Oliver Ebenhöh

Summary

Affiliation: Humboldt University
Country: Germany

Publications

  1. pmc MetaPath Online: a web server implementation of the network expansion algorithm
    Thomas Handorf
    Department of Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
    Nucleic Acids Res 35:W613-8. 2007
  2. ncbi request reprint Structural analysis of expressed metabolic subnetworks
    Oliver Ebenhöh
    Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
    Genome Inform 17:163-72. 2006
  3. ncbi request reprint Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems
    O Ebenhöh
    Humboldt Universitat zu Berlin, Institut für Biologie Theoretische Biophysik, Invalidenstrasse 42, D 10115 Berlin, Germany
    Bull Math Biol 63:21-55. 2001
  4. ncbi request reprint Evolutionary changes of metabolic networks and their biosynthetic capacities
    O Ebenhöh
    Department of Biology, Humboldt University, Berlin, Germany
    Syst Biol (Stevenage) 153:354-8. 2006
  5. ncbi request reprint A cross species comparison of metabolic network functions
    Oliver Ebenhöh
    Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Germany
    Genome Inform 16:203-13. 2005
  6. ncbi request reprint Structural analysis of expanding metabolic networks
    Oliver Ebenhöh
    Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Germany
    Genome Inform 15:35-45. 2004
  7. ncbi request reprint Expanding metabolic networks: scopes of compounds, robustness, and evolution
    Thomas Handorf
    Institute of Biology, Department of Theoretical Biophysics, Humboldt University Berlin, Invalidenstr 42, 10115 Berlin, Germany
    J Mol Evol 61:498-512. 2005
  8. ncbi request reprint Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds
    Kai Kruse
    Theoretical Biophysics, Insitute for Biology, Humboldt University, Berlin, Germany
    Genome Inform 20:91-101. 2008
  9. ncbi request reprint Measuring correlations in metabolomic networks with mutual information
    Jorge Numata
    Macromolecular Modeling Group, Freie Universitat Berlin, Takustr 6, Berlin, 14195, Germany
    Genome Inform 20:112-22. 2008
  10. ncbi request reprint Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness
    Oliver Ebenhöh
    Department of Theoretical Biophysics, Institute of Biology, Humboldt University, Invalidenstrasse 42, 10115 Berlin, Germany
    Bull Math Biol 65:323-57. 2003

Detail Information

Publications14

  1. pmc MetaPath Online: a web server implementation of the network expansion algorithm
    Thomas Handorf
    Department of Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
    Nucleic Acids Res 35:W613-8. 2007
    ..The web server is accessible through http://scopes.biologie.hu-berlin.de...
  2. ncbi request reprint Structural analysis of expressed metabolic subnetworks
    Oliver Ebenhöh
    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...
  3. ncbi request reprint Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems
    O Ebenhöh
    Humboldt Universitat zu Berlin, Institut für Biologie Theoretische Biophysik, Invalidenstrasse 42, D 10115 Berlin, Germany
    Bull Math Biol 63:21-55. 2001
    ..A distance measure and a measure for the internal ordering of reactions are introduced to study differences and similarities in the stoichiometries of metabolic pathways...
  4. ncbi request reprint Evolutionary changes of metabolic networks and their biosynthetic capacities
    O Ebenhöh
    Department of Biology, Humboldt University, Berlin, Germany
    Syst Biol (Stevenage) 153:354-8. 2006
    ..The evolutionary dynamics of one particular network function: the metabolic expansion of glucose is investigated...
  5. ncbi request reprint A cross species comparison of metabolic network functions
    Oliver Ebenhöh
    Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Germany
    Genome Inform 16:203-13. 2005
    ..The presented concepts allow for a systematic investigation of structure-function relationships of metabolic networks and may put forth valuable hints on the evolution of metabolic pathways...
  6. ncbi request reprint Structural analysis of expanding metabolic networks
    Oliver Ebenhöh
    Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Germany
    Genome Inform 15:35-45. 2004
    ..The expansion provides efficient tools for detecting new structural characteristics such as substrate-product relationships over long distances...
  7. ncbi request reprint Expanding metabolic networks: scopes of compounds, robustness, and evolution
    Thomas Handorf
    Institute of Biology, Department of Theoretical Biophysics, Humboldt University Berlin, Invalidenstr 42, 10115 Berlin, Germany
    J Mol Evol 61:498-512. 2005
    ..It is hypothesized that the expansion process displays characteristics of the evolution of metabolism such as the temporal order of the emergence of metabolic pathways...
  8. ncbi request reprint Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds
    Kai Kruse
    Theoretical Biophysics, Insitute for Biology, Humboldt University, Berlin, Germany
    Genome Inform 20:91-101. 2008
    ..In conclusion, we state that network expansion, due to its enormous advantages in computational speed, is a valuable alternative to determining producible metabolites with FBA...
  9. ncbi request reprint Measuring correlations in metabolomic networks with mutual information
    Jorge Numata
    Macromolecular Modeling Group, Freie Universitat Berlin, Takustr 6, Berlin, 14195, Germany
    Genome Inform 20:112-22. 2008
    ..We analyze experimental data on metabolite concentrations from Arabidopsis thaliana by using these procedures. The mutual information was able to detect additional non-linear correlations undetectable for the Pearson coefficient...
  10. ncbi request reprint Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness
    Oliver Ebenhöh
    Department of Theoretical Biophysics, Institute of Biology, Humboldt University, Invalidenstrasse 42, 10115 Berlin, Germany
    Bull Math Biol 65:323-57. 2003
    ..Under changing environmental conditions multifunctional networks prove to be optimal and will be selected...
  11. ncbi request reprint Metabolic synergy: increasing biosynthetic capabilities by network cooperation
    Nils Christian
    Institute for Biology, Humboldt University Berlin, Germany
    Genome Inform 18:320-9. 2007
    ....
  12. ncbi request reprint Patterns of interactions of reaction pairs in metabolic networks
    József Bruck
    Theoretical Biophysics, Institute of Biology, Humboldt University, Invalidenstr 42, D 10115 Berlin, Germany
    Genome Inform 17:208-18. 2006
    ..In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism...
  13. pmc Bioinformatics meets systems biology
    Carlos Salazar
    Theoretical Biophysics, Institute for Biology, Humboldt University, Invalidenstrasse 42, 10115 Berlin, Germany
    Genome Biol 7:303. 2006
  14. ncbi request reprint An environmental perspective on metabolism
    Thomas Handorf
    Theoretical Biophysics, Department of Biology, Humboldt University Berlin, Invalidenstr 42, 10115 Berlin, Germany
    J Theor Biol 252:530-7. 2008
    ..Using these types we predict broad nutritional requirements for 447 organisms, providing clues for possible environments from the knowledge of their metabolic networks...