Welcome to the Homepage of Molecular Systems Biology


February 2015


New Research platform at the University of Vienna

Metabolomics, the unbiased profiling of all small molecules in biological samples, has developed into a core technology for functional genomics, biobased economy and personalized medicine in the last decade. Recently, ecological metabolomics has emerged in ecosystem research and metagenomic studies. The quality of state-of-the-art metabolomics technology depends on the quality of the preparation workflows, the quality of metabolite libraries and workflows for structural elucidation of novel structures. Because of the diversity of the metabolomes from organisms in functional and biomedical studies as well as the complexity of exo-metabolomes in environmental samples from marine, fresh water and terrestrial ecosystems an interdisciplinary approach is necessary to tackle this problem. Internationally recognized labs at the University of Vienna distributed over three faculties for Chemistry, Geosciences and Life Sciences consolidate their specific and complementary metabolomics platforms and application fields to build a Vienna Metabolomics Center.

April 2014

NEW PAPER in PLOS ONE: Solving the Differential Biochemical Jacobian from Metabolomics Covariance Data

Januar 2014

NEW PAPER in New Phytologist: Metabolism and development integration of micro computed tomography data and metabolite profiling reveals metabolic reprogramming from floral initiation to silique development

April 2013


From April 1st, 2013 on, we are part of the new Department of

"Ecogenomics and Systems Biology"

This department consists now of two divisions:

"Archaea Biology and Ecogenomics"

(Formerly the department of Genetics in Ecology)


"Molecular Systems Biology"

(Formerly the department of Molecular Systems Biology").

November 2012

NEW PAPER: Metabolomic analysis of medicinal plants using GC-MS and LC-MS data integration

Phytochemical composition of Potentilla anserina L. analyzed by an integrative GC-MS and LC-MS metabolomics platform.

Juni 2012

NEW PAPER: COVAIN - a metabolomics toolbox for data integration, multivariate statistics and metabolic modelling

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.

July 2012

ICAR LOGO 2012International Conference on Arabidopsis Research in Vienna

The conference took place in hot July at the HOFBURG in Vienna. About 900 participants from all over the world came to the conference and made an exciting and stimulating program of lectures and workshops possible.

June 2012

Stefanie WienkoopHabilitation awarded to Stefanie Wienkoop

After a public lecture on Friday, June 22, the habilitation was awarded to Stefanie. We congratulate!

March 2012

Green Systems Biology (W. Weckwerth)

This article belongs to the the most downloaded articles from SciVerse ScienceDirect in the last 90 days.

July 2011

Green Systems Biology

Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. Weckwerth W. J Proteomics. 2011 Jul 23. ... Abstract Pubmed

Plants have shaped our human life form from the outset. With the emerging recognition of world population feeding, global climate change and limited energy resources with fossil fuels, the relevance of plant biology and biotechnology is becoming dramatically important. One key issue is to improve plant productivity and abiotic/biotic stress resistance in agriculture due to restricted land area and increasing environmental pressures. ......

June 2011

Unpredictability of Metabolism – a genotype-phenotype equation

Unpredictability of metabolism-the key role of metabolomics science in combination with next-generation genome sequencing. Weckwerth W. Anal Bioanal Chem. 2011 Jun;400(7):1967-78. ... Abstract Pubmed

Next generation sequencing (NGS) provides technologies to sequence whole prokaryotic and eukaryotic genomes in days, to perform genome-wide association (GWA) studies, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and RNA sequencing (RNA-seq) for transcriptome studies. An exponential growing volume of sequence data can be anticipated, yet, functional interpretation does not keep pace with the amount of data produced. In principle, these data contain all the secrets of living systems, the genotype-phenotype-relationship. ......

Strategy for functional interpretation of genotype data and environmental phenotypes based on molecular data.

Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Wienkoop S, Weiss J, May P, Kempa S, Irgang S, Recuenco-Munoz L, Pietzke M, Schwemmer T, Rupprecht J, Egelhofer V, Weckwerth W. Mol Biosyst. 2010 Jun 18;6(6):1018-31. ... Abstract Pubmed

Profiling Platform MoSys to combine proteomics-assisted genome annotation (May et al., 2008), targeted proteomics (Mass Western (Wienkoop and Weckwerth, 2006; Lehmann et al., 2008; Wienkoop et al., 2008a)), subcellular fractionation, untargeted proteomics (MAPA: mass accuracy precursor alignment (Hoehenwarter et al., 2008)) for analysis of dynamic proteomes as well as to integrate the data with metabolomics and metabolic flux data (Weckwerth, 2008). ......

Workflow Metabolomics

Unpredictability of metabolism-the key role of metabolomics science in combination with next-generation genome sequencing. Weckwerth W. Anal Bioanal Chem. 2011 Jun;400(7):1967-78.
... Abstract Pubmed




Workflow Proteomics

Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. Weckwerth W. J Proteomics. 2011 Jul 23.
... Abstract Pubmed




November 2010

Technologierevolution in der Biodiversitätsforschung

"Nach Genom und Proteom folgt nun Entschlüsselung des Metabolom."

Mit neuartigen Analyseverfahren, der sogenannten Metabolomics-Technologie, ist es möglich, Einblicke in den Stoffwechsel von Organismen zu erhalten. Die Gruppe um Wolfram Weckwerth, Leiter des Departments für Molekulare Systembiologie der Universität Wien, hat hochkomplexe Verfahren eingesetzt, um grundlegende Fragen zur Biodiversität zu klären. Forschungsobjekt war eine der größten wissenschaftlichen Anbauflächen für Biodiversität in Europa – das Jena-Experiment; untersucht wurden die Vielfalt der dortigen Wiesenvegetation und deren Pflanzeninteraktionen. Die Ergebnisse sind im internationalen Fachmagazin "PLoS ONE" erschienen.

Juni 2010


Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses.

Stefanie Wienkoop, Julia Weiß, Patrick May, Stefan Kempa, Susann Irgang, Luis Recuenco-Munoz, Matthias Pietzke, Thorsten Schwemmer, Jens Rupprecht, Volker Egelhofer and Wolfram Weckwerth


Workshop "Teach The Teachers" on 19.03.2010 ... more (in deutsch)

November 2009

COVER STORY: Molecular Plant-Microbe Interaction

Metabolomics and targeted proteomics reveal mechanistic metabolic marker for plant-microbe interaction under drought stress.

Juli 2009

Mechanistic insight into the beneficial interaction of bacteria and plants for increased growth/biomass production revealed by metabolomic technology

Beneficial endophyte-plant interaction revealed by Metabolomics.

März 2009

Pathonet - plant immunity signalling. An international plant systems biology project hosted by the GEN-AU (Genome Research in Austria)

Plant Immunity Signalling.

February 2009

Proteomics in genome annotation and systems biology

Recent Review about the proteomics platform of MoSys in BIOSPEKTRUM.

September 2008

Journal of Proteome Research editorial about MASC proteomics activities

The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology.

March 2008

UNIPROT cross-references have been added to the Protein Mass spectra EXtraction database.

November 2007

Database for the phosphoproteome of Arabidopsis thaliana.

October 2007

Proteome Analysis of Arabidopsis Leaf Peroxisomes Reveals Novel Targeting Peptides, Metabolic Pathways, and Defense Mechanisms.

July 2007

ProMEX: a step towards a central mass spectral reference library for plant proteomics

The article outlining the mass spectral database ProMEX (BMC Bioinformatics 2007, 8:216) has been recently highlighted as a "Highly Accessed"publication by BioMed Central. The ProMEX database was released to the public in June 2007 by the Weckwerth group and provides access to a mass spectral reference library from a variety of proteomic studies as well as the ability to query stored data with newly derived experimental data.


April 2014

Erbgut entschluesseln per Knopfdruck

Augenfarbe, Haarfarbe, Blütenfarbe, Blattform, Stressresistenz, Stoffwechsel ... das Genom ist Träger aller Erbanlagen von Mensch, Pflanzen, Tieren und Mikroorganismen. Der Systembiologe Wolfram Weckwerth und sein Team praesentieren neue Erkenntnisse zur Erforschung des Erbguts. Die vollständige funktionale Aufklarung und Interpretation eines ganzen Genoms eines Organismus ist der "Heilige Gral" in der Biologie der nächsten Dekaden und stellt eine Herausforderung dar, die jene der Genomsequenzierung des Menschen oder der Pflanze vor rund zehn Jahren bei weitem übertrifft. "Die Dynamik von Lebewesen, wie z.B. ihr Stoffwechsel und ihre Entwicklung, kann man nicht einfach aus dem Erbgut ablesen", so Wolfram Weckwerth vom Department für Ökogenomik und Systembiologie der Universität Wien. Um diese Dynamik auf molekularer Ebene zu verstehen, mit der Genominformation zu verknüpfen und eine funktionale Interpretation des Genoms zu ermöglichen, werden sogenannte "Big Data" (genomweite molekulare Analysen) generiert.

September 2012

Die Zukunft der globalen Versorgung mit Nahrungsmitteln und biogenen Rohstoffen

Die Herausforderung, mit Produkten biogenen Ursprungs sowohl Welternährung als auch Rohstoffversorgung sicherzustellen, bringt die Biowissenschaften an ihre Grenzen. Die Gregor-Mendel-Gesellschaft prämiert Ideen für visionäre Ansätze.

22.05.2012 - "DER STANDARD"

"Hier bahnt sich eine echte Revolution an"

Wie sich verschiedene Pflanzenarten gegenseitig beeinflussen, untersucht der Biochemiker Wolfram Weckwerth ...

Interview mit Prof. Dr. Wolfram Weckwerth

September 2011

2. Platz beim beim Österreichischen Bundeslehrlingswettbewerb

Dominik Soukup

Dominik Soukup hat beim österreichischen Bundeslehrlingswettbewerb den 2. Platz belegt und ist für den europaweiten Wettbewerb nominiert.
Wir gratulieren recht herzlich.


Dominik Soukup has won the second place of the austrian competition of gardener and florists prentices. We congratulate him. He is nominated for the Europe-wide competition in the next year.

01.05.2011 - "Die Presse"

Feine Signale der Pflanze.

Die Erforschung des Metaboloms macht den Stoffwechsel einer Pflanze sichtbar. Dadurch kann man studieren, in welchem Zustand sich ein Organismus befindet.

Interview mit Prof. Dr. Wolfram Weckwerth

November 2010


Interview mit Prof. Dr. Wolfram Weckwerth

November 2010

Pflanzenforschung - Stress im grünen Bereich

Wer unter Stress leidet, kann eine Menge dagegen tun: Zum Beispiel weniger arbeiten, Entspannungstechniken lernen oder im Grünen die Seele baumeln lassen . Doch auch hier - auf einer Blumenwiese oder im Wald - herrscht eine Menge Stress . Denn selbst Gräser, Bäume und Kräuter stehen unter Druck. Umweltfaktoren wie Dürre, Frost und Mineralienmangel machen dem Grünzeug zu schaffen . Auch Krankheitserreger schreiten ständig zum Angriff. Glücklicherweise sind Pflanzen derartigen Attacken nicht hilflos ausgeliefert. Sie verfügen über ein angeborenes Immunsystem, das Viren, Bakterien und Pilze erkennt und Alarm schlägt . Wie diese Abwehrreaktionen im Detail funktionieren, will GEN-AU Forscher Wolfram Weckwerth herausfinden . Er untersucht die Protein- und Stoffwechselprofile von gestressten Pflanzen - gemeinsam mit drei Wissenschaftsteams im Rahmen des europäischen Konsortiums PathoNet. .

29.08. 2010 - 03.09.2010

International Metabolomics Austria

The first international metabolomics-symposium "International Metabolomics Austria" in conjunction with the "4th Central and Eastern European Proteomics Conference" will be held from 29.08. 2010 - 03.09.2010 in Vienna, Austria. For program, registration and abstract submission see


MoSys Portrait im "Standard"


MoSys Scientist in "USA Today"

May 2010....

Chinese Government Award for MoSys PhD student Dr. Yanmei Chen, a PhD student under the supervision of Professor Wolfram Weckwerth in the Department of Molecular Systems Biology, has received the highly-prestigious Chinese Government Award for Outstanding Self-Financed Students Abroad.



MoSys Pressemitteilung "Pappeln als Biotreibstofflieferanten von morgen"