S Knudsen

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. pmc Alternative mapping of probes to genes for Affymetrix chips
    Laurent Gautier
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 5:111. 2004
  2. ncbi request reprint Promoter2.0: for the recognition of PolII promoter sequences
    S Knudsen
    Center for Biological Sequence Analysis, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 15:356-61. 1999
  3. pmc GenePublisher: Automated analysis of DNA microarray data
    Steen Knudsen
    Center for Biological Sequence Analysis, BioCentrum DTU, 2800 Lyngby, Denmark
    Nucleic Acids Res 31:3471-6. 2003
  4. ncbi request reprint Neural network predicts sequence of TP53 gene based on DNA chip
    Jeppe S Spicker
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Bioinformatics 18:1133-4. 2002
  5. ncbi request reprint Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
    H Willenbrock
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Leukemia 18:1270-7. 2004
  6. ncbi request reprint Implementation of a gene expression index calculation method based on the PDNN model
    Henrik Bjørn Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU Technical University of Denmark Building 208, DK 2800 Lyngby, Denmark
    Bioinformatics 21:687-8. 2005
  7. pmc Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Henrik Bjørn Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Nucleic Acids Res 31:3491-6. 2003
  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 New weakly expressed cell cycle-regulated genes in yeast
    Ulrik de Lichtenberg
    Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Yeast 22:1191-201. 2005
  10. 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

Publications19

  1. pmc Alternative mapping of probes to genes for Affymetrix chips
    Laurent Gautier
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 5:111. 2004
    ..However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available...
  2. ncbi request reprint Promoter2.0: for the recognition of PolII promoter sequences
    S Knudsen
    Center for Biological Sequence Analysis, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 15:356-61. 1999
    ..Through the use of genetic algorithms, the weights in the neural networks are optimized to discriminate maximally between promoters and non-promoters...
  3. pmc GenePublisher: Automated analysis of DNA microarray data
    Steen Knudsen
    Center for Biological Sequence Analysis, BioCentrum DTU, 2800 Lyngby, Denmark
    Nucleic Acids Res 31:3471-6. 2003
    ..The results of the entire analysis are summarized in report form and returned to the user...
  4. ncbi request reprint Neural network predicts sequence of TP53 gene based on DNA chip
    Jeppe S Spicker
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Bioinformatics 18:1133-4. 2002
    ....
  5. ncbi request reprint Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
    H Willenbrock
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Leukemia 18:1270-7. 2004
    ..Further studies should focus on prediction of MRD, as this prediction would relate strongly to long-term outcome and could thus determine the intensity of induction therapy...
  6. ncbi request reprint Implementation of a gene expression index calculation method based on the PDNN model
    Henrik Bjørn Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU Technical University of Denmark Building 208, DK 2800 Lyngby, Denmark
    Bioinformatics 21:687-8. 2005
    ..2003). Here we describe an open source implementation of the PDNN method for the statistical language R...
  7. pmc Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Henrik Bjørn Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Nucleic Acids Res 31:3491-6. 2003
    ..Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/...
  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 New weakly expressed cell cycle-regulated genes in yeast
    Ulrik de Lichtenberg
    Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Yeast 22:1191-201. 2005
    ..Several of the gene products are believed to be phosphorylated by Cdc28. For many of these new genes, homologues exist in Schizosaccharomyces pombe and Homo sapiens for which the expression also varies with cell cycle progression...
  10. 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...
  11. ncbi request reprint Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
    H B Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 18:321-2. 2002
    ..The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end...
  12. pmc Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering
    Christoffer Bro
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 71:6465-72. 2005
    ..This conclusion was supported by measurements of sugar phosphates, which showed that there were increased concentrations of glucose-6-phosphate, galactose-6-phosphate, and fructose-6-phosphate in the strain construct overexpressing PGM2...
  13. ncbi request reprint Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions
    Hanne Jarmer
    BioCentrum DTU, Technical University of Denmark, Lyngby
    FEMS Microbiol Lett 206:197-200. 2002
    ..Based on these observations we propose a simplification of previously designed one-step transformation procedures for B. subtilis strain 168...
  14. ncbi request reprint The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing
    Kim Theilgaard-Monch
    The Granulocyte Research Laboratory, Department of Hematology 9322, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK 2100 Copenhagen, Denmark
    J Immunol 172:7684-93. 2004
    ..These findings demonstrate that migration of PMNs to skin lesions induces a transcriptional activation program, which regulates cellular fate and function, and promotes wound healing...
  15. pmc A new non-linear normalization method for reducing variability in DNA microarray experiments
    Christopher Workman
    Genedata AG, Basel, Switzerland
    Genome Biol 3:research0048. 2002
    ..Current normalization techniques are most often linear and therefore not capable of fully correcting for these effects...
  16. ncbi request reprint Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae
    Matthew D W Piper
    Kluyver Laboratory of Biotechnology, Technical University of Delft, Julianalaan 26, Delft 2628BC, The Netherlands
    J Biol Chem 277:37001-8. 2002
    ....
  17. ncbi request reprint Classification of Dukes' B and C colorectal cancers using expression arrays
    Casper Møller Frederiksen
    Dept of Clinical Biochemistry, Aarhus University Hospital, 8200, Skejby, Aarhus N, Denmark
    J Cancer Res Clin Oncol 129:263-71. 2003
    ..Classification of substages based on DNA microarray technology is currently the most promising approach. We therefore investigated if gene expression microarrays could be used to classify colorectal tumors...
  18. ncbi request reprint Identification of novel genes regulated in the developing human ventral mesencephalon
    Jesper Roland Jørgensen
    NsGene A S, Baltorpvej 154, DK 2750 Ballerup, Denmark
    Exp Neurol 198:427-37. 2006
    ..The data presented here may help to device cell replacement and regenerative therapies for Parkinson's disease (PD)...
  19. ncbi request reprint Reduced expression of nuclear-encoded genes involved in mitochondrial oxidative metabolism in skeletal muscle of insulin-resistant women with polycystic ovary syndrome
    Vibe Skov
    Department of Biochemistry, Genetics, and Pharmacology, Odense University Hospital and Human Microarray Centre, University of Southern Denmark, Odense, Denmark
    Diabetes 56:2349-55. 2007
    ..These abnormalities may contribute to the increased risk of type 2 diabetes observed in women with PCOS...