1925 - 1933 (2013)
Journal Article
Reciprocal Enzyme Regulation as a Source of Bistability in Covalent Modification Cycles. Journal of Theoretical Biology 330, pp. 56 - 74 (2013)
2012
Journal Article
Minimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 28 (3), pp. 381 - 387 (2012)
Journal Article
Switching in mass action networks based on linear inequalities. SIAM Journal on Applied Dynamical Systems 11 (1), pp. 110 - 134 (2012)
Journal Article
Multistationarity in Mass Action Networks with Applications to ERK Activation. Journal of Mathematical Biology 65 (1), pp. 107 - 156 (2012)
Journal Article
Rapid selection of glucose-utilizing variants of the polyhydroxyalkanoate producer Ralstonia eutropha H16 by incubation with high substrate levels. Letters in Applied Microbiology 54 (1), pp. 45 - 51 (2012)
Journal Article
An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279 (18), pp. 3290 - 3313 (2012)
Journal Article
The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 13, p. 251 (2012)
Journal Article
Analysis and Design of Stimulus Response Curves of E. coli. Metabolites 2 (4), pp. 844 - 871 (2012)
Journal Article
Iac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. Journal of Biotechnology 157 (1), pp. 82 - 88 (2012)
Journal Article
An extended model for the repression of photosynthesis genes by the AppA/PpsR system in Rhodobacter sphaeroides. FEBS Journal 279 (18), pp. 3449 - 3461 (2012)
Journal Article
Chemical Reaction Systems with Toric Steady States. Bulletin of Mathematical Biology 74 (5), pp. 1027 - 1065 (2012)
Journal Article
Fructose metabolism of the purple non-sulfur bacterium Rhodospirillum rubrum: Effect of carbon dioxide on growth, and production of bacteriochlorophyll and organic acids. Enzyme and Microbial Technology 50 (4-5), pp. 238 - 246 (2012)
Journal Article
Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. Journal of Bacteriology 194 (21), pp. 5897 - 5908 (2012)
Journal Article
Comment on "Load-induced modulation of signal transduction networks": Reconciling ultrasensitivity with bifunctionality? Science Signaling 5 (205), p. Ic1 (2012)
Journal Article
High-Level Production of the Industrial Product Lycopene by the Photosynthetic Bacterium Rhodospirillum rubrum. Applied and Environmental Microbiology 78 (20), pp. 7205 - 7215 (2012)
2011
Journal Article
Glutathione Redox Effect on Photosynthetic Membrane Expression in Rhodospirillum rubrum. Journal of Bacteriology 193 (8), pp. 1893 - 1900 (2011)
Journal Article
Experimental validation of a new integrated simulated moving bed process for the production of single enantiomers. Journal of Chromatography A 2218 (16), pp. 2232 - 2239 (2011)
Journal Article
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, p. 150 (2011)
Journal Article
Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), pp. 204 - 213 (2011)
Journal Article
An application programming interface for CellNetAnalyzer. Biosystems 105 (2), pp. 162 - 168 (2011)
Journal Article
Modeling the Light- and Redox-Dependent Interaction of PpsR/AppA in Rhodobacter sphaeroides. Biophysical Journal 100 (10), pp. 2347 - 2355 (2011)
Journal Article
Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 7 (12), pp. 3253 - 3270 (2011)
Journal Article
Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels. Journal of Biotechnology 154 (1), pp. 35 - 45 (2011)
Journal Article
Brownian diffusion of ion channels in different membrane patch geometries. Physical review E 83 (2), p. 021919 (2011)
2010
Journal Article
From Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 7 (1), p. 151 (2010)
Journal Article
CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), pp. 88 - 101 (2010)
Journal Article
TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), pp. 2160 - 2168 (2010)
Journal Article
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 17 (1), pp. 39 - 53 (2010)
2009
Journal Article
Hypergraphs and cellular networks. PLoS Computational Biology 5 (5), p. e1000385 (2009)
Journal Article
Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, p. 181 (2009)
Journal Article
Logical network of genotoxic stress-induced NF-kB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and Applications in Bioinformatics and Chemistry 2, pp. 125 - 138 (2009)
Journal Article
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5, p. 331 (2009)
Journal Article
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5 (8), e1000438 (2009)
Journal Article
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 3, 98 (2009)
Book Chapter (5)
2020
Book Chapter
Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering. In: Advances in Microbial Physiology, Vol. 77, pp. 37 - 88 (Ed. Poole, R. K.). Academic Press (2020)
2014
Book Chapter
Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli. In: Advances in Microbial Physiology, Vol. 64, pp. 65 - 114 (Ed. Poole, R. K.). Elsevier/Academic Press, Amsterdam (2014)
Book Chapter
Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. In: Large-Scale Networks in Engineering and Life Sciences, pp. 263 - 316. Springer International Publishing, Cham (2014)
2013
Book Chapter
Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic Data. In: Gene Network Inference: Verification of Methods for Systems Genetic Data., pp. 33 - 47. Springer, Heidelberg (2013)
Book Chapter
Host-pathogen interactions. In: Systems Biology of Tuberculosis, pp. 107 - 126. Springer, New York (2013)