Nicole Cloonan

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. pmc MicroRNAs and their isomiRs function cooperatively to target common biological pathways
    Nicole Cloonan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
    Genome Biol 12:R126. 2011
  2. pmc RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
    Nicole Cloonan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
    Bioinformatics 25:2615-6. 2009
  3. pmc MicroRNA-182-5p targets a network of genes involved in DNA repair
    Keerthana Krishnan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
    RNA 19:230-42. 2013
  4. pmc The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition
    Nicole Cloonan
    Institute for Molecular Bioscience, The University of Queensland, Carmody Road, St Lucia, 4072, Australia
    Genome Biol 9:R127. 2008
  5. pmc Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
    Gabriel Kolle
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Queensland 4072, Australia
    Genome Res 21:2014-25. 2011
  6. doi Stem cell transcriptome profiling via massive-scale mRNA sequencing
    Nicole Cloonan
    Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
    Nat Methods 5:613-9. 2008
  7. pmc Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
    Rathi D Thiagarajan
    Institute for Molecular Bioscience, The University of Queensland, St, Lucia QLD 4072, Australia
    BMC Genomics 12:441. 2011
  8. doi The regulated retrotransposon transcriptome of mammalian cells
    Geoffrey J Faulkner
    Institute for Molecular Bioscience, University of Queensland, Australia
    Nat Genet 41:563-71. 2009
  9. pmc Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data
    David L A Wood
    Queensland Centre for Medical Genomics, University of Queensland, Brisbane, Australia
    PLoS ONE 10:e0126911. 2015
  10. doi Genomic analyses identify molecular subtypes of pancreatic cancer
    Peter Bailey
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
    Nature 531:47-52. 2016

Detail Information

Publications19

  1. pmc MicroRNAs and their isomiRs function cooperatively to target common biological pathways
    Nicole Cloonan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
    Genome Biol 12:R126. 2011
    ..Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules...
  2. pmc RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
    Nicole Cloonan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
    Bioinformatics 25:2615-6. 2009
    ..This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context...
  3. pmc MicroRNA-182-5p targets a network of genes involved in DNA repair
    Keerthana Krishnan
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
    RNA 19:230-42. 2013
    ..Finally, we show that miR-182-5p is highly expressed in a panel of human breast cancer samples, highlighting its role as a potential oncomir in breast cancer...
  4. pmc The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition
    Nicole Cloonan
    Institute for Molecular Bioscience, The University of Queensland, Carmody Road, St Lucia, 4072, Australia
    Genome Biol 9:R127. 2008
    ....
  5. pmc Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
    Gabriel Kolle
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Queensland 4072, Australia
    Genome Res 21:2014-25. 2011
    ....
  6. doi Stem cell transcriptome profiling via massive-scale mRNA sequencing
    Nicole Cloonan
    Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
    Nat Methods 5:613-9. 2008
    ....
  7. pmc Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
    Rathi D Thiagarajan
    Institute for Molecular Bioscience, The University of Queensland, St, Lucia QLD 4072, Australia
    BMC Genomics 12:441. 2011
    ..These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models...
  8. doi The regulated retrotransposon transcriptome of mammalian cells
    Geoffrey J Faulkner
    Institute for Molecular Bioscience, University of Queensland, Australia
    Nat Genet 41:563-71. 2009
    ..We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome...
  9. pmc Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data
    David L A Wood
    Queensland Centre for Medical Genomics, University of Queensland, Brisbane, Australia
    PLoS ONE 10:e0126911. 2015
    ..The methods evaluated in this study will be of use to researchers performing highly conservative quantification of ASE, and the genes and isoforms identified as ASE of interest to researchers studying those loci. ..
  10. doi Genomic analyses identify molecular subtypes of pancreatic cancer
    Peter Bailey
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
    Nature 531:47-52. 2016
    ..These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development. ..
  11. doi Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling
    Gabriel Kolle
    Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
    Stem Cells 27:2446-56. 2009
    ....
  12. pmc Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH
    Chikako Ragan
    The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia
    PLoS ONE 4:e5745. 2009
    ..These results confirm and extend the scope of miRNA-mediated species- and transcript-specific regulation in different cell types, tissues and developmental conditions...
  13. pmc Whole genomes redefine the mutational landscape of pancreatic cancer
    Nicola Waddell
    1 Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia 2 QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
    Nature 518:495-501. 2015
    ..Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. ..
  14. pmc X-MATE: a flexible system for mapping short read data
    David L A Wood
    The University of Queensland, Queensland, Australia
    Bioinformatics 27:580-1. 2011
    ....
  15. pmc Transcriptome content and dynamics at single-nucleotide resolution
    Nicole Cloonan
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    Genome Biol 9:234. 2008
    ..Massively parallel short-tag sequencing of cDNA libraries--RNAseq--is being used to study the dynamics and complexity of eukaryotic transcriptomes, giving new biological insights into the 'active genome'...
  16. pmc A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
    Michael R Tallack
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Genome Res 20:1052-63. 2010
    ..Additionally, we suggest new mechanisms for KLF1 cooperation with other transcription factors, in particular the erythroid transcription factor GATA1, to maintain homeostasis in the erythroid compartment...
  17. doi Tiny RNAs associated with transcription start sites in animals
    Ryan J Taft
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
    Nat Genet 41:572-8. 2009
    ..tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes...
  18. ncbi The clinical potential and challenges of sequencing cancer genomes for personalized medical genomics
    Nicole Cloonan
    The University of Queensland, Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, 306 Carmody Road, St Lucia, QLD 4072, Australia
    IDrugs 13:778-81. 2010
    ..This feature review explores the clinical potential and challenges of studying cancer genomes for personalized medical genomics...
  19. doi A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing
    Kelly Quek
    Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD, Australia
    Biotechniques 57:31-8. 2014
    ..Furthermore, the proposed workflow allows hundreds of events to be processed in a shorter time frame compared with the conventional workflow...