Molecular Systems Biology

Stefanie Wienkoop | Curriculum Vitae | Publications ...

Stfanie Wienkoop

Contact:
University of Vienna
Dept for Molecular Systems Biology
1090 Vienna, Austria
Phone + 43-1-4277-577 03
e-mail: stefanie.wienkoop@univie.ac.at

 

Projects:

  • Multilevel analysis towards drought tolerance in Legumes ... more

Present Position:

Assistant Professor "Plant Systems Interaction"
Department of Molecular Systems Biology

Place and
Year of Birth:

Alfaz del Pi (Spain), 1971

Marital Status:

Married, 1 daughter (born 1993)

Education:

1996

Diploma Degree in Biology, Technical University Darmstadt, Germany
 

1996 - 2000

Doctorate (Dr. rer. nat.), Technical University Darmstadt, Germany

Academic Appointments:

4 – 11/ 2000

Post Doctoral Fellowship, University of British Columbia, Dept. of Botany, Vancouver, Canada (Lab of Anthony Glass)
 

2000 - 2002

Post Doctoral Position at National Laboratory Risø, Plant Research Dept., Denmark (Lab of Hans Thordal-Christensen)
 

2002 - 2008

Post Doctoral Position at Max-Planck Institute of Molecular Plant Physiology, Golm/Potsdam, Germany (Lab of Wolfram Weckwerth)
 

since 10/2008

Assistant Professor "Plant Systems Interaction", Dept. of Molecular Systems Biology, University of Vienna, Austria

Professional duties and functions:
  • Research Group Leader, Plant Systems Interactions, Department Molecular Systems Biology, University of Vienna, Austria
  • Teaching and Supervision, GC- and LC Mass Spectrometry, Molecular Plant Physiology, University of Vienna, Austria
  • Memberships: a) European Plant Proteomics COST action, b) Deutsche Gesellschaft für Massenspektrometrie (DGMS), c) Austrien Society of Plant Biology (ATSPB), d) Austrian Society of Molecular Bioscience and Biotechnology (ÖGMBT)
  • Regular Reviewer of International Journals: Proteomics, Plant Physiology, Plant Cell, Phytochemistry, Bioinformatics etc.
  • Reviewer of the Netherlands Organisation for Scientific Research foundation (NWO)

Complete List of Publications (40)

  • * Corresponding author (6)
  • # Equal contribution to first author (3)
  • First author (16)

Scientific Journals

34.

MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data.

H.J. Joshi, M. Hirsch-Hoffmann, K. Baerenfaller , W. Gruissem , S. Baginsky , R. Schmidt, W.X. Shulze, O. Sun , K.J. van Wijk, V. Egelhofer, S. Wienkoop, W. Weckwerth, C. Bruley, N. Rolland, T Toyoda, H. Nakagami, A.M.E. Jones, S.P. Briggs, I.Castleden, S.K. Tanz, A.H. Millar and J.L. Heazlewood (2010).

Plant Physiology DOI:10.1104/pp.110.168195

33.

Spectral counting robust on high mass accuracy mass spectrometers

W. Hoehenwarter, S. Wienkoop (2010).

Rapid Commun. Mass Spectrom. 24: 3609-14

32.

Arabidopsis thaliana as a model organism for plant proteome research.

S. Wienkoop*, S. Baginsky, W. Weckwerth (2010).

J Proteomics 73 (11): 2239-48

31.

Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics.

W. Hoehenwarter, Y. Chen, L. Recuenco-Munoz, S Wienkoop, W. Weckwerth (2010).

Amino Acids. DOI 10.1007/s00726-010-0669-1

30.

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

S. Wienkoop*, J. Weiss, P. May, S. Kempa, S. Irgang, L. Recuenco-Munoz, M. Pietzke, T. Schwemmer, J. Rupprecht, V. Egelhofer, W. Weckwerth (2010).

Mol Biosyst. 18;6(6):1018-31

29.

A Proteomics Toolbox.

S. Wienkoop, W. Weckwerth. (2010)

Analytica Pro, Sonderheft 01.2010

28.

Carbon metabolism and bacteroid functioning are involved in the regulation of nitrogen fixation in Medicago truncatula under drought and recovery.

E. Larrainzar, S Wienkoop*#, C Scherling, S Kempa, R Ladrera, C Arrese-Igor, W Weckwerth and EM González, (2009).

Mol Plant Microbe Interact. 22(12):1565-76.

27.

Proteomik-Toolbox: Proteomics in Genomannotation und Systembiologie.

S. Wienkoop, W. Weckwerth. (2009).

Biospektrum Special: Protein-Aufreinigung und –Analytik pp. 148-151

26.

An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential 13C-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells.

S. Kempa, J Hummel, T Schwemmer, M Pietzke, N Strehmel, S Wienkoop, J Kopka, W Weckwerth (2009)

J Basic Microbiol. 49(1):82-91.

25.

Evidence for novel tomato seed allergens: IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling.

O.Y. Bässler, J Weiss, S Wienkoop, K Lehmann, C Scheler, S Dölle, D Schwarz, P Franken, E George, M Worm, W Weckwerth (2009).

J Proteome Res. 2009 Mar;8(3):1111-22.

24.

Absolute quantification of Medicago truncatula sucrose synthase isoforms and N-metabolism enzymes in symbiotic root nodules and the detection of novel nodule phosphoproteins by mass spectrometry.

S. Wienkoop*, E. Larrainzar, M. Glinski, E. M. Gonzalez, C. Arrese-Igor and W. Weckwerth (2008)./p>

J Exp Bot 59(12):3307-15.

23.

A Cytosolic Pathway for the Conversion of Hydroxypyruvate to Glycerate during Photorespiration in Arabidopsis

S. Timm, A. Nunes-Nesi, T. Pärnik, K. Morgenthal, S. Wienkoop, O. Keerberg, W. Weckwerth, L.A. Kleczkowski, A.R. Fernie, H. Bauwe (2008).

Plant Cell 20(10):2848-59.

22.

A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment.

W. Hoehenwarter, J.T.van Dongen, S. Wienkoop, M. Steinfath, J. Hummel, A. Erban, R. Sulpice, B. Regierer, J. Kopka, P. Geigenberger, W. Weckwerth (2008).

Proteomics. 8(20):4214-25.

21.

Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii.

P. May, S. Wienkoop# S. Kempa, B. Usadel, N. Christian, J. Rupprecht, J. Weiss, L. Recuenco-Munoz, O. Ebenhöh, W. Weckwerth, D. Walther (2008).

Genetics 179(1): 157-66.

20.

If the antibody fails - a Mass Western approach

U. Lehmann, S. Wienkoop, W. Weckwerth (2008)

Plant J. 55(6):1039-46.

19.

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.

S. Wienkoop, K. Morgenthal, F. Wolschin, M. Scholz, J. Selbig, W. Weckwerth (2008).

Mol Cell Proteomics 7(9):1725-36.

18.

Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms.

S. Reumann, L Babujee, C. Ma, S. Wienkoop, T. Siemsen, G.E. Antonicelli, N. Rasche, F. Lüder, W. Weckwerth, O. Jahn (2007).

Plant Cell. 19(10):3170-93.

17.

ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.

J. Hummel, M. Niemann, S. Wienkoop, W. Schulze, D. Steinhauser, J. Selbig, D. Walther, W. Weckwerth. (2007)

BMC Bioinformatics. 23;8:216.

16.

Medicago truncatula Root Nodule Proteome Analysis Reveals Differential Plant and Bacteroid Responses to Drought Stress.

E. Larrainzar, S. Wienkoop#, W. Weckwerth, R. Ladrera, C. Arrese-Igor and E. M. Gonzalez (2007)

Plant Phys. Vol. 144, 1495-1507

15.

Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostic

S. Wienkoop, E. Larrainzar, M. Niemann, E. Gonzalez and W. Weckwerth (2006).

J Sep Sci. 29(18):2793-801.

14.

Drug target discovery in low abundance Proteins.

S. Wienkoop and W. Weckwerth (2006).

DrugPlusInternational 09; 14-17.

13.

Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidopsis thaliana

S. Wienkoop and W. Weckwerth (2006)

J Exp Bot 57(7): 1529-35.

12.

D-Glycerate 3-Kinase, the Last Unknown Enzyme in the Phytorespiratory Cycle in Arabidopsis, belonging to a novel kinase family.

R. Boldt, C. Edner, U. Kolukisaoglu, M. Hagemann, W. Weckwerth, S. Wienkoop,.K. Morgenthal, and H. Bauwe (2005).

Plant Cell, Vol. 17, 2413-20.

11.

Metal oxide affinity chromatography: Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography.

F. Wolschin, S. Wienkoop and W. Weckwerth (2005).

Proteomics 5, 4389-97.

10.

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.

K. Morgenthal, S. Wienkoop, M. Scholz, J. Selbig, and W, Weckwerth (2005)

Metabolomics 1, 109-121.

9.

Cell-specific protein profiling in Arabidopsis thaliana trichomes: Identification of trichome-located proteins involved in sulfur metabolism and detoxification.

S. Wienkoop, D. Zoeller, B. Ebert, U. Simon-Rosin, J. Fisahn, M. Glinski, W. Weckwerth (2004).

Phytochemistry 65: 1641-49.

8.

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.

S. Wienkoop M. Glinski, N. Tanaka, V. Tolstikov, O. Fiehn, W. Weckwerth (2004).

Rapid Commun Mass Spectrom.;18(6):643-50.

7.

Stable isotope labeling of phosphopeptides for multiparallel kinase target analysis and identification of phosphorylation sites.

M. Glinski, T. Romeis, C.P. Witte, S. Wienkoop, W. Weckwerth (2003).

Rapid Commun Mass Spectrom. 2003;17(14):1579-84.

Proteome analysis. Novel proteins identified at the peribacteroid membrane from Lotus japonicus root nodules.

S. Wienkoop and G. Saalbach (2003).

Plant Physiology 131(3):1080-90.

5.

Differentiation of plant cells during symbiotic nitrogen fixation.

B. Trevaskis, G. Colebatch, G. Desbrosses, M. Wandrey, S. Wienkoop, G. Saalbach, and M. Udvardi (2002).

J. of Comparative and Functional Genomics 3: 151-157.

4.

Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea (Pisum sativum) symbiosomes.

G. Saalbach, P. Erik and S. Wienkoop (2002).

Proteomics 2: 325 – 337>

3.

Different diurnal cycles of the expression of two nitrate reductase transcripts in tobacco roots.

S. Wienkoop, R. Schlichting, W.R. Ullrich and C. Stöhr (2001).

Protoplasma 217:15-19.

2.

Nitrate reductase in roots: Succinate- and NADH-dependent plasma membrane-bound forms.

C. Stöhr, S. Wienkoop and W.R. Ullrich (2000).

Plant and Soil 00: 1 – 4

1.

Kinetic characterization of succinate-dependent plasma membrane-bound nitrate reductase in tobacco roots.

S. Wienkoop, W.R. Ullrich and C. Stöhr (1999).

Physiologia Plantarum 105: 609 – 614.

Book Chapters

6.

Proteomics and metabolomics for systems biology in Legumes.

S. Wienkoop* (2010).

In: Perez de la Vega M., Cubero J.I. (Eds.). Cool Season Grain Legumes. Springer, Heidelberg. Chapter 10. (in press)

5.

Integrative profiling of metabolites and proteins: improving pattern recognition and biomarker selection for systems level approaches in "Metabolomics: Methods and Protocols." Book series: Methods in Molecular Biology.

K. Morgenthal, S. Wienkoop, F. Wolschin and W. Weckwerth (2006).

Humana Press. Ed. W. Weckwerth.

4.

Nitrate reduction at the plasma membrane of plant roots. In Avances en el Metabolismo del Nitrogeno: De los Microorganismos a las Plantas.

W. Ullrich, S. Wienkoop, U. Reck, C. Stöhr (2005).

Universidad de Huelva Publicaciones Ed. J.M. Vega Piqueres et al.

3.

Isolation of the peribacteroid membrane in Lotus japonicus.

S. Wienkoop* (2005).

In Lotus japonicus Handbook. Kluwer Academic Publishers: Dordrecht Ed. AJ Marquez.

2.

Plasma membrane-bound nitrate reductase in roots of higher plants.

C. Stöhr, S. Wienkoop and W.R. Ullrich (1998).

In Proceedings 5th Intern. Symposium on Inorganic Nitrogen Assimilation. Kluwer Scientific Publishers, Dortrecht.

1.

Nitrate reductase in roots: Succinate- and NADH-dependent plasma membrane-bound forms.

C. Stöhr, S. Wienkoop and W.R.Ullrich (1998).

In Proceedings 5th Intern. Symposium on Structure and Function of Roots. Kluwer Scientific Publishers, Dortrecht.