General information about GABI

GABI, acronym for "Genomanalyse im biologischen System Pflanze", is the name of a large collaborative network of different plant genomic research projects. The projects are funded by the Federal Ministry of Education and Research (BMBF) with the purpose to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research.
GabiPD (The GABI Primary Database) is part of the large GABI network.
For more information: http://www.gabi.de; http://www.bmbf.de/pub/gabi.pdf

Aims of GabiPD (The GABI Primary Database)

GabiPD collects, integrates and links all relevant primary information from the GABI projects and makes them accessible via internet. For data searches interfaces are developed. GreenCards is the main interface for text based retrieval of sequence, snp, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensy agency are facilitated. Besides bioinformatics services are offered to the GABI community.
GabiPD is funded by the Federal Ministry of Education and Research (BMBF).

Data submission and access to the data

Registered users can submit data via secure file upload. To submit data, please go to: Submit data The owner of the data can define who gets access to the data.
All data which are achieved with materials or services of the GABI resource centers are subjected to the rules laid out by the BMBF. That is, the submitted data are only accessible for the owner of the data and an owner-defined usergroup up to six month. After this time the patent- and licensing agency (PLA) and the Wirtschaftsverbund Pflanzengenom (WPG) get the authorization to access your data for three month prior to publication.

Team members

GabiPD Team in the Bioinformatics group at the MPIMP:

	Dr. Birgit Kersten	Team leader, Biologist	Email:
	Dr. Diego Riano-Pachon	Postdoc, Bioinformatician	Email:
	Axel Nagel	Computer scientist	Email:
	Rico Basekow	Computer scientist	Email:
	Robert Wagner	Computer scientist	Email:
	Jost Neigenfind	PhD student, Bioinformatician	Email:
	Sabrina Kleessen	Student worker	Email:

Former members:
Oezguer Demir
Dr. Svenja Diehl (Meyer)
Sebastian Koehler
Daniel Walaschewski
Elke Weber

Current projects of the GabiPD Team

GABI-FUTURE GabiPD:
GABI Primary Database (GabiPD)
(BMBF, single project, 2007-2010, project coordinator: Dr. Birgit Kersten)
GabiPD home

Current posters:

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Publications of the GabiPD Team

• Pajerowska-Mukhtar K, Stich B, Achenbach U, Ballvora A, Luebeck J, Strahwald J, Tacke E, Hofferbert H-R, Ilarionova E, Bellin D, Walkemeier B, Basekow R, Kersten B and C Gebhardt ( ) Genetics, Submitted

• Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D and R Rakwal (2008) Plant phosphoproteomics: An update. Proteomics, In press

• Arvidsson S, Kwasniewski M, Riano-Pachon DM and B Mueller-Roeber B (2008) QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 9(1):465. BMC Bioinformatics

• Kersten B and T Feilner (2008) Protein microarrays for phosphorylation studies. In: Walker J, ed, Protein protocols handbook. Humana Press, Totowa. Springer

• Riano-Pachon DM, Nagel A, Neigenfind J, Basekow R, Wagner R, Weber E, Mueller-Roeber B, Diehl S and B Kersten (2008) GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database. Nucleic Acids Research, DOI 10.1093/nar/gkn611 Nucleic Acids Research

• Lohse M, Krueger P, Hannemann J, Nagel A, Stitt M, Walther D and B Usadel (2008) Robin - Microarray Experimentanalyse leicht gemacht. GenomXPress 3/08:16-17 (In German). GenomXPress

• Balazadeh S, Riano-Pachon DM and B Mueller-Roeber (2008) Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biology. 10(s1):63-75. Plant Biology

• Kersten B (2008) Time to search for kinase substrates. In: Rakwal R, Agrawal GK, eds, Plant Proteomics: Technologies, Strategies, and Applications:485-498. Wiley-Interscience, Hoboken, USA. WILEY

• Correa LGG, Riano-Pachon DM, Schrago CG, dos Santos RV, Mueller-Roeber B and M Vincentz (2008) The role of bZIP transcription factors in green plant evolution: Adaptive features emerging from four founder genes. PLoS ONE. 3(8):e2944. PubMed

• Neigenfind J, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J and B Kersten (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 9:356. BMC Genomics

•Kersten B, Nagel A, Riano-Pachon DM, Neigenfind J, Weber E, Wagner R and S Diehl (2008) Die GABI-Primaerdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXPress 1/08:17-19 (In German). GenomXPress

• Riano-Pachon DM, Correa LGG, Trejos-Espinosa R and B Mueller-Roeber (2008) Green transcription factors: a Chlamydomonas overview. Genetics 179(1):31-9. PubMed

• Kersten B and EE Wanker (2008) Klinische Proteomik. In: Ganten D, Ruckpaul K, eds, Grundlagen der Molekularen Medizin:Section 3.1, Springer, Berlin, Heidelberg, New York (In German). Springer

• Feilner T and B Kersten (2007) Phosphorylation studies using plant protein microarrays. In: Thiellement H, Zivy M, Damerval C, Mechin V, eds, Plant Proteomics. Methods and Protocols. Series: Methods in Molecular Biology 355:379-90. Humana Press Inc., Totowa. PubMed   

• Kersten B and T Feilner (2007) Generation of plant protein micorarrays and investigation of antigen-antibody interactions. In: Thiellement H, Zivy M, Damerval C, Mechin V, eds, Plant Proteomics. Methods and Protocols. Series: Methods in Molecular Biology 355:365-78. Humana Press Inc., Totowa. PubMed   

• Kersten B and T Feilner (2007) High-throughput identification of plant protein kinase substrates. In: Šamaj J, Thelen J, eds, Plant proteomics:53-70, Springer, Berlin, Heidelberg, New York. Springer

• Kersten B, Agrawal GK, Iwahashi H and R Rakwal (2006) Plant phosphoproteomics: A long road ahead. Proteomics 6(20):5517-5528. PubMed

• Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR and M Stitt (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7:535. PubMed

• Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blaesing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M and AR Fernie (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: Effects of genetic and environmental alterations in energy metabolism in the Leaf. Plant Molecular Biology 60(5):773-92. PubMed

• Wanker EE and B Kersten (2006) Proteomics: from proteins to disease mechanisms and the development of novel therapeutic strategies. In: Ganten D, Ruckpaul K, eds, Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, Springer, Berlin, Heidelberg, New York. Springer

• Feilner T, Hultschig C, Lee J, Meyer S, Immink RGH, Koenig A, Possling A, Seitz H, Beveridge A, Scheel D, Cahill DJ, Lehrach H, Kreutzberger J and B Kersten (2005) High-throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Molecular & Cellular Proteomics 4(10):1558-1568. PubMed

• Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S and M Stitt (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiology 138(3):1195-204. PubMed

• Meyer S, Nagel A and C Gebhardt (2005) PoMaMo - A comprehensive database for potato genome data. Nucleic Acids Research 33(Database issue):D666-70. PubMed

• Buerkle L, Meyer S, Dortay H, Lehrach H and A Heyl (2005) In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system. Functional & Integrative Genomics 5(3):175-183. PubMed

• Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krueger P, Selbig J, Mueller LA, Rhee SY and M Stitt (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal 37(6):914-39. PubMed
Selected as fast breaking paper in plant and animal sciences: ESI topics
(183 times cited in August 2008)

• Rickert AM, Kim JH, Meyer S, Nagel A, Ballvora A, Oefner PJ and C Gebhardt (2003) First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnology Journal 1(6):399-410. PubMed

Publications of Birgit Kersten

• Pajerowska-Mukhtar K, Stich B, Achenbach U, Ballvora A, Luebeck J, Strahwald J, Tacke E, Hofferbert H-R, Ilarionova E, Bellin D, Walkemeier B, Basekow R, Kersten B and C Gebhardt ( ) Genetics, Submitted

• Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D and R Rakwal (2008) Plant phosphoproteomics: An update. Proteomics, In press

• Kersten B and T Feilner (2008) Protein microarrays for phosphorylation studies. In: Walker J, ed, Protein protocols handbook. Humana Press, Totowa. Springer

• Riano-Pachon DM, Nagel A, Neigenfind J, Basekow R, Wagner R, Weber E, Mueller-Roeber B, Diehl S and B Kersten (2008) GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database. Nucleic Acids Research, DOI 10.1093/nar/gkn611 Nucleic Acids Research

•Kersten B (2008) Time to search for kinase substrates. In: Rakwal R, Agrawal GK, eds, Plant Proteomics: Technologies, Strategies, and Applications:485-498. Wiley-Interscience, Hoboken, USA. WILEY

• Neigenfind J, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J and B Kersten (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 9:356. BMC Genomics

•Kersten B, Nagel A, Riano-Pachon DM, Neigenfind J, Weber E, Wagner R and S Diehl (2008) Die GABI-Primärdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXPress 1/08:17-19 (In German). GenomXPress

• Kersten B and EE Wanker (2008) Klinische Proteomik. In: Ganten D, Ruckpaul K, eds, Grundlagen der Molekularen Medizin:Section 3.1, Springer, Berlin, Heidelberg, New York (In German). Springer

• Feilner T and B Kersten (2007) Phosphorylation studies using plant protein microarrays. In: Thiellement H, Zivy M, Damerval C, Mechin V, eds, Plant Proteomics. Methods and Protocols. Series: Methods in Molecular Biology 355:379-90. Humana Press Inc., Totowa. PubMed   

• Kersten B and T Feilner (2007) Generation of plant protein micorarrays and investigation of antigen-antibody interactions. In: Thiellement H, Zivy M, Damerval C, Mechin V, eds, Plant Proteomics. Methods and Protocols. Series: Methods in Molecular Biology 355:365-78. Humana Press Inc., Totowa. PubMed   

• Kersten B and T Feilner (2007) High-throughput identification of plant protein kinase substrates. In: Šamaj J, Thelen J, eds, Plant proteomics:53-70, Springer, Berlin, Heidelberg, New York. Springer

• Kersten B, Agrawal GK, Iwahashi H and R Rakwal (2006) Plant phosphoproteomics: A long road ahead. Proteomics 6(20):5517-5528. PubMed

• Grelle G, Kostka S, Otto A, Kersten B, Genser KF, Mueller EC, Waelter S, Boeddrich A, Stelzl U, Haenig C, Volkmer-Engert R, Landgraf C, Alberti S, Hoehfeld J, Stroedicke M and EE Wanker (2006) Identification of VCP/p97, CHIP and amphiphysin II interaction partners using membrane-based human proteome arrays. Molecular & Cellular Proteomics 5(2):234-244. PubMed

• Wanker EE and B Kersten (2006) Proteomics: from proteins to disease mechanisms and the development of novel therapeutic strategies. In: Ganten D, Ruckpaul K, eds, Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, Springer, Berlin, Heidelberg, New York. Springer

• Kersten B, Wanker EE, Hoheisel JD and P Angenendt (2005) Multiplex approaches in protein microarray technology. Expert Review of Proteomics 2(4):499-510. PubMed

• Feilner T, Hultschig C, Lee J, Meyer S, Immink RGH, Koenig A, Possling A, Seitz H, Beveridge A, Scheel D, Cahill DJ, Lehrach H, Kreutzberger J and B Kersten (2005) High-throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Molecular & Cellular Proteomics 4(10):1558-1568. PubMed

• Kramer A, Feilner T, Possling A, Radchuk V, Weschke W, Buerkle L and B Kersten (2004) Identification of barley CK2alpha targets by using protein microarray technology. Phytochemistry 65(12):1777-1784. PubMed

• Kersten B, Feilner T, Angenendt P, Giavalisco P, Brenner W and L Buerkle (2004) Proteomic approaches in plant biology. Current Proteomics 1(2):131-144. Bentham

• Kersten B, Possling A, Blaesing F, Mirgorodskaya E, Gobom J and H Seitz (2004) Protein microarray technology and UV-crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions. Analytical Biochemistry 331:303-313. PubMed

• Feilner T, Kreutzberger J, Niemann B, Kramer A, Possling A, Seitz H and B Kersten (2004) Proteomic studies using microarrays. Current Proteomics 1(4):283-295. Bentham

• Kersten B, Feilner T, Kramer A, Wehrmeyer S, Possling A, Witt I, Zanor MI, Stracke R, Lueking A, Kreutzberger J, Lehrach H and DJ Cahill (2003) Generation of Arabidopsis protein chips for antibody and serum screening. Plant Molecular Biology 52(5):999-1010. PubMed

• Buerkle L, Feilner T, Brenner W, Giavalisco P, Lehrach H and B Kersten (2003) Genomic and proteomic approaches in plant research. In: Pandalai SG, ed, Recent Research Developments in Plant Molecular Biology 1:239-263, Research Signpost, Kerala, India. Research Signpost

• Kersten B, Buerkle L, Kuhn EJ, Giavalisco P, Konthur Z, Lueking A, Walter G, Eickhoff H and U Schneider (2002) Large-scale plant proteomics. Plant Molecular Biology 48:(1-2) 133-141. PubMed

• Kersten B, Kasper P, Brendler-Schwaab SY and L Mueller (2002) Use of the photo-micronucleus assay in Chinese hamster V79 cells to study photochemical genotoxicity. Mutation Research 519(1-2):49-66. PubMed

• Kersten B, Niemann B and S Jahn (2001) Development of single-chain Fv fragments from a human anti-double-stranded DNA antibody to study the influence of somatic mutations on antigen binding. Experimental and Clinical Immunogenetics 18(2):96-99. PubMed

• Mueller L, Brendler-Schwaab S, Kasper P and B Kersten (2001) In vitro methods for phototoxicity and photocarcinogenicity testing of drugs. Altex-Alternativen Zu Tierexperimenten 18(2):117-121. PubMed

• Zhang J, Kersten B, Kasper P and L Mueller (2001) Photogenotoxicity and apoptosis in human HaCaT keratinocytes induced by 8-methoxypsoralen and lomefloxacin. Environmental Mutagen Research 23(Special issue):89-96. ingentaconnect

• Kersten B, Kasper P, Brendler-Schwaab SY and L Mueller (2001) Effects of visible light absorbing chemicals in the photo-micronucleus test in Chinese hamster V79 cells. Environmental Mutagen Research 23(Special issue):97-102. ScienceDirect

• Kersten B, Zhang J, Brendler-Schwaab SY, Kasper P and L Mueller (1999) The application of the micronucleus test in Chinese hamster V79 cells to detect drug-induced photogenotoxicity. Mutation Research 445(1):55-71. PubMed

• Mueller L, Kasper P, Kersten B and J Zhang (1998) Photochemical genotoxicity and photochemical carcinogenesis-Two sides of a coin? Toxicology Letters 102-103:383-387. PubMed

• Leibiger H, Kersten B, Albersheim P and A Darvill (1998) Structural characterization of the oligosacharides of a human monoclonal anti-lipopolysaccharide immunoglobulin M. Glycobiology 8(5):497-507. PubMed

• Tilgner J, Golembowski S, Kersten B, Sterry W and S Jahn (1997) VH genes expressed in peripheral blood IgE-producing B cells from patients with atopic dermatitis. Clinical and Experimental Immunology 107(3):528-535. PubMed

• Mueller-Tegethoff K, Kersten B, Kasper P and L Mueller (1997) Application of the in vitro rat hepatocyte micronucleus assay in genetic toxicology testing. Mutation Research 392(1-2):125-138. PubMed

Selected publications referencing GabiPD

• Tellstroem V, Usadel B, Thimm O, Stitt M, Kuester H and K Niehaus (2007) The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula. Plant Physiol. 143(2):825-37. PubMed

• Schneider K, Kulosa D, Soerensen TR, Moehring S, Heine M, Durstewitz G, Polley A, Weber E, Jamsari, Lein J, Hohmann U, Tahiro E, Weisshaar B, Schulz B, Koch G, Jung C and M Ganal (2007) Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor Appl Genet. 115(5):601-15. PubMed

• Ballvora A, Joecker A, Viehoever P, Ishihara H, Paal J, Meksem K, Bruggmann R, Schoof H, Weisshaar B and C Gebhardt (2007) Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics 2(8):112. PubMed

• Sattarzadeh A, Achenbach U, Luebeck J, Strahwald J, Tacke E, Hofferbert HR, Rothsteyn T and C Gebhardt (2006) Single nucleotide polymorphism (SNP) genotyping as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida pathotype Pa2/3. Mol. Breeding 18:301-312. Springer

• Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I and A Graner (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Journal of Theoretical and Applied Genetics 114:823-839. PubMed

• Hilson P (2006) Cloned sequence repertoires for small- and large-scale biology. Trends in Plant Science 11:133-141. PubMed

• Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M and AR Fernie (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Mol. Biol. 60(5):773-92. PubMed

• Feilner T, Hultschig C, Lee J, Meyer S, Immink RG, Koenig A, Possling A, Seitz H, Beveridge A, Scheel D, Cahill DJ, Lehrach H, Kreutzberger J and B Kersten (2005) High throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Molecular and Cellular Proteomics 4(10):1558-68. PubMed

• Giavalisco P, Wilson D, Kreitler T, Lehrach H, Klose J, Gobom J and P Fucini (2005) High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome. Plant Mol Biol. 57(4):577-91. PubMed

• Giavalisco P, Nordhoff E, Kreitler T, Kloppel KD, Lehrach H, Klose J and J Gobom (2005) Proteome analysis of Arabidopsis thaliana by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. Proteomics 5(7):1902-13. PubMed

• Buerkle L, Meyer S, Dortay H, Lehrach H and A Heyl (2005) In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system. Functional & Integrative Genomics 5(3), 175-183. PubMed

• Meyer S, Nagel A and C Gebhardt (2005) PoMaMo-a comprehensive database for potato genome data. Nucleic Acids Research 33(Database issue):D666-70. PubMed

• Nagel A, Usadel B, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S and M Stitt (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiology 138(3):1195-204. PubMed

• Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krueger P, Selbig J, Mueller LA, Rhee SY and M Stitt (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal 37(6):914-39 (fast breaking paper). PubMed

• Rickert AM, Jeong HK, Meyer S, Nagel A, Ballvora A, Oefner PJ and C Gebhardt (2003) First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnology Journal 1(6):399-410. PubMed