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