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Animal & Bioscience Research Papers


Animal Breeding and Genomics

Meredith B.K., Kearney F.J, Finlay E.K., Bradley D.G., Fahey A.G., Berry D.P. and Lynn D.J. (2012). Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland. BMC Genetics 13: 21.

Mullen, M.P., Creevey, C.J., McCabe, M.J., Berry, D.P., Magee, D.A., Killeen, A.P., Park, S.D., McGettigan, P.A., Lucy, M.C., MacHugh, D.E. and Waters, S.M. (2012). Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. BMC Genomics 13: 16.

Mullen, M.P., Berry, D.P., Howard, D.J., Diskin, M.G., Lynch, C.O., Giblin, L., Kenny, D.A., Magee, D.A., Meade, K.G. and Waters, S.M. (2011). Single nucleotide polymorphisms in the insulin-like growth factor 1 (IGF-1) gene are associated with performance in Holstein-Friesian dairy cattle. Frontiers in Genetics 2: 3.

Berry, D.P., Meade, K.G., Mullen, M.P., Butler, S., Diskin, M.G., Morris, D. and Creevey, C.J. (2011). The integration of “omic” disciplines and systems biology in cattle breeding. Animal 5: 493-505.

Foley, C., O'Farrelly, C. and Meade, K.G. (2011). Technical note: Comparative analyses of the quality and yield of genomic DNA from invasive and noninvasive, automated and manual extraction methods. Journal of Dairy Science 94: 3159-3165.

McHugh, N., Meuwissen, T.H.E., Cromie, A.R. and Sonesson, A.K. (2011). Use of female information in dairy cattle genomic breeding programs. Journal of Dairy Science 94: 4109-4118.

Waters, S.M., McCabe, M.S., Howard, D.J., Giblin, L., Magee, D.A., MacHugh, D.E. and Berry, D.P. (2011). Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle. Animal Genetics 42: 39-49.


Animal Health and Welfare

Mee, J.F. (2012). Bovine neonatal survival – Is improvement possible? Advances in Dairy Technology 23: 161-174.

Lynch, E.M., McGee, M., Doyle, S. and Earley, B. (2012). Effect of pre-weaning concentrate supplementation on peripheral distribution of leukocytes, functional activity of neutrophils, acute phase protein and behavioural responses of abruptly weaned and housed beef calves. BMC Veterinary Research 8: 1.

O’Loughlin, A., Lynn, D.J., McGee, M., Doyle, S., McCabe, M. and Earley, B. (2012). Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology. BMC Genomics 13: 250.

Earley, B., Murray, M., Prendiville, D.J., Pintado, B., Borque, C. and Canali, E. (2012). The effect of transport by road and sea on physiology, immunity and behaviour of beef cattle. Research in Veterinary Science 92: 531-541.

O’Loughlin, A., McGee, M., Waters, S.M., Doyle, S. and Earley, B. (2011). Examination of the bovine leukocyte environment using immunogenetic biomarkers to assess immunocompetence following exposure to weaning stress. BMC Veterinary Research 7: 45.

Pang, W.Y., Earley, B., Murray, M., Sweeney, T., Gath, V. and Crowe, M.A. (2011). Banding or burdizzo castration and carprofen administration on peripheral leukocyte inflammatory cytokine transcripts. Research in Veterinary Science 90: 127-132.

Mazurek, M., McGee, M., Crowe, M.A., Prendiville, D.J., Boivin, X. and Earley, B. (2011). Consistency and stability of behavioural fear responses of heifers to different fear-eliciting situations involving humans. Applied Animal Behaviour Science 131: 21-28.


Infection & Disease

Magee D.A., Taraktsoglou M., Killick K.E., Nalpas N.C., Browne J.A., Park S.D.E., Conlon K.M., Lynn D.J., Hokamp K., Gordon S.V., Gormley E. and MacHugh D. (2012). Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis. PLoS One 7: e32034.

Meade, K.G., O'Gorman, G.M., Narciandi, F., MacHugh, D.E. and O'Farrelly, C. (2012). Functional characterisation of bovine interleukin 8 promoter haplotypes in vitro. Molecular Immunology 50: 108-116.

Waters, S. M., Berry, D. P. and Mullen, M.P. (2012). Polymorphisms in genes of the somatotrophic axis are independently associated with milk production, udder health, survival and animal size in Holstein-Friesian Dairy cattle. Journal of Animal Breeding and Genetics 129: 70-78.

Yang, J., Sang, Y., Meade, K.G. and Ross, C. (2011). The role of oct-1 in the regulation of tracheal antimicrobial peptide (TAP) and lingual antimicrobial peptide (LAP) expression in bovine mammary epithelial cells. Immunogenetics 63: 715-725.

Shaughnessy, R.G., Meade, K.G., McGivney, B.A., Allan, B. and O'Farrelly, C. (2011). Global gene expression analysis of chicken caecal response to Campylobacter jejuni. Veterinary Immunology and Immunopathology 142: 64-71.

Whelehan, C.J., Meade, K.G., Eckersall, P.D., Young, F.J. and O'Farrelly C. (2011). Experimental Staphylococcus aureus infection of the mammary gland induces region-specific changes in innate immune gene expression. Veterinary Immunology and Immunopathology 140: 181-189.

Waters, W.R., Palmer, M.V., Thacker, T.C., Davis, W.C., Sreevatsan, S., Coussens, P., Meade, K.G., Hope, J.C. and Estes, D.M. (2011). Tuberculosis immunity: opportunities from studies with cattle. Clinical and Developmental Immunology 2011: 768542.


Computational Biology

Orchard S., Kerrien S., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F.S.L., Cesareni G., Chatr-aryamontri A., Chautard E., Dumousseau M., Eisenberg D., Goll J., Hancock R.E.W., Hannick L.I., Jurisica I., Khadake J., Lynn, D.J., et al., (2012). Coordinating Molecular Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). Nature Methods 9: 345-350.

Creevey, C.J., Muller, J., Doerks, T., Thompson, J.D., Arendt, D. and Bork, P. (2011). Identifying single copy orthologs in Metazoa. PLoS Computational Biology 7: e1002269.

Creevey, C.J., Doerks, T., Fitzpatrick, D.A., Raes, J. and Bork, P. (2011). Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS ONE 6: e22099.

Procter, J.B., Thompson, J., Letunic, I., Creevey, C., Jossinet, F. and Barton, G.J. (2010). Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods 7: 16-25.

Soyer, O.S. and Creevey, C.J. (2010). Duplicate retention in signalling proteins and constraints from network dynamics. Journal of Evolutionary Biology 23: 2410-2421.

Lynn, D.J., Chan, C., Naseer, M., Yau, M., Lo, R., Sribnaia, A., Ring, G., Que, J., Wee, K., Winsor, G.L., Laird, M.R., Breuer, K., Foroushani, A.K., Brinkman, F.S.L. and Hancock, R.E.W. (2010). Curating the innate immunity interactome. BMC Systems Biology 4: 117.

Geeleher, P., Morris, D.G., Hinde, J.P. and Golden, A. (2009). BioconductorBuntu - A linux distribution that implements a web-based DNA microarray analysis server. Bioinformatics 25: 1438-1439.


Fertility and Reproduction

Cummins, S.B., Waters, S.M., Evans, A.C.O., Lonergan, P. and Butler, S.T. (2012). The Effect of Genetic Merit for Fertility Traits on Regulation of the Somatotropic Axis in Hepatic Tissue in Holstein cows. Journal of Dairy Science 95: 3711-3721.

Mullen, M.P., Elia, G., Hilliard, M., Parr, M.H., Diskin, M.G., Evans, A.C.O. and Crowe M.A. (2012). Proteomic characterization of histotroph during the preimplantation phase of the estrous cycle in cattle. Journal of Proteome Research 11: 3004-3018.

Parr, M.H., Mullen, M.P., Crowe, M.A., Roche, J.F., Lonergan, P., Evans, A.C.O. and Diskin, M.G. (2012). The relationship between progesterone during the early luteal phase and embryo survival in dairy heifers. Journal of Dairy Science 95: 2390-2396.

Mullen, M.P., Forde, N., Parr, M.H., Diskin, M.G., Morris, D.G., Godkin, J.D., Nally, J. E., Evans, A.C.O., Crowe, M. A. (2012). Alterations in systemic concentrations of progesterone during the early luteal phase affect RBP4 expression in the bovine uterus. Reproduction, Fertility and Development 24: 715-722.

Faulkner, S., Elia, G., Mullen, M.P., O’Boyle, P., Dunn, M. and Morris, D. (2012). A comparison of the bovine uterine and plasma proteome using iTRAQ proteomics. Proteomics 12: 2014-2023.

Narciandi, F., Lloyd, A.T., Chapwanya, A., O' Farrelly, C. and Meade, K.G. (2011). Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster. Immunogenetics 63: 641-651.

Coyne, G.S., Kenny, D.A. and Waters, S.M. (2011). Effect of dietary n-3 polyunsaturated fatty acid supplementation on bovine uterine endometrial and hepatic gene expression of the insulin-like growth factor system. Theriogenology 75: 500-512.

Herlihy, M.M., Berry, D.P., Crowe, M.A., Diskin, M.G. and Butler, S.T. (2011). Evaluation of protocols to synchronize estrus and ovulation in seasonal calving pasture-based dairy production systems. Journal of Dairy Science 94: 4488-4501.

Hutchinson, I.A., De Veth, M.J., Stanton, C., Dewhurst, R.J., Lonergan, P., Evans, A.C.O. and Butler, S.T. (2011). Effects of lipid encapsulated Conjugated Linoleic Acid supplementation on milk production, bioenergetic status, and indicators of reproductive performance in lactating dairy cows. Journal of Dairy Research 78: 308-317.


Feed Efficiency and Nutrition

Carberry, C.A., Kenny, D.A., McCabe, M.S. and Waters, S.M. (2012). The effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Applied and Environmental Microbiology 78: 4949-4958.

Alam, T., Kenny, D.A., Sweeney, T., Buckley, F., Prendiville, R., McGee, M. and Waters, S.M. (2012). Expression of genes involved in energy homeostasis in the duodenum and liver of Holstein-Friesian and Jersey cows and their F1 hybrid. Physiological Genomics 44: 198-209.

McCabe M.S., Waters S.M., Morris D.G., Kenny D.A., Lynn D.J. and Creevey C. (2012). RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 13: 193.

Keady, S.M., Kenny, D.A., Keane, M.G. and Waters, S.M. (2011). Effect of sire breed and genetic merit for carcass weight on the transcriptional regulation of the somatotropic axis in longissimus dorsi of crossbred steers. Journal of Animal Science 89: 4007-4016.

Harrison, S.M., Schmidt, O., Moloney, A.P., Kelly, S.D., Rossmann, A., Schellenberg, A., Camin, F., Perini, M., Hoogewerff, J. and Monahan, F.J. (2011). Tissue turnover in ovine muscles and lipids as recorded by multiple (H,C,O,S) stable isotope ratios. Food Chemistry 124: 291-297.

Kelly, A.K., Waters, S.M., McGee, M., Fonseca, R.G., Carberry, C. and Kenny, D.A. (2011). mRNA expression of genes regulating oxidative phosphorylation in the muscle of beef cattle divergently ranked on residual feed intake. Physiological Genomics 43: 12-23.

Gill, F.L., Dewhurst, R.J., Dungait, J.A.J., Evershed, R.P., Ives, L., Li, C.S., Pancost, R.D., Sullivan, M., Bera, S. and Bull, I.D. (2010). Archaeol – a biomarker for foregut fermentation in modern and ancient herbivorous mammals? Organic Geochemistry 41: 467-472.