A Krogh

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. ncbi request reprint Two methods for improving performance of an HMM and their application for gene finding
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proc Int Conf Intell Syst Mol Biol 5:179-86. 1997
  2. ncbi request reprint Hidden neural networks
    A Krogh
    Department of Chemistry, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Neural Comput 11:541-63. 1999
  3. pmc Using database matches with for HMMGene for automated gene detection in Drosophila
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Genome Res 10:523-8. 2000
  4. ncbi request reprint Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
  5. ncbi request reprint Genome organisation and chromatin structure in Escherichia coli
    D Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Biochimie 83:201-12. 2001
  6. ncbi request reprint Prediction of signal peptides and signal anchors by a hidden Markov model
    H Nielsen
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proc Int Conf Intell Syst Mol Biol 6:122-30. 1998
  7. ncbi request reprint On the total number of genes and their length distribution in complete microbial genomes
    M Skovgaard
    Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
    Trends Genet 17:425-8. 2001
  8. ncbi request reprint Sigma A recognition sites in the Bacillus subtilis genome
    H Jarmer
    Center for Biological Sequence Analysis, Building 208, and Section for Molecular Microbiology, Building 301, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
    Microbiology 147:2417-24. 2001
  9. ncbi request reprint Prediction of human protein function from post-translational modifications and localization features
    L J Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 319:1257-65. 2002

Collaborators

Detail Information

Publications9

  1. ncbi request reprint Two methods for improving performance of an HMM and their application for gene finding
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proc Int Conf Intell Syst Mol Biol 5:179-86. 1997
    ..A new (approximative) algorithm is described, which finds the most probable prediction summed over all paths yielding the same prediction. We show that these methods contribute significantly to the high performance of HMMgene...
  2. ncbi request reprint Hidden neural networks
    A Krogh
    Department of Chemistry, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Neural Comput 11:541-63. 1999
    ..An evaluation of the HNN on the task of recognizing broad phoneme classes in the TIMIT database shows clear performance gains compared to standard HMMs tested on the same task...
  3. pmc Using database matches with for HMMGene for automated gene detection in Drosophila
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Genome Res 10:523-8. 2000
    ..The specificity drops more than the sensitivity increases when ESTs are used. This is due to the high noise level in EST matches, and it is discussed in more detail why this is and how it might be improved...
  4. ncbi request reprint Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  5. ncbi request reprint Genome organisation and chromatin structure in Escherichia coli
    D Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Biochimie 83:201-12. 2001
    ..We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus...
  6. ncbi request reprint Prediction of signal peptides and signal anchors by a hidden Markov model
    H Nielsen
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Proc Int Conf Intell Syst Mol Biol 6:122-30. 1998
    ....
  7. ncbi request reprint On the total number of genes and their length distribution in complete microbial genomes
    M Skovgaard
    Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
    Trends Genet 17:425-8. 2001
    ..Although it is often claimed that Escherichia coli has about 4300 genes, we show that it probably has only approximately 3800 genes, and that a similar discrepancy exists for almost all published genomes...
  8. ncbi request reprint Sigma A recognition sites in the Bacillus subtilis genome
    H Jarmer
    Center for Biological Sequence Analysis, Building 208, and Section for Molecular Microbiology, Building 301, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
    Microbiology 147:2417-24. 2001
    ..Some of the response-regulator aspartate phosphatases were among the predictions of promoters containing extended sites. The expression of rapA and rapB was confirmed by site-directed mutagenesis to depend on the extended -10 region...
  9. ncbi request reprint Prediction of human protein function from post-translational modifications and localization features
    L J Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 319:1257-65. 2002
    ..These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects such as the length, isoelectric point and composition of the polypeptide chain...