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About Us



Contact

Webmaster
to_gabi

Dr. Björn Usadel Marie Bolger
to_bjoern to_marie
Phone: + 49-(0)241-80-26634
Fax: + 49-(0)241-80-22637
Phone: + 49-(0)2461-61-2628
RWTH Aachen University
Institute for Biology I
Worringer Weg 1
52056 Aachen
Forschungszentrum Jülich
IBG-2: Plant Sciences
Wilhelm-Johnen-Straße
52428 Jülich
Germany
phone: +49-(0)2461-61-2628
web: http://www.usadellab.org
Forschungszentrum Jülich
IBG-2: Plant Sciences
Wilhelm-Johnen-Straße
52425 Jülich
Germany



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



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

Dr. Björn Usadel Head of GabiPD team, Biologist
Email:
to_bjoern

Former members:
Axel Nagel
Jost Neigenfind
Rico Basekow
Oezguer Demir
Dr. Svenja Diehl (Meyer)
Dr. Oliver Drechsel
Dr. Pawel Durek
Alex Finck
Maren Imhoff
Dr. Birgit Kersten
Sabrina Kleeßen
Sebastian Koehler
Doreen Pahlke
Dr. Diego Mauricio Riaño-Pachón
Robert Wagner
Daniel Walaschewski
Elke Weber


Current projects of the GabiPD Team

GABI-FUTURE GabiPD:
GABI Primary Database (GabiPD)
(BMBF; single project, 2007-2011; project coordinator: Dr. Björn Usadel)
Current posters:
Download (0.2M)

Download (7.4M)

Download (10M)

Download (4.4M)

GABI-FUTURE MapMen:
A portfolio of user-driven tools to design, handle, visualize and analyze functional genomics experiments against a background of existing knowledge: Tuning in Arabidopsis and application to crop genomics
(BMBF; subproject, 2007-2010; project coordinator: Prof. Mark Stitt, MPIMP)
MapMan in GabiPD
Current posters: Download (1.3M) Download (13M) Download (22M)

GABI-FUTURE Papatomics:
Validation of association between DNA-based markers and quantitative traits in advanced breeding populations of potato by marker-assisted selection and "Papatomics" (potato transcriptomics, proteomics, metabolomics)
(BMBF; subproject, 2008-2010; project coordinator: PD Dr. Christiane Gebhardt, MPIZ)
PoMaMo in GabiPD
SATlotyper in GabiPD
Current posters: Download (0.8M) Download (2M)

GABI-FUTURE GABI-GAIN:
Biometric and bioinformatic tools for genomics-based plant breeding
(BMBF; subproject, 2008-2011; project coordinator: Prof. Dr. Albrecht Melchinger, Universität Hohenheim)
Current posters: Download (0.8M) Download (2.8M)

Climate 2010:
Climate tolerance of barley – From gene induction to function
(StMELF, Bayerisches Staatsministerium für Ernährung, Landwirtschaft und Forsten; subcontract, 2009-2011; project coordination: Dr. Guenther Schweizer, LFL)

GABI Plant-KBBE II ExpResBar:
Exploiting genetic variation for resistance to important pathogens in barley
(BMBF; subproject, 2010-2013; project coordination: Jutta Förster, Saaten-Union BIOTEC GmbH)

Arabidopsis WebServices:
Participation in Arabidopsis WebServices http://bioinfo.mpiz-koeln.mpg.de/jabba
WebServices in GabiPD



Publications of the GabiPD Team


• Usadel B, Schwacke R, Nagel A and B Kersten (2012) GabiPD - The GABI Primary Database integrates plant proteomic data with gene-centric information. Frontiers in Plant Science 3:154. doi: 10.3389/fpls.2012.00154. Frontiers

• Gyetvai G, Sønderkær M, Göbel U, Basekow R, Ballvora A, Imhoff M, Kersten B, Nielsen KL and Gebhardt C. (2012) The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis. PLoS ONE 7(2): e31526. doi:10.1371/journal.pone.0031526. PubMed

• Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño-Pachón DM, Corrêa LG, Reski R, Mueller-Roeber B and SA Rensing (2010) Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2:488-503. PubMed

• Kryvych S, Kleeßen S, Ebert B, Kersten B and J Fisahn (2010) Proteomics - the key to understanding systems biology of Arabidopsis trichomes. Phytochemistry, doi: 10.1016/j.phytochem.2010.09.003. PubMed

• Riaño-Pachón DM, Kleeßen S, Neigenfind J, Durek P, Weber E, Walther D, Selbig J, Engelsberger W, Schulze W and B Kersten (2010) Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11(1):411. PubMed

• Durek P, Schmidt R, Heazlewood J, Jones A, MacLean D, Nagel A, Kersten B and W Schulze (2010) PhosPhAt: The Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Research 38 (Database issue): D828-D834. PubMed

• Pérez-Rodriguez P, Riaño-Pachón DM, Corrêa LGG, Rensing S, Kersten B and B Mueller-Roeber (2010) PlntTFDB: Updated content and new features in the Plant Transcription Factor Database. Nucleic Acids Research 38 (Database issue):D822-7. PubMed

• Kim JA, Cho K, Singh R, Jung YH, Jeong SH, Kim SH, Lee JE, Cho YS, Agrawal GK, Rakwal R, Tamogami S, Kersten B, Jeon JS, An G and NS Jwa (2009) Rice OsACDR1 (Oryza sativa Accelerated Cell Death and Resistance 1) is a potential positive regulator of disease resistance. Molecules and Cells 28, 431-439. PubMed

• Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A and M Stitt (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ. 32(9):1211-29. PubMed

• Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D and R Rakwal (2009) Plant phosphoproteomics: An update. Proteomics 9(4):964-88. PubMed

• 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 (2009) Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics 181(3):1115-27. PubMed

• Riano-Pachon DM, Nagel A, Neigenfind J, Basekow R, Wagner R, Weber E, Mueller-Roeber B, Diehl S and B Kersten (2009) GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database. Nucleic Acids Research 37(Database issue):D954-9. PubMed

• Kersten B and T Feilner (2009) Protein microarrays for phosphorylation studies. In: Walker J, ed, Protein protocols handbook. Humana Press, Totowa. Springer

• 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

• 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. PubMed

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

• 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. PubMed

•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
(257 times cited in August 2009)

• 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



Selected publications referencing GabiPD

For an up to date list check Google Scholar

• 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 (2009) Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics 181(3):1115-27. PubMed

• Vizeacoumar FJ, Chong Y, Boone C and BJ Andrews (2009) A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett. 583(11):1656-61. PubMed

• Achenbach U, Paulo J, Ilarionova E, Lübeck J, Strahwald J, Tacke E, Hofferbert HR and C Gebhardt (2008) Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V. Theor Appl Genet. 118(3):619-29. PubMed PMID: 19020852. PubMed

• Pestsova E, Meinhard J, Menze A, Fischer U, Windhövel A and P Westhoff (2008) Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds. BMC Plant Biol. 8:122. PubMed

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

• Lange C, Holtgräwe D, Schulz B, Weisshaar B, Himmelbauer H. (2008) Construction and characterization of a sugar beet (Beta vulgaris) fosmid library. Genome 51(11):948-51. PubMed

• 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

• 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

• 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

• 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
br> • 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


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