Molecular Systems Biology

Wolfram Weckwerth | Curriculum Vitae | Publications ...

Wolfram Weckwerth

University of Vienna
Dept for Molecular Systems Biology
1090 Vienna, Austria
Phone + 43-1-4277-577 00





Solanaceae Pollen Thermotolerance (SPOT-ITN) more ...

MERIT Metabolomic

Metabolic Reprogramming by Induction of Transcription (MERIT) more ...

China Scholarship Council
EMBO Felloships
Marie Curie Actions
Intra-European Fellowships for career development (IEF) - Marie Curie Actions more ...
Metabolomics platform for nutritional and medicinal plants
Flower and Pollen Development
EPISYSBIOL – Adaptation strategies of Chlamydomonas reinhardtii to changing environments and stress </p>



  • Development of genome-wide metabolomics and proteomics/phosphoproteomics technologies as elementary systems biology techniques, high throughput profiling (HTP) in systems biology, data integration; combining experimental approaches with multivariate statistics, pattern recognition and modeling of metabolism: "synergetics".
  • Development of theoretical models based on multivariate statistics for the biological interpretation of HTP data, calculation of biochemical regulation – the “differential Jacobian" - from HTP data.
  • Plant genotype-phenotype interaction; plant phenotypic plasticity including stress, growth, developmental and nutritional physiology.
  • Personalzed medicine: metabolomic and proteomic analysis of biofluids, data integration and human physiology.
  • Metabolomics and proteomics – assisted genome annotation and reconstruction of genome-wide metabolic and regulatory networks in plant, microbial and other model systems like Arabidopsis thaliana (dicot), Chlamydomonas reinhardtii (green alga), Medicago truncatula (legume) and others, applications of metabolomics and proteomics to non-sequenced species like tomato, potato, plant communities, microbiomes etc.
  • Databases, data management and data mining.

Detailed CV

1994                     Diploma in Chemistry, Institute of Molecular Biology and Biochemistry, Technical University Berlin, Germany.
1998 PhD in Biochemistry, Institute of Molecular Biology and Biochemistry, Technical University Berlin, Germany.
2000 Postdoc at the Max-Planck-Institute of Molecular Plant Physiology, Department Lothar Willmitzer, Potsdam, Germany.
2002 Research Group Leader at the Max-Planck-Institute of Molecular Plant Physiology, Department Mark Stitt, Potsdam, Germany.
2007 Habilitation in Molecular Plant Physiology and Systems biology, Lecturer Systems Biology, University of Potsdam, Germany.
2007 Head of Central Infrastructure Systems Biology Lab, GOFORSYS, University Potsdam, Germany.
2006 - 2007 Offerships for Professorship at the Department of Plant Biology, Michigan State University, USA and Professorship at the University of Vienna, Austria.
since 2008 Since 2008 – Full professor and founding chair of the Department of Molecular Systems Biology (MOSYS) at the University of Vienna, Austria.



Professional Duties and Functions

  • Chair of MASC (Multi-National Arabidopsis Steering Committee), Co-Chair of the Proteomics and Metabolomics Subcommittees (MASCP; MASCPM).
  • Scientific Advisory Board Czech Globe.
  • Scientific Advisory Board Austrian Society of Analytical Chemistry (ASAC).
  • Scientific Advisory Board “Open Science”, Vienna, Austria.
  • Scientific Advisory Board Gregor-Mendel-Society.
  • Editorial and Review Board Member of Current Metabolomics, Frontiers in Plant Proteomics, Frontiers in Plant Physiology, Frontiers of Plant Systems Biology, Journal of Personalized Medicine
  • Recent reviewing panels: European Systems Biology (EUSYSBIO) Foresight Workshop, Heidelberg, Germany 2005; Steering Committee of the systems biology programme GoFORSYS, Potsdam, Germany 2006-2007; “New technologies in Systems Biology”, Federal Ministry of Education and Research in Germany (BMBF) Berlin, Germany 2008; Steering Committee ISTA (Institute of Science and Technology), Maria-Gugging, Austria 2009; Steering Committee of the Systems Biology Programme 2011, Federal Ministry of Education and Research in Germany (BMBF), Berlin, Germany 2011
  • Editor of the first edition “Metabolomics: Methods and Protocols”, in the series “Methods in Molcular Biology”, Humana Press 2007

Conference Organization

  • Organization of the International Conference on Arabidopsis Research, ICAR 2012, Vienna, Austria
  • Initiation and Organization of the first International Metabolomics Conference Austria, InMetA 2010, Vienna, Austria
  • Organization of the MASC-Proteomics Workshop in Beijing, China, International Arabidopsis Conference 2007, 2009

Key-Publications (for a full publication list see here ...)

  • Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54: 669-689
  • 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
  • Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci U S A 101: 7809-7814
  • Morgenthal K, Wienkoop S, Scholz M, Selbig J, Weckwerth W (2005) Correlative GC-TOF-MS based metabolite profiling and LC-MS based protein profiling reveal time-related systemic regulation of metabolite-protein networks and improve pattern recognition for multiple biomarker selection. Metabolomics 1: 109-121
  • Wienkoop S, Morgenthal K, Wolschin F, Scholz M, Selbig J, Weckwerth W (2008) Integration of metabolomic and proteomic phenotypes: analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana. Mol Cell Proteomics 7: 1725-1736
  • Scherling C, Ulrich K, Ewald D, Weckwerth W (2009) A Metabolic Signature of the Beneficial Interaction of the Endophyte Paenibacillus sp Isolate and In Vitro-Grown Poplar Plants Revealed by Metabolomics. Molecular Plant-Microbe Interactions 22: 1032-1037
  • Scherling C, Roscher C, Giavalisco P, Schulze ED, Weckwerth W (2010) Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species. Plos One 5: e12569
  • Wienkoop S, Weiss J, May P, Kempa S, Irgang S, Recuenco-Munoz L, Pietzke M, Schwemmer T, Rupprecht J, Egelhofer V, Weckwerth W (2010) Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Mol Biosyst 6: 1018-1031
  • Weckwerth W (2011) Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics 75: 284-305
  • Weckwerth W (2011) Unpredictability of metabolism - the key role of metabolomics science in combination with next-generation genome sequencing. Anal Bioanal Chem 400: 1967-1978
  • Sun X, Weckwerth W (2012) COVAIN: a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data. Metabolomics doi:10.1007/s11306-012-0399-3 Patents
  • Mari A, Lyon D, Fragner L, Montoro P, Piacente S, Wienkoop S, Egelhofer V, & Weckwerth W (2012) Phytochemical composition of Potentilla anserina L. analyzed by an integrative GC-MS and LC-MS metabolomics platform. Metabolomics:1-9
  • Doerfler H, Lyon D, Nägele T, Sun X, Fragner L, Hadacek F, Egelhofer V, & Weckwerth W (2012) Granger causality in integrated GC–MS and LC–MS metabolomics data reveals the interface of primary and secondary metabolism. Metabolomics:1-11.

Invited national and international talks since 2002

  • Mass spectrometry Methods in Proteomics 2002. Free University Berlin, Germany.
    Title: Stable isotope labelling for quantitative proteomics.
  • Summerschool Proteomics. Canacale, Turkey 2002.
    Title: Biochemical Networks and quantitative proteomics.
  • Institute of Plant Biochemistry. Halle, Germany 2003.
    Title: Shotgun Proteomics.
  • NATO Advanced Research Workshop. Genomics for Biosafety: New Challenges. Bansko, Bulgaria 2003.
    Title: Biochemical Profiling in Plant Systems.
  • Potential of Metabolic Profiling in Plant Science. Turin, Italy 2003.
    Title: Integrating Metabolomics and Proteomics in Plant Systems Biology.
  • Plant Proteomics Workshop. Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA 2004.
    Title: Plant proteomics embedded in dynamic metabolic networks – an integrative approach.
  • Gordon Research Conference Macromolecular Organization & Cell Function. Queen´s College, Oxford, UK 2004.
    Title: Metabolic networks and their structural characteristics at a plant-systems level.
  • Genomes to Systems. 2nd Conference. The Consortium for Post-Genome Science. Manchester, UK 2004.
    Title: Causal connectivities in metabolomic networks: An integrative approach.
  • The 14th FESPB Congress (Federation of European Societies of Plant Biology). Cracow, Poland 2004.
    Title: Differential Metabolic Correlation Networks in Plant Physiology.
  • Summer School 2004, DFG Research Training Group "Communication in Biological Systems". Hirschegg, Germany.
    Title: Structural principles in biochemical networks at a systems level.
  • Proteomics Workshop Thermoelectron. Berlin, Germany 2004.
    Title: Plant Proteomics.
  • Plant Research International Institute. Wagningen, Netherlands 2005.
    Title: GC-TOF-MS metabolite profiling in Arabidopsis thaliana.
  • Proteomics Workshop "Protnet" Jena, Germany 2005.
    Title: Shotgun proteomics in plants.
  • Semestervortrag Universität Rostock, Germany 2005.
    Titel: Integration of metabolomics and proteomics based on mass spectrometry and multivariate data mining.
  • Symposium Metabolomics IPK Gatersleben, Germany 2005.
    Title: Systems biology in plants.
  • Society of Experimental Biology, Barcelona, Spain 2005.
    Title: Signalling and plant proteomics.
  • International Congress of Botany, Vienna, Austria 2005.
    1. Session Metabolic Profiling: Metabolomics and proteomics in Arabidopsis thaliana– integration improves pattern recognition and biological interpretation.
    2. Session Nonlinear Dynamics: Metabolomics or How to find  causal connectivity in metabolic networks?
  • International Arabidopsis Conference Madison, Wisconsin, USA 2005.
    Title: Metabolomics and proteomics in Arabidopsis thaliana– transitions from pattern recognition to biological interpretation.
  • European Network Summerschool, Ljubljana, Slowenia 2005.
    Title: Mass Spectrometry - a major tool for functional genomics research.
  • DFG SPP Workshop "Dynamics of Chemically Mediated Interaction Webs in Aquatic Communities: Regulation, Variability and Plasticity.", Wilhelmshaven, Germany 2005.
  • DFG SPP Workshop "Experimentelle und theoretische Metabolomforschung - metabolische Netze", Köln, Germany 2005.
  • Leibniz Institute of Plant Biochemistry, Halle, Germany 2005.
    Title: Metabolomics and proteomics in Arabidopsis thaliana– integration improves pattern recognition and biological interpretation.
  • Deutsche Gesellschaft für Massenspektrometrie (DGMS), Mainz, Germany 2006.
    Keynote lecture: "Massenspektrometrie im Zeitalter der Systembiologie: Metabolit- und Protein-Profilanalyse in biologischen Modellsystemen"
  • "MassSpecNet", FU Berlin, Germany 2006.
    Title: "Qualitative and quantitative protein phosphorylation analysis using liquid chromatography coupled to fast scanning ion trap and triple quadrupole mass spectrometry."
  • Yokohama Riken Institute, Japan 2006
    Workshop on "Plant Metabolomics and Functional Genomics.
    Title: Mass spectrometry and Systems biology: Integration of metabolomics, proteomics and multivariate data mining reveals insights into systemic responses of a biochemical network."
  • Kyoto Research Technology Institute, internal Seminar organized by Nobuo Tanaka, Japan 2006
    Title: "High-resolution chromatography coupled to mass spectrometry and application in metabolomics and proteomics."
  • 4th International Conference on Plant Metabolomics, Reading, UK 2006
    Title: "Integration of metabolomics and proteomics based on mass spectrometry and multivariate data mining: Can we learn from the systems-approach?"
  • University of Vienna, Department Ecology and Ecosystem Research, Austria 2006
  • DKFZ Heidelberg, "MSClub", Germany 2006
  • The 3rd International Workshop on Biochips and Environmental Monitoring, Osaka, Japan 2006, invited AIST-Fellow (Advanced Industrial Science and Technology, Tsukuba)
  • IPK Gatersleben, Germany 2006
  • Deutsch-Tunesischer Workshop "Plants and Bioinformatics", Tunesien 2006
  • Missouri Plant Biology Symposium on Protein Phosphorylation, USA, 2007
  • Departmental Seminar, Cornell University, USA, 2007
  • Symposium "Comprehensive Gas Chromatography-Time-of-Flight Mass Spectrometry in Biomedical Research", University Regensburg, Germany, 2007
  • International Arabidopsis Conference China, 2007
  • Hinxton UK, British society of proteome research, 2007
  • München Martinsried, Arbeitstagung Proteomics, 2007
  • Deutsche Gesellschaft für Massenspektrometrie Tagung, Bremen, Germany, 2007
  • Proteomics Workshop, Bremen, 2007
  • Göttinger Proteomics Forum, Göttingen MPI, Germany, 2007
  • Botanisches Colloquium, LMU München, Germany, 2007
  • Institutsseminar Polnische Akademie der Wissenschaften, Posen, Polen 2007
  • Seminar Mass spectrometry in Life Science, Warschau, Polen, 2007
  • Robert-Koch-Institut, Berlin, Germany, 2007
  • European Plant Proteomics Conference, Cordoba, Spain2008
  • Grand Opening Event, Thermo Proteomics Seminar, Basel, 2008
  • FORSYS BMBF, Forschungseinrichtungen fuer Systembiologie in Deutschland, Berlin, Germany, 2008
  • NUGO meeting, European network for nutrigenomics, Munich, Germany, 2008
  • IRTG, international research training group, Germany-USA-Japan, Genomics and Systems Biology of molecular networks, Berlin, Germany, 2008
  • Molecular interactions, Berlin, Germany, 2008
  • URGV Plant genomics research unit, Paris, France, 2008
  • Austrian platform proteomics, Seefeld, Österreich, 2008
  • European Proteomics Seminar Series, Thermo Fisher Scientific, Kunsthistorisches Museum Wien, Österreich, 2008
  • Center for Systems Biology, University of Warwick, UK, 2008
  • International Conference for Peptide Chemistry, Shenzen China, 2008 – abgesagt
  • Metabolomics Symposium, Dalian China, 2008 – abgesagt
  • 8th international plant metabolism symposium, Jeju Island, Korea, 2008 – abgesagt, confirmed for next year
  • KEYNOTE speaker, Proteomlux, Luxemburg, 2008

External funding


Funding source

Grant title

Grant is a collaborative grant with...

Period covered

Total volume (EUR)



Institutsübergreifende Forschungsinitiative Arabidopsis-Proteomprojekt

Tina Romeis, Berlin





BMBF "Nutrigenomics": "Allergenicity in crop plants"

Charité Berlin, Proteome Factory and IGZ Grossbeeren


900.000 (AG Weckwerth 200.000)



BMBF "Quantpro": Innovative diagnostic tools to optimise potato breeding: Systemic analysis of cellular processes and their relation to plant internal oxygen concentrations

Peter Geigenberger, Joost van Dongen, Potsdam


1.472.000 (AG Weckwerth 250.000)



DFG "Photorespiration and metabolite profiling"

Hermann Bauwe, University Rostock





Forschungseinrichtungen fuer Systembiologie in Deutschland (FORSYS)

GoFORSYS consortium, Potsdam


13 million (AG Weckwerth 3.369.000)



Analyse der Sekundärmodifikationen der Phytochrom-Signaltransduktion

Mathias Zeidler, Göttingen





Eranet Plant Genomics PATHONET

Irute Mieskene, Universität Wien, Cyril Zipfel, UK, Dirk Scheel, Germany


1.1 million (AG Weckwerth 220.000)




Emilio Montesinos, Spain, Uwe Sonnewald, Germany


2 million (AG Weckwerth 250.000)


Leibniz Instituts Förderung

Gemüseallergene: Detektion, Analyse und Steuerung im modernen Gartenbau

Phillip Franken, Germany, Margitta Worm Germany, Christian Scheler, Germany


1.1 million (AG Weckwerth 250.000)










Michael Schagerl, University of Vienna







TOTAL (AG Weckwerth own contribution)

5.1 million