Research Topics
| Christoph KaletaSummaryAffiliation: Friedrich Schiller University Country: Germany Publications
| Collaborators
|
Detail Information
Publications
Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regionsChristoph Kaleta
Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Jena, Germany
Int J Circumpolar Health 71:1-2. 2012..It is of particular relevance for understanding the metabolic state of natives of the arctic regions due to the very high fat content of their traditional diet only containing negligible amounts of carbohydrates...- Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysisChristoph Kaleta
Systems Biology Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Beutenbergstr, 11A, D 07745 Jena, Germany
BMC Syst Biol 4:116. 2010..There exist many approaches to reconstruct regulatory interaction networks from gene expression experiments. Mutual information based approaches are most useful for large-scale network inference... - More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coliAnna Katharina Göhler
Department of Genetics, University of Osnabruck, Osnabruck, Germany
BMC Syst Biol 5:197. 2011..To achieve an extended understanding of its gene regulatory network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach... - In silico evidence for gluconeogenesis from fatty acids in humansChristoph Kaleta
Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Jena, Germany
PLoS Comput Biol 7:e1002116. 2011..Moreover, the energetic loss associated to the usage of gluconeogenesis from fatty acids can help explain the efficiency of carbohydrate reduced and ketogenic diets such as the Atkins diet... - Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patternsChristoph Kaleta
Department of Bioinformatics, Friedrich Schiller University Jena, Germany
Genome Res 19:1872-83. 2009..Finally, we give an outlook on further applications like the computation of minimal media, the development of knockout strategies, and the analysis of combined genome-scale networks... 
Computing chemical organizations in biological networksFlorian Centler
Bio Systems Analysis Group, Jena Centre for Bioinformatics JCB and Department of Mathematics and Computer Science, Friedrich Schiller University Jena, D 07743 Jena, Germany
Bioinformatics 24:1611-8. 2008..The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states...
Can sugars be produced from fatty acids? A test case for pathway analysis toolsLuis F de Figueiredo
Department of Bioinformatics, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
Bioinformatics 25:152-8. 2009..This shows that, for metabolic pathway analysis, it is important to consider the topology (including bimolecular reactions) and stoichiometry of metabolic systems, as is done in EMA...- Can sugars be produced from fatty acids? A test case for pathway analysis toolsLuis F de Figueiredo
Department of Bioinformatics, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
Bioinformatics 24:2615-21. 2008..Using this example, we can compare the various methods in pathway analysis... - Computing the shortest elementary flux modes in genome-scale metabolic networksLuis F de Figueiredo
Friedrich Schiller University Jena, 07743 Jena, Germany
Bioinformatics 25:3158-65. 2009..In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity... - Using chemical organization theory for model checkingChristoph Kaleta
Department of Mathematics and Computer Science, Bio Systems Analysis Group, Jena Centre for Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, D 07743 Jena, Germany
Bioinformatics 25:1915-22. 2009..In formalisms like Systems Biology Markup Language (SBML), however, information about the stoichiometric coefficients required for an analysis of chemical organizations can be hidden in kinetic laws... - Hands-on metabolism analysis of complex biochemical networks using elementary flux modesSascha Schäuble
Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
Methods Enzymol 500:437-56. 2011..Finally, we give an overview of applications of EFM analysis in biotechnology and other fields and discuss issues arising when applying methods from metabolic pathway analysis to genome-scale metabolic networks... - Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costsFrank Wessely
Department of Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, Jena, Germany
Mol Syst Biol 7:515. 2011.... - Phenotype prediction in regulated metabolic networksChristoph Kaleta
Bio Systems Analysis Group, Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany
BMC Syst Biol 2:37. 2008..By this, the phenotypes implied by a metabolic network can be predicted without the need for explicit knowledge of the detailed reaction kinetics... - Predicting novel pathways in genome-scale metabolic networksStefan Schuster
Department of Bioinformatics, School of Biology and Pharmacy, University of Jena, Ernst Abbe Pl 2, D 07743 Jena, Germany
Biochem Soc Trans 38:1202-5. 2010..The subsystem can be made up by reactions in which we are interested in, for example, reactions producing a certain metabolite. This allows one to predict novel metabolic pathways in genome-scale networks... - Detecting and investigating substrate cycles in a genome-scale human metabolic networkJuliane Gebauer
Department of Bioinformatics, School of Biology and Pharmaceutics and JenAge Research Core, Friedrich Schiller University of Jena, Germany
FEBS J 279:3192-202. 2012..This selective force is particularly strong against futile cycles that have a high flux as a result of thermodynamic principles... - Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysisDimitar Kenanov
Department of Bioinformatics, Friedrich Schiller University, Jena, Germany
FEBS J 277:1023-34. 2010..The loss of the outer membrane in the cell wall-free mutant, however, shows that lipid A is dispensable as the main component of the outer surface structure in this particular E. coli strain... - Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approachStefan Schuster
Department of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz, Jena, Germany
Biosystems 105:147-53. 2011..This provides a straightforward explanation of the Warburg effect in tumour cells... - Integrated network reconstruction, visualization and analysis using YANAsquareRoland Schwarz
Department of Bioinformatics, Biocenter Am Hubland, D 97074 University of Würzburg, Germany
BMC Bioinformatics 8:313. 2007..Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network...