Research Topics
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Publications
A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancerShivashankar 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...- Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscleAshley J Waardenberg
CSIRO, Food Futures Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, QLD 4067, Australia
BMC Syst Biol 2:88. 2008.... - Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscleQuan 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... 
Construction and validation of a Bovine Innate Immune MicroarrayLaurelea 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...- Gene expression studies of developing bovine longissimus muscle from two different beef cattle breedsSigrid A Lehnert
Cooperative Research Centre for Cattle and Beef Quality, Australia
BMC Dev Biol 7:95. 2007.... 
Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression dataAntonio 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...- Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networksAntonio 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... 
A gene coexpression network for bovine skeletal muscle inferred from microarray dataAntonio 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...- Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancerAntonio Reverter
CSIRO Livestock Industries, Queensland Bioscience Precinct 306 Carmody Road, Brisbane, Queensland 4067, Australia
Bioinformatics 22:2396-404. 2006.... - Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattleA 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... - A mixture model-based cluster analysis of DNA microarray gene expression data on Brahman and Brahman composite steers fed high-, medium-, and low-quality dietsA 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... - Validation of alternative methods of data normalization in gene co-expression studiesAntonio 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... - A rapid method for computationally inferring transcriptome coverage and microarray sensitivityA Reverter
Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
Bioinformatics 21:80-9. 2005..In the absence of large-scale sequencing, the majority of the tags detected by the latter approaches will remain unidentified until the genome sequence is available... - Gene expression profiling of muscle tissue in Brahman steers during nutritional restrictionK 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.... - Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutritionS A Lehnert
Cooperative Research Centre for Cattle and Beef Quality, Australia
J Anim Sci 84:3239-50. 2006.... - Gene expression patterns during intramuscular fat development in cattleY 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... - A differential wiring analysis of expression data correctly identifies the gene containing the causal mutationNicholas 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... - The heritability of the expression of two stress-regulated gene fragments in pigsC 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... - Identification of a gene network contributing to hypertrophy in callipyge skeletal muscleTony 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... - Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networksNicholas 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... - A mixed-model approach for the analysis of cDNA microarray gene expression data from extreme-performing pigs after infection with Actinobacillus pleuropneumoniaeR 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... - The evolution of tropical adaptation: comparing taurine and zebu cattleE 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... - A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheepWendy 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... - Gene expression profiling of porcine peripheral blood leukocytes after infection with Actinobacillus pleuropneumoniaeRalf J Moser
CSIRO Livestock Industries, St Lucia 4067, Australia
Vet Immunol Immunopathol 121:260-74. 2008.... - The interplay between evolution, regulation and tissue specificity in the Human Hereditary DiseasomeShivashankar H Nagaraj
CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
BMC Genomics 11:S23. 2010.... - Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattleMaxy 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... - PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approachesNathan 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... - Transcriptional profiling of skeletal muscle tissue from two breeds of cattleYong 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... - Differential gene expression of wheat progeny with contrasting levels of transpiration efficiencyGang 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... - Identification of immune genes and proteins involved in the response of bovine mammary tissue to Staphylococcus aureus infectionYlva 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... - Gastrointestinal nematode challenge induces some conserved gene expression changes in the gut mucosa of genetically resistant sheepAaron Ingham
CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
Int J Parasitol 38:431-42. 2008.... - The combined effect of SNP-marker and phenotype attributes in genome-wide association studiesE 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.... - Effects of grouping unfamiliar cohorts, high ambient temperature and stocking density on live performance of growing pigsC 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... - Purebred-crossbred performance and genetic evaluation of postweaning growth and carcass traits in Bos indicus x Bos taurus crosses in AustraliaS Newman
Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, North Rockhampton, QLD, Australia
J Anim Sci 80:1801-8. 2002.... - Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarraySiok 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... - Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animalsPhilippa 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... - A validated whole-genome association study of efficient food conversion in cattleW 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... - Nematode challenge induces differential expression of oxidant, antioxidant and mucous genes down the longitudinal axis of the sheep gutM 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... - Potential for recombinant Babesia bovis antigens to protect against a highly virulent isolateM 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... - Parasitic castration by the digenian trematode Allopodocotyle sp. alters gene expression in the brain of the host mollusc Haliotis asininaTamika 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... - Association weight matrix for the genetic dissection of puberty in beef cattleMarina 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... - Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodonEnrique 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...