Rasmus Wernersson

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. ncbi request reprint Probe selection for DNA microarrays using OligoWiz
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Lyngby 2800, Denmark
    Nat Protoc 2:2677-91. 2007
  2. pmc Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
    Jan Gorodkin
    Division of Genetics and Bioinformatics, IBHV, Grønnegårdsvej 3, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
    Genome Biol 8:R45. 2007
  3. pmc Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotation
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 34:W385-8. 2006
  4. pmc OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800, Lyngby, Denmark
    Nucleic Acids Res 33:W611-5. 2005
  5. pmc FeatureExtract--extraction of sequence annotation made easy
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 33:W567-9. 2005
  6. pmc Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
    Rasmus Wernersson
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    BMC Genomics 6:70. 2005
  7. pmc Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments
    Nicholas Paul Gauthier
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 36:D854-9. 2008
  8. 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
  9. doi request reprint InterMap3D: predicting and visualizing co-evolving protein residues
    Rodrigo Gouveia-Oliveira
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 25:1963-5. 2009
  10. pmc An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
    Henrik Nielsen
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    BMC Genomics 7:256. 2006

Detail Information

Publications17

  1. ncbi request reprint Probe selection for DNA microarrays using OligoWiz
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Lyngby 2800, Denmark
    Nat Protoc 2:2677-91. 2007
    ..The protocol requires limited computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h...
  2. pmc Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
    Jan Gorodkin
    Division of Genetics and Bioinformatics, IBHV, Grønnegårdsvej 3, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
    Genome Biol 8:R45. 2007
    ..The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages...
  3. pmc Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotation
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 34:W385-8. 2006
    ..The software is available for both download and online use at http://www.cbs.dtu.dk/services/VirtualRibosome/...
  4. pmc OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800, Lyngby, Denmark
    Nucleic Acids Res 33:W611-5. 2005
    ..Furthermore, we show that probes designed using OligoWiz 2.0 give rise to consistent hybridization results (http://www.cbs.dtu.dk/services/OligoWiz2)...
  5. pmc FeatureExtract--extraction of sequence annotation made easy
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 33:W567-9. 2005
    ..The FeatureExtract web server is freely available for both academic and commercial use at http://www.cbs.dtu.dk/services/FeatureExtract/...
  6. pmc Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
    Rasmus Wernersson
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    BMC Genomics 6:70. 2005
    ..Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls...
  7. pmc Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments
    Nicholas Paul Gauthier
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 36:D854-9. 2008
    ..Cyclebase is available at http://www.cyclebase.org...
  8. 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...
  9. doi request reprint InterMap3D: predicting and visualizing co-evolving protein residues
    Rodrigo Gouveia-Oliveira
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 25:1963-5. 2009
    ..Finally, InterMap3D generates high-quality images of the protein with the predicted co-evolving residues highlighted...
  10. pmc An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
    Henrik Nielsen
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    BMC Genomics 7:256. 2006
    ..A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes...
  11. doi request reprint Probe design for expression arrays using OligoWiz
    Rasmus Wernersson
    Center for Biological Sequence Analysis, Technical University of Denmark, Kgs, Lyngby, Denmark
    Methods Mol Biol 529:23-36. 2009
    ..For an in-depth review of the entire field of probe design (including a comparison of different probe design packages) as well as instructions on how to produce special purpose arrays (e.g., splice detection arrays), please refer to (1)...
  12. pmc Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
    Aron C Eklund
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 38:e27. 2010
    ..This optimized matrix may be useful in the design of microarray probes, and in other BLASTN-based searches for hybridization partners...
  13. 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/...
  14. pmc FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 34:W84-8. 2006
    ..FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/...
  15. pmc RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    Rasmus Wernersson
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800, Lyngby, Denmark
    Nucleic Acids Res 31:3537-9. 2003
    ..RevTrans also accepts user-provided protein alignments for greater control of the alignment process. The RevTrans web server is freely available at http://www.cbs.dtu.dk/services/RevTrans/...
  16. doi request reprint The strength of intron donor splice sites in human genes displays a bell-shaped pattern
    Kai Wang
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 27:3079-84. 2011
    ..Increased understanding of the mechanisms controlling pre-mRNA splicing is thus important for a wide range of aspects relating to gene expression...
  17. pmc PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
    Lars Rønn Olsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 39:W61-7. 2011
    ..Furthermore, PHUSER offers the option to insert linkers between DNA fragments, as well as highly flexible cassette options. PHUSER is publicly available at http://www.cbs.dtu.dk/services/phuser/...