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  1. Targeting PHGDH reverses the immunosuppressive phenotype of tumor-associated macrophages through α-ketoglutarate and mTORC1 signaling.
    Cai Z, Li W, Hager S, Wilson JL, Afjehi-Sadat L, Heiss EH, Weichhart T, Heffeter P, Weckwerth W. Cell Mol Immunol. 2024 Feb 27. doi: 10.1038/s41423-024-01134-0.
  2. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Microb Cell Fact. 2024 Feb 8;23(1):43. doi: 10.1186/s12934-024-02314-3.
  3. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Zuffa S et al, Nat Microbiol. 2024 Feb;9(2):336-345. doi: 10.1038/s41564-023-01575-9.
  4. Sulforaphane impedes mitochondrial reprogramming and histone acetylation in polarizing M1 (LPS) macrophages. Bahiraii S, Brenner M, Weckwerth W, Heiss EH. Free Radic Biol Med. 2024 Mar;213:443-456. doi: 10.1016/j.freeradbiomed.2024.01.029.
  5. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. RNA Biol. 2024 Jan;21(1):1-15. doi: 10.1080/15476286.2023.2298532.
  6. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Schwarzerova J, Zeman M, Babak V, Jureckova K, Nykrynova M, Varga M, Weckwerth W, Dolejska M, Provaznik V, Rychlik I, Cejkova D. Microbiol Spectr. 2024 Jan 11;12(1):e0196423. doi: 10.1128/spectrum.01964-23.
  7. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Plant Biotechnol J. 2024 Mar;22(3):555-571. doi: 10.1111/pbi.14203.
  8. Metabolic support by macrophages sustains colonic epithelial homeostasis. Fritsch SD, Sukhbaatar N, Gonzales K, Sahu A, Tran L, Vogel A, Mazic M, Wilson JL, Forisch S, Mayr H, Oberle R, Weiszmann J, Brenner M, Vanhoutte R, Hofmann M, Pirnes-Karhu S, Magnes C, Kühnast T, Weckwerth W, Bock C, Klavins K, Hengstschläger M, Moissl-Eichinger C, Schabbauer G, Egger G, Pirinen E, Verhelst SHL, Weichhart T. Cell Metab. 2023 Nov 7;35(11):1931-1943.e8. doi: 10.1016/j.cmet.2023.09.010.
  9. Candidate pathogenicity factor/effector proteins of 'Candidatus Phytoplasma solani' modulate plant carbohydrate metabolism, accelerate the ascorbate-glutathione cycle, and induce autophagosomes. Dermastia M, Tomaž Š, Strah R, Lukan T, Coll A, Dušak B, Anžič B, Čepin T, Wienkoop S, Kladnik A, Zagorščak M, Riedle-Bauer M, Schönhuber C, Weckwerth W, Gruden K, Roitsch T, Pompe Novak M, Brader G. Front Plant Sci. 2023 Aug 18;14:1232367. doi: 10.3389/fpls.2023.1232367.
  10. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Zuffa S, et al Res Sq [Preprint]. 2023 Aug doi: 10.21203/
  11. Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.). Wolfe TM, Balao F, Trucchi E, Bachmann G, Gu W, Baar J, Hedrén M, Weckwerth W, Leitch AR, Paun O. Mol Ecol. 2023 Jul 15. doi: 10.1111/mec.17070.

  12. COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks.
    Li J, Waldherr S, Weckwerth W. Bioinformatics. 2023 Jul 1; doi: 10.1093/bioinformatics/btad397. .
  13. Norbergenin prevents LPS-induced inflammatory responses in macrophages through inhibiting NFκB, MAPK and STAT3 activation and blocking metabolic reprogramming. Li W, Cai Z, Schindler F, Bahiraii S, Brenner M, Heiss EH, Weckwerth W. Front Immunol. 2023 May 12;14:1117638. doi: 10.3389/fimmu.2023.1117638.
  14. Scrutinizing different ionization responses of polar lipids in a reversed-phase gradient by implementing a counter-gradient. Hildebrand F, Schoeny H, Rampler E, Koellensperger G.  Anal Chim Acta. 2023 Jul 18;1265:341274. doi: 10.1016/j.aca.2023.341274.
  15. Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. Weiszmann J, Walther D, Clauw P, Back G, Gunis J, Reichardt I, Koemeda S, Jez J, Nordborg M, Schwarzerova J, Pierides I, Nägele T, Weckwerth W. Plant Physiol. 2023 May 23:kiad298. doi: 10.1093/plphys/kiad298.
  16. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK.  Plant Genome. 2023 May 10:e20337. doi: 10.1002/tpg2.20337.
  17. Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems. Retzer K, Weckwerth W. Front Plant Sci. 2023 Mar 16;14:1154088. doi:10.3389/fpls.2023.1154088.
  18. Evaluation of Sustainable Recycled Products to Increase the Production of Nutraceutical and Antibacterial Molecules in Basil Plants by a Combined Metabolomic Approach. Verrillo M, Koellensperger G, Puehringer M, Cozzolino V, Spaccini R, Rampler E. Plants (Basel). 2023 Jan 23;12(3):513. doi: 10.3390/plants12030513.
  19. Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes. Kumar R, Ghatak A, Goyal I, Sarkar NK, Weckwerth W, Grover A, Chaturvedi P. Front Plant Sci. 2023 Jan 13;13:1083971. doi:10.3389/fpls.2022.1083971.
  20. Interpretable machine learning methods for predictions in systems biology from omics data. Sidak D, Schwarzerová J, Weckwerth W, Waldherr S. Front Mol Biosci. 2022 Oct 17;9:926623. doi: 10.3389/fmolb.2022.926623.
  21. Branched-chain ketoacids derived from cancer cells modulate macrophage polarization and metabolic reprogramming. Cai Z, Li W, Brenner M, Bahiraii S, Heiss EH, Weckwerth W.  Front Immunol. 2022 Oct 13;13:966158. doi: 10.3389/fimmu.2022.966158.
  22. PANOMICS at the interface of root-soil microbiome and BNI. Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. Trends Plant Sci. 2023 Jan;28(1):106-122. doi: 10.1016/j.tplants.2022.08.016.
  23. Perspectives of (/memorandum for) systems thinking on COVID-19 pandemic and pathology. Tretter F, Peters EMJ, Sturmberg J, Bennett J, Voit E, Dietrich JW, Smith G, Weckwerth W, Grossman Z, Wolkenhauer O, Marcum JA. J Eval Clin Pract. 2023 Apr;29(3):415-429. doi: 10.1111/jep.13772.
  24. Influence of the environment on ragweed pollen and their sensitizing capacity in a mouse model of allergic lung inflammation. Liu SH, Kazemi S, Karrer G, Bellaire A, Weckwerth W, Damkjaer J, Hoffmann O, Epstein MM. Front Allergy. 2022 Aug 5;3:854038. doi: 10.3389
  25. Sulforaphane diminishes moonlighting of pyruvate kinase M2 and interleukin 1β expression in M1 (LPS) macrophages.Bahiraii S, Brenner M, Yan F, Weckwerth W, Heiss EH. Front Immunol. 2022 Aug 2;13:935692. doi: 10.3389
  26. Systematic Investigation of LC Miniaturization to Increase Sensitivity in Wide-Target LC-MS-Based Trace Bioanalysis of Small Molecules. Fitz V, El Abiead Y, Berger D, Koellensperger G. Front Mol Biosci. 2022 Jul 18;9:857505. doi: 10.3389
  27. Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity. Ghatak A, Schindler F, Bachmann G, Engelmeier D, Bajaj P, Brenner M, Fragner L, Varshney RK, Subbarao GV, Chaturvedi P, Weckwerth W. Biol Fertil Soils. 2022;58(3):291-306. doi: 10.1007
  28. Editorial: Sorghum and Pearl Millet as Climate Resilient Crops for Food and Nutrition Security.
    Chaturvedi P, Govindaraj M, Govindan V, Weckwerth W. Front Plant Sci. 2022 Mar 11;13:851970. doi: 10.3389
  29. (±)-Catechin-A Mass-Spectrometry-Based Exploration Coordination Complex Formation with FeII and FeIII. Kubicova L, Bachmann G, Weckwerth W, Chobot V. Cells. 2022 Mar 11;11(6):958. doi: 10.3390
  30. Throttling Growth Speed: Evaluation of aux1-7 Root Growth Profile by Combining D-Root system and Root Penetration Assay.  García-González J, Lacek J, Weckwerth W, Retzer K. Plants (Basel). 2022 Feb 27;11(5):650. doi: 10.3390
  31. A Potential Citrate Shunt in Erythrocytes of PKAN Patients Caused by Mutations in Pantothenate Kinase 2. Werning M, Dobretzberger V, Brenner M, Müllner EW, Mlynek G, Djinovic-Carugo K, Baron DM, Fragner L, Bischoff AT, Büchner B, Klopstock T, Weckwerth W, Salzer U. Biomolecules. 2022 Feb 18;12(2):325. doi: 10.3390
  32. Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions. Moors KA, Ott E, Weckwerth W, Milojevic T. Life (Basel). 2021 Dec 24;12(1):23. doi: 10.3390
  33. Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study.
    Schoeny H, Rampler E, Binh Chu D, Schoeberl A, Galvez L, Blaukopf M, Kosma P, Koellensperger G. Anal Chem. 2022 Jan 25;94(3):1618-1625. doi: 10.1021
  34. Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination.
    Lacek J, García-González J, Weckwerth W, Retzer K. Int J Mol Sci. 2021 Nov 26;22(23):12784.
  35. Yeast-based reference materials for quantitative metabolomics. Wasito H, Hermann G, Fitz V, Troyer C, Hann S, Koellensperger G. Anal Bioanal Chem. 2021 Oct 13. doi: 10.1007/s00216-021-03694-w.
  36. Rapid delivery systems for future food security. Varshney RK, Bohra A, Roorkiwal M, Barmukh R, Cowling W, Chitikineni A, Lam HM, Hickey LT, Croser J, Edwards D, Farooq M, Crossa J, Weckwerth W, Millar AH, Kumar A, Bevan MW, Siddique KHM. Nat Biotechnol. 2021 Oct;39(10):1179-1181. doi: 10.1038/s41587-021-01079-z.
  37. Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor. Herpell JB, Vanwijnsberghe S, Peeters C, Schindler F, Fragner L, Bejtović M, Weckwerth W, Vandamme P. Int J Syst Evol Microbiol. 2021 Sep;71(9). doi: 10.1099/ijsem.0.004969.
  38. Fast-forward breeding for a food-secure world. Varshney RK, Bohra A, Roorkiwal M, Barmukh R, Cowling WA, Chitikineni A, Lam HM, Hickey LT, Croser JS, Bayer PE, Edwards D, Crossa J, Weckwerth W, Millar H, Kumar A, Bevan MW, Siddique KHM. Trends Genet. 2021 Sep 14:S0168-9525(21)00226-2. doi: 10.1016/j.tig.2021.08.002.
  39. Tissue-Specific Proteome and Subcellular Microscopic Analyses Reveal the Effect of High Salt Concentration on Actin Cytoskeleton and Vacuolization in Aleurone Cells during Early Germination of Barley. Dermendjiev G, Schnurer M, Weiszmann J, Wilfinger S, Ott E, Gebert C, Weckwerth W, Ibl V. Int J Mol Sci. 2021 Sep 6;22(17):9642. doi: 10.3390/ijms22179642.
  40. Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer. Herrmann HA, Rusz M, Baier D, Jakupec MA, Keppler BK, Berger W, Koellensperger G, Zanghellini J. Cancers (Basel). 2021 Aug 17;13(16):4130. doi: 10.3390/cancers13164130.
  41. Exogenous carbon source supplementation counteracts root and hypocotyl growth limitations under increased cotyledon shading, with glucose and sucrose differentially modulating growth curves. García-González J, Lacek J, Weckwerth W, Retzer K. Plant Signal Behav. 2021 Aug 24:1969818. doi: 10.1080/15592324.2021.1969818.
  42. Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata. Schindler F, Fragner L, Herpell JB, Berger A, Brenner M, Tischler S, Bellaire A, Schönenberger J, Li W, Sun X, Schinnerl J, Brecker L, Weckwerth W. Front Mol Biosci. 2021 Jul 30;8:683671. doi: 10.3389/fmolb.2021.683671.
  43. Morpho-metabotyping the oxidative stress response. Rusz M, Del Favero G, El Abiead Y, Gerner C, Keppler BK, Jakupec MA, Koellensperger G. Sci Rep. 2021 Jul 29;11(1):15471. doi: 10.1038/s41598-021-94585-8.
  44. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Plant J. 2021 Aug;107(3):669-687. doi: 10.1111/tpj.15410.
  45. The Quest for System-Theoretical Medicine in the COVID-19 Era. Tretter F, Wolkenhauer O, Meyer-Hermann M, Dietrich JW, Green S, Marcum J, Weckwerth W. Front Med (Lausanne). 2021 Mar 29;8:640974. doi: 10.3389/fmed.2021.640974.
  46. Heat stress response mechanisms in pollen development. Chaturvedi P, Wiese AJ, Ghatak A, Záveská Drábková L, Weckwerth W, Honys D. New Phytol. 2021 Jul;231(2):571-585. doi: 10.1111/nph.17380.
  47. Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries. Rampler E, Hermann G, Grabmann G, El Abiead Y, Schoeny H, Baumgartinger C, Köcher T, Koellensperger G. Metabolites. 2021 Mar 10;11(3):160. doi: 10.3390/metabo11030160.
  48. A combined flow injection/reversed-phase chromatography-high-resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C internal standards. Schoeny H, Rampler E, El Abiead Y, Hildebrand F, Zach O, Hermann G, Koellensperger G. Analyst. 2021 Apr 26;146(8):2591-2599. doi: 10.1039/d0an02443k.
  49. Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat. Ghatak A, Chaturvedi P, Bachmann G, Valledor L, Ramšak Ž, Bazargani MM, Bajaj P, Jegadeesan S, Li W, Sun X, Gruden K, Varshney RK, Weckwerth W. Front Plant Sci. 2021 Jan 13;11:600278. doi: 10.3389/fpls.2020.600278.
  50. The TOR-Auxin Connection Upstream of Root Hair Growth. Retzer K, Weckwerth W. Plants (Basel). 2021 Jan 13;10(1):150. doi: 10.3390/plants10010150.
  51. In Vitro Evaluation of Pro- and Antioxidant Effects of Flavonoid Tricetin in Comparison to Myricetin. Chobot V, Hadacek F, Bachmann G, Weckwerth W, Kubicova L. Molecules. 2020 Dec 11;25(24):5850. doi: 10.3390/molecules25245850.
  52. Multiomics approach unravels fertility transition in a pigeonpea line for a two-line hybrid system. Pazhamala LT, Chaturvedi P, Bajaj P, Srikanth S, Ghatak A, Chitikineni A, Bellaire A, Hingane A, Kumar CVS, Saxena KB, Weckwerth W, Saxena RK, Varshney RK. Plant Genome. 2020 Jul;13(2):e20028. doi: 10.1002/tpg2.20028.
  53. Actaea racemosa L. extract inhibits steroid sulfation in human breast cancer cells: Effects on androgen formation. Poschner S, Wackerlig J, Dobusch D, Pachmann B, Banh SJ, Thalhammer T, Jäger W. Phytomedicine. 2020 Dec;79:153357. doi: 10.1016/j.phymed.2020.153357.
  54. Chasing the Major Sphingolipids on Earth: Automated Annotation of Plant Glycosyl Inositol Phospho Ceramides by Glycolipidomics. Panzenboeck L, Troppmair N, Schlachter S, Koellensperger G, Hartler J, Rampler E. Metabolites. 2020 Sep 19;10(9):375. doi: 10.3390/metabo10090375.
  55. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. FEMS Microbiol Rev. 2020 Nov 24;44(6):874-908. doi: 10.1093/femsre/fuaa037.
  56. Structural and Functional Heat Stress Responses of Chloroplasts of Arabidopsis thaliana. Paul P, Mesihovic A, Chaturvedi P, Ghatak A, Weckwerth W, Böhmer M, Schleiff E. Genes (Basel). 2020 Jun 12;11(6):650. doi: 10.3390/genes11060650.
  57. Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. Front Microbiol. 2019 Apr 29;10:909. doi: 10.3389/fmicb.2019.00909.
  58. Combination of Hypoglycemia and Metformin Impairs Tumor Metabolic Plasticity and Growth by Modulating the PP2A-GSK3β-MCL-1 Axis. Elgendy M, Cirò M, Hosseini A, Weiszmann J, Mazzarella L, Ferrari E, Cazzoli R, Curigliano G, DeCensi A, Bonanni B, Budillon A, Pelicci PG, Janssens V, Ogris M, Baccarini M, Lanfrancone L, Weckwerth W, Foiani M, Minucci S. Cancer Cell. 2019 May 13;35(5):798-815.e5. doi: 10.1016/j.ccell.2019.03.007. Epub 2019 Apr 25.
  59. Metabolomics in Plant Stress Physiology. Ghatak A, Chaturvedi P, Weckwerth W. Adv Biochem Eng Biotechnol. 2018;164:187-236. doi: 10.1007/10_2017_55.
  60. Resveratrol and other dietary polyphenols are inhibitors of estrogen metabolism in human breast cancer cells. Poschner S, Maier-Salamon A, Thalhammer T, Jäger W. J Steroid Biochem Mol Biol. 2019 Jun;190:11-18. doi: 10.1016/j.jsbmb.2019.03.001. Epub 2019 Mar 6.
  61. Proteomics and metabolomics identify molecular mechanisms of aging potentially predisposing for chronic lymphocytic leukemia. Mayer RL, Schwarzmeier JD, Gerner MC, Bileck A, Mader JC, Meier-Menches SM, Gerner SM, Schmetterer KG, Pukrop T, Reichle A, Slany A, Gerner C. Mol Cell Proteomics. 2018 Feb;17(2):290-303. doi: 10.1074/mcp.RA117.000425. Epub 2017 Dec 1.
  62. Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation. Wilson JL, Nägele T, Linke M, Demel F, Fritsch SD, Mayr HK, Cai Z, Katholnig K, Sun X, Fragner L, Miller A, Haschemi A, Popa A, Bergthaler A, Hengstschläger M, Weichhart T, Weckwerth W. Cell Rep. 2020 Feb 4;30(5):1542-1552.e7. doi: 10.1016/j.celrep.2020.01.011.
  63. Chronic signaling via the metabolic checkpoint kinase mTORC1 induces macrophage granuloma formation and marks sarcoidosis progression. Linke M, Pham HT, Katholnig K, Schnöller T, Miller A, Demel F, Schütz B, Rosner M, Kovacic B, Sukhbaatar N, Niederreiter B, Blüml S, Kuess P, Sexl V, Müller M, Mikula M, Weckwerth W, Haschemi A, Susani M, Hengstschläger M, Gambello MJ, Weichhart T. Nat Immunol. 2017 Mar;18(3):293-302. doi: 10.1038/ni.3655. Epub 2017 Jan 16.
  64. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Anal Chem. 2021 Jan 12;93(1):519-545. doi: 10.1021/acs.analchem.0c04698. Epub 2020 Nov 28.
  65. Studying AMPK in an Evolutionary Context. Jain A, Roustan V, Weckwerth W, Ebersberger I. Methods Mol Biol. 2018;1732:111-142. doi: 10.1007/978-1-4939-7598-3_8.
  66. Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation. De La Harpe M, Paris M, Hess J, Barfuss MHJ, Serrano-Serrano ML, Ghatak A, Chaturvedi P, Weckwerth W, Till W, Salamin N, Wai CM, Ming R, Lexer C. Plant Cell Environ. 2020 Jul 16. doi: 10.1111/pce.13847. Online ahead of print.
  67. Mexicanolide-type limonoids from the twigs and leaves of Cipadessa baccifera.
    Cao DH, Liao SG, Sun P, Xiao YD, Xiao CF, Hu HB, Weckwerth W, Xu YK. Phytochemistry. 2020 Sep;177:112449. doi: 10.1016/j.phytochem.2020.112449. Epub 2020 Jun 26.
  68. Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Zhao, Z., F. Baltar, and G.J. Herndl, Sci Adv, 2020. 6(16): p. eaaz4354.
  69. The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato. Herpell JB et al., Front Microbiol. 2020 Apr 21;11:581. doi: 10.3389/fmicb.2020.00581.
  70. Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks. Chen Y, Weckwerth W. Trends Plant Sci. 2020 Apr 28:S1360-1385(20)30113-8. doi: 10.1016/j.tplants.2020.03.013.
  71. Adjustment of photosynthetic activity to drought and fluctuating light in wheat. Grieco M, Roustan V, Dermendjiev G, Rantala S, Jain A, Leonardelli M, Neumann K, Berger V, Engelmeier D, Bachmann G, Ebersberger I, Aro EM, Weckwerth W, Teige M. Plant Cell Environ. 2020 Jun;43(6):1484-1500. doi: 10.1111/pce.13756.
  72. PANOMICS meets germplasm. Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. Plant Biotechnol J. 2020 Mar 12. doi: 10.1111/pbi.13372.
  73. Molecular Mechanisms of Microbial Survivability in Outer Space: A Systems Biology Approach. Milojevic, T. and W. Weckwerth, Front Microbiol, 2020. 11: p. 923.
  74. Preparative supercritical fluid chromatography for lipid class fractionation-a novel strategy in high-resolution mass spectrometry based lipidomics. Schoeny H, Rampler E, Hermann G, Grienke U, Rollinger JM, Koellensperger G. Anal Bioanal Chem. 2020 Apr;412(10):2365-2374. doi: 10.1007/s00216-020-02463-5.
  75. Metabolism of Estrogens: Turnover Differs Between Platinum-Sensitive and -Resistant High-Grade Serous Ovarian Cancer Cells. Poschner Set al., Cancers (Basel). 2020 Jan 23;12(2). pii: E279. doi: 10.3390/cancers12020279.
  76. Single Spheroid Metabolomics: Optimizing Sample Preparation of Three-Dimensional Multicellular Tumor Spheroids. Rusz M, Rampler E, Keppler BK, Jakupec MA, Koellensperger G. Metabolites. 2019 Dec 14;9(12). pii: E304. doi: 10.3390/metabo9120304.
  77. Proposing a validation scheme for (13)C metabolite tracer studies in high-resolution mass spectrometry. Schwaiger-Haber, M., et al., Anal Bioanal Chem, 2019. 411(14): p. 3103-3113.
  78. Molecular response of Deinococcus radiodurans to simulated microgravity explored by proteometabolomic approach. Ott E, Fuchs FM, Moeller R, Hemmersbach R, Kawaguchi Y, Yamagishi A, Weckwerth W, Milojevic T. Sci Rep. 2019 Dec 5;9(1):18462. doi: 10.1038/s41598-019-54742-6.
  79. Coordination Complex Formation and Redox Properties of Kynurenic and Xanthurenic Acid Can Affect Brain Tissue Homeodynamics Kubicova L, Hadacek F, Bachmann G, Weckwerth W, Chobot V. Antioxidants (Basel). 2019 Oct 11;8(10). pii: E476. doi: 10.3390/antiox8100476.
  80. The Power of LC-MS Based Multiomics: Exploring Adipogenic Differentiation of Human Mesenchymal Stem/Stromal Cells. Rampler E, Egger D, Schoeny H, Rusz M, Pacheco MP, Marino G, Kasper C, Naegele T, Koellensperger G. Molecules. 2019 Oct 8;24(19). pii: E3615. doi: 10.3390/molecules24193615.
  81. Male Sterility in Maize after Transient Heat Stress during the Tetrad Stage of Pollen Development. Begcy K, Nosenko T, Zhou LZ, Fragner L, Weckwerth W, Dresselhaus T. Plant Physiol. 2019 Oct;181(2):683-700. doi: 10.1104/pp.19.00707.
  82. Subcellular dynamics of proteins and metabolites under abiotic stress reveal deferred response of the Arabidopsis thaliana hexokinase-1 mutant gin2-1 to high light. Kustner, L., et al., Plant J, 2019. 100(3): p. 456-472.
  83. Resolving subcellular plant metabolism. Fürtauer L, Küstner L, Weckwerth W, Heyer AG, Nägele T.Plant J. 2019 Jul 30. doi: 10.1111/tpj.14472. [Epub ahead of print]
  84. Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. Front Microbiol. 2019 Apr 29;10:909. doi: 10.3389/fmicb.2019.00909.
  85. Dynamics of Plant Metabolism during Cold Acclimation. Furtauer, L., et al., Int J Mol Sci, 2019. 20(21).
  86. Combination of Hypoglycemia and Metformin Impairs Tumor Metabolic Plasticity and Growth by Modulating the PP2A-GSK3β-MCL-1 Axis. Elgendy M, et al., Cancer Cell. 2019 Apr 10. pii: S1535-6108(19)30152-7. doi: 10.1016/j.ccell.2019.03.007. [Epub ahead of print]
  87. Resveratrol and other dietary polyphenols are inhibitors of estrogen metabolism in human breast cancer cells. Poschner S, Maier-Salamon A, Thalhammer T, Jäger W. J Steroid Biochem Mol Biol. 2019 Mar 6;190:11-18. doi: 10.1016/j.jsbmb.2019.03.001. [Epub ahead of print]
  88. Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells. Warth B et al., Metabolites. 2019 Jan 2;9(1). pii: E7. doi: 10.3390/metabo9010007.
  89. Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. Bayer, B., et al., mSystems, 2019. 4(4).
  90. The SnRK1 Kinase as Central Mediator of Energy Signaling between Different Organelles. Wurzinger, B., et al., Plant Physiol, 2018. 176(2): p. 1085-1094.
  91. Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii. Roustan V, Weckwerth W. Front Plant Sci. 2018 Nov 28;9:1590. doi: 10.3389/fpls.2018.01590. eCollection 2018.
  92. Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field. Nagler M, Nägele T, Gilli C, Fragner L, Korte A, Platzer A, Farlow A, Nordborg M, Weckwerth W. Front Plant Sci. 2018 Nov 6;9:1556. doi: 10.3389/fpls.2018.01556. eCollection 2018.
  93. Using RT-qPCR, Proteomics, and Microscopy to Unravel the Spatio-Temporal Expression and Subcellular Localization of Hordoindolines Across Development in Barley Endosperm. Shabrangy, A., et al., Front Plant Sci, 2018. 9: p. 775.
  94. Monitoring Early Life Mycotoxin Exposures via LC-MS/MS Breast Milk Analysis. Braun D, Ezekiel CN, Abia WA, Wisgrill L, Degen GH, Turner PC, Marko D, Warth B. Anal Chem. 2018 Dec 18;90(24):14569-14577. doi: 10.1021/acs.analchem.8b04576. Epub 2018 Nov 30.
  95. Merging metabolomics and lipidomics into one analytical run. Schwaiger M, Schoeny H, El Abiead Y, Hermann G, Rampler E, Koellensperger G. Analyst. 2018 Nov 9. doi: 10.1039 [Epub ahead of print]
  96. Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics. Hassan H, Amiruddin MD, Weckwerth W, Ramli US. Electrophoresis. 2018 Oct 29. doi: 10.1002 [Epub ahead of print]
  97. Microscopic and Proteomic Analysis of Dissected Developing Barley Endosperm Layers Reveals the Starchy Endosperm as Prominent Storage Tissue for ER-Derived Hordeins Alongside the Accumulation of Barley Protein Disulfide Isomerase (HvPDIL1-1). Roustan V, Roustan PJ, Weidinger M, Reipert S, Kapusi E, Shabrangy A, Stoger E, Weckwerth W, Ibl V. Front Plant Sci. 2018 Sep 10;9:1248. doi:  10.3389
  98. Vacuolar sucrose cleavage prevents limitation of cytosolic carbohydrate metabolism and stabilizes photosynthesis under abiotic stress.
    Weiszmann J, Fürtauer L, Weckwerth W, Nägele T. FEBS J. 2018 Sep 14. doi: 10.1111/febs.14656. [Epub ahead of print]
  99. Snf1-RELATED KINASE1-Controlled C/S1-bZIP Signaling Activates Alternative Mitochondrial Metabolic Pathways to Ensure Plant Survival in Extended Darkness. Pedrotti, L., et al., Plant Cell, 2018. 30(2): p. 495-509.
  100. Complementary intestinal mucosa and microbiota responses to caloric restriction.
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  101. Resveratrol Inhibits Key Steps of Steroid Metabolism in a Human Estrogen-Receptor Positive Breast Cancer Model: Impact on Cellular Proliferation.
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  102. Glycolate Induces Redox Tuning Of Photosystem II in Vivo: Study of a Photorespiration Mutant. Messant, M., et al., Plant Physiol, 2018. 177(3): p. 1277-1285.
  103. Autonomous Multimodal Metabolomics Data Integration for Comprehensive Pathway Analysis and Systems Biology. Huan T, et al., Anal Chem. 2018 Jul 17;90(14):8396-8403. doi: 10.1021
  104. Proteomics of Heat-Stress and Ethylene-Mediated Thermotolerance Mechanisms in Tomato Pollen Grains. Jegadeesan, S., et al., Front Plant Sci, 2018. 9: p. 1558.
  105. Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry. Palermo A1, Forsberg EM2, Warth B3, Aisporna AE1, Billings E1, Kuang E2, Benton HP1, Berry D4, Siuzdak G1,5. ACS Nano. 2018 Jul 24;12(7):6938-6948. doi: 10.1021
  106. A Novel Lipidomics Workflow for Improved Human Plasma Identification and Quantification Using RPLC-MSn Methods and Isotope Dilution Strategies. Rampler E, Criscuolo A, Zeller M, El Abiead Y, Schoeny H, Hermann G, Sokol E, Cook K, Peake DA, Delanghe B, Koellensperger G. (2018) Anal Chem. 2018 May 10.
  107. 13C-labelled yeast as internal standard for LC-MS/MS and LC high resolution MS based amino acid quantification in human plasma. Hermann G, Schwaiger M, Volejnik P, Koellensperger G., J Pharm Biomed Anal. 2018 Jun 5;155:329-334
  108. Altered membrane rigidity via enhanced endogenous cholesterol synthesis drives cancer cell resistance to destruxins. Heilos, D., et al., Oncotarget, 2018. 9(39): p. 25661-25680.
  109. Metabolomics Reveals that Dietary Xenoestrogens Alter Cellular Metabolism Induced by Palbociclib/Letrozole Combination Cancer Therapy. Warth B, Raffeiner P, Granados A, Huan T, Fang M, Forsberg EM, Benton HP, Goetz L, Johnson CH, & Siuzdak G (2018) Cell Chem Biol.
  110. Mathematical Modeling Approaches in Plant Metabolomics. Furtauer, L., et al., Methods Mol Biol, 2018. 1778: p. 329-347.
  111. Proteomics and metabolomics identify molecular mechanisms of aging potentially predisposing for chronic lymphocytic leukemia. Mayer RL et al., (2018) Mol Cell Proteomics 17(2):290-303.
  112. Studying AMPK in an Evolutionary Context. Jain A, Roustan V, Weckwerth W, & Ebersberger I (2018) Methods Mol Biol 1732:111-142.
  113. Metabolomics in Plant Stress Physiology. Ghatak A, Chaturvedi P, & Weckwerth W (2018) Adv Biochem Eng Biotechnol.
  114. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism. Wang, L., et al., Front Plant Sci, 2017. 8: p. 1066.
  115. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Varshney RK et al. (2017) Nat Biotechnol 35(10):969-976.
  116. Anion-Exchange Chromatography Coupled to High-Resolution Mass Spectrometry: A Powerful Tool for Merging Targeted and Non-targeted Metabolomics. Schwaiger M, Rampler E, Hermann G, Miklos W, Berger W, & Koellensperger G (2017) Anal Chem 89(14):7667-7674.
  117. Combined Metabolomic Analysis of Plasma and Urine Reveals AHBA, Tryptophan and Serotonin Metabolism as Potential Risk Factors in Gestational Diabetes Mellitus (GDM). Leitner M,  Fragner L,  Danner S,  Holeschofsky N,  Leitner K,  Tischler S,  Doerfler H,  Bachmann G,  Sun X,  Jaeger W,  Kautzky-Willer A,  Weckwerth W (2017) Front Mol Biosci. 2017; 4: 84.
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  118. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Bergauer K, Fernandez-Guerra A, Garcia JAL, Sprenger RR, Stepanauskas R, Pachiadaki MG, Jensen ON, Herndl GJ,   Front. Pharmacol., 05 October 2017
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  119. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Kerou, M., Offre, P., Valledor, L., Abby, S. S., Melcher, M., Nagler, M., Weckwerth, W.,Schleper, C. (2016).  Proc Natl Acad Sci U S A 113, E7937-E46.
  120. Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii.  Roustan V, Bakhtiari S, Roustan PJ, & Weckwerth W (2017) Biotechnol Biofuels 10:280.
  121. Protein sumoylation and phosphorylation intersect in Arabidopsis signaling. Nukarinen, E., et al., Plant J, 2017. 91(3): p. 505-517.
  122. LILY-lipidome isotope labeling of yeast: in vivo synthesis of (13)C labeled reference lipids for quantification by mass spectrometry. Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, & Koellensperger G (2017) Analyst 142(11):1891-1899.
  123. The Impacts of Genistein and Daidzein on Estrogen Conjugations in Human Breast Cancer Cells: A Targeted Metabolomics Approach.  Poschner S, Maier-Salamon A, Zehl M, Wackerlig J, Dobusch D, Pachmann B, Sterlini KL, & Jager W (2017) Front Pharmacol 8:699.
  124. Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata. Pascual J, Canal MJ, Escandon M, Meijon M, Weckwerth W, & Valledor L (2017) Mol Cell Proteomics 16(3):485-501.
  125. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. Ghatak, A., P. Chaturvedi, and W. Weckwerth, Front Plant Sci, 2017. 8: p. 757.
  126. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. Ott E, Kawaguchi Y, Kolbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, & Milojevic T (2017) Plos One 12(12):e0189381.
  127. Chronic signaling via the metabolic checkpoint kinase mTORC1 induces macrophage granuloma formation and marks sarcoidosis progression. Linke M et al. (2017) Nature immunology 18(3):293-302.
  128. Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana. Hoermiller, II, Naegele T, Augustin H, Stutz S, Weckwerth W, & Heyer AG (2017) Plant Cell Environ 40(5):602-610.
  129. Proteomics survey of Solanaceae family: Current status and challenges ahead. Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, & Gupta R (2017) J Proteomics 169:41-57.
  130. PPARgamma Modulates Long Chain Fatty Acid Processing in the Intestinal Epithelium. Duszka K, Oresic M, Le May C, Konig J, & Wahli W (2017) Int J Mol Sci 18(12).
  131. System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance. Wang L, Nagele T, Doerfler H, Fragner L, Chaturvedi P, Nukarinen E, Bellaire A, Huber W, Weiszmann J, Engelmeier D, Ramsak Z, Gruden K, & Weckwerth W (2016) Plant J 87(3):318-332.
  132. Longer telomeres in chronic, moderate, unconjugated hyperbilirubinaemia: insights from a human study on Gilbert's Syndrome. Tosevska A, Moelzer C, Wallner M, Janosec M, Schwarz U, Kern C, Marculescu R, Doberer D, Weckwerth W, & Wagner KH (2016) Scientific reports 6:22300.
  133. An evolutionary perspective of AMPK-TOR signaling in the three domains of life. Roustan V, Jain A, Teige M, Ebersberger I, & Weckwerth W (2016) J Exp Bot 67(13):3897-3907.
  134. Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. "Modra frankinja" with Flavescence Doree Phytoplasma. Prezelj N, Covington E, Roitsch T, Gruden K, Fragner L, Weckwerth W, Chersicola M, Vodopivec M, & Dermastia M (2016) Front Plant Sci 7:711.
  135. The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata. Pascual J, Alegre S, Nagler M, Escandon M, Annacondia ML, Weckwerth W, Valledor L, & Canal MJ (2016) J Proteomics 143:390-400.
  136. Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. Nukarinen E, Nagele T, Pedrotti L, Wurzinger B, Mair A, Landgraf R, Bornke F, Hanson J, Teige M, Baena-Gonzalez E, Droge-Laser W, & Weckwerth W (2016) Scientific reports 6:31697.
  137. Primary Metabolism, Phenylpropanoids and Antioxidant Pathways Are Regulated in Potato as a Response to Potato virus Y Infection. Kogovsek P, Pompe-Novak M, Petek M, Fragner L, Weckwerth W, & Gruden K (2016) Plos One 11(1):e0146135.
  138. Comprehensive tissue-specific proteome analysis of drought stress responses in Pennisetum glaucum (L.) R. Br. (Pearl millet).  Ghatak A, Chaturvedi P, Nagler M, Roustan V, Lyon D, Bachmann G, Postl W, Schrofl A, Desai N, Varshney RK, & Weckwerth W (2016) J Proteomics 143:122-135.
  139. Biodiesel and poly-unsaturated fatty acids production from algae and crop plants - a rapid and comprehensive workflow for lipid analysis. Furuhashi T, Nakamura T, Fragner L, Roustan V, Schon V, & Weckwerth W (2016) Biotechnol J 11(10):1262-1267.
  140. Approximating the stabilization of cellular metabolism by compartmentalization. Furtauer L & Nagele T (2016) Theory Biosci 135(1-2):73-87.
  141.  A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information.  Nagele T, Furtauer L, Nagler M, Weiszmann J, & Weckwerth W (2016) Front Mol Biosci 3:6.
  142.  Pollen proteomics: from stress physiology to developmental priming. Chaturvedi P, Ghatak A, & Weckwerth W (2016) Plant Reprod 29(1-2):119-132.
  143. Cajanus cajan–a source of PPARγ activators leading to anti-inflammatory and cytotoxic effects. Schuster R, Holzer W, Doerfler H, Weckwerth W, Viernstein H, Okonogi S, & Mueller M (2016) Food & Function. 7 (9), 3798-3806
  144. Metabolomic and Proteomic Profiles Reveal the Dynamics of Primary Metabolism during Seed Development of Lotus (Nelumbo nucifera).  Wang L, Fu J, Li M, Fragner L, Weckwerth W, & Yang P (2016) Front Plant Sci 7:750.
  145. A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. Furtauer, L., W. Weckwerth, and T. Nagele, Front Plant Sci, 2016. 7: p. 1912.
  146. Exploring natural variation of Pinus pinaster Aiton using metabolomics: Is it possible to identify the region of origin of a pine from its metabolites? Meijon M, Feito I, Oravec M, Delatorre C, Weckwerth W, Majada J, & Valledor L (2016) Mol Ecol 25(4):959-976.
  147. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Kawakatsu T et al. (2016) Cell 166(2):492-505.
  148. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Genomes Consortium. Electronic address mngoaa & Genomes C (2016)   Genomes Consortium. Electronic address mngoaa & Genomes C (2016) Cell.166(2):481-491
  149. Dataset of UV induced changes in nuclear proteome obtained by GeLC-Orbitrap/MS in Pinus radiata needles. Alegre S, Pascual J, Nagler M, Weckwerth W, Canal MJ, & Valledor L (2016) Data Brief 7:1477-1482.
  150. Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interaction. Stare T, Ramsak Z, Blejec A, Stare K, Turnsek N, Weckwerth W, Wienkoop S, Vodnik D, & Gruden K (2015) BMC Genomics 16:716.
  151. Challenges of Inversely Estimating Jacobian from Metabolomics Data. Sun X, Langer B, & Weckwerth W (2015) Frontiers in bioengineering and biotechnology 3:188.
  152. Integrative molecular profiling indicates a central role of transitory starch breakdown in establishing a stable C/N homeostasis during cold acclimation in two natural accessions of Arabidopsis thaliana. Nagler M, Nukarinen E, Weckwerth W, & Nagele T (2015) BMC Plant Biol 15:284.
  153. SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants. Mair A et al., (2015)   Elife 4.