John Mattick

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. pmc Clusters of internally primed transcripts reveal novel long noncoding RNAs
    Masaaki Furuno
    Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America
    PLoS Genet 2:e37. 2006
  2. pmc Non-coding RNAs in the nervous system
    Mark F Mehler
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    J Physiol 575:333-41. 2006
  3. pmc Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data
    Chol hee Jung
    Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    BMC Genomics 11:77. 2010
  4. pmc Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
    Esteban Marcellin
    Australian Institute for Bioengineering and Nanotechnology AIBN, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Genomics 14:15. 2013
  5. pmc The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization
    Ryan J Taft
    Department of Molecular and Experimental Medicine, The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Epigenetics Chromatin 4:13. 2011
  6. pmc Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
    Tim R Mercer
    Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
    BMC Neurosci 11:14. 2010
  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. pmc A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
    Alessandro Guffanti
    Institute of Biomedical Technologies, National Research Council, Milan, Italy
    BMC Genomics 10:163. 2009
  9. pmc Maintenance of transposon-free regions throughout vertebrate evolution
    Cas Simons
    Australian Research Council Special Research Center for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    BMC Genomics 8:470. 2007
  10. pmc GONOME: measuring correlations between GO terms and genomic positions
    Stefan M Stanley
    Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
    BMC Bioinformatics 7:94. 2006

Detail Information

Publications86

  1. pmc Clusters of internally primed transcripts reveal novel long noncoding RNAs
    Masaaki Furuno
    Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America
    PLoS Genet 2:e37. 2006
    ..Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like Xist and Air...
  2. pmc Non-coding RNAs in the nervous system
    Mark F Mehler
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    J Physiol 575:333-41. 2006
    ..Non-coding RNAs may provide the key to understanding the multi-tiered links between neural development, nervous system function, and neurological diseases...
  3. pmc Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data
    Chol hee Jung
    Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    BMC Genomics 11:77. 2010
    ..We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences...
  4. pmc Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
    Esteban Marcellin
    Australian Institute for Bioengineering and Nanotechnology AIBN, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Genomics 14:15. 2013
    ..Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes...
  5. pmc The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization
    Ryan J Taft
    Department of Molecular and Experimental Medicine, The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Epigenetics Chromatin 4:13. 2011
    ..abstract:..
  6. pmc Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
    Tim R Mercer
    Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
    BMC Neurosci 11:14. 2010
    ..Long non-protein-coding RNAs (ncRNAs) are emerging as important regulators of cellular differentiation and are widely expressed in the brain...
  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. pmc A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
    Alessandro Guffanti
    Institute of Biomedical Technologies, National Research Council, Milan, Italy
    BMC Genomics 10:163. 2009
    ..This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts...
  9. pmc Maintenance of transposon-free regions throughout vertebrate evolution
    Cas Simons
    Australian Research Council Special Research Center for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    BMC Genomics 8:470. 2007
    ..These regions are significantly associated with loci involved in developmental and transcriptional regulation...
  10. pmc GONOME: measuring correlations between GO terms and genomic positions
    Stefan M Stanley
    Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
    BMC Bioinformatics 7:94. 2006
    ..However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions...
  11. ncbi request reprint RNA regulation: a new genetics?
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nat Rev Genet 5:316-23. 2004
  12. ncbi request reprint Mathematics/computation. Accelerating networks
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Science 307:856-8. 2005
  13. doi request reprint Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms
    John S Mattick
    Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
    Ann N Y Acad Sci 1178:29-46. 2009
    ..Moreover, the observations that RNA-directed epigenetic changes can be inherited raises the intriguing question: has evolution learnt how to learn?..
  14. ncbi request reprint Small regulatory RNAs in mammals
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Hum Mol Genet 14:R121-32. 2005
    ....
  15. ncbi request reprint The functional genomics of noncoding RNA
    John S Mattick
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Science 309:1527-8. 2005
    ..It appears likely that ncRNAs constitute a critical hidden layer of gene regulation in complex organisms, the understanding of which requires new approaches in functional genomics...
  16. ncbi request reprint A new paradigm for developmental biology
    John S Mattick
    ARC Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    J Exp Biol 210:1526-47. 2007
    ....
  17. ncbi request reprint Non-coding RNA
    John S Mattick
    Australian Research Council Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Hum Mol Genet 15:R17-29. 2006
    ..RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species...
  18. doi request reprint RNAs as extracellular signaling molecules
    Marcel E Dinger
    Institute for Molecular Bioscience, ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072, Australia
    J Mol Endocrinol 40:151-9. 2008
    ..As such, RNA signaling may play a central but previously hidden role in multicellular ontogeny, homeostasis, and transmitted epigenetic memory...
  19. ncbi request reprint Profile of the Institute for Molecular Bioscience, University of Queensland
    John Mattick
    Institute for Molecular Bioscience and Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Australia
    Int J Dev Biol 46:357-9. 2002
  20. ncbi request reprint Type IV pili and twitching motility
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Annu Rev Microbiol 56:289-314. 2002
    ..Twitching motility is also controlled by a range of signal transduction systems, including two-component sensor-regulators and a complex chemosensory system...
  21. doi request reprint 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...
  22. pmc The genetic signatures of noncoding RNAs
    John S Mattick
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    PLoS Genet 5:e1000459. 2009
    ..There is every possibility that many of these variations will alter the interactions between regulatory RNAs and their targets, a prospect that should be borne in mind in future functional analyses...
  23. ncbi request reprint The central role of RNA in the genetic programming of complex organisms
    John S Mattick
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    An Acad Bras Cienc 82:933-9. 2010
    ..Moreover, many RNAs are edited, especially in the nervous system, which may be the basis of epigenome-environment interactions and the function of the brain...
  24. pmc Non-coding RNAs: the architects of eukaryotic complexity
    J S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
    EMBO Rep 2:986-91. 2001
    ..This system has interesting and perhaps informative analogies with small world networks and dataflow computing...
  25. ncbi request reprint The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms
    J S Mattick
    Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Mol Biol Evol 18:1611-30. 2001
    ....
  26. ncbi request reprint The human genome and the future of medicine
    John S Mattick
    Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Med J Aust 179:212-6. 2003
    ....
  27. ncbi request reprint Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Bioessays 25:930-9. 2003
    ..This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoietic development and phenotypic variation...
  28. doi request reprint The central role of RNA in human development and cognition
    John S Mattick
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    FEBS Lett 585:1600-16. 2011
    ..Thus, it appears that what was dismissed as 'junk' because it was not understood holds the key to understanding human evolution, development, and cognition...
  29. doi request reprint 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...
  30. ncbi request reprint The hidden genetic program of complex organisms
    John S Mattick
    University of Queensland, Institute for Molecular Bioscience
    Sci Am 291:60-7. 2004
  31. pmc Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome
    Khairina Tajul-Arifin
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
    Genome Res 13:1416-29. 2003
    ..The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family...
  32. pmc Specific expression of long noncoding RNAs in the mouse brain
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Proc Natl Acad Sci U S A 105:716-21. 2008
    ..Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs...
  33. ncbi request reprint The relationship between non-protein-coding DNA and eukaryotic complexity
    Ryan J Taft
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    Bioessays 29:288-99. 2007
    ..We suggest that the informational paradox in complex organisms may be explained by the expansion of cis-acting regulatory elements and genes specifying trans-acting non-protein-coding RNAs...
  34. ncbi request reprint Evidence for control of splicing by alternative RNA secondary structures in Dipteran homothorax pre-mRNA
    Evgeny A Glazov
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    RNA Biol 3:36-9. 2006
    ....
  35. ncbi request reprint Raising the estimate of functional human sequences
    Michael Pheasant
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
    Genome Res 17:1245-53. 2007
    ..Thus, it is likely that much more than 5% of the genome encodes functional information, and although the upper bound is unknown, it may be considerably higher than currently thought...
  36. ncbi request reprint Isolation and characterization of a new nucleolar protein, Nrap, that is conserved from yeast to humans
    Budi Utama
    Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Genes Cells 7:115-32. 2002
    ..The nucleolus is the site of rRNA synthesis and processing in eukaryotic cells, but its composition remains poorly understood...
  37. doi request reprint Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans
    Ryan J Taft
    Institute for Molecular Bioscience, School of Integrative Biology, University of Queensland, St Lucia, Australia
    Nat Struct Mol Biol 17:1030-4. 2010
    ..We propose that nuclear-localized tiny RNAs are involved in the epigenetic regulation of gene expression...
  38. doi request reprint A global view of genomic information--moving beyond the gene and the master regulator
    John S Mattick
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072 QLD, Australia
    Trends Genet 26:21-8. 2010
    ....
  39. ncbi request reprint Prediction of protein solvent accessibility using support vector machines
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Special Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, Australia
    Proteins 48:566-70. 2002
    ..In addition, our results further suggest that this system may be combined with other prediction methods to achieve more reliable results, and that the Support Vector Machine method is a very useful tool for biological sequence analysis...
  40. doi request reprint 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
    ....
  41. ncbi request reprint SVMtm: support vector machines to predict transmembrane segments
    Zheng Yuan
    ARC Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, Australia
    J Comput Chem 25:632-6. 2004
    ..This method can be used to complement current transmembrane helix prediction methods and can be used for consensus analysis of entire proteomes. The predictor is located at http://genet.imb.uq.edu.au/predictors/SVMtm...
  42. doi request reprint 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
    ....
  43. pmc Differentiating protein-coding and noncoding RNA: challenges and ambiguities
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    PLoS Comput Biol 4:e1000176. 2008
    ..Therefore, the functionality of any transcript at the RNA level should not be discounted...
  44. doi request reprint Multiple evolutionary rate classes in animal genome evolution
    Christopher Oldmeadow
    School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
    Mol Biol Evol 27:942-53. 2010
    ....
  45. ncbi request reprint Evolution, biogenesis and function of promoter-associated RNAs
    Ryan J Taft
    Institute for Molecular Bioscience, The University of Queensland, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
    Cell Cycle 8:2332-8. 2009
    ..elegans. We suggest that tiRNAs may be intimately connected RNAPII backtracking, nucleosome marking, and gene regulation...
  46. ncbi request reprint Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Trends Genet 22:1-5. 2006
    ..Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function...
  47. doi request reprint Delineating slowly and rapidly evolving fractions of the Drosophila genome
    Jonathan M Keith
    School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
    J Comput Biol 15:407-30. 2008
    ..Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format...
  48. doi request reprint Noncoding RNAs in Long-Term Memory Formation
    Tim R Mercer
    Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia
    Neuroscientist 14:434-45. 2008
    ..Taken together, the emerging evidence suggests a central role for ncRNAs in memory formation and provokes novel research directions in this field...
  49. doi request reprint Non-coding RNAs: regulators of disease
    Ryan J Taft
    Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    J Pathol 220:126-39. 2010
    ....
  50. doi request reprint Genome-wide identification of long noncoding RNAs in CD8+ T cells
    Ken C Pang
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    J Immunol 182:7738-48. 2009
    ..Taken together, our findings represent the first systematic discovery of long ncRNAs expressed in CD8(+) T cells and suggest that many of these transcripts are likely to play a role in adaptive immunity...
  51. pmc tonB3 is required for normal twitching motility and extracellular assembly of type IV pili
    Bixing Huang
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    J Bacteriol 186:4387-9. 2004
    ..Three mutants with Tn5-B21 insertion in tonB3 (PA0406) of Pseudomonas aeruginosa exhibited defective twitching motility and reduced assembly of extracellular pili. These defects could be complemented with wild-type tonB3...
  52. ncbi request reprint Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
    Stuart Stephen
    ARC Special Research Centre for Functional and Applied Genomics and ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    Mol Biol Evol 25:402-8. 2008
    ..These elements are different from other conserved noncoding elements and appear to be important regulatory innovations that became fixed following the emergence of vertebrates from the sea to the land...
  53. doi request reprint Long non-coding RNAs: insights into functions
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nat Rev Genet 10:155-9. 2009
    ..We also consider the medical implications, and the emerging recognition that any transcript, regardless of coding potential, can have an intrinsic function as an RNA...
  54. pmc Transposon-free regions in mammalian genomes
    Cas Simons
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Genome Res 16:164-72. 2006
    ....
  55. pmc Small RNAs derived from snoRNAs
    Ryan J Taft
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    RNA 15:1233-40. 2009
    ..These findings indicate that there is interplay between the RNA silencing and snoRNA-mediated RNA processing systems, and that sdRNAs comprise a novel and ancient class of small RNAs in eukaryotes...
  56. pmc Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
    Timothy Ravasi
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Genome Res 16:11-9. 2006
    ..Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome...
  57. ncbi request reprint Characterization of a complex chemosensory signal transduction system which controls twitching motility in Pseudomonas aeruginosa
    Cynthia B Whitchurch
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Mol Microbiol 52:873-93. 2004
    ..The Chp system is also required for full virulence in a mouse model of acute pneumonia...
  58. doi request reprint Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs
    Chol hee Jung
    Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD, Australia
    Genomics 96:154-66. 2010
    ..This work reports the existence of Drosophila genus-specific sequence motifs, and suggests that many more novel functional elements may be discovered in genomes using the general approach outlined herein...
  59. pmc Phosphorylation of the Pseudomonas aeruginosa response regulator AlgR is essential for type IV fimbria-mediated twitching motility
    Cynthia B Whitchurch
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
    J Bacteriol 184:4544-54. 2002
    ..aeruginosa...
  60. pmc Effect of site-specific mutations in different phosphotransfer domains of the chemosensory protein ChpA on Pseudomonas aeruginosa motility
    Andrew J Leech
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    J Bacteriol 188:8479-86. 2006
    ..aeruginosa motility that are not evident from the conventional twitching stab assay. Together, these results suggest that ChpA plays a central role in the complex regulation of type IV pilus-mediated motility in P. aeruginosa...
  61. doi request reprint Molecular evolution of the HBII-52 snoRNA cluster
    Satu Nahkuri
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
    J Mol Biol 381:810-5. 2008
    ..By analysing these snoRNAs in marsupial and eutherian mammal genomes, we reconstruct the likely evolutionary history of the HBII-52 cluster and SNORD119 and suggest that they have evolved from a common ancestor...
  62. 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...
  63. pmc Dynamic isomiR regulation in Drosophila development
    Selene L Fernandez-Valverde
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
    RNA 16:1881-8. 2010
    ..This work suggests that isomiR expression is an important aspect of miRNA biology, which warrants further investigation...
  64. pmc FimX, a multidomain protein connecting environmental signals to twitching motility in Pseudomonas aeruginosa
    Bixing Huang
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    J Bacteriol 185:7068-76. 2003
    ..These data suggest that fimX is involved in the regulation of twitching motility in response to environmental cues...
  65. doi request reprint RNA editing, DNA recoding and the evolution of human cognition
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Trends Neurosci 31:227-33. 2008
    ....
  66. pmc RNAdb--a comprehensive mammalian noncoding RNA database
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nucleic Acids Res 33:D125-30. 2005
    ..The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation...
  67. ncbi request reprint Nucleosomes are preferentially positioned at exons in somatic and sperm cells
    Satu Nahkuri
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
    Cell Cycle 8:3420-4. 2009
    ..These findings show that the location of exons is recorded in the chromatin structure and may be inherited across generations. Such embedded information may underpin transcriptionally coupled exon recognition and splice site selection...
  68. pmc Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    Evgeny A Glazov
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Genome Res 15:800-8. 2005
    ....
  69. 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...
  70. pmc Differential regulation of twitching motility and elastase production by Vfr in Pseudomonas aeruginosa
    Scott A Beatson
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    J Bacteriol 184:3605-13. 2002
    ..We suggest that Vfr controls twitching motility and quorum sensing via independent pathways in response to these different signals, bound by the same cyclic nucleotide monophosphate-binding pocket...
  71. pmc NRED: a database of long noncoding RNA expression
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nucleic Acids Res 37:D122-6. 2009
    ..Taken together, NRED should significantly advance the study and understanding of long ncRNAs, and provides a timely and valuable resource to the scientific community...
  72. pmc RNAdb 2.0--an expanded database of mammalian non-coding RNAs
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nucleic Acids Res 35:D178-82. 2007
    ..To access RNAdb, visit http://research.imb.uq.edu.au/RNAdb...
  73. doi request reprint 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...
  74. pmc RNA: Networks & Imaging
    Marc Kenzelmann
    Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
    Mol Syst Biol 2:44. 2006
    ....
  75. ncbi request reprint Splicing bypasses 3' end formation signals to allow complex gene architectures
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Gene 403:188-93. 2007
    ..This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes...
  76. ncbi request reprint Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
    ....
  77. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  78. ncbi request reprint Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  79. pmc Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse
    Igor V Makunin
    Australian Research Council ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    PLoS ONE 2:e1133. 2007
    ..MicroRNAs (miRNAs) are short non-coding RNAs that regulate differentiation and development in many organisms and play an important role in cancer...
  80. pmc Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
    Neil F W Saunders
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    Genome Res 13:1580-8. 2003
    ..This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles...
  81. ncbi request reprint Macropodid herpesvirus 1 encodes genes for both thymidylate synthase and ICP34.5
    Sandeep Guliani
    Queensland Agricultural Biotechnology Centre, Gehrmann Laboratories, St Lucia, Brisbane, Australia
    Virus Genes 24:207-13. 2002
    ..5, identifying it as the MaHV-1 ICP34.5 homologue. This is the first report of a herpesvirus that encodes for both TS and ICP34.5...
  82. ncbi request reprint Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease
    Mark F Mehler
    Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Physiol Rev 87:799-823. 2007
    ....
  83. ncbi request reprint Proteome analysis of extracellular proteins regulated by the las and rhl quorum sensing systems in Pseudomonas aeruginosa PAO1
    Amanda S Nouwens
    Australian Proteome Analysis Facility, Level 4, Building F7B, Macquarie University, Australia 2109
    Microbiology 149:1311-22. 2003
    ..Known QS-regulated extracellular proteins, including elastase (lasB), LasA protease (lasA) and alkaline metalloproteinase (aprA) were also detected...
  84. pmc Pseudomonas aeruginosa fimL regulates multiple virulence functions by intersecting with Vfr-modulated pathways
    Cynthia B Whitchurch
    Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
    Mol Microbiol 55:1357-78. 2005
    ..Our studies indicate that Vfr and FimL are components of intersecting pathways that control twitching motility, TTSS and autolysis in P. aeruginosa...
  85. ncbi request reprint The amazing complexity of the human transcriptome
    Martin C Frith
    Eur J Hum Genet 13:894-7. 2005
  86. pmc Quorum sensing is not required for twitching motility in Pseudomonas aeruginosa
    Scott A Beatson
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    J Bacteriol 184:3598-604. 2002
    ..This problem may have compromised some past studies of regulatory hierarchies controlled by quorum sensing and of bacterial regulatory systems in general...