Pål Sætrom

Summary

Affiliation: Norwegian University of Science and Technology
Country: Norway

Publications

  1. pmc Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
    Javier Pena-Diaz
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491 Trondheim, Norway
    Nucleic Acids Res 41:2846-56. 2013
  2. pmc A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS ONE 6:e18430. 2011
  3. pmc Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation
    Laurent F Thomas
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS Comput Biol 8:e1002621. 2012
  4. doi request reprint Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and microRNA-like targeting
    Pål Sætrom
    Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway
    Methods Mol Biol 942:169-77. 2013
  5. pmc Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments
    Takaya Saito
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Prinsesse Kristinsgt, 1, NO 7491 Trondheim, Norway
    Silence 3:3. 2012
  6. pmc Cell-type specificity of ChIP-predicted transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491, Trondheim, Norway
    BMC Genomics 13:372. 2012
  7. pmc Inferring causative variants in microRNA target sites
    Laurent F Thomas
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    Nucleic Acids Res 39:e109. 2011
  8. pmc Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Biol 9:80. 2011
  9. pmc A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
    Morten Beck Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    Nucleic Acids Res 39:e25. 2011
  10. doi request reprint Multiple microRNAs may regulate the DNA repair enzyme uracil-DNA glycosylase
    Siv A Hegre
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    DNA Repair (Amst) 12:80-6. 2013

Collaborators

Detail Information

Publications13

  1. pmc Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
    Javier Pena-Diaz
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491 Trondheim, Norway
    Nucleic Acids Res 41:2846-56. 2013
    ..We also find similar patterns in foreskin fibroblasts, indicating that replication-dependent expression of Polycomb-silenced genes is a prevalent but unrecognized regulatory mechanism...
  2. pmc A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS ONE 6:e18430. 2011
    ..Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial...
  3. pmc Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation
    Laurent F Thomas
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS Comput Biol 8:e1002621. 2012
    ..Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease...
  4. doi request reprint Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and microRNA-like targeting
    Pål Sætrom
    Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway
    Methods Mol Biol 942:169-77. 2013
    ..The procedure can be used to create siRNAs that robustly target pairs of genes...
  5. pmc Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments
    Takaya Saito
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Prinsesse Kristinsgt, 1, NO 7491 Trondheim, Norway
    Silence 3:3. 2012
    ..abstract:..
  6. pmc Cell-type specificity of ChIP-predicted transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491, Trondheim, Norway
    BMC Genomics 13:372. 2012
    ..But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding?..
  7. pmc Inferring causative variants in microRNA target sites
    Laurent F Thomas
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    Nucleic Acids Res 39:e109. 2011
    ..A database of predicted SNP effects is available at http://www.bigr.medisin.ntnu.no/mirsnpscore/. The database is based on haplotype data from the CEU HapMap population and miRNAs from miRBase 16.0...
  8. pmc Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Biol 9:80. 2011
    ....
  9. pmc A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
    Morten Beck Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    Nucleic Acids Res 39:e25. 2011
    ..Our results showed that ChIP-seq peaks should be narrowed down to 100-400 bp, which is sufficient to identify unique peaks and binding sites. Based on these results, we propose a meta-approach that gives improved peak definitions...
  10. doi request reprint Multiple microRNAs may regulate the DNA repair enzyme uracil-DNA glycosylase
    Siv A Hegre
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    DNA Repair (Amst) 12:80-6. 2013
    ..Down-regulation was dependent on the 3'UTR, indicating that the miRNAs directly target the conserved seed sites in the 3'UTR. These results add miRNAs as a new modality to UNG's increasing list of complex regulatory mechanisms...
  11. pmc The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences
    Sabry Razick
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Prinsesse Kristinasgt 1, NO 7491 Trondheim, Norway and Department of Computer and Information Science, Norwegian University of Science and Technology, Sem Sælands vei 9, NO 7491 Trondheim, Norway
    Database (Oxford) 2014:bau027. 2014
    ..Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/...
  12. pmc A two-step site and mRNA-level model for predicting microRNA targets
    Takaya Saito
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    BMC Bioinformatics 11:612. 2010
    ..To address this possible fault, we developed a miRNA target prediction model that recognizes the individual characteristics of functional binding sites and the global characteristics of miRNA-targeted mRNAs...
  13. ncbi request reprint Error-free versus mutagenic processing of genomic uracil-Relevance to cancer
    Hans E Krokan
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway Electronic address
    DNA Repair (Amst) 19:38-47. 2014
    ..In conclusion, genomic uracil is an essential intermediate in adaptive immunity and innate antiviral responses, but may also be a fundamental cause of a wide range of malignancies. ..