Pål Sætrom

Summary

Affiliation: Norwegian University of Science and Technology
Country: Norway

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. doi request reprint AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature
    Henrik Sahlin Pettersen
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491 Trondheim, Norway Liaison Committee between the Central Norway Regional Health Authority RHA and the Norwegian University of Science and Technology NTNU, Trondheim, Norway St Olav s Hospital, Trondheim University Hospital, NO 7006 Trondheim, Norway
    DNA Repair (Amst) 25:60-71. 2015
  9. 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
  10. 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

Collaborators

Detail Information

Publications15

  1. 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...
  2. 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:..
  3. 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?..
  4. 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...
  5. 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...
  6. 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
    ....
  7. 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...
  8. doi request reprint AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature
    Henrik Sahlin Pettersen
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491 Trondheim, Norway Liaison Committee between the Central Norway Regional Health Authority RHA and the Norwegian University of Science and Technology NTNU, Trondheim, Norway St Olav s Hospital, Trondheim University Hospital, NO 7006 Trondheim, Norway
    DNA Repair (Amst) 25:60-71. 2015
    ..In conclusion, AID-induced mutagenic U:G mismatches in DNA may be a fundamental and common cause of mutations in B-cell malignancies. ..
  9. 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...
  10. 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/...
  11. 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...
  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. pmc Circular RNAs are depleted of polymorphisms at microRNA binding sites
    Laurent F Thomas
    Department of Cancer Research and Molecular Medicine and Department of Computer and Information Science, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    Bioinformatics 30:2243-6. 2014
    ..As it is unclear whether these thousands of predicted miRNA binding sites are functional, we investigated whether miRNA seed sites within human circRNAs are under selective pressure...
  14. 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...
  15. doi 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. ..