Ines Thiele

Summary

Publications

  1. pmc Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells
    Swagatika Sahoo
    Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, 101 Reykjavik, Iceland
    Hum Mol Genet 22:2705-22. 2013
  2. pmc Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    Almut Heinken
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Gut Microbes 4:28-40. 2013
  3. pmc A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
    Gunnar Sigurdsson
    Center for Systems Biology, University of Iceland, Reykajavik, Iceland
    PLoS ONE 7:e34337. 2012
  4. pmc Contextualization procedure and modeling of monocyte specific TLR signaling
    Maike K Aurich
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    PLoS ONE 7:e49978. 2012
  5. pmc Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks
    Juan Nogales
    Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
    Bioengineered 4:158-63. 2013
  6. pmc Consensus and conflict cards for metabolic pathway databases
    Miranda D Stobbe
    Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, Amsterdam 1100 DE, The Netherlands
    BMC Syst Biol 7:50. 2013
  7. pmc A community-driven global reconstruction of human metabolism
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Nat Biotechnol 31:419-25. 2013
  8. doi request reprint A systems biology approach to studying the role of microbes in human health
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Curr Opin Biotechnol 24:4-12. 2013
  9. pmc Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    PLoS ONE 7:e45635. 2012
  10. pmc Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Biophys J 98:2072-81. 2010

Detail Information

Publications27

  1. pmc Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells
    Swagatika Sahoo
    Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, 101 Reykjavik, Iceland
    Hum Mol Genet 22:2705-22. 2013
    ..Taken together, the sIEC model represents a comprehensive, biochemically accurate platform for studying the function of sIEC and their role in whole body metabolism...
  2. pmc Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    Almut Heinken
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Gut Microbes 4:28-40. 2013
    ..This systems approach represents a powerful tool for modeling metabolic interactions between a gut microbe and its host in health and disease...
  3. pmc A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
    Gunnar Sigurdsson
    Center for Systems Biology, University of Iceland, Reykajavik, Iceland
    PLoS ONE 7:e34337. 2012
    ....
  4. pmc Contextualization procedure and modeling of monocyte specific TLR signaling
    Maike K Aurich
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    PLoS ONE 7:e49978. 2012
    ..Thus, a cell-type and condition-specific signaling network can provide functional insight into signaling cascades. Furthermore, we demonstrate the energy dependence of TLR signaling pathways in monocytes...
  5. pmc Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks
    Juan Nogales
    Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
    Bioengineered 4:158-63. 2013
    ....
  6. pmc Consensus and conflict cards for metabolic pathway databases
    Miranda D Stobbe
    Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, Amsterdam 1100 DE, The Netherlands
    BMC Syst Biol 7:50. 2013
    ..We can use these different descriptions to our advantage by identifying conflicting information and combining their knowledge into a single, more accurate, and more complete description. This task is, however, far from trivial...
  7. pmc A community-driven global reconstruction of human metabolism
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Nat Biotechnol 31:419-25. 2013
    ..Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/...
  8. doi request reprint A systems biology approach to studying the role of microbes in human health
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Curr Opin Biotechnol 24:4-12. 2013
    ..Such host-microbe models, combined with experimental data, will ultimately further our understanding of how microbes influence human health...
  9. pmc Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    PLoS ONE 7:e45635. 2012
    ..This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors...
  10. pmc Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    Biophys J 98:2072-81. 2010
    ..These reactions contribute significant variance among AOS. These results show that constraint-based modeling can be applied to gain insight into the systemic properties of E. coli's transcriptional and translational machinery...
  11. pmc Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
    Jan Schellenberger
    Bioinformatics Program, University of California San Diego, La Jolla, California, USA
    Nat Protoc 6:1290-307. 2011
    ..A suite of test scripts can now be used to learn the core functionality of the toolbox and validate results. This toolbox lowers the barrier of entry to use powerful COBRA methods...
  12. pmc Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
    Juan Nogales
    Center for Systems Biology, University of Iceland, 101 Reykjavik, Iceland
    Proc Natl Acad Sci U S A 109:2678-83. 2012
    ..The results and modeling approach presented here may promote a better understanding of the photosynthetic process. They can also guide bioengineering projects toward optimal biofuel production in photosynthetic organisms...
  13. pmc The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    Ottar Rolfsson
    Center for Systems Biology, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
    BMC Syst Biol 5:155. 2011
    ..At the same time, a major challenge in the post genomic era involves characterisation of missing biological components to complete genome annotation...
  14. doi request reprint Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity
    Ottar Rolfsson
    Center for Systems Biology, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
    Biochem J 449:427-35. 2013
    ..Furthermore, we illustrate how incomplete human metabolic knowledge can be coupled with gene annotation in order to prioritize and confirm gene functions...
  15. pmc A protocol for generating a high-quality genome-scale metabolic reconstruction
    Ines Thiele
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    Nat Protoc 5:93-121. 2010
    ..Therefore, this protocol provides a helpful manual for all stages of the reconstruction process...
  16. doi request reprint Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies
    Giuseppe Paglia
    Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
    J Chromatogr B Analyt Technol Biomed Life Sci 898:111-20. 2012
    ..A higher number of metabolites could be detected when analyzing the platelet samples with two different LC-MS methods or when using complementary extraction methods in parallel...
  17. pmc Computationally efficient flux variability analysis
    Steinn Gudmundsson
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    BMC Bioinformatics 11:489. 2010
    ..However, its use has been somehow limited by the long computation time compared to other constraint-based modeling methods...
  18. pmc Three-dimensional structural view of the central metabolic network of Thermotoga maritima
    Ying Zhang
    Joint Center for Molecular Modeling JCMM, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    Science 325:1544-9. 2009
    ..Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks...
  19. pmc Identification of potential pathway mediation targets in Toll-like receptor signaling
    Fan Li
    Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000292. 2009
    ..The results of this study are expected to yield meaningful avenues for further research in the task of mediating the Toll-like receptor signaling network and its effects...
  20. doi request reprint rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
    Stefan Gretar Thorleifsson
    Center for Systems Biology, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland
    Bioinformatics 27:2009-10. 2011
    ..Genome-scale metabolic networks are widely used in systems biology. However, to date no freely available tool exists that ensures quality control during the reconstruction process...
  21. pmc A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
    Martin I Sigurdsson
    Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
    BMC Syst Biol 4:140. 2010
    ..Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms...
  22. pmc von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
    Ronan M T Fleming
    Science Institute, University of Iceland, Reykjavik, Iceland
    Bioinformatics 27:142-3. 2011
    ....
  23. pmc Global reconstruction of the human metabolic network based on genomic and bibliomic data
    Natalie C Duarte
    Bioengineering Department, University of California at San Diego, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 104:1777-82. 2007
    ..These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology...
  24. pmc Reconstruction of biochemical networks in microorganisms
    Adam M Feist
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    Nat Rev Microbiol 7:129-43. 2009
    ..This review should aid the growing number of researchers who are carrying out reconstructions for particular target organisms...
  25. pmc A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    BMC Syst Biol 5:8. 2011
    ..Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem...
  26. doi request reprint Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS)
    Giuseppe Paglia
    Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik 101, Iceland
    Anal Bioanal Chem 402:1183-98. 2012
    ..Our data suggest that the method presented can be used for qualitative and quantitative analysis of extracellular metabolites and it is suitable for routine applications such as in vitro drug screening...
  27. ncbi request reprint A compendium of inborn errors of metabolism mapped onto the human metabolic network
    Swagatika Sahoo
    Center for Systems Biology, University of Iceland, Iceland
    Mol Biosyst 8:2545-58. 2012
    ..The presented comprehensive knowledge base of IEMs will provide a valuable tool in studying metabolic changes involved in inherited metabolic diseases...