Christoph Kaleta

Summary

Affiliation: Friedrich Schiller University
Country: Germany

Publications

  1. doi request reprint Metabolic costs of amino acid and protein production in Escherichia coli
    Christoph Kaleta
    Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Jena, Germany
    Biotechnol J 8:1105-14. 2013
  2. pmc Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions
    Christoph Kaleta
    Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Jena, Germany
    Int J Circumpolar Health 71:1-2. 2012
  3. pmc More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
    Anna Katharina Göhler
    Department of Genetics, University of Osnabruck, Osnabruck, Germany
    BMC Syst Biol 5:197. 2011
  4. pmc In silico evidence for gluconeogenesis from fatty acids in humans
    Christoph Kaleta
    Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Jena, Germany
    PLoS Comput Biol 7:e1002116. 2011
  5. pmc Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
    Christoph 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
  6. pmc Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
    Christoph Kaleta
    Department of Bioinformatics, Friedrich Schiller University Jena, Germany
    Genome Res 19:1872-83. 2009
  7. doi request reprint Computing chemical organizations in biological networks
    Florian 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
  8. ncbi request reprint Can sugars be produced from fatty acids? A test case for pathway analysis tools
    Luis F de Figueiredo
    Department of Bioinformatics, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 25:152-8. 2009
  9. doi request reprint Can sugars be produced from fatty acids? A test case for pathway analysis tools
    Luis F de Figueiredo
    Department of Bioinformatics, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 24:2615-21. 2008
  10. doi request reprint Hands-on metabolism analysis of complex biochemical networks using elementary flux modes
    Sascha Schäuble
    Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
    Methods Enzymol 500:437-56. 2011

Collaborators

Detail Information

Publications19

  1. doi request reprint Metabolic costs of amino acid and protein production in Escherichia coli
    Christoph Kaleta
    Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Jena, Germany
    Biotechnol J 8:1105-14. 2013
    ..Moreover, we show that the biosynthesis of a large number of amino acids from glucose and particularly from glycerol provides a surplus of energy, which can be used to balance the high energetic cost of amino acid polymerization. ..
  2. pmc Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions
    Christoph 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...
  3. pmc More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
    Anna 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...
  4. pmc In silico evidence for gluconeogenesis from fatty acids in humans
    Christoph 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...
  5. pmc Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
    Christoph 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...
  6. pmc Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
    Christoph 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...
  7. doi request reprint Computing chemical organizations in biological networks
    Florian 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...
  8. ncbi request reprint Can sugars be produced from fatty acids? A test case for pathway analysis tools
    Luis F de Figueiredo
    Department of Bioinformatics, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 25:152-8. 2009
    ..Using this example, we can compare the various methods in pathway analysis...
  9. doi request reprint Can sugars be produced from fatty acids? A test case for pathway analysis tools
    Luis 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...
  10. doi request reprint Hands-on metabolism analysis of complex biochemical networks using elementary flux modes
    Sascha 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...
  11. doi request reprint Computing the shortest elementary flux modes in genome-scale metabolic networks
    Luis 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...
  12. pmc Using chemical organization theory for model checking
    Christoph 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...
  13. pmc Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
    Frank Wessely
    Department of Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, Jena, Germany
    Mol Syst Biol 7:515. 2011
    ....
  14. doi request reprint Detecting and investigating substrate cycles in a genome-scale human metabolic network
    Juliane 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...
  15. doi request reprint Predicting novel pathways in genome-scale metabolic networks
    Stefan 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...
  16. pmc Phenotype prediction in regulated metabolic networks
    Christoph 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...
  17. doi request reprint Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis
    Dimitar 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...
  18. doi request reprint Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach
    Stefan 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...
  19. pmc Integrated network reconstruction, visualization and analysis using YANAsquare
    Roland 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...