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  2009
  1. Kind T, Wohlgemuth G, Lee DY, Lu L, Palazoglu M, Shahbaz S, Fiehn O (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal. Chem. (in press)
  2. Kind T, Leamy T, Leary J, Fiehn O (2009) Software platform virtualization in chemistry research and university teaching. J. Cheminformatics 1:18
  3. Kind T, Scholz M, Fiehn O (2009) How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS ONE 4(5): e5440
  4. Hartman A, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen J (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. Proc. Natl. Acad. Sci. USA 106, 17187-17192
  5. Skogerson K, Runnebaum R, Wohlgemuth G, de Ropp J, Heymann H, Fiehn O (2009) Comparison of GC-TOF MS and 1H-NMR metabolite identification in white wines from a sensory study investigating wine body. J. Agric. Food Sci. 57, 6899-6907
  6. Burke G, Fiehn O, Moran N (2009) Effects of facultative symbionts and heat stress on the metabolome of pea aphids. ISME Journal (in press, doi:10.1038/ismej.2009.114)
  7. Shin MH, Lee DY, Skogerson K, Wohlgemuth G, Choi IG, Fiehn O, Kim KH. (2009) Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans. Biotechnology and Bioengineering (in press, doi:10.1002/bit.22557)
  8. Martinelli F, Uratsu SL, Reagan RL, Chen Y, Tricoli D, Fiehn O, Rocke DM, Gasser CS, Dandekar AM (2009) Gene regulation in parthenocarpic tomato fruit. J. Exp. Bot. 60, 3873-3890

  9. Dandekar AM, Martinelli F, Davis C, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D’Souza R, Roy S, Reagan RL, Lin D, Cary RB, Pardington P, Gupta G (2009) Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Critical Reviews in Immunology (in press)



     2008
  10. Denkert C, Budczies J, Weichert W, Wohlgemuth G, Scholz M, Kind T, Niesporek S, Noske A, Buckendahl A, Dietel M, Fiehn O (2008) Metabolic profiling of human colon carcinoma - Deregulation of TCA and amino acid turnover. Mol. Cancer 7: 72
  11. Taylor CF et al (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnol. 26, 889-896
  12. Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau BJ (2008) Quality control for plant metabolomics: Reporting MSI-compliant studies. Plant J. 53, 691-704
  13. Lee DY, Fiehn O (2008) High quality metabolomic data for Chlamydomonas reinhardtii. Plant Methods 4: 7
  14. Fiehn O (2008) Extending the breadth of metabolite profiling by gas chromatography/mass spectrometry. TrAC - Trends Anal. Chem. 27, 261-269
  15. Ikegami T, Horie K, Saad N, Hosoya N,  Fiehn O, Tanaka N (2008) Highly efficient analysis of underivatized carbohydrates using monolithic silica-based capillary hydrophilic interaction (HILIC) HPLC. Anal. Bioanal. Chem. 391, 2533-2542
  16. Lisec J, Meyer RC, Steinfath M, Redestig H, Becher M, Witucka-Wall H, Fiehn O, Torjek O, Selbig J, Altmann T, Willmitzer L. (2008) Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant J. 53, 960-972

  17. Ulu A, Davis BB, Tsai HJ, Kim IH, Morisseau C, Inceoglu B, Fiehn O, Hammock BD, Weiss RH. (2008) Soluble epoxide hydrolase inhibitors reduce the development of atherosclerosis in apolipoprotein e-knockout mouse model. J Cardiovasc Pharmacol. 52,314-23.

      

    2007
  18. Kose F, Budczies J, Holschneider M, Fiehn O (2007) Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors. BMC Bioinformatics 8:162

  19. Kind T, Fiehn O (2007) Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8: 115  (supporting information and freeware)

  20. Horie K, Kimura H, Ikegami T, Iwatsuka A, Saad N, Fiehn O, Tanaka N (2007) Calculating optimal modulation periods to maximize the peak capacity in two-dimensional HPLC. Anal. Chem. 79, 3764-3770

  21. Huster D, Purnat TD, Burkhead JL, Ralle M, Fiehn O, Stuckert F, Olson NE, Teupser D, Lutsenko S (2007) Higher copper selectivity alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease. J. Biol. Chem. 282, 8343-8355
  22. Horie K, Ikegami T, Hosoya K, Saad N, Fiehn O, Tanaka N (2007) Highly efficient monolithic silica capillary columns modified with poly(acrylic acid) for hydrophilic interaction chromatography. J. Chromatogr. A 1164, 198-205

  23. Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner LW, Goodacre R, Hardy NW, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon JC, Sansone S-A (2007) The Metabolomics Standards Initiative (MSI). Metabolomics 3, 175-178

  24. Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3, 195-201

  25. Sumner LW, Amberg A, Barrett D, Beger R, Beale MH, Daykin C, Fan TWM, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Higashi R, Kopka J, Lindon JC, Lane AN, Marriott P, Nicholls AW, Reilly MD, Viant M (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3, 211-221
  26. Sansone S-A, Nikolau B, van Ommen B, Taylor C, Robertson D, Lindon J, Griffin JL, Sumner LW, van der Werf M, Hardy NW, Morrison N, Mendes P, Kaddurah-Daouk R, Goodacre R, Fan T, Fiehn O (2007) The Metabolomics Standards Initiative. Nature Biotechnol. 25, 846-848

  27. Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H, Toerjek O, Fiehn O, Eckardt A, Willmitzer L,  Selbig J, Altmann T (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104, 4759-4764

  28. Scholz M, Fiehn O (2007) SetupX - A Public Study Design Database for Metabolomic Projects. Pacific Symp. Biocomp. 12, 169-180

  29. Frey I, Rubio-Aliaga I, Siewert A, Sailer D, Drobyshev A, Beckers J, Aubert J, Bar Hen A, Fiehn O, Eichinger H, Daniel H (2007) Profiling at mRNA, protein and metabolite level reveals alterations in renal amino acid handling and glutathione metabolism in kidney tissue of Pept2-/- mice. Physiol. Genomics 28, 301-310

  30. Kind T, Tolstikov VV, Fiehn O, Weiss RH (2007) A comprehensive urinary metabolomics approach for identifying kidney cancer. Anal. Biochem. 363, 185-195
  31. Fiehn O (2007) Cellular Metabolomics: The Quest for Pathway Structure. In: The Handbook of Metabonomics and Metabolomics, Chapter 2. Eds. Lindon JC, Nicholson JK, Holmes E. Elsevier BV, Amsterdam and Oxford, ISBN-13: 978-0-44-452841-4, pp. 35-54
  32. Dixon RA, Gang DR, Charlton AJ, Fiehn O, Kuiper HA, Reynolds TL, Tjeerdema RS, Jeffery EH, German JB, Ridley WP, Seiber JN (2007) Applications of Metabolomics in Agriculture. J. Agr. Food Sci. 54, 8984-8994
  33. Fiehn, O (2007) Validated high quality automated metabolome analysis of Arabidopsis thaliana leaf disks. In: Concepts in Plant Metabolomics. Chapter 1. Eds. Nikolau BJ, Wurtele ES. Springer, New York, 1-18

    2006
  34. Denkert C, Budczies J, Kind T, Weichert W, Tablack P, Sehouli J, Niesporek S, Koensgen D, Dietel M, Fiehn O (2006) GC-TOF based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors. Cancer Res. 66, 10795-10804
  35. Fiehn O (2006) Study of metabolic control in plants by metabolomics. In: Control of Primary Metabolism in Plants. Eds. Plaxton WC and McManus MT. Blackwell, Annual Plant Reviews 22, 60-84
  36. Kind T, Fiehn O (2006) Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 7:234; see supplemental material 

  37. Fiehn O, Kristal B, v Ommen B, Sumner LW, Sansone SA, Taylor C, Hardy N, Kaddurah-Daouk R (2006) Establishing Reporting Standards for Metabolomic and Metabonomic Studies: A Call for Participation. OMICS 10, 158-163

  38. Perroud B, Lee J, Valkova N, Dhirapong A, Lin P-Y, Fiehn O, Kueltz D, Weiss RH (2006) Pathway analysis of kidney cancer using proteomics and metabolic profiling. BMC Mol. Cancer 5:64
  39. Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ, ISBN13: 978-1-59745-244-1. Methods in Molecular Biology 358, 3-18
  40. Fiehn O, Weckwerth W (2006) Mass spectrometry: Quantitation. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. Ganten D, Ruckpaul K (eds.), Springer, New York/Heidelberg, ISBN: 3-540-44244-8, DOI 10.1007/3-540-29623-9_3550, part 13, 1030-1034
  41. Fiehn O (2006) Metabolite Profiling in Arabidopsis. In: Arabidopsis Protocols 2nd edition. Salinas J, Sanchez-Serrano JJ (eds.), Methods in Molecular Biology ser., Humana Press, Totowa NJ, 439-447

  42. Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK (2006) Natural Genetic Variation of Freezing Tolerance in Arabidopsis   Plant Physiol. 142, 98-112

  43. Castle LA, Fiehn O, Kaddurah-Daouk R, Lindon JC (2006) Metabolomics standards workshop and the development of international standards for reporting metabolomics experimental results. Brief. Bioinformatics 7, 159-165

    2005
  44. Fiehn O, Wohlgemuth G, Scholz M (2005) Setup and Annotation of Metabolomic Experiments by Integrating Biological and Mass Spectrometric Metadata. Proc. Lect. Notes Bioinformatics 3615, 224-239 
  45. Boelling C, Fiehn O (2005) Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol. 139, 1995-2005
  46. Catchpole G, Beckmann M, Enot DP, Mondhe M, Zywicki B, Taylor J, Hardy N, Smith A, King RD, Kell DB, Fiehn O, Draper J. (2005) Phenotyping by hierarchical metabolomics to assess similarity of genetically modified and conventional crops. Proc. Natl. Acad. Sci.  USA  102, 14458-14462
  47. Schad M., Mungur R., Fiehn O., Kehr J. (2005) Metabolic profiling of laser microdissected vascular bundles of Arabidopsis thaliana. Plant Methods 1:2
  48. Shellie RA, Welthagen W, Zrostlikova J, Spranger J, Ristow M, Fiehn O, Zimmermann R (2005) Statistical methods for comparing GC x GC-TOFMS chromatograms: metabolomic analysis of mouse tissue extracts. J. Chromatogr. A 1086,83-90 
  49. Nikiforova VJ, Kopka J, Tolstikov V, Fiehn O, L Hopkin L, Hawkesford MJ, Hesse H, Hoefgen R. (2005) Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol. 138, 304-318
  50. Welthagen W, Shellie R, Ristow M, Spranger J, Zimmermann R, Fiehn O (2005) Comprehensive two dimensional gas chromatography – time of flight mass spectrometry, GCxGC-TOF for high resolution metabolomics: Biomarker discovery on spleen tissue extracts of obese NZO compared to lean C57BL/6 mice. Metabolomics 1, 57-65 
  51. Zywicki B, Catchpole G, Draper J, Fiehn O (2005) Comparison of rapid liquid chromatography-electrospray ionization-tandem mass spectrometry methods for determination of glycoalkaloids in transgenic field-grown potatoes. Anal. Biochem. 336, 178-186

    2004
  52. Cook D, Fowler S, Fiehn O, Tomashow M (2004) Role of the CBF cold response pathway in configuring the low temperature metabolome of Arabidopsis. Proc. Natl. Acad Sci. USA 101, 15243-15248 
  53. Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Metabolic networks unravel the effects of silent plant phenotypes. Proc. Natl. Acad. Sci. USA 101, 7809-7814
  54. Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino R, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BG, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 22, 1601-1605 
  55. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau B, Mendes P, Roessner-Tunali U, Beale M, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9, 418-425
  56. Wienkoop S, Glinski M, Tanaka N, Tolstikov VV, Fiehn O, Weckwerth W (2004) Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins. Rapid Commun. Mass Spectrom. 18, 643–650
  57. Weckwerth W, Wenzel K, Fiehn O (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83 
  58. Scholz M, Gatzek S, Sterling A., Fiehn O, Selbig J (2004) Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20, 2447 - 2454

    2003
  59. Tolstikov VV, Lommen A, Nakanishi K, Tanaka N, Fiehn O (2003) Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics. Anal. Chem. 75, 6737-6740 
  60. Fiehn O (2003) Metabolic networks of Cucurbita maxima phloem. Phytochemistry 62, 875-886 
  61. Fiehn O, Spranger J (2003) Can metabolomics be used for assessing nutritional dependent human diseases? Phytochem. Rev. 1, 223-230 
  62. Fiehn O, Spranger J (2003) Use of metabolomics to discover metabolic patterns associated with human diseases. In: Metabolic Profiling. Its role in biomarker discovery and gene function analysis. Harrigan GG, Godacre R. Kluwer Academic Publishers, Boston/Dordrecht/London. Chapter 11 pp 199-215 
  63. Steuer R, Kurths J, Fiehn O, Weckwerth W (2003) Interpreting correlations in metabolomic networks. Biochem. Soc. Trans. 31, 1476-1478
  64. Steuer R, Kurth J, Fiehn O, Weckwerth W (2003) Observing and interpreting correlations in metabolic networks. Bioinformatics 19, 1019-1026 
  65. Weckwerth W, Fiehn O (2003) Deciphering metabolic networks Eur. J. Biochem (270, 579-588

    2002 
  66. Taylor J, King RD, Altmann T, Fiehn O (2002) Application of metabolomics to plant genotype discrimination using statistics and machine learning. Bioinformatics 18, S241-S248 Suppl. S 
  67. Fiehn O, Weckwerth W (2002) Can we discover novel pathways using metabolomic analysis? Curr. Opin. Biotechnol. 13, 156-160 
  68. Tolstikov VV, Fiehn O (2002) Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Anal Biochem 301, 298-307

    2001
  69. Kose F, Weckwerth W, Linke T, Fiehn O (2001) Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 17, 1198-1208 
  70. Fiehn O (2002) Metabolomics – the link between genotype and phenotype. Plant Mol. Biol. 48, 155-171 
  71. Vogel G, Fiehn O, Jean-Richard-dit-Bressel L, Boller T, Wiemken A, Aeschbacher RA, Wingler A (2001) Trehalose metabolism in Arabidopsis: occurrence of trehalose and molecular cloning and characterization of trehalose-6-phosphate synthase homologues. J. Exp. Bot. 52,, 1817-1826 
  72. Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genom. 2, 155-168 
  73. Fiehn O, Kloska S, Altmann T (2001) Integrated studies on plant biology using multi parallel techniques. Curr. Opin. Biotechnol. 12, 82-86 
  74. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11-29

    2000
  75. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18, 1157-1161 
  76. Weckwerth W, Willmitzer L, Fiehn O (2000) Comparative quantification and identification of phosphoproteins using stable isotope labeling and liquid chromatography/mass spectrometry. Rapid Comm. Mass Spectrom. 14, 1677-1681 
  77. Fiehn O, Kopka J, Trethewey RN, Willmitzer L (2000) Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal. Chem. 72, 3573-3580 
  78. Goodlett DR, Bruce JE, Anderson GA, Rist B, Pasa-Tolic L, Fiehn O, Smith RD, Aebersold R (2000) Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal. Chem. 72, 1112-1118

    1999 and earlier
  79. Reemtsma T, Fiehn O, Jekel M (1999) A modified method for the analysis of organics in industrial waste water as directed by their toxicity to Vibrio fischeri. Fresen. J. Anal. Chem. 363, 771-776 
  80. Fiehn O, Wegener G, Jochimsen J, Jekel M (1998) Analysis of the ozonation of 2-mercaptobenzothiazole in water and tannery waste water using sum parameters, liquid and gas chromatography, and capillary electrophoresis. Wat. Res. 32, 1075-1084 
  81. Fiehn O, Wegener G, Jekel M (1998) Capillary electrophoretic analysis of organic anions in tannery waste water including high contents of chloride and sulfate. Intern. J. Environ. Anal. Chem. 69, 257-271 
  82. Fiehn O, Vigelahn L, Kalnowski G, Reemtsma T, Jekel M (1997) Toxicity directed fractionation of tannery waste water using solid-phase extraction and luminescence inhibition in microtiter plates. Acta Hydrochim. Hydrobiol. 254, 1-6 
  83. Fiehn O, Jekel M (1997) Analysis of phenolic compounds in industrial waste water with HPLC and post-column reaction detection. J. Chromatogr. 769, 189-200 
  84. Fiehn O, Jekel M (1996) Comparison of sorbents using semipolar to highly hydrophilic compounds for a sequential solid-phase extraction procedure of industrial waste waters. Anal. Chem. 68, 3083-3089 
  85. Reemtsma T, Fiehn O, Kalnowski G, Jekel M (1995) Microbial transformations and biological effects of fungicide-derived benzothiazoles determined in industrial waste water. Environ. Sci. Technol. 29, 478-485 
  86. Fiehn O, Reemtsma T, Jekel M (1994) Extraction and analysis of various benzothiazoles from industrial wastewater. Anal. Chim. Acta 295, 297-305 
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