@article{SteuerKurthsFiehnetal.2003,
  author    = {Steuer, Ralf and Kurths, J{\"u}rgen and Fiehn, Oliver and Weckwerth, Wolfram},
  title     = {Interpreting correlations in metabolomic networks},
  issn      = {0300-5127},
  year      = {2003},
  abstract  = {Correlations, as observed between the concentrations of metabolites in a biological sample, may be used to gain additional information about the physiological state of a given tissue. in this mini-review, we discuss the integration of these observed correlations into metabolomic networks and their relationships with the underlying biochemical pathways},
  language  = {en}
}
@article{RoessnerLuedemannBrustetal.2001,
  author    = {Roessner, Ute and Luedemann, A. and Brust, D. and Fiehn, Oliver and Linke, Thomas and Willmitzer, Lothar and Fernie, Alisdair R.},
  title     = {Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems},
  issn      = {1040-4651},
  year      = {2001},
  language  = {en}
}
@article{PattersonHeFolzetal.2020,
  author    = {Patterson, Jenelle A. and He, Hai and Folz, Jacob S. and Li, Qiang and Wilson, Mark A. and Fiehn, Oliver and Bruner, Steven D. and Bar-Even, Arren and Hanson, Andrew D.},
  title     = {Thioproline formation as a driver of formaldehyde toxicity in Escherichia coli},
  series = {Biochemical Journal},
  volume    = {477},
  journal   = {Biochemical Journal},
  number    = {9},
  publisher = {Portland Press},
  address   = {London},
  issn      = {1470-8728},
  doi       = {10.1042/BCJ20200198},
  pages     = {1745 -- 1757},
  year      = {2020},
  abstract  = {Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.},
  language  = {en}
}
@article{MeyerWituckaWallBecheretal.2012,
  author    = {Meyer, Rhonda C. and Witucka-Wall, Hanna and Becher, Martina and Blacha, Anna Maria and Boudichevskaia, Anastassia and D{\"o}rmann, Peter and Fiehn, Oliver and Friedel, Svetlana and von Korff, Maria and Lisec, Jan and Melzer, Michael and Repsilber, Dirk and Schmidt, Renate and Scholz, Matthias and Selbig, Joachim and Willmitzer, Lothar and Altmann, Thomas},
  title     = {Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids},
  series = {The plant journal},
  volume    = {71},
  journal   = {The plant journal},
  number    = {4},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/j.1365-313X.2012.05021.x},
  pages     = {669 -- 683},
  year      = {2012},
  abstract  = {Heterosis-associated cellular and molecular processes were analyzed in seeds and seedlings of Arabidopsis thaliana accessions Col-0 and C24 and their heterotic hybrids. Microscopic examination revealed no advantages in terms of hybrid mature embryo organ sizes or cell numbers. Increased cotyledon sizes were detectable 4 days after sowing. Growth heterosis results from elevated cell sizes and numbers, and is well established at 10 days after sowing. The relative growth rates of hybrid seedlings were most enhanced between 3 and 4 days after sowing. Global metabolite profiling and targeted fatty acid analysis revealed maternal inheritance patterns for a large proportion of metabolites in the very early stages. During developmental progression, the distribution shifts to dominant, intermediate and heterotic patterns, with most changes occurring between 4 and 6 days after sowing. The highest incidence of heterotic patterns coincides with establishment of size differences at 4 days after sowing. In contrast, overall transcript patterns at 4, 6 and 10 days after sowing are characterized by intermediate to dominant patterns, with parental transcript levels showing the largest differences. Overall, the results suggest that, during early developmental stages, intermediate gene expression and higher metabolic activity in the hybrids compared to the parents lead to better resource efficiency, and therefore enhanced performance in the hybrids.},
  language  = {en}
}
@article{KoseWeckwerthLinkeetal.2001,
  author    = {Kose, F. and Weckwerth, Wolfram and Linke, Thomas and Fiehn, Oliver},
  title     = {Visualizing plant metabolomic correlation networks using clique-metabolite matrices},
  year      = {2001},
  language  = {en}
}
@article{AltmannTaylorKingetal.2003,
  author    = {Altmann, Thomas and Taylor, Janet and King, Ross. D. and Fiehn, Oliver},
  title     = {Application of metabolomics to plant genotype discrimination using statistics and machine learning},
  year      = {2003},
  language  = {en}
}
@article{AltmannFiehnKloska2001,
  author    = {Altmann, Thomas and Fiehn, Oliver and Kloska, Sebastian},
  title     = {Integrated studies on plant biology using multiparallel techniques},
  year      = {2001},
  language  = {en}
}