Wolfram Weckwerth

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. pmc Comprehensive cell-specific protein analysis in early and late pollen development from diploid microsporocytes to pollen tube growth
    Till Ischebeck
    Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090, Vienna, Austria
    Mol Cell Proteomics 13:295-310. 2014
  2. pmc Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species
    Christian Scherling
    Department of Bioinformatics and Biochemistry, Technical University of Braunschweig, Braunschweig, Germany
    PLoS ONE 5:e12569. 2010
  3. doi request reprint Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology
    Wolfram Weckwerth
    Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    J Proteomics 75:284-305. 2011
  4. doi request reprint Metabolomics: an integral technique in systems biology
    Wolfram Weckwerth
    Molecular Systems Biology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    Bioanalysis 2:829-36. 2010
  5. ncbi request reprint Tandem metal-oxide affinity chromatography for enhanced depth of phosphoproteome analysis
    Gerold J M Beckers
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:621-32. 2014
  6. doi request reprint The different proteomes of Chlamydomonas reinhardtii
    Luis Valledor
    Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
    J Proteomics 75:5883-7. 2012
  7. ncbi request reprint From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform
    Wolfram Weckwerth
    Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:15-27. 2014
  8. pmc Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography
    Wolfgang Hoehenwarter
    Department Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Mol Cell Proteomics 12:369-80. 2013
  9. doi request reprint Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments
    Volker Egelhofer
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Nat Protoc 8:595-601. 2013
  10. doi request reprint MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber
    Wolfgang Hoehenwarter
    Department of Molecular Systems Biology, University of Vienna, Faculty of Life Sciences, Althanstrasse 14, A 1090, Vienna, Austria
    J Proteome Res 10:2979-91. 2011

Collaborators

Detail Information

Publications25

  1. pmc Comprehensive cell-specific protein analysis in early and late pollen development from diploid microsporocytes to pollen tube growth
    Till Ischebeck
    Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090, Vienna, Austria
    Mol Cell Proteomics 13:295-310. 2014
    ....
  2. pmc Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species
    Christian Scherling
    Department of Bioinformatics and Biochemistry, Technical University of Braunschweig, Braunschweig, Germany
    PLoS ONE 5:e12569. 2010
    ..Taken together, our study demonstrates that metabolite profiling is a strong diagnostic tool to assess individual metabolic phenotypes in response to plant diversity and ecophysiological adjustment...
  3. doi request reprint Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology
    Wolfram Weckwerth
    Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    J Proteomics 75:284-305. 2011
    ....
  4. doi request reprint Metabolomics: an integral technique in systems biology
    Wolfram Weckwerth
    Molecular Systems Biology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    Bioanalysis 2:829-36. 2010
    ..Especially, the systematic relation between high-throughput metabolomic data and their interpretation with respect to the underlying biochemical regulatory network is discussed...
  5. ncbi request reprint Tandem metal-oxide affinity chromatography for enhanced depth of phosphoproteome analysis
    Gerold J M Beckers
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:621-32. 2014
    ..Thus, tandem MOAC effectively targets the phosphate moiety of phosphoproteins and phosphopeptides and, thus, allows probing of the phosphoproteome to unprecedented depth...
  6. doi request reprint The different proteomes of Chlamydomonas reinhardtii
    Luis Valledor
    Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
    J Proteomics 75:5883-7. 2012
    ..Lists of protein accessions exclusively assigned to individual C. reinhardtii genome assemblies and annotations are provided as a resource for proteogenomic studies...
  7. ncbi request reprint From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform
    Wolfram Weckwerth
    Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:15-27. 2014
    ..All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html...
  8. pmc Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography
    Wolfgang Hoehenwarter
    Department Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Mol Cell Proteomics 12:369-80. 2013
    ....
  9. doi request reprint Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments
    Volker Egelhofer
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Nat Protoc 8:595-601. 2013
    ..This procedure also includes the recommended MS settings for complex quantitative MAPA analysis using ProtMAX (http://www.univie.ac.at/mosys/software.html)...
  10. doi request reprint MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber
    Wolfgang Hoehenwarter
    Department of Molecular Systems Biology, University of Vienna, Faculty of Life Sciences, Althanstrasse 14, A 1090, Vienna, Austria
    J Proteome Res 10:2979-91. 2011
    ..We identified nearly 4000 proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date...
  11. ncbi request reprint Cell-specific analysis of the tomato pollen proteome from pollen mother cell to mature pollen provides evidence for developmental priming
    Palak Chaturvedi
    Department of Molecular Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, A 1090, Vienna, Austria
    J Proteome Res 12:4892-903. 2013
    ....
  12. ncbi request reprint An improved detergent-compatible gel-fractionation LC-LTQ-Orbitrap-MS workflow for plant and microbial proteomics
    Luis Valledor
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:347-58. 2014
    ....
  13. doi request reprint Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics
    Wolfgang Hoehenwarter
    Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
    Amino Acids 41:329-41. 2011
    ..We present a mathematical technique that delivers a good approximation for shotgun proteomics data...
  14. pmc Systemic cold stress adaptation of Chlamydomonas reinhardtii
    Luis Valledor
    Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria, Althanstrasse 14, A 1090, Vienna, Austria
    Mol Cell Proteomics 12:2032-47. 2013
    ..Twenty percent of the proteins responsive to cold are uncharacterized proteins. This presents a considerable resource for new discoveries in cold stress biology in alga and plants. ..
  15. pmc Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data
    David Lyon
    Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
    PLoS ONE 9:e94692. 2014
    ..To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover. ..
  16. ncbi request reprint Mass Western for absolute quantification of target proteins and considerations about the instrument of choice
    David Lyon
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Methods Mol Biol 1072:199-208. 2014
    ..Here, we present a detailed workflow including tips and we discuss advantages and disadvantages of using different types of MS for absolute quantification. ..
  17. pmc ProMEX - a mass spectral reference database for plant proteomics
    Stefanie Wienkoop
    Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Front Plant Sci 3:125. 2012
    ..Direct links at the protein level to the most relevant databases are present in ProMEX. Furthermore, the spectral sequence information are linked to their respective pathways and can be viewed in pathway maps...
  18. pmc Solving the differential biochemical Jacobian from metabolomics covariance data
    Thomas Nagele
    Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
    PLoS ONE 9:e92299. 2014
    ....
  19. pmc mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data
    Hannes Doerfler
    Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
    PLoS ONE 9:e96188. 2014
    ..The mzGroupAnalyzer is implemented in the graphical user interface (GUI) of the metabolomics toolbox COVAIN (Sun & Weckwerth, 2012, Metabolomics 8: 81-93). The strategy can be extended to any biological system. ..
  20. doi request reprint Arabidopsis thaliana as a model organism for plant proteome research
    Stefanie Wienkoop
    Department of Molecular Systems Biology, University of Vienna, Faculty of Life Sciences, Vienna, Austria
    J Proteomics 73:2239-48. 2010
    ..Consequently, insights into plant proteome dynamics and cell functions are rapidly increasing. A proteomics-toolbox developed for systems biology research on Arabidopsis will be introduced...
  21. doi request reprint Metabolism and development - integration of micro computed tomography data and metabolite profiling reveals metabolic reprogramming from floral initiation to silique development
    Anke Bellaire
    Department of Structural and Functional Botany, Faculty of Life Sciences, University of Vienna, Rennweg 14, Vienna, Austria
    New Phytol 202:322-35. 2014
    ..Based on these observations a model for metabolic adjustment during flower development is proposed. ..
  22. pmc Unpredictability of metabolism--the key role of metabolomics science in combination with next-generation genome sequencing
    Wolfram Weckwerth
    Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
    Anal Bioanal Chem 400:1967-78. 2011
    ..In this context, a systematic equation is derived based on metabolomics covariance data and the genome-scale stoichiometric matrix which describes the genotype-phenotype relationship...
  23. doi request reprint Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses
    Stefanie Wienkoop
    Dept of Molecular Systems Biology, University of Vienna, Vienna, Austria
    Mol Biosyst 6:1018-31. 2010
    ..This indicates its role as one of the strongest CO2-responsive proteins in the crosstalk of air-adapted mixotrophic chloroplast and mitochondrial metabolism in Chlamydomonas reinhardtii...