A Reverter

Summary

Country: Australia

Publications

  1. doi request reprint Breeding and Genetics Symposium: building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies
    A Reverter
    CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, Brisbane, QLD 4067, Australia
    J Anim Sci 91:530-6. 2013
  2. pmc A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer
    Shivashankar H Nagaraj
    Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation, Division of Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, Brisbane, Queensland 4067, Australia
    BMC Syst Biol 5:35. 2011
  3. pmc Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle
    Ashley J Waardenberg
    CSIRO, Food Futures Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, QLD 4067, Australia
    BMC Syst Biol 2:88. 2008
  4. pmc Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle
    Quan Gu
    Computational and Systems Biology, CSIRO Food Futures Flagship and CSIRO Livestock Industries, 306 Carmody Rd, St Lucia, Brisbane, Queensland 4067, Australia
    BMC Genomics 12:23. 2011
  5. pmc Construction and validation of a Bovine Innate Immune Microarray
    Laurelea Donaldson
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia 4067, QLD, Australia
    BMC Genomics 6:135. 2005
  6. pmc Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds
    Sigrid A Lehnert
    Cooperative Research Centre for Cattle and Beef Quality, Australia
    BMC Dev Biol 7:95. 2007
  7. doi request reprint Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data
    Antonio Reverter
    Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Brisbane, Queensland 4067, Australia
    Bioinformatics 26:896-904. 2010
  8. doi request reprint Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
    Antonio Reverter
    CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, Brisbane, Queensland 4067, Australia
    Bioinformatics 24:2491-7. 2008
  9. ncbi request reprint A gene coexpression network for bovine skeletal muscle inferred from microarray data
    Antonio Reverter
    Bioinformatics Group, Commonwealth Scientific and Industrial Research Organisation Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Physiol Genomics 28:76-83. 2006
  10. ncbi request reprint Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
    Antonio Reverter
    CSIRO Livestock Industries, Queensland Bioscience Precinct 306 Carmody Road, Brisbane, Queensland 4067, Australia
    Bioinformatics 22:2396-404. 2006

Collaborators

Detail Information

Publications43

  1. doi request reprint Breeding and Genetics Symposium: building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies
    A Reverter
    CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, Brisbane, QLD 4067, Australia
    J Anim Sci 91:530-6. 2013
    ..We argue that these new approaches are holistic and therefore more appropriate than traditional approaches for investigating genetic mechanisms underlying complex phenotypes of importance in livestock species...
  2. pmc A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer
    Shivashankar H Nagaraj
    Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation, Division of Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, Brisbane, Queensland 4067, Australia
    BMC Syst Biol 5:35. 2011
    ..We introduce a systems biology approach to study cancer that formally integrates the available genetic, transcriptomic, epigenetic and molecular knowledge on cancer biology and, as a proof of concept, we apply it to colorectal cancer...
  3. pmc Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle
    Ashley J Waardenberg
    CSIRO, Food Futures Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, QLD 4067, Australia
    BMC Syst Biol 2:88. 2008
    ....
  4. pmc Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle
    Quan Gu
    Computational and Systems Biology, CSIRO Food Futures Flagship and CSIRO Livestock Industries, 306 Carmody Rd, St Lucia, Brisbane, Queensland 4067, Australia
    BMC Genomics 12:23. 2011
    ..To better understand how the genetic code controls gene expression in bovine muscle we associated gene expression data from developing Longissimus thoracis et lumborum skeletal muscle with bovine promoter sequence information...
  5. pmc Construction and validation of a Bovine Innate Immune Microarray
    Laurelea Donaldson
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia 4067, QLD, Australia
    BMC Genomics 6:135. 2005
    ..This knowledge may allow the development of strategies that exploit these genes to enhance resistance to disease in an individual or animal population...
  6. pmc Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds
    Sigrid A Lehnert
    Cooperative Research Centre for Cattle and Beef Quality, Australia
    BMC Dev Biol 7:95. 2007
    ....
  7. doi request reprint Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data
    Antonio Reverter
    Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Brisbane, Queensland 4067, Australia
    Bioinformatics 26:896-904. 2010
    ..We argue that RIF has universal applicability, and advocate its use as a promising hypotheses generating tool for the systematic identification of novel TF not yet documented as critical...
  8. doi request reprint Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
    Antonio Reverter
    CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, Brisbane, Queensland 4067, Australia
    Bioinformatics 24:2491-7. 2008
    ..The properties of PCIT are examined in the context of the topology of the reconstructed network including connectivity structure, clustering coefficient and sensitivity...
  9. ncbi request reprint A gene coexpression network for bovine skeletal muscle inferred from microarray data
    Antonio Reverter
    Bioinformatics Group, Commonwealth Scientific and Industrial Research Organisation Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Physiol Genomics 28:76-83. 2006
    ..Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle...
  10. ncbi request reprint Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
    Antonio Reverter
    CSIRO Livestock Industries, Queensland Bioscience Precinct 306 Carmody Road, Brisbane, Queensland 4067, Australia
    Bioinformatics 22:2396-404. 2006
    ..The purpose of this communication is to introduce an analytical procedure to simultaneously identify genes that are differentially expressed (DE) as well as differentially connected (DC) in two or more classes of interest...
  11. ncbi request reprint A mixture model-based cluster analysis of DNA microarray gene expression data on Brahman and Brahman composite steers fed high-, medium-, and low-quality diets
    A Reverter
    Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland 4067, Australia
    J Anim Sci 81:1900-10. 2003
    ..Results from the HIGH vs. LOW contrast identified 27 genes with a greater than 95% posterior probability of belonging to the cluster of differentially expressed genes...
  12. ncbi request reprint Validation of alternative methods of data normalization in gene co-expression studies
    Antonio Reverter
    Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
    Bioinformatics 21:1112-20. 2005
    ..We conclude that normalization methods based on mixed-model equations are optimal...
  13. ncbi request reprint Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle
    A Reverter
    The Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland 4067, Australia
    J Anim Sci 82:3430-9. 2004
    ..These results contribute to our understanding of the mechanistic processes involved in adipogenesis and nutrient partitioning...
  14. ncbi request reprint A rapid method for computationally inferring transcriptome coverage and microarray sensitivity
    A Reverter
    Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Bioinformatics 21:80-9. 2005
    ..We address the question of what level of coverage is required to exploit the sensitivity of the different technologies, and what is the sensitivity of the different approaches in the experimental study...
  15. ncbi request reprint Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction
    K A Byrne
    Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland 4067, Australia
    J Anim Sci 83:1-12. 2005
    ....
  16. ncbi request reprint Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutrition
    S A Lehnert
    Cooperative Research Centre for Cattle and Beef Quality, Australia
    J Anim Sci 84:3239-50. 2006
    ....
  17. doi request reprint Gene expression patterns during intramuscular fat development in cattle
    Y H Wang
    Commonwealth Scientific and Industrial Research Organisation CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Queensland 4067, Australia
    J Anim Sci 87:119-30. 2009
    ..In addition, the genes found to be highly expressed during development of marbling could be used to develop genetic markers or biomarkers to assist with beef production strategies...
  18. pmc A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    Nicholas J Hudson
    Food Futures Flagship and Livestock Industries, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia Brisbane, Queensland, Australia
    PLoS Comput Biol 5:e1000382. 2009
    ..In contrast to other published methods that compare co-expression networks, significance testing is not used to eliminate connections...
  19. ncbi request reprint The heritability of the expression of two stress-regulated gene fragments in pigs
    C A Kerr
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
    J Anim Sci 83:1753-65. 2005
    ..09 +/- 0.07). Estimates of heritability did not increase in the subset of low expression data. The limitations of using gene expression measures as potential selection criteria in commercial situations are discussed...
  20. ncbi request reprint Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle
    Tony Vuocolo
    Commonwealth Scientific and Industrial Research Organisation Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
    Physiol Genomics 28:253-72. 2007
    ..A model is proposed describing a core network of genes and histone epigenetic modifications that is likely to underpin the fiber type changes and muscle hypertrophy characteristic of callipyge sheep...
  21. pmc Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks
    Nicholas J Hudson
    Food Futures Flagship and Livestock Industries, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Brisbane, Queensland, Australia
    PLoS ONE 4:e7249. 2009
    ..In muscle a small number of well characterised transcription factors are proposed to regulate development. Therefore, muscle appears to be a tractable system for proposing new computational approaches...
  22. ncbi request reprint A mixed-model approach for the analysis of cDNA microarray gene expression data from extreme-performing pigs after infection with Actinobacillus pleuropneumoniae
    R J Moser
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland 4067, Australia
    J Anim Sci 82:1261-71. 2004
    ..These results provide evidence that the proposed statistical approach was useful in enhancing the knowledge of the mechanisms involved in the genetics of the immune response...
  23. doi request reprint The evolution of tropical adaptation: comparing taurine and zebu cattle
    E K F Chan
    Cooperative Research Centre for Beef Genetic Technologies CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD 4067, Australia
    Anim Genet 41:467-77. 2010
    ..We anticipate this investigation to be a stepping-stone for future studies to identify genomic regions specific to the two cattle groups, and to subsequently assist in the discrimination between temperate and tropically adapted cattle...
  24. pmc A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep
    Wendy J M Smith
    CSIRO Livestock Industries, 306 Carmody Rd, St Lucia, QLD 4067, Australia
    BMC Vet Res 6:27. 2010
    ..The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP) that were genotyped across three populations for their associations with fleece rot resistance...
  25. pmc Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle
    Maxy Mariasegaram
    CSIRO Livestock Industries, St Lucia, Queensland, Australia
    BMC Genomics 11:370. 2010
    ..This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts...
  26. pmc The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome
    Shivashankar H Nagaraj
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
    BMC Genomics 11:S23. 2010
    ....
  27. doi request reprint PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
    Nathan S Watson-Haigh
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
    Bioinformatics 26:411-3. 2010
    ..AVAILABILITY AND IMPLEMENTATION: Source code and binaries freely available (under GPL-3) for download via CRAN at http://cran.r-project.org/package=PCIT, implemented in R and supported on Linux and MS Windows...
  28. pmc Identification of immune genes and proteins involved in the response of bovine mammary tissue to Staphylococcus aureus infection
    Ylva C Strandberg Lutzow
    Co operative Research Centre for Innovative Dairy Products, Australia
    BMC Vet Res 4:18. 2008
    ..Moreover, the effect of infection on the presence of bioactive innate immune proteins in milk is also unclear. The nature of these responses may determine the susceptibility of the tissue and its ability to resolve the infection...
  29. ncbi request reprint Gene expression profiling of porcine peripheral blood leukocytes after infection with Actinobacillus pleuropneumoniae
    Ralf J Moser
    CSIRO Livestock Industries, St Lucia 4067, Australia
    Vet Immunol Immunopathol 121:260-74. 2008
    ....
  30. ncbi request reprint Gastrointestinal nematode challenge induces some conserved gene expression changes in the gut mucosa of genetically resistant sheep
    Aaron Ingham
    CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Int J Parasitol 38:431-42. 2008
    ....
  31. ncbi request reprint Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency
    Gang Ping Xue
    CSIRO Plant Industry, 306 Carmody Road, St Lucia, QLD, 4067, Australia
    Plant Mol Biol 61:863-81. 2006
    ..These data indicate that some of these TE differentially expressed genes are candidates for investigating processes that underlie the high TE trait or for use as expression quantitative trait loci (eQTLs) for TE...
  32. ncbi request reprint Transcriptional profiling of skeletal muscle tissue from two breeds of cattle
    Yong Hong Wang
    Cooperative Research Center for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, Queensland, 4067, Australia
    Mamm Genome 16:201-10. 2005
    ..By discovering as yet uncharacterized genes that are differentially regulated in this comparison, the work may lead us to a better understanding of the regulatory pathways involved in the development of intramuscular adipose tissue...
  33. ncbi request reprint Purebred-crossbred performance and genetic evaluation of postweaning growth and carcass traits in Bos indicus x Bos taurus crosses in Australia
    S Newman
    Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, North Rockhampton, QLD, Australia
    J Anim Sci 80:1801-8. 2002
    ....
  34. pmc The combined effect of SNP-marker and phenotype attributes in genome-wide association studies
    E K F Chan
    Cooperative Research Centre for Beef Genetic Technologies, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Anim Genet 40:149-56. 2009
    ....
  35. ncbi request reprint Effects of grouping unfamiliar cohorts, high ambient temperature and stocking density on live performance of growing pigs
    C A Kerr
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
    J Anim Sci 83:908-15. 2005
    ..38 vs. 7.49 +/- 0.29 kg). In conclusion, under the conditions of this study, the grouping of unfamiliar cohorts and high ambient temperature treatments had a detrimental effect on pig performance, and these effects were reversible...
  36. ncbi request reprint Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray
    Siok Hwee Tan
    The Cooperative Research Center for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
    Funct Integr Genomics 6:235-49. 2006
    ..This analysis was able to indicate the importance of different gene categories at various stages of adipogenic conversion, thereby providing further insights into the molecular changes during bovine adipogenesis...
  37. doi request reprint Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals
    Philippa J M Jack
    CSIRO Livestock Industries, Australian Animal Health Laboratory, Private Bag 24, Geelong, Victoria 3220, Australia
    Vet Microbiol 133:145-53. 2009
    ..The results indicate that with further development this microarray assay could be a valuable tool for the diagnosis of vesicular and vesicular-like diseases...
  38. pmc A validated whole-genome association study of efficient food conversion in cattle
    W Barendse
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia 4067, Australia
    Genetics 176:1893-905. 2007
    ..Successful validation depended on the sign of the allelic association in different populations rather than on the strength of the initial association or its size of effect...
  39. doi request reprint Nematode challenge induces differential expression of oxidant, antioxidant and mucous genes down the longitudinal axis of the sheep gut
    M Menzies
    CSIRO Livestock Industries, St Lucia, QLD 4067, Australia
    Parasite Immunol 32:36-46. 2010
    ..Other aspects of the response were parasite-specific, with T. colubriformis challenge inducing expression peaks at times corresponding to nematode life-stage transitions...
  40. ncbi request reprint Potential for recombinant Babesia bovis antigens to protect against a highly virulent isolate
    M Hope
    CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Australia
    Parasite Immunol 27:439-45. 2005
    ..Control of parasites correlated with high monocyte numbers late in infection. The results thus confirm the potential usefulness of both antigens but also demonstrate the limitations of current formulations...
  41. ncbi request reprint Parasitic castration by the digenian trematode Allopodocotyle sp. alters gene expression in the brain of the host mollusc Haliotis asinina
    Tamika Rice
    School of Integrative Biology, University of Queensland, Brisbane, QLD 4072, Australia
    FEBS Lett 580:3769-74. 2006
    ..A number of the regulatory genes are differentially expressed in parasitised H. asinina, but in only a few cases do expression patterns in infected animals match those occurring in animals where reproduction is normally repressed...
  42. pmc Association weight matrix for the genetic dissection of puberty in beef cattle
    Marina R S Fortes
    Cooperative Research Centre for Beef Genetic Technologies, Queensland Bioscience Precinct, Brisbane, QLD, Australia
    Proc Natl Acad Sci U S A 107:13642-7. 2010
    ..Applied to our case, the AWM results recapitulate the known biology of puberty, captured experimentally validated binding sites, and identified candidate genes and gene-gene interactions for further investigation...
  43. ncbi request reprint Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon
    Enrique de la Vega
    Australian Institute of Marine Science, Townsville, Queensland, Australia
    Physiol Genomics 31:126-38. 2007
    ..These expression data agree with observed differences in shrimp physical appearance and behavior following exposure to stress conditions...