Florian Gnad

Summary

Country: Germany

Publications

  1. ncbi request reprint Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression
    Florian Gnad
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Bioinformatics 22:2577-9. 2006
  2. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
  3. doi request reprint Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
  4. ncbi request reprint Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    Boris Macek
    Max Planck Institut for Biochemistry, Department of Proteomics and Signal Transduction, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:299-307. 2008
  5. doi request reprint Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis
    Boumediene Soufi
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 9:3638-46. 2010
  6. pmc Large-scale proteomics analysis of the human kinome
    Felix S Oppermann
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 8:1751-64. 2009
  7. doi request reprint Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover
    Sidney B Cambridge
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich Martinsried, Germany
    J Proteome Res 10:5275-84. 2011
  8. doi request reprint High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 9:4642-52. 2009
  9. doi request reprint Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
    Mol Cell 46:542-8. 2012
  10. doi request reprint Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors
    Cuiping Pan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 8:4534-46. 2008

Detail Information

Publications28

  1. ncbi request reprint Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression
    Florian Gnad
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Bioinformatics 22:2577-9. 2006
    ....
  2. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
    ..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...
  3. doi request reprint Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
    ..In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells...
  4. ncbi request reprint Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    Boris Macek
    Max Planck Institut for Biochemistry, Department of Proteomics and Signal Transduction, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:299-307. 2008
    ..Our results establish Ser/Thr/Tyr phosphorylation as a common posttranslational modification in Eubacteria, present since the onset of cellular life...
  5. doi request reprint Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis
    Boumediene Soufi
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 9:3638-46. 2010
    ....
  6. pmc Large-scale proteomics analysis of the human kinome
    Felix S Oppermann
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 8:1751-64. 2009
    ..In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis...
  7. doi request reprint Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover
    Sidney B Cambridge
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich Martinsried, Germany
    J Proteome Res 10:5275-84. 2011
    ..Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover...
  8. doi request reprint High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 9:4642-52. 2009
    ..We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com)...
  9. doi request reprint Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
    Mol Cell 46:542-8. 2012
    ..Many N-glycosylated proteins coevolved with the rise of extracellular processes that are specific within corresponding phylogenetic groups and essential for organismal development, body growth, and organ formation...
  10. doi request reprint Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors
    Cuiping Pan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 8:4534-46. 2008
    ..Finally, we devised a triple labeling strategy comprising control cells, stimulated cells, and phosphatase treated cells to derive an upper bound on phosphorylation occupancy...
  11. doi request reprint Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Proteome Res 8:4039-49. 2009
    ..Availability of the C. elegans phosphoproteome should add a novel dimension to functional data obtained by genetic screens in this organism...
  12. pmc Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life
    Michalis Aivaliotis
    Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS ONE 4:e4777. 2009
    ....
  13. pmc Predicting post-translational lysine acetylation using support vector machines
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Bioinformatics 26:1666-8. 2010
    ..This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico prediction of acetylated lysine residues...
  14. ncbi request reprint Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry
    Sara Zanivan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 7:5314-26. 2008
    ..Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies...
  15. pmc Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 8:611. 2012
    ..Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer...
  16. pmc MAPU 2.0: high-accuracy proteomes mapped to genomes
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 37:D902-6. 2009
    ..MAPU 2.0 is a model for a database specifically designed for high-accuracy proteomics and a member of the ProteomExchange Consortium. It is available on line at http://www.mapuproteome.com...
  17. doi request reprint Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
    ..Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications...
  18. doi request reprint Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif
    Ivan Matic
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried D 82152, Germany
    Mol Cell 39:641-52. 2010
    ..In 16 proteins we identified a hydrophobic cluster SUMOylation motif (HCSM). SUMO conjugation of RanGAP1 and ZBTB1 via HCSMs is remarkably efficient...
  19. ncbi request reprint The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
    Boris Macek
    Max Planck Institute for Biochemistry, Proteomics, and Signal Transduction, Am Klopferspitz 18a, D 82152 Martinsried, Germany
    Mol Cell Proteomics 6:697-707. 2007
    ....
  20. doi request reprint Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle
    Henrik Daub
    Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell 31:438-48. 2008
    ..These results provide a vastly extended knowledge base for functional studies on kinases and their regulation through site-specific phosphorylation...
  21. doi request reprint Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried near Munich, Germany
    J Proteome Res 9:3280-9. 2010
    ..Together with the glycosylation sites from a recent large-scale study, they can confirm or correct predicted membrane topologies of these proteins, as we show for the examples calcium channels and glutamate receptors...
  22. pmc Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics
    Maximiliane Hilger
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 8:1908-20. 2009
    ..Our analysis highlights a connection of Ptp61F to cytoskeletal regulation through GTPase regulating proteins and focal adhesion components...
  23. ncbi request reprint Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried D 82152, Germany
    Cell 141:897-907. 2010
    ..The N-glycoproteome contains a plethora of modification sites on factors important in development, organ-specific functions, and disease...
  24. ncbi request reprint Phosphoproteins of the chicken eggshell calcified layer
    Karlheinz Mann
    Max Planck Institute for Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany
    Proteomics 7:106-15. 2007
    ..Among the major phosphorylated proteins of the chicken eggshell matrix were osteopontin and the eggshell-specific proteins ovocleidin-17, ovocleidin-116, and ovocalyxin-32...
  25. pmc PHOSIDA 2011: the posttranslational modification database
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 39:D253-60. 2011
    ..The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets...
  26. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  27. doi request reprint The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins
    Boumediene Soufi
    Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, Lyngby, Denmark
    Proteomics 8:3486-93. 2008
    ....
  28. ncbi request reprint Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
    Cell 127:635-48. 2006
    ..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...