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Wolfram Weckwerth

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Proteomics

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TOP 3
Volker Egelhofer; Wolfgang Hoehenwarter; David Lyon; Wolfram Weckwerth; Stefanie Wienkoop
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments.
Wolfgang Hoehenwarter; Ella Nukarinen; Horst Röhrig; Martin Thomas; Wolfram Weckwerth; Uwe Conrath; Volker Egelhofer; Gerold J M Beckers
Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography.
Luis Valledor; Volker Egelhofer; Luis Recuenco-Munoz; Stefanie Wienkoop; Wolfram Weckwerth
The different proteomes of Chlamydomonas reinhardtii.

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All Publications

2013: Volker Egelhofer; Wolfgang Hoehenwarter; David Lyon; Wolfram Weckwerth; Stefanie Wienkoop
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments.
Nature protocols 2013;8(3):595-601.
2013: Wolfgang Hoehenwarter; Ella Nukarinen; Horst Röhrig; Martin Thomas; Wolfram Weckwerth; Uwe Conrath; Volker Egelhofer; Gerold J M Beckers
Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography.
Molecular & cellular proteomics : MCP 2013;12(2):369-80.
2012: Luis Valledor; Volker Egelhofer; Luis Recuenco-Munoz; Stefanie Wienkoop; Wolfram Weckwerth
The different proteomes of Chlamydomonas reinhardtii.
Journal of proteomics 2012;75(18):5883-7.
2012: Ganesh Kumar Agrawal; Raj Agrawal; Bronwyn J Barkla; Niranjan Chakraborty; Sixue Chen; Rainer Cramer; Renu Deswal; Michael J Dunn; Joshua L Heazlewood; Dominique Job; Thomas Kieselbach; Bongani Kaiser Ndimba; Mohammed Suhail Rafudeen; Jenny Renaut; Abhijit Sarkar; Georgia Tanou; Wolfram Weckwerth; Stefanie Wienkoop; Randeep Rakwal
Boosting the globalization of plant proteomics through INPPO: current developments and future prospects.
Proteomics 2012;12(3):359-68.
2012: Stefanie Wienkoop; Wolfgang Hoehenwarter; Christiana Staudinger; Wolfram Weckwerth; Volker Egelhofer
ProMEX - a mass spectral reference database for plant proteomics.
Frontiers in plant science 2012;3():125.
2011: Víctor M Beato; M Begoña Herrera-Rodríguez; Juan J Camacho-Cristóbal; Stefan Kempa; Jesús Rexach; M Teresa Navarro-Gochicoa; Wolfram Weckwerth; Agustín González-Fontes
Expression of root glutamate dehydrogenase genes in tobacco plants subjected to boron deprivation.
Plant physiology and biochemistry : PPB / Société française de physiologie végétale 2011;49(11):1350-4.
2011: Sabine Dölle; Eckhard George; Karola Lehmann; Dietmar Schwarz; Wolfram Weckwerth; Margitta Worm; Philipp Franken
Tomato allergy: impact of genotype and environmental factors on the biological response.
Journal of the science of food and agriculture 2011;91(12):2234-40.
2011: Wolfgang Hoehenwarter; Jan Hummel; Abdelhalim Larhlimi; Joachim Selbig; Joost T van Dongen; Volker Egelhofer; Stefanie Wienkoop; Wolfram Weckwerth
MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber.
Journal of proteome research 2011;10(7):2979-91.
2011: Dietmar Schwarz; Wolfram Weckwerth; Saskia Welter; Sabine Dölle; Philipp Franken; Eckhard George; Karola Lehmann; Margitta Worm
Impact of arbuscular mycorrhizal fungi on the allergenic potential of tomato.
Mycorrhiza 2011;21(5):341-9.
2011: Wolfgang Hoehenwarter; Yanmei Chen; Luis Recuenco-Munoz; Stefanie Wienkoop; Wolfram Weckwerth
Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics.
Amino acids 2011;41(2):329-41.
2011: Wolfram Weckwerth
Unpredictability of metabolism--the key role of metabolomics science in combination with next-generation genome sequencing.
Analytical and bioanalytical chemistry 2011;400(7):1967-78.
2011: Patrick May; Nils Christian; Oliver Ebenhöh; Wolfram Weckwerth; Dirk Walther
Integration of proteomic and metabolomic profiling as well as metabolic modeling for the functional analysis of metabolic networks.
Methods in molecular biology (Clifton, N.J.) 2011;694():341-63.
2010: Stefanie Wienkoop; Sacha Baginsky; Wolfram Weckwerth
Arabidopsis thaliana as a model organism for plant proteome research.
Journal of proteomics 2010;73(11):2239-48.
2010: Jakob Prestele; Georg Hierl; Christian Scherling; Stefan Hetkamp; Claus Schwechheimer; Erika Isono; Wolfram Weckwerth; Gerhard Wanner; Christine Gietl
Different functions of the C3HC4 zinc RING finger peroxins PEX10, PEX2, and PEX12 in peroxisome formation and matrix protein import.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(33):14915-20.
2010: Yanmei Chen; Wolfgang Hoehenwarter; Wolfram Weckwerth
Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and mass accuracy precursor alignment.
The Plant journal : for cell and molecular biology 2010;63(1):1-17.
2010: Stefanie Wienkoop; Julia Weiss; Patrick May; Stefan Kempa; Susann Irgang; Luis Recuenco-Munoz; Matthias Pietzke; Thorsten Schwemmer; Jens Rupprecht; Volker Egelhofer; Wolfram Weckwerth
Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses.
Molecular bioSystems 2010;6(6):1018-31.
2010: Wolfram Weckwerth
Metabolomics: an integral technique in systems biology.
Bioanalysis 2010;2(4):829-36.
2010: Christian Scherling; Christiane Roscher; Patrick Giavalisco; Ernst-Detlef Schulze; Wolfram Weckwerth
Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species.
PloS one 2010;5(9):e12569.
2009: Estíbaliz Larrainzar; Stefanie Wienkoop; Christian Scherling; Stefan Kempa; Rubén Ladrera; Cesar Arrese-Igor; Wolfram Weckwerth; Esther Gonzalez
Carbon metabolism and bacteroid functioning are involved in the regulation of nitrogen fixation in Medicago truncatula under drought and recovery.
Molecular plant-microbe interactions : MPMI 2009;22(12):1565-76.
2009: Jun Ito; Nicolas L Taylor; Ian Castleden; Wolfram Weckwerth; A Harvey Millar; Joshua L Heazlewood
A survey of the Arabidopsis thaliana mitochondrial phosphoproteome.
Proteomics 2009;9(17):4229-40.
2009: Christian Scherling; Kristina Ulrich; Dietrich Ewald; Wolfram Weckwerth
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 : MPMI 2009;22(8):1032-7.
2009: Olivia Y Bässler; Julia Weiss; Stefanie Wienkoop; Karola Lehmann; Christian Scheler; Sabine Dölle; Dietmar Schwarz; Philipp Franken; Eckhard George; Margitta Worm; Wolfram Weckwerth
Evidence for novel tomato seed allergens: IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling.
Journal of proteome research 2009;8(3):1111-22.
2009: Stefan Kempa; Jan Hummel; Thorsten Schwemmer; Matthias Pietzke; Nadine Strehmel; Stefanie Wienkoop; Joachim Kopka; Wolfram Weckwerth
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.
Journal of basic microbiology 2009;49(1):82-91.
2009: Pawel Durek; Christian Schudoma; Wolfram Weckwerth; Joachim Selbig; Dirk Walther
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
BMC bioinformatics 2009;10():117.
2008: Stefan Timm; Adriano Nunes-Nesi; Tiit Pärnik; Katja Morgenthal; Stefanie Wienkoop; Olav Keerberg; Wolfram Weckwerth; Leszek A Kleczkowski; Alisdair R Fernie; Hermann Bauwe
A cytosolic pathway for the conversion of hydroxypyruvate to glycerate during photorespiration in Arabidopsis.
The Plant cell 2008;20(10):2848-59.
2008: Wolfram Weckwerth; Sacha Baginsky; Klaas van Wijk; Joshua L Heazlewood; Harvey Millar
The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology.
Journal of proteome research 2008;7(10):4209-10.
2008: Ute Lehmann; Stefanie Wienkoop; Hendrik Tschoep; Wolfram Weckwerth
If the antibody fails--a mass western approach.
The Plant journal : for cell and molecular biology 2008;55(6):1039-46.
2008: Stefanie Wienkoop; Katja Morgenthal; Florian Wolschin; Matthias Scholz; Joachim Selbig; Wolfram Weckwerth
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.
Molecular & cellular proteomics : MCP 2008;7(9):1725-36.
2008: Patrick May; Stefanie Wienkoop; Stefan Kempa; Björn Usadel; Nils Christian; Jens Rupprecht; Julia Weiss; Luis Recuenco-Munoz; Oliver Ebenhöh; Wolfram Weckwerth; Dirk Walther
Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
Genetics 2008;179(1):157-66.
2008: Wolfram Weckwerth
Integration of metabolomics and proteomics in molecular plant physiology--coping with the complexity by data-dimensionality reduction.
Physiologia plantarum 2008;132(2):176-89.
2008: Stefanie Wienkoop; Estíbaliz Larrainzar; Mirko Glinski; Esther Gonzalez; Cesar Arrese-Igor; Wolfram Weckwerth
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.
Journal of experimental botany 2008;59(12):3307-15.
2008: Joshua L Heazlewood; Pawel Durek; Jan Hummel; Joachim Selbig; Wolfram Weckwerth; Dirk Walther; waltraud Schulze
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor.
Nucleic acids research 2008;36(Database issue):D1015-21.
2007: Sigrun Reumann; Lavanya Babujee; Changle Ma; Stefanie Wienkoop; Tanja Siemsen; Gerardo E Antonicelli; Nicolas Rasche; Franziska Lüder; Wolfram Weckwerth; Olaf Jahn
Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms.
The Plant cell 2007;19(10):3170-93.
2007: Wolf D Lehmann; Ralf Krüger; Mogjiborahman Salek; Chien-Wen Hung; Florian Wolschin; Wolfram Weckwerth
Neutral loss-based phosphopeptide recognition: a collection of caveats.
Journal of proteome research 2007;6(7):2866-73.
2007: Estíbaliz Larrainzar; Stefanie Wienkoop; Wolfram Weckwerth; Rubén Ladrera; Cesar Arrese-Igor; Esther Gonzalez
Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress.
Plant physiology 2007;144(3):1495-507.
2007: Nadja Engel; Kirsten van den Daele; Uner Kolukisaoglu; Katja Morgenthal; Wolfram Weckwerth; Tiit Pärnik; Olav Keerberg; Hermann Bauwe
Deletion of glycine decarboxylase in Arabidopsis is lethal under nonphotorespiratory conditions.
Plant physiology 2007;144(3):1328-35.
2007: Ralf Krüger; Florian Wolschin; Wolfram Weckwerth; Jörg Bettmer; Wolf D Lehmann
Plant protein phosphorylation monitored by capillary liquid chromatography--element mass spectrometry.
Biochemical and biophysical research communications 2007;355(1):89-96.
2007: Mark Müller-Linow; Wolfram Weckwerth; Marc-Thorsten Hütt
Consistency analysis of metabolic correlation networks.
BMC systems biology 2007;1():44.
2007: Jan Hummel; Michaela Niemann; Stefanie Wienkoop; waltraud Schulze; Dirk Steinhauser; Joachim Selbig; Dirk Walther; Wolfram Weckwerth
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.
BMC bioinformatics 2007;8():216.
2007: Ralf Steuer; Katja Morgenthal; Wolfram Weckwerth; Joachim Selbig
A gentle guide to the analysis of metabolomic data.
Methods in molecular biology (Clifton, N.J.) 2007;358():105-26.
2007: Katja Morgenthal; Stefanie Wienkoop; Florian Wolschin; Wolfram Weckwerth
Integrative profiling of metabolites and proteins: improving pattern recognition and biomarker selection for systems level approaches.
Methods in molecular biology (Clifton, N.J.) 2007;358():57-75.
2006: Stefanie Wienkoop; Estibaliz Larrainzar; Michaela Niemann; Esther M Gonzalez; Ute Lehmann; Wolfram Weckwerth
Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostics.
Journal of separation science 2006;29(18):2793-801.
2006: Mirko Glinski; Wolfram Weckwerth
The role of mass spectrometry in plant systems biology.
Mass spectrometry reviews 2006;25(2):173-214.
2006: Katja Morgenthal; Wolfram Weckwerth; Ralf Steuer
Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation.
Bio Systems 2006;83(2-3):108-17.
2006: Florian Wolschin; Wolfram Weckwerth
Methionine oxidation in peptides--a source for false positive phosphopeptide identification in neutral loss driven MS3.
Rapid communications in mass spectrometry : RCM 2006;20(16):2516-8.
2006: Stefanie Wienkoop; Wolfram Weckwerth
Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidopsis thaliana.
Journal of experimental botany 2006;57(7):1529-35.
2005: Wolfram Weckwerth; Katja Morgenthal
Metabolomics: from pattern recognition to biological interpretation.
Drug discovery today 2005;10(22):1551-8.
2005: Florian Wolschin; Stefanie Wienkoop; Wolfram Weckwerth
Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC).
Proteomics 2005;5(17):4389-97.
2005: Mirko Glinski; Wolfram Weckwerth
Differential multisite phosphorylation of the trehalose-6-phosphate synthase gene family in Arabidopsis thaliana: a mass spectrometry-based process for multiparallel peptide library phosphorylation analysis.
Molecular & cellular proteomics : MCP 2005;4(10):1614-25.
2005: Ralf Boldt; Christoph Edner; Uner Kolukisaoglu; Martin Hagemann; Wolfram Weckwerth; Stefanie Wienkoop; Katja Morgenthal; Hermann Bauwe
D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family.
The Plant cell 2005;17(8):2413-20.
2005: Joachim Kopka; Nicolas Schauer; Stephan Krueger; Claudia Birkemeyer; Björn Usadel; Eveline Bergmüller; Peter Dörmann; Wolfram Weckwerth; Yves Gibon; Mark Stitt; Lothar Willmitzer; Alisdair R Fernie; Dirk Steinhauser
GMD@CSB.DB: the Golm Metabolome Database.
Bioinformatics (Oxford, England) 2005;21(8):1635-8.
2005: Florian Wolschin; Ute Lehmann; Mirko Glinski; Wolfram Weckwerth
An integrated strategy for identification and relative quantification of site-specific protein phosphorylation using liquid chromatography coupled to MS2/MS3.
Rapid communications in mass spectrometry : RCM 2005;19(24):3626-32.
2005: Florian Wolschin; Wolfram Weckwerth
Combining metal oxide affinity chromatography (MOAC) and selective mass spectrometry for robust identification of in vivo protein phosphorylation sites.
Plant methods 2005;1(1):9.
2005: Jan Hummel; Nima Keshvari; Wolfram Weckwerth; Joachim Selbig
Species-specific analysis of protein sequence motifs using mutual information.
BMC bioinformatics 2005;6():164.
2004: Stefanie Wienkoop; Daniela Zoeller; Berit Ebert; Ulrike Simon-Rosin; Joachim Fisahn; Mirko Glinski; Wolfram Weckwerth
Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification.
Phytochemistry 2004;65(11):1641-9.
2004: Wolfram Weckwerth; Marcelo Ehlers Loureiro; Kathrin Wenzel; Oliver Fiehn
Differential metabolic networks unravel the effects of silent plant phenotypes.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(20):7809-14.
2004: Joachim Kopka; Alisdair R Fernie; Wolfram Weckwerth; Yves Gibon; Mark Stitt
Metabolite profiling in plant biology: platforms and destinations.
Genome biology 2004;5(6):109.
2004: Stefanie Wienkoop; Mirko Glinski; Nobuo Tanaka; Vladimir V Tolstikov; Oliver Fiehn; Wolfram Weckwerth
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.
Rapid communications in mass spectrometry : RCM 2004;18(6):643-50.
2004: Wolfram Weckwerth; Kathrin Wenzel; Oliver Fiehn
Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks.
Proteomics 2004;4(1):78-83.
2003: Ralf Steuer; Jürgen Kurths; Oliver Fiehn; Wolfram Weckwerth
Interpreting correlations in metabolomic networks.
Biochemical Society transactions 2003;31(Pt 6):1476-8.
2003: Wolfram Weckwerth; Joachim Selbig
Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information.
Biochemical and biophysical research communications 2003;307(3):516-21.
2003: Ralf Steuer; Jürgen Kurths; Oliver Fiehn; Wolfram Weckwerth
Observing and interpreting correlations in metabolomic networks.
Bioinformatics (Oxford, England) 2003;19(8):1019-26.
2003: Oliver Fiehn; Wolfram Weckwerth
Deciphering metabolic networks.
European journal of biochemistry / FEBS 2003;270(4):579-88.
2003: Wolfram Weckwerth
Metabolomics in systems biology.
Annual review of plant biology 2003;54():669-89.
2003: Mirko Glinski; Tina Romeis; Claus-Peter Witte; Stefanie Wienkoop; Wolfram Weckwerth
Stable isotope labeling of phosphopeptides for multiparallel kinase target analysis and identification of phosphorylation sites.
Rapid communications in mass spectrometry : RCM 2003;17(14):1579-84.
2002: Wolfram Weckwerth; Oliver Fiehn
Can we discover novel pathways using metabolomic analysis?
Current opinion in biotechnology 2002;13(2):156-60.
2001: F Kose; Wolfram Weckwerth; T Linke; Oliver Fiehn
Visualizing plant metabolomic correlation networks using clique-metabolite matrices.
Bioinformatics (Oxford, England) 2001;17(12):1198-208.
2000: Wolfram Weckwerth; K Miyamoto; K Iinuma; M Krause; Mirko Glinski; Thomas Storm; Gerhard Bonse; Horst Kleinkauf; Rainer Zocher
Biosynthesis of PF1022A and related cyclooctadepsipeptides.
The Journal of biological chemistry 2000;275(23):17909-15.
2000: Wolfram Weckwerth; Lothar Willmitzer; Oliver Fiehn
Comparative quantification and identification of phosphoproteins using stable isotope labeling and liquid chromatography/mass spectrometry.
Rapid communications in mass spectrometry : RCM 2000;14(18):1677-81.