Nikolaj Blom

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. pmc PhosphoBase: a database of phosphorylation sites
    N Blom
    Center for Biological Sequence Analysis, Department of Chemistry, Building 207, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 26:382-6. 1998
  2. ncbi request reprint Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    Nikolaj Blom
    Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark
    Proteomics 4:1633-49. 2004
  3. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
  4. pmc Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Lars Kiemer
    Center for Biological Sequence Analysis BioCentrum DTU, Technical University of Denmark DK 2800 Lyngby
    BMC Bioinformatics 5:72. 2004
  5. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
  6. ncbi request reprint Kinase-specific prediction of protein phosphorylation sites
    Martin L Miller
    Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
    Methods Mol Biol 527:299-310, x. 2009
  7. doi request reprint NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proteomics 9:116-25. 2009
  8. ncbi request reprint Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK 2800 Lyngby, Denmark
    Mol Cell Proteomics 7:181-92. 2008
  9. ncbi request reprint NetAcet: prediction of N-terminal acetylation sites
    Lars Kiemer
    Center for Biological Sequence Analysis, BioCentrum DTU Building 208 Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 21:1269-70. 2005
  10. ncbi request reprint Feature-based prediction of non-classical and leaderless protein secretion
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:349-56. 2004

Collaborators

Detail Information

Publications11

  1. pmc PhosphoBase: a database of phosphorylation sites
    N Blom
    Center for Biological Sequence Analysis, Department of Chemistry, Building 207, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 26:382-6. 1998
    ..PhosphoBase is available on the WWW at http://www.cbs.dtu.dk/databases/PhosphoBase/..
  2. ncbi request reprint Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    Nikolaj Blom
    Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark
    Proteomics 4:1633-49. 2004
    ..The new server, NetPhosK, is made publicly available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The issues of underestimation, over-prediction and strategies for improving prediction specificity are also discussed...
  3. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
    ..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
  4. pmc Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Lars Kiemer
    Center for Biological Sequence Analysis BioCentrum DTU, Technical University of Denmark DK 2800 Lyngby
    BMC Bioinformatics 5:72. 2004
    ..Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods...
  5. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..The atlas is available as a community resource (http://netphorest.info)...
  6. ncbi request reprint Kinase-specific prediction of protein phosphorylation sites
    Martin L Miller
    Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
    Methods Mol Biol 527:299-310, x. 2009
    ..Finally, we point to possible developments with the intention of providing the community with improved and additional phosphorylation predictors for large-scale modeling of cellular signaling networks...
  7. doi request reprint NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proteomics 9:116-25. 2009
    ..In conclusion, NetPhosBac clearly illustrates the advantage of taxa-specific predictors and we hope it will provide a useful asset to the microbiological community...
  8. ncbi request reprint Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK 2800 Lyngby, Denmark
    Mol Cell Proteomics 7:181-92. 2008
    ..Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding...
  9. ncbi request reprint NetAcet: prediction of N-terminal acetylation sites
    Lars Kiemer
    Center for Biological Sequence Analysis, BioCentrum DTU Building 208 Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 21:1269-70. 2005
    ..We obtain correlation coefficients close to 0.7 on yeast data and a sensitivity up to 74% on mammalian data, suggesting that the method is valid for eukaryotic NatA orthologs...
  10. ncbi request reprint Feature-based prediction of non-classical and leaderless protein secretion
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:349-56. 2004
    ..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP...
  11. ncbi request reprint Prediction of proprotein convertase cleavage sites
    Peter Duckert
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:107-12. 2004
    ..The method predicts cleavage sites in independent sequences with a sensitivity of 95% for the furin neural network and 62% for the general PC network. The ProP method is made publicly available at http://www.cbs.dtu.dk/services/ProP...