Nikolaj Blom

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. ncbi 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 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. ncbi Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
  4. ncbi 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. ncbi 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 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. ncbi 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 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 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 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

Publications10

  1. ncbi 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 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. ncbi 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. ncbi 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. ncbi 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 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. ncbi 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 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 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 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...