Paulo P Amaral

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. pmc Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Genome Res 18:1433-45. 2008
  2. doi Noncoding RNA in development
    Paulo P Amaral
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Mamm Genome 19:454-92. 2008
  3. doi Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
    Dennis K Gascoigne
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
    Bioinformatics 28:3042-50. 2012
  4. doi RNA regulation of epigenetic processes
    John S Mattick
    Australian Research Council Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
    Bioessays 31:51-9. 2009
  5. doi Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications
    Marcel E Dinger
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Brief Funct Genomic Proteomic 8:407-23. 2009
  6. pmc Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
    Paulo P Amaral
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    RNA 15:2013-27. 2009
  7. doi The eukaryotic genome as an RNA machine
    Paulo P Amaral
    Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Science 319:1787-9. 2008
  8. pmc lncRNAdb: a reference database for long noncoding RNAs
    Paulo P Amaral
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Nucleic Acids Res 39:D146-51. 2011
  9. pmc The reality of pervasive transcription
    Michael B Clark
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    PLoS Biol 9:e1000625. 2011

Detail Information

Publications9

  1. pmc Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Genome Res 18:1433-45. 2008
    ..Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery...
  2. doi Noncoding RNA in development
    Paulo P Amaral
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Mamm Genome 19:454-92. 2008
    ....
  3. doi Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
    Dennis K Gascoigne
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
    Bioinformatics 28:3042-50. 2012
    ..We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets...
  4. doi RNA regulation of epigenetic processes
    John S Mattick
    Australian Research Council Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
    Bioessays 31:51-9. 2009
    ..Moreover, RNA-directed regulatory processes may also transfer epigenetic information not only within cells but also between cells and organ systems, as well as across generations...
  5. doi Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications
    Marcel E Dinger
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Brief Funct Genomic Proteomic 8:407-23. 2009
    ....
  6. pmc Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
    Paulo P Amaral
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    RNA 15:2013-27. 2009
    ..These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development...
  7. doi The eukaryotic genome as an RNA machine
    Paulo P Amaral
    Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Science 319:1787-9. 2008
    ..In parallel, it is increasingly evident that many of these RNAs have regulatory functions. Here, we highlight recent advances that illustrate the diversity of ncRNA control of genome dynamics, cell biology, and developmental programming...
  8. pmc lncRNAdb: a reference database for long noncoding RNAs
    Paulo P Amaral
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Nucleic Acids Res 39:D146-51. 2011
    ..lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/...
  9. pmc The reality of pervasive transcription
    Michael B Clark
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    PLoS Biol 9:e1000625. 2011
    ..Despite recent controversies, the evidence that the majority of the human genome is transcribed into RNA remains strong...