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researcher

David MacHugh

Associate Dean For Research, Innovation and Impact

School of Agriculture & Food Science

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Biography

1984-1988: B.A. (Mod. Genetics), Trinity College Dublin, Dublin 2. Ireland.

1988-1989:
Research worker, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, UK.

1990-1995:
Postgraduate student (Ph.D.), Molecular Population Genetics Laboratory, Genetics Department, Trinity College Dublin, Dublin 2. Ireland. PhD thesis: Molecular Biogeography and Genetic Structure of Domesticated Cattle. Available in PDF format at the following URL: http://www.animalgenomics.ucd.ie/dmachugh/thesis/

1995-1995:
Research consultant, Food and Agriculture Organisation of the United Nations, Rome, Italy.

1996-1999:
Wellcome Trust Postdoctoral Research Fellow in Bioarchaeology, Genetics Department, Trinity College Dublin, Dublin 2. Ireland.

1998-2000: Research Director, IdentiGEN Ltd., U2, Trinity Enterprise Centre, Pearse St, Dublin 2 Ireland. www.identigen.com

1999-present:
College Lecturer, Senior Lecturer, Associate Professor and Professor of Genomics, UCD School of Agriculture, Food Science and Veterinary Medicine and Conway Institute, University College Dublin.

2010-2016:
Scientific Director, Equinome Ltd., NovaUCD, Belfield, Dublin 4, Ireland.

2010-present: Shareholder and Member of Scientific Advisory Board, Plusvital Ltd., NovaUCD, Belfield, Dublin 4, Ireland. www.plusvital.com
 
2012-present: Member of Scientific Advisory Board, IdentiGEN Ltd., Unit 2, Trinity Enterprise Centre, Pearse St, Dublin 2. Ireland. www.identigen.com

2013-present:
Associate Dean for Research, Innovation and Impact, UCD School of Agriculture, Food Science and Veterinary Medicine and Conway Institute, University College Dublin.

Professional

 

Associations

Association: American Society of Animal Science, Function/Role: Member
Association: International Society of Animal Genetics, Function/Role: Member
Association: American Genetic Association, Function/Role: Member

Patents

Patent 20110262915 : Method for predicting the athletic performance potential of a subject
Patent WO200012008-A1 : Biopsy device for obtaining tissue specimens
Patent IE980164, EP097 : A method and system of identification of a meat product by genotyping
   

Conference Contributions

Bahar, B., Monahan, F.J., Moloney, A.P., Schmidt, O., MacHugh, D.E. & Sweeney, T.; (2006) Stability of gene transcripts in post-mortem bovine skeletal muscle. [Poster Presentation], 2nd International Symposium on Animal Functional Genomics, Michigan State University, East Lansing, U.S , 16-MAY-06 - 19-MAY-06.
Quinn, K.M., Hennessy, K., MacHugh, D.E., Feely, D. and Brophy, P.O.; (2007) Sport horse and pony breeding in Ireland. [Poster Presentation (Refereed)], 58th Annual Meeting of the European Association for Animal Production (EAAP), University College Dublin, Dublin. Ireland , 26-AUG-07 - 29-AUG-07.
Quinn, K.M., Hennessy, K., MacHugh, D.E., Feely, D. and Brophy, P.O.; (2007) Genetic parameters for show jumping ability in young horse competitions in Ireland. [Poster Presentation (Refereed)], 58th Annual Meeting of the European Association for Animal Production (EAAP), University College Dublin, Dublin. Ireland , 26-AUG-07 - 29-AUG-07.
MacHugh, D.E.; (2007) A symposium is to identify critical needs and opportunities to advance the use of animal genomics to solve problems in animal health. [Invited Lecture], International Symposium on Animal Genomics for Animal Health, World Organisation for Animal Health, Paris, France , 23-OCT-07 - 25-OCT-07.
MacHugh, D.E.,Loftus, R.T.,Sharp, P.M.,Cunningham, E.P.; (1990) Proceedings of the First Conference on DNA Fingerprinting. [Published Abstract], Bovine microsatellites for studies of genetic diversity in cattle, Berne, Switzerland .
Bradley, D.G.,Sharp, P.M.,Loftus, R.T.,MacHugh, D.E.,Cunningham, E.P.; (1991) Proceedings of a workshop held at ILRAD. [Published Abstract], Bovine genome mapping and trypanotolerance, Nairobi, Kenya .
Cunningham, E.P.,Loftus, R.T.,MacHugh, D.E.,Bradley, D.G.; (1994) Proceedings of the 5th World Congress on Genetics Applied to Livestock Production. [Published Abstract], Molecular evolution of African, European and Asian cattle, .
MacHugh, D.E.; (2004) Proceedings of the International Food Conference, Thinking Beyond Tomorrow: A Safe and Nutritious Food Chain for the Consumer. [Published Abstract], Genomic approaches to animal breeding: thinking inside the box, Dublin, Ireland .
Hill, E.W.,O'Gorman, G.M.,Gormley, E.,Fitzpatrick, T.,Rosa, G J.M.,Coussens P.M.,MacHugh, D.E.; (2003) Proceedings of the International Symposium on Animal Functional Genomics. [Published Abstract], Functional genomics analysis of the bovine immune response to in vitro co-culture with trypanosomes (Trypanosoma brucei), Michigan State University, USA .
MacHugh, D.E.; (2003) Proceedings of Wellcome Trust Host/Pathogen Meeting. [Published Abstract], Functional genomics of the bovine immune system and trypanosomiasis II, Roslin Institute, Roslin, Midlothian, Scotland .
Meade, K.,Gormley, E.,Fitzpatrick, T.,Rosa, G.J.M.,Coussens, P.M.,MacHugh, D.E.; (2003) Proceedings of the International Symposium on Animal Functional Genomics. [Published Abstract], Analysis of host gene expression in tuberculosis-infected cattle using in vitro stimulation of peripheral blood mononuclear cells (PBMC) and cDNA microarrays, Michigan State University, USA .
Fitzpatrick, R.,Casey, O.,MacHugh, D. E.; (2004) Proceedings of the Agricultural Research Forum. [Published Abstract], Bovine genomics: challenges and applications, Tullamore, Co. Offaly, Ireland .
MacHugh, D.E.; (2002) Proceedings of Wellcome Trust Host/Pathogen Meeting. [Published Abstract], Functional genomics of the bovine immune system and trypanosomiasis I, Roslin Institute, Roslin, Midlothian, Scotland .
Freeman, A.R.,MacHugh, D.E.,McKeown, S.,Walzer, C.,McConnell, D.J.,Bradley, D.G.; (2000) Proceedings of the 27th International Conference on Animal Genetics. [Published Abstract], Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus), Minneapolis, USA .
MacHugh, D.E.; (1999) Proceedings of Wellcome Trust Symposium on Bioarchaeology. [Published Abstract], Genetic analysis of cattle faunal material from a range of archaeological contexts, London, UK .
Meghen, C.N.,Scott, C.S.,Bradley, D.G.,MacHugh, D.E.,Loftus, R.T.,Cunningham, E.P.; (1998) Proceedings of the 8th World Conference on Animal Production. [Published Abstract], DNA-based traceability for the meat industry, Seoul, South Korea .
Loftus, R.T.,Bradley, D.G.,MacHugh, D.E.,Troy, C.S.,Meghen, C.N.,Cunningham, E.P.; (1998) Proceedings of the 8th World Conference on Animal Production. [Published Abstract], Molecular genetics and the evolution of domesticated cattle, .
MacHugh, D.E.,Loftus, R.T.,Troy, C.S.,Bradley, D.G.; (1996) Proceedings of the Conference on the Archaeozoology of Southwest Asia and Adjacent Areas Working Group. [Published Abstract], DNA Analysis and the Origins and History of Domesticated Cattle, Budapest, Hungary .
MacHugh, D.E.,Meghen, C.,Loftus, R.T.,Cunningham P.,Bradley, D.G.; (1996) Proceedings of the 25th International Conference on Animal Genetics. [Published Abstract], Molecular biogeography of domesticated cattle revealed with microsatellite DNA polymorphisms, Tours, France .
Bradley, D.G.,Loftus, R.T.,MacHugh, D.E.,Cunningham, P.; (1997) The molecular evolution of domestic cattle. [Published Abstract], Proceedings of the Symposium on Mediterranean Animal Germplasm and Future Human Challenges, Italy .

Committees

Committee : UCD Research, Innovation and Impact Group
Committee : Scientific Advisory Board, IdentiGEN Ltd.
Committee : UCD College of Health and Agricultural Sciences Research, Innovation and Impact Group
Committee : UCD School of Agriculture and Food Science Research, Innovation and Impact Committee
Committee : UCD Conway Institute Genomics Steering Committee
Committee : UCD Conway IT/Bioinformatics Steering Committee
Committee : UCD Research IT Steering Committee
Committee : UCD School of Agiculture and Food Science Postgraduate Education Committee
Committee : UCD College of Life Sciences Graduate School Board

Employment

Employer: University College Dublin
Position: Senior Lecturer
Employer: University College Dublin
Position: College Lecturer
Employer: IdentiGEN
Position: Research Director
Employer: Trinity College Dublin
Position: Welcome Trust Research Fellow
Employer: United Nations
Position: Consultant to the Food and Agriculture Organisation

Education

Year 1988 Institution: Dublin University
Qualification: BA Subject: Genetics
Year 1996 Institution: Dublin University
Qualification: PhD Subject: Molecular Biogeography and Genetic Structure of Domesticated Cattle.

Languages

English:
French:

Consultancy

Client: Equinome Ltd.
Client: IdentiGEN Ltd

Outreach Activities

11th November 2010, Science Week presentation to 5th and 6th class students in Willow Park School, Blackrock, Co. Dublin. Genomics and the Work of a Genome Scientist.
27th March 2012, Presentation to 1st year students in St. Brendan's College, Bray, Co. Wicklow. Genomics and the Work of a Genome Scientist.
 

Other Activities

Founder, shareholder and Scientific Director; Equinome Ltd.; www.equinome.com
Founder and shareholder, IdentiGEN Genetic Testing Services Ltd. www.identigen.com
Founded 1996

Publications

 

Book Chapters

Magee, D. A., MacHugh, D. E. and Edwards, C. J. (2017) 'Animal domestication, genetic diversity and genomic analysis' In: Hunter, D., Guarino, L., Spillane, C. and McKeown, P. C (eds). Routledge Handbook of Agricultural Biodiversity. Oxford, UK: Routledge, Taylor & Francis Group. Available Online [Details]
Hill EW, Katz LM, MacHugh DE; (2013) 'Genomics of Performance' In: Chowdhary B (eds). Equine Genomics. Hoboken, NJ: Wiley-Blackwell. , pp.265-284 [Details]
Meghen, C.,MacHugh, D.E.,Sauveroche, B.,Kana, G.,Bradley, D.G.; (2000) 'Characterisation of the Kuri cattle of Lake Chad using molecular genetic techniques' In: Meghen, C.,MacHugh, D.E.,Sauveroche, B.,Kana, G.,Bradley, D.G.; (eds). The origins and development of African livestock : archaeology, genetics, linguistics, and ethnography. London ; New York, NY: UCL Press. , pp.259-268 [Details]
MacHugh, D.E.,Loftus, R.T.,Troy, C.S.,Bradley, D.G.; (1998) 'DNA analysis and the origins and history of domesticated cattle' In: MacHugh, D.E.,Loftus, R.T.,Troy, C.S.,Bradley, D.G.; (eds). Archaeozoology of the Near East III. Groningen, The Netherlands: ARC-Publications 18. , pp.8 [Details]
Bradley, D. G., Loftus, R. T., Machugh, D. E., Cunningham, P. (1997) 'The molecular evolution of domestic cattle' In: Bradley, D. G., Loftus, R. T., Machugh, D. E., Cunningham, P (eds). EAAP Publication; International Symposium on Mediterranean Animal Germplasm and Future Human Challenges. , pp.55-59 Available Online [Details]
Bradley, D.G.,MacHugh, D.E.,Loftus, R.T.,Meghen, C.,Sharp, P.M.,Cunningham, E. P.; (1993) 'Genetic characterisation of indigenous cattle breeds: first results and implications for genetic improvement' In: Bradley, D.G.,MacHugh, D.E.,Loftus, R.T.,Meghen, C.,Sharp, P.M.,Cunningham, E. P.; (eds). Amélioration génétique des bovins en Afrique de l'Ouest. Rome: FAO Animal Production and Health Paper. , pp.37-45 [Details]
 

Peer Reviewed Journals

Braud, M., Magee, D. A., Park, S. D., Sonstegard, T. S., Waters, S. M., MacHugh, D. E., Spillane, C. (2017) 'Genome-wide microRNA binding site variation between extinct wild aurochs and modern cattle identifies candidate microRNA-regulated domestication genes'. Frontiers in Genetics, 8 (3):3. [DOI] [Details]
Correia, C. N., Nalpas, N. C., McLoughlin, K. E., Browne, J. A., Gordon, S. V., MacHugh, D. E., Shaughnessy, R. G. (2017) 'Circulating microRNAs as potential biomarkers of infectious disease'. Frontiers in Immunology, 8 :118. [DOI] [Details]
MacHugh D.E., Larson G., Orlando L. (2017) 'Taming the Past: Ancient DNA and the Study of Animal Domestication'. Annual review of animal biosciences, 5 :329-351. [DOI] [Details]
Bryan K., McGivney B.A., Farries G. McGettigan P.A.. McGivney C.L., Gough K.F., MacHugh D.E., Katz L.M., Hill E.W. (2017) 'Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components'. BMC Genomics, 18 (1). [DOI] [Details]
Upadhyay MR, Chen W, Lenstra JA, Goderie CR, MacHugh DE, Park SD, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JA, Groenen MA (2017) 'Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle'. Heredity, 118 (2):169-176. [DOI] [Details]
Aulicino A, Dinan AM, Miranda-CasoLuengo AA, Browne JA, Rue-Albrecht K, MacHugh DE, Loftus BJ (2015) 'High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants'. BMC Genomics, 16 :1-15. [DOI] [Details]
Rue-Albrecht K, McGettigan PA, Hernández B, Nalpas NC, Magee DA, Parnell AC, Gordon SV, MacHugh DE (2016) 'GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data'. BMC Bioinformatics, 17 :126. [DOI] [Details]
Healy C, Golby P, MacHugh DE, Gordon SV (2016) 'The MarR family transcription factor Rv1404 coordinates adaptation of Mycobacterium tuberculosis to acid stress via controlled expression of Rv1405c, a virulence-associated methyltransferase'. Tuberculosis, 97 :154-162. [DOI] [Details]
Casey, M. E., Meade, K. G., Nalpas, N. C., Taraktsoglou, M., Browne, J. A., Killick, K. E., Park, S. D. E., Gormley, E., Hokamp, K., Magee, D. A., MacHugh, D. E. (2015) 'Analysis of the bovine monocyte-derived macrophage response to Mycobacterium avium subspecies paratuberculosis infection using RNA-seq'. Frontiers in Immunology, 6:23 . Available Online [DOI] [Details]
Vegh, P., Magee, D. A., Nalpas, N. C., Bryan, K., McCabe, M. S., Browne, J. A., Conlon, K. M., Gordon, S. V., Bradley, D. G., MacHugh, D. E., Lynn, D. J. (2015) 'MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking'. Tuberculosis, 95 (1):60-67. Available Online [DOI] [Details]
Park, S. D., Magee, D. A., McGettigan, P. A., Teasdale, M. D., Edwards, C. J., Lohan, A. J., Murphy, A., Braud, M., Donoghue, M. T., Liu, Y., Chamberlain, A. T., Rue-Albrecht, K., Schroeder, S., Spillane, C., Tai, S., Bradley, D. G., Sonstegard, T. S., Loftus, B. J., MacHugh, D. E. (2015) 'Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle'. Genome Biology, 16:234 . Available Online [DOI] [Details]
O'Doherty, A. M., MacHugh, D. E., Spillane, C., Magee, D. A. (2015) 'Genomic imprinting effects on complex traits in domesticated animal species'. Frontiers in Genetics, 6:156 . Available Online [DOI] [Details]
Nalpas, N. C., Magee, D. A., Conlon, K. M., Browne, J. A., Healy, C., McLoughlin, K. E., Rue-Albrecht, K., McGettigan, P. A., Killick, K. E., Gormley, E., Gordon, S. V., MacHugh, D. E. (2015) 'RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli'. Scientific Reports, 5:13629 . Available Online [DOI] [Details]
Moran, B., Butler, S. T., Moore, S. G., MacHugh, D. E., Creevey, C. J. (2015) 'Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits'. Reproduction, Fertility and Development, [Online early] . Available Online [DOI] [Details]
McGovern, F. M., Magee, D. A., Browne, J. A., MacHugh, D. E., Boland, T. M. (2016) 'Iodine supplementation of the pregnant dam alters intestinal gene expression and immunoglobulin uptake in the newborn lamb'. Animal, (4):598-606. Available Online [DOI] [Details]
Farrell, D., Shaughnessy, R. G., Britton, L., MacHugh, D. E., Markey, B., Gordon, S. V. (2015) 'The identification of circulating miRNA in bovine serum and their potential as novel biomarkers of early Mycobacterium avium subsp paratuberculosis infection'. PLoS ONE, 10 (7). Available Online [DOI] [Details]
Fariello, M. I., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., San Cristobal, M., Boitard, S. International Sheep Genomics Consortium (2014) 'Selection signatures in worldwide sheep populations'. PLoS ONE, 9 (8):e103813. Available Online [DOI] [Details]
Schubert, M., Jonsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., Fumagalli, M., Raghavan, M., Seguin-Orlando, A., Korneliussen, T. S., Velazquez, A. M., Stenderup, J., Hoover, C. A., Rubin, C. J., Alfarhan, A. H., Alquraishi, S. A., Al-Rasheid, K. A., MacHugh, D. E., Kalbfleisch, T., MacLeod, J. N., Rubin, E. M., Sicheritz-Ponten, T., Andersson, L., Hofreiter, M., Marques-Bonet, T., Gilbert, M. T., Nielsen, R., Excoffier, L., Willerslev, E., Shapiro, B., Orlando, L. (2014) 'Prehistoric genomes reveal the genetic foundation and cost of horse domestication'. Proceedings of the National Academy of Sciences USA, 111 (52):5661-9. Available Online [DOI] [Details]
Sanderson, N. D., Norman, P. J., Guethlein, L. A., Ellis, S. A., Williams, C., Breen, M., Park, S. D., Magee, D. A., Babrzadeh, F., Warry, A., Watson, M., Bradley, D. G., MacHugh, D. E., Parham, P., Hammond, J. A. (2014) 'Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts'. Journal of Immunology, 193 (12):6016-6030. Available Online [DOI] [Details]
Rue-Albrecht, K., Magee, D. A., Killick, K. E., Nalpas, N. C., Gordon, S. V., MacHugh, D. E. (2014) 'Comparative functional genomics and the bovine macrophage response to strains of the Mycobacterium genus'. Frontiers in Immunology, 5:536 . Available Online [DOI] [Details]
McLoughlin, K. E., Nalpas, N. C., Rue-Albrecht, K., Browne, J. A., Magee, D. A., Killick, K. E., Park, S. D., Hokamp, K., Meade, K. G., O'Farrelly, C., Gormley, E., Gordon, S. V., MacHugh, D. E. (2014) 'RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis'. Frontiers in Immunology, 5:396 . Available Online [DOI] [Details]
Magee, D. A., Spillane, C., Berkowicz, E. W., Sikora, K. M., MacHugh, D. E. (2014) 'Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits'. Animal Genetics, 45 Suppl 1 :25-39. Available Online [DOI] [Details]
Magee, D. A., MacHugh, D. E., Edwards, C. J. (2014) 'Interrogation of modern and ancient genomes reveals the complex domestic history of cattle'. Frontiers, 4 (3):7-22. Available Online [DOI] [Details]
Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., Pirson, C., Healy, C., McLoughlin, K. E., Chen, J., Vordermeier, H. M., Gormley, E., MacHugh, D. E., Gordon, S. V. (2014) 'Innate cytokine profiling of bovine alveolar macrophages reveals commonalities and divergence in the response to Mycobacterium bovis and Mycobacterium tuberculosis infection'. Tuberculosis, 94 (4):441-450. Available Online [DOI] [Details]
Killick, K. E., Magee, D. A., Park, S. D., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Nalpas, N. C., Gormley, E., Gordon, S. V., MacHugh, D. E., Hokamp, K. (2014) 'Key hub and bottleneck genes differentiate the macrophage response to virulent and attenuated Mycobacterium bovis'. Frontiers in Immunology, 5:422 . Available Online [DOI] [Details]
Heaton, M. P., Leymaster, K. A., Kalbfleisch, T. S., Kijas, J. W., Clarke, S. M., McEwan, J., Maddox, J. F., Basnayake, V., Petrik, D. T., Simpson, B., Smith, T. P., Chitko-McKown, C. G. International Sheep Genomics Consortium. (2014) 'SNPs for parentage testing and traceability in globally diverse breeds of sheep'. PLoS ONE, 9 (4):e94851. Available Online [DOI] [Details]
Killick, K. E., Ni Cheallaigh, C., O'Farrelly, C., Hokamp, K., MacHugh, D. E., Harris, J. (2013) 'Receptor-mediated recognition of mycobacterial pathogens'. Cellular Microbiology, 15 (9):1484-1495. Available Online [DOI] [Details]
Nalpas, N. C., Park, S. D., Magee, D. A., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Rue-Albrecht, K., Killick, K. E., Hokamp, K., Lohan, A. J., Loftus, B. J., Gormley, E., Gordon, S. V., Machugh, D. E. (2013) 'Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro'. BMC Genomics, 14 (1):230. [Details]
Orr, N., Hill, E. W., Gu, J., Govindarajan, P., Conroy, J., van Grevenhof, E. M., Ducro, B. J., van Arendonk, J. A., Knaap, J. H., van Weeren, P. R., Machugh, D. E., Ennis, S., Brama, P. A. (2013) 'Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10'. Animal Genetics, 44 (4):408-12. [Details]
Vegh, P., Foroushani, A. B., Magee, D. A., McCabe, M. S., Browne, J. A., Nalpas, N. C., Conlon, K. M., Gordon, S. V., Bradley, D. G., Machugh, D. E., Lynn, D. J. (2013) 'Profiling microRNA expression in bovine alveolar macrophages using RNA-seq'. Veterinary Immunology and Immunopathology, 155 (4):238-44. [Details]
Waters, Sinead M., Coyne, Gerard S., Kenny, David A., MacHugh, David E., Morris, Dermot G. (2012) 'Dietary n-3 polyunsaturated fatty acid supplementation alters the expression of genes involved in the control of fertility in the bovine uterine endometrium'. Physiological Genomics, 44 (18):878-888. Available Online [Details]
Berkowicz, E. W., Magee, D. A., Berry, D. P., Sikora, K. M., Howard, D. J., Mullen, M. P., Evans, R. D., Spillane, C., MacHugh, D. E. (2012) 'Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle'. Animal Genetics, 43 (1):81-87. Available Online [Details]
M. A. Bower, B. A. McGivney, M. G. Campana, J. Gu, L. S. Andersson, E. Barrett, C. R. Davis, S. Mikko, F. Stock, V. Voronkova, D. G. Bradley, A. G. Fahey, G. Lindgren, D. E. MacHugh, G. Sulimova and E. W. Hill; (2012) 'The genetic origin and history of speed in the Thoroughbred racehorse'. Nature Communications, 3 :643. Available Online [DOI] [Details]
Eivers, S. S., McGivney, B. A., Gu, J., MacHugh, D. E., Katz, L. M., Hill, E. W. (2012) 'PGC-1 alpha encoded by the PPARGC1A gene regulates oxidative energy metabolism in equine skeletal muscle during exercise'. Animal Genetics, 43 (2):153-162. Available Online [Details]
Hill, Emmeline W., Fonseca, Rita G., McGivney, Beatrice A., Gu, Jingjing, MacHugh, David E., Katz, Lisa M. (2012) 'MSTN genotype (g.66493737C/T) association with speed indices in Thoroughbred racehorses'. Journal of Applied Physiology, 112 (1):86-90. Available Online [Details]
Hill, Emmeline W., Ryan, Donal P., MacHugh, David E. (2012) 'Horses for Courses: a DNA-based Test for Race Distance Aptitude in Thoroughbred Racehorses'. Recent patents on DNA & gene sequences, 6 (3):203-8. Available Online [Details]
Kijas, James W., Lenstra, Johannes A., Hayes, Ben, Boitard, Simon, Porto Neto, Laercio R., San Cristobal, Magali, Servin, Bertrand, McCulloch, Russell, Whan, Vicki, Gietzen, Kimberly, Paiva, Samuel, Barendse, William, Ciani, Elena, Raadsma, Herman, McEwan, John, Dalrymple, Brian, International Sheep Genomics Consortium, Members (2012) 'Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection'. PLoS Biology, 10 (2). Available Online [Details]
MacHugh, David E., Taraktsoglou, Maria, Killick, Kate E., Nalpas, Nicolas C., Browne, John A., Park, Stephen D. E., Hokamp, Karsten, Gormley, Eamonn, Magee, David A. (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 . Available Online [Details]
Magee, David A., Taraktsoglou, Maria, Killick, Kate E., Nalpas, Nicolas C., Browne, John A., Park, Stephen D. E., Conlon, Kevin M., Lynn, David J., Hokamp, Karsten, Gordon, Stephen V., Gormley, Eamonn, MacHugh, David E. (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 (2). Available Online [Details]
B McGivney, J Browne, R Fonseca, D MacHugh, R Whiston, L Katz, E Hill ; (2012) 'MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance'. Animal Genetics, 43 (6):810-2. [DOI] [Details]
Meade, Kieran G., O'Gorman, Grace M., Narciandi, Fernando, MacHugh, David E., O'Farrelly, Cliona (2012) 'Functional characterisation of bovine interleukin 8 promoter haplotypes in vitro'. Molecular Immunology, 50 (1-2):108-116. Available Online [Details]
Mullen, M. P., Creevey, C. J., Berry, D. P., McCabe, M. S., Magee, D. A., Howard, D. J., Killeen, A. P., Park, S. D., McGettigan, P. A., Lucy, M. C., Machugh, D. E., 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. Available Online [Details]
Sheridan, Michael P., Browne, John A., MacHugh, David E., Costello, Eamon, Gormley, Eamonn (2012) 'Impact of delayed processing of bovine peripheral blood on differential gene expression'. Veterinary Immunology and Immunopathology, 145 (1-2):199-205. Available Online [Details]
Sikora, K. M., Magee, D. A., Berkowicz, E. W., Lonergan, P., Evans, A. C. O., Carter, F., Comte, A., Waters, S. M., MacHugh, D. E., Spillane, C. (2012) 'PHLDA2 is an imprinted gene in cattle'. Animal Genetics, 43 (5):587-590. Available Online [Details]
Waters, S. M., McCabe, M. S., Howard, D. J., Giblin, L., Magee, D. A., MacHugh, D. E., Berry, D. P. (2011) 'Associations between newly discovered polymorphisms in the Bos taurusgrowth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle'. Animal Genetics, 42 (1):39-49. Available Online [Details]
Berkowicz, Erik W., Magee, David A., Sikora, Klaudia M., Berry, Donagh P., Howard, Dawn J., Mullen, Michael P., Evans, Ross D., Spillane, Charles, MacHugh, David E. (2011) 'Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle'. Journal of Dairy Research, 78 (1):1-8. Available Online [Details]
Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O'Farrelly C, Hokamp K, MacHugh DE (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . [DOI] [Details]
Magee, David A., Berry, Donagh P., Berkowicz, Erik W., Sikora, Klaudia M., Howard, Dawn J., Mullen, Michael P., Evans, Ross D., Spillane, Charles, MacHugh, David E. (2011) 'Single Nucleotide Polymorphisms within the Bovine DLK1-DIO3 Imprinted Domain Are Associated with Economically Important Production Traits in Cattle'. Journal of Heredity, 102 (1):94-101. Available Online [Details]
Mullen, M. P., Berry, D. P., Howard, D. J., Diskin, M. G., Lynch, C. O., Berkowicz, E. W., Magee, D. A., MacHugh, D. E., Waters, S. M. (2011) 'Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle (vol 93, pg 5959, 2010)'. Journal of Dairy Science, 94 (2):1069-1069. Available Online [Details]
Sikora, Klaudia M., Magee, David A., Berkowicz, Erik W., Berry, Donagh P., Howard, Dawn J., Mullen, Michael P., Evans, Ross D., MacHugh, David E., Spillane, Charles (2011) 'DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gs alpha)-encoding (GNAS) genomic imprinting domain are associated with performance traits'. BMC Genetics, 12 . Available Online [Details]
Taraktsoglou M, Szalabska U, Magee DA, Browne JA, Sweeney T, Gormley E, MacHugh DE (2011) 'Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens'. Veterinary Immunology and Immunopathology, 140 :130-139. [Details]
Orr N, Back W, Gu J, Leegwater P, Govindarajan P, Conroy J, Ducro B, Van Arendonk JAM, MacHugh DE, Ennis S, Hill EW, Brama PAJ ; (2010) 'Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses'. Animal Genetics, 41 (suppl. 2):2-7. Available Online [DOI] [Details]
Edwards, Ceiridwen J., Magee, David A., Park, Stephen D. E., McGettigan, Paul A., Lohan, Amanda J., Murphy, Alison, Finlay, Emma K., Shapiro, Beth, Chamberlain, Andrew T., Richards, Martin B., Bradley, Daniel G., Loftus, Brendan J., MacHugh, David E. (2010) 'A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius)'. PLoS ONE, 5 (2). Available Online [Details]
Eivers, S. S., McGivney, B. A., Fonseca, R. G., MacHugh, D. E., Menson, K., Park, S. D., Rivero, J. L. L., Taylor, C. T., Katz, L. M., Hill, E. W. (2010) 'Alterations in oxidative gene expression in equine skeletal muscle following exersise and training (vol 40, pg 83, 2010)'. Physiological Genomics, 41 (2):201-201. Available Online [Details]
Eivers, Suzanne S., McGivney, Beatrice A., Fonseca, Rita G., MacHugh, David E., Menson, Katie, Park, Stephen D., Rivero, Jose-Luis L., Taylor, Cormac T., Katz, Lisa M., Hill, Emmeline W. (2010) 'Alterations in oxidative gene expression in equine skeletal muscle following exercise and training'. Physiological Genomics, 40 (2):83-93. Available Online [Details]
Gu, J., MacHugh, D. E., McGivney, B. A., Park, S. D. E., Katz, L. M., Hill, E. W. (2010) 'Association of sequence variants in CKM (creatine kinase, muscle) and COX4I2 (cytochrome c oxidase, subunit 4, isoform 2) genes with racing performance in Thoroughbred horses'. Equine Veterinary Journal, 42 :569-575. Available Online [Details]
Hill, E. W., Eivers, S. S., McGivney, B. A., Fonseca, R. G., Gu, J., Smith, N. A., Browne, J. A., MacHugh, D. E., Katz, L. M. (2010) 'Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle'. Equine Veterinary Journal Supplement, 42 :576-581. Available Online [Details]
Hill, Emmeline W., Gu, Jingjing, Eivers, Suzanne S., Fonseca, Rita G., McGivney, Beatrice A., Govindarajan, Preethi, Orr, Nick, Katz, Lisa M., MacHugh, David (2010) 'A Sequence Polymorphism in MSTN Predicts Sprinting Ability and Racing Stamina in Thoroughbred Horses'. PLoS ONE, 5 (1). Available Online [Details]
Hill, E.W., Gu, J., McGivney, B.A., MacHugh, D.E.; (2010) 'Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance'. Animal Genetics, 41 (Suppl 2):56-63. Available Online [DOI] [Details]
Hill EW, McGivney BA, Gu J, Whiston R, MacHugh DE; (2010) 'A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses'. BMC Genomics, 11 (1):552-null. Available Online [DOI] [Details]
Magee, DA,Berkowicz, EW,Sikora, KM,Berry, DP,Park, SDE,Kelly, AK,Sweeney, T,Kenny, DA,Evans, RD,Wickham, BW,Spillane, C,MacHugh, DE; (2010) 'A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits'. Animal, 4 :1958-1970. [DOI] [Details]
Magee, D. A., Berkowicz, E. W., Sikora, K. M., Sweeney, T., Kenny, D. A., Kelly, A. K., Evans, R. D., Wickham, B. W., Bradley, D. G., Spillane, C., MacHugh, D. E. (2010) 'High concordance of bovine single nucleotide polymorphism genotypes generated using two independent genotyping strategies'. Animal Biotechnology, 21 (4):257-262. Available Online [Details]
Magee, D. A., Park, S. D. E., Scraggs, E., Murphy, A. M., Doherty, M. L., Kijas, J. W., MacHugh, D. E., Int Sheep Genomics, Consortium (2010) 'Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform'. Journal of Animal Science, 88 (10):3183-3186. Available Online [Details]
Magee, David A., Sikora, Klaudia M., Berkowicz, Erik W., Berry, Donagh P., Howard, Dawn J., Mullen, Michael P., Evans, Ross D., Spillane, Charles, MacHugh, David E. (2010) 'DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle'. BMC Genetics, 11 . Available Online [Details]
Mullen, M. P., Berry, D. P., Howard, D. J., Diskin, M. G., Lynch, C. O., Berkowicz, E. W., Magee, D. A., MacHugh, D. E., Waters, S. M. (2010) 'Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle'. Journal of Dairy Science, 93 (12):5959-5969. Available Online [Details]
Sikora, Klaudia Maria, Magee, David, Berkowicz, Eric, MacHugh, David, Spillane, Charles (2009) 'Genomic imprinting in mammals and quality traits in cattle'. Cellular Oncology, 31 (2):131-132. Available Online [Details]
Gu, Jingjing, Orr, Nick, Park, Stephen D., Katz, Lisa M., Sulimova, Galina, MacHugh, David E., Hill, Emmeline W. (2009) 'A Genome Scan for Positive Selection in Thoroughbred Horses'. PLoS ONE, 4 (6). Available Online [Details]
MacHugh, D. E., Gormley, E., Park, S. D. E., Browne, J. A., Taraktsoglou, M., O'Farrelly, C., Meade, K. G. (2009) 'Gene Expression Profiling of the Host Response to Mycobacterium bovis Infection in Cattle'. Transboundary and Emerging Diseases, 56 (6-7):204-214. Available Online [Details]
McGivney, Beatrice A., Eivers, Suzanne S., MacHugh, David E., MacLeod, James N., O'Gorman, Grace M., De Park, Stephen, Katz, Lisa M., Hill, Emmeline W. (2009) 'Transcriptional adaptations following exercise in Thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy'. BMC Genomics, 10 . Available Online [Details]
Meade, Kieran G., O'Gorman, Grace M., Hill, Emmeline W., Narciandi, Fernando, Agaba, Morris, Kemp, Stephen J., O'Farrelly, Cliona, MacHugh, David E. (2009) 'Divergent antimicrobial peptide (AMP) and acute phase protein (APP) responses to Trypanosoma congolense infection in trypanotolerant and trypanosusceptible cattle'. Molecular Immunology, 47 (2-3):196-204. Available Online [Details]
O'Gorman, Grace M., Park, Stephen D. E., Hill, Emmeline W., Meade, Kieran G., Coussens, Paul M., Agaba, Morris, Naessens, Jan, Kemp, Stephen J., MacHugh, David E. (2009) 'Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility'. BMC Genomics, 10 . Available Online [Details]
Murphy, Angela M., Meade, Kieran G., Hayes, Patricia A., Park, Stephen D. E., Evans, Alex C. O., Lonergan, Patrick, MacHugh, David E. (2008) 'Transmission ratio distortion at the growth hormone gene (GH1) in bovine preimplantation embryos: An in vitro culture-induced phenomenon?'. Molecular Reproduction and Development, 75 (5):715-722. Available Online [Details]
Mc Parland, S., Kearney, J. F., MacHugh, D. E., Berry, D. P. (2008) 'Inbreeding effects on postweaning production traits, conformation, and calving performance in Irish beef cattle'. Journal of Animal Science, 86 (12):3338-3347. Available Online [Details]
Meade, Kieran G., Gormley, Eamonn, O'Farrelly, Cliona, Park, Stephen D., Costello, Eamon, Keane, Joseph, Zhao, Yingdong, MacHugh, David E. (2008) 'Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program'. BMC Genomics, 9 . Available Online [Details]
Murphy, Angela M., MacHugh, David E., Park, Stephen D. E., Scraggs, Erik, Haley, Chris S., Lynn, David J., Boland, Maurice P., Doherty, Michael L. (2007) 'Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep Chromosome 5'. Mammalian Genome, 18 (1):43-52. Available Online [Details]
Bahar, Bojlul, Monahan, Frank J., Moloney, Aidan P., Schmidt, Olaf, MacHugh, David E., Sweeney, Torres (2007) 'Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues'. Bmc Molecular Biology, 8 . Available Online [Details]
Edwards, C. J., Baird, J. F., MacHugh, D. E. (2007) 'Taurine and zebu admixture in Near Eastern cattle: a comparison of mitochondrial, autosomal and Y-chromosomal data'. Animal Genetics, 38 (5):520-524. Available Online [Details]
Fitzgerald, D. C., Meade, K. G., McEvoy, A. N., Lillis, L., Murphy, E. P., MacHugh, D. E., Baird, A. W. (2007) 'Tumour necrosis factor-alpha (TNF-alpha) increases nuclear factor kappa B (NF kappa B) activity in and interleukin-8 (IL-8) release from bovine mammary epithelial cells'. Veterinary Immunology and Immunopathology, 116 (1-2):59-68. Available Online [Details]
Meade, Kieran G., Gormley, Eamonn, Doyle, Mairead B., Fitzsimons, Tara, O'Farrelly, Cliona, Costello, Eamon, Keane, Joseph, Zhao, Yingdong, MacHugh, David E. (2007) 'Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease'. BMC Genomics, 8 . Available Online [Details]
O'Gorman, Grace M., Park, Stephen D. E., Hill, Emmeline W., Meade, Kieran G., Mitchell, Laura C., Agaba, Morris, Gibson, John P., Hanotte, Olivier, Naessens, Jan, Kemp, Stephen J., MacHugh, David E. (2006) 'Cytokine mRNA profiling of peripheral blood mononuclear cells from trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense'. Physiological Genomics, 28 (1):53-61. Available Online [Details]
McGahern, A., Bower, M. A. M., Edwards, C. J., Brophy, P. O., Sulimova, G., Zakharov, I., Vizuete-Forster, M., Levine, M., Li, S., MacHugh, D. E., Hill, E. W. (2006) 'Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations'. Animal Genetics, 37 (5):494-497. Available Online [Details]
McGahern, A. M., Edwards, C. J., Bower, M. A., Heffernan, A., Park, S. D. E., Brophy, P. O., Bradley, D. G., MacHugh, D. E., Hill, E. W. (2006) 'Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses'. Animal Genetics, 37 (5):498-502. Available Online [Details]
Meade, Kieran G., Gormley, Eamonn, Park, Stephen D. E., Fitzsimons, Tara, Rosa, Guilherme J. M., Costello, Eamon, Keane, Joseph, Coussens, Paul M., MacHugh, David E. (2006) 'Gene expression profiling of peripheral blood mononuclear cells (PBMC) from Mycobacterium bovis infected cattle after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD)'. Veterinary Immunology and Immunopathology, 113 (1-2):73-89. Available Online [Details]
Meade, K. G.,Hill, E. W.,Buckley, F.,MacHugh, D. E.; (2005) 'Convenient detection of single nucleotide polymorphism haplotypes in the bovine growth hormone gene using amplification-created restriction sites'. Anim Genet, 36 (2):175-7. [Details]
Hill, E. W., O'Gorman, G. M., Agaba, M., Gibson, J. P., Hanotte, O., Kemp, S. J., Naessens, J., Coussens, P. M., MacHugh, D. E. (2005) 'Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics'. Veterinary Immunology and Immunopathology, 105 (3-4):247-258. Available Online [Details]
Meade, K. G., Hill, E. W., Buckley, F., MacHugh, D. E. (2005) 'Convenient detection of single nucleotide polymorphism haplotypes in the bovine growth hormone gene using amplification-created restriction sites'. Animal Genetics, 36 (2):175-177. Available Online [Details]
Freeman, A. R., Meghen, C. M., MacHugh, D. E., Loftus, R. T., Achukwi, M. D., Bado, A., Sauveroche, B., Bradley, D. G. (2004) 'Admixture and diversity in West African cattle populations'. Molecular Ecology, 13 (11):3477-3487. Available Online [Details]
Edwards, C. J., MacHugh, D. E., Dobney, K. M., Martin, L., Russell, N., Horwitz, L. K., McIntosh, S. K., MacDonald, K. C., Helmer, D., Tresset, A., Vigne, J. D., Bradley, D. G. (2004) 'Ancient DNA analysis of 101 cattle remains: limits and prospects'. Journal of Archaeological Science, 31 (6):695-710. Available Online [Details]
Edwards, C. J., Connellan, J., Wallace, P. F., Park, S. D. E., McCormick, F. M., Olsaker, I., Eythorsdottir, E., MacHugh, D. E., Bailey, J. F., Bradley, D. G. (2003) 'Feasibility and utility of microsatellite markers in archaeological cattle remains from a Viking Age settlement in Dublin'. Animal Genetics, 34 (6):410-416. Available Online [Details]
Troy, C. S., MacHugh, D. E., Bailey, J. F., Magee, D. A., Loftus, R. T., Cunningham, P., Chamberlain, A. T., Sykes, B. C., Bradley, D. G. (2001) 'Genetic evidence for Near-Eastern origins of European cattle'. Nature, 410 (6832):1088-1091. Available Online [Details]
Freeman, A. R., MacHugh, D. E., McKeown, S., Walzer, C., McConnell, D. J., Bradley, D. G. (2001) 'Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus)'. Heredity, 86 :355-362. Available Online [Details]
MacHugh, D. E., Bradley, D. G. (2001) 'Livestock genetic origins: goats buck the trend'. Proceedings of the National Academy of Sciences of the United States of America, 98 (10):5382-5384. Available Online [Details]
MacHugh, D.E., Edwards, C.J., Bailey, J.F., Bancroft, D.R., Bradley, D.G. (2000) 'The extraction and analysis of ancient DNA from bone and teeth: a survey of current methodologies'. Ancient Biomolecules, 3 :81-102. [Details]
Edwards, C. J., Gaillard, C., Bradley, D. G., MacHugh, D. E. (2000) 'Y-specific microsatellite polymorphisms in a range of bovid species'. Animal Genetics, 31 (2):127-130. Available Online [Details]
Ritz, L. R., Glowatzki-Mullis, M. L., MacHugh, D. E., Gaillard, C. (2000) 'Phylogenetic analysis of the tribe Bovini using microsatellites'. Animal Genetics, 31 (3):178-185. Available Online [Details]
Millard, A., MacHugh, D., Harris, D. R., Jones, M., Eglinton, G., Renfrew, C. (1999) 'Early medieval cattle remains from a Scandinavian settlement in Dublin: Genetic analysis and comparison with extant breeds - Discussion'. Philosophical Transactions of the Royal Society B-Biological Sciences, 354 (1379):108-109. Available Online [Details]
Loftus, R. T., Ertugrul, O., Harba, A. H., El-Barody, M. A. A., Machugh, D. E., Park, S. D. E., Bradley, D. G. (1999) 'A microsatellite survey of cattle from a centre of origin: the Near East'. Molecular Ecology, 8 (12):2015-2022. Available Online [Details]
Loftus, R. T., MacHugh, D. E., Cunningham, P., Bradley, D. G. (1999) 'Animal domestication'. Science, 283 (5400):329-330. Available Online [Details]
MacHugh, D. E., Troy, C. S., McCormick, F., Olsaker, I., Eythorsdottir, E., Bradley, D. G. (1999) 'Early medieval cattle remains from a Scandinavian settlement in Dublin: Genetic analysis and comparison with extant breeds'. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 354 (1379):99-108. Available Online [Details]
Meghen, C. N., Scott, C. S., Bradley, D. G., Machugh, D. E., Loftus, R. T., Cunningham, E. P. (1998) 'DNA based traceability techniques for the meat industry'. Animal Genetics, 29 (SUPPL. 1):48-49. Available Online [Details]
Bradley, D. G., Loftus, R. T., Cunningham, P., MacHugh, D. E. (1998) 'Genetics and domestic cattle origins'. Evolutionary Anthropology, 6 (3):79-86. Available Online [Details]
MacHugh, D. E., Loftus, R. T., Cunningham, P., Bradley, D. G. (1998) 'Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers'. Animal Genetics, 29 (5):333-340. Available Online [Details]
MacHugh, D. E., Shriver, M. D., Loftus, R. T., Cunningham, P., Bradley, D. G. (1997) 'Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and Zebu cattle (Bos taurus and Bos indicus)'. Genetics, 146 (3):1071-1086. Available Online [Details]
Machugh, D. E., Loftus, R. T., Cunningham, P., Bradley, D. G. (1996) 'Molecular biogeography of domesticated cattle revealed with microsatellite DNA polymorphisms'. Animal Genetics, 27 (SUPPL. 2):23-23. Available Online [Details]
Bradley, D. G., MacHugh, D. E., Cunningham, P., Loftus, R. T. (1996) 'Mitochondrial diversity and the origins of African and European cattle'. Proceedings of the National Academy of Sciences of the United States of America, 93 (10):5131-5135. Available Online [Details]
Bradley, D. G., Machugh, D. E., Cunningham, P., Loftus, R. T. (1996) 'Mitochondrial DNA sequence variation and the origins of domestic cattle'. Animal Genetics, 27 (SUPPL. 2):19-19. Available Online [Details]
Hendrickx, G., Meghen, C., Napala, A., Machugh, D. E., Bradley, D. G., Dao, B. (1996) 'Phenotypic designations of Togolese cattle correlate strongly with microsatellite allele frequency data'. Animal Genetics, 27 (SUPPL. 2):21-21. Available Online [Details]
Meghen, C., Machugh, D. E., Bradley, D. G. (1994) 'Genetic characterization and West African cattle'. World Animal Review (Multilingual Edition), 78 (1):59-66. Available Online [Details]
Bradley, D. G., Machugh, D. E., Loftus, R. T., Sow, R. S., Hoste, C. H., Cunningham, E. P. (1994) 'Zebu-taurine variation in Y-chromosomal DNA - a sensitive assay for genetic introgression in West African trypanotolerant cattle populations'. Animal Genetics, 25 (1):7-12. Available Online [Details]
Loftus, R. T., Machugh, D. E., Bradley, D. G., Sharp, P. M., Cunningham, P. (1994) 'Evidence for two independent domestications of cattle'. Proceedings of the National Academy of Sciences of the United States of America, 91 (7):2757-2761. Available Online [Details]
Loftus, R. T., Machugh, D. E., Ngere, L. O., Balain, D. S., Badi, A. M., Bradley, D. G., Cunningham, E. P. (1994) 'Mitochondrial genetic variation in European, African and Indian cattle populations'. Animal Genetics, 25 (4):265-271. Available Online [Details]
Machugh, D. E., Loftus, R. T., Bradley, D. G., Sharp, P. M., Cunningham, P. (1994) 'Microsatellite DNA variation within and among European cattle breeds'. Proceedings of the Royal Society B-Biological Sciences, 256 (1345):25-31. Available Online [Details]
Loftus, R., Machugh, D., Bradley, D., Sharp, P., Cunningham, P. (1993) 'Mitochondrial Genetic Distances among European, African and Indian Cattle'. Resistance or Tolerance of Animals to Disease and Veterinary Epidemiology and Diagnostic Methods, :72. Available Online [Details]
Machugh, D., Bradley, D., Loftus, R., Meghan, C., Sharp, P., Cunningham, P. (1993) 'Molecular Biogeography of West-African Cattle Breeds'. Resistance or Tolerance of Animals to Disease and Veterinary Epidemiology and Diagnostic Methods, :17. Available Online [Details]
 

Conference Publications

MacHugh, D. E. (2016) Network-based integration of gene expression and genome-wide association data to prioritize genomic variants associated with susceptibility/resistance to bovine tuberculosis EMBO: From Functional Genomics to Systems Biology EMBL Heidelberg, Germany, [Details]
Bryan, K., McGivney, B., Farries, G., Gough, K., McGivney, C., MacHugh, D., Katz, L., Hill E. (2017) Evidence for a transcriptome-driven variant-specific functional effect of the equine myostatin (MSTN) performance SNP (g.66493737C>T) Cell Symposium on Exercise Metabolism Gothenburg, Sweden, [Details]
Killick, K. E., Mullen, M. P., Hall, T. J., Nalpas, N. C., Richardson, I. W., Magee, D. A., Correia, C. N., Browne, J. A., Berry, D. P., Bradley, D. G., Naranbhai, V., Hill, A. V., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) Integrative genomics of human and bovine tuberculosisIntegrative genomics of human and bovine tuberculosis 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., Vordermeier, H. M., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2017) Globin mRNA depletion is an unnecessary step in RNA-seq transcriptomics studies of peripheral blood from cattle 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
Faherty O'Donnell, S. L., McLoughlin, K. E., Correia, C. N., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., Vordermeier, H. M., Villarreal-Ramos , B., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) RNA transcript biomarker development for bovine tuberculosis using the NanoString nCounter® Analysis System UCD Conway Festival of Research and Innovation Dublin, Ireland, [Details]
Hall, T. J., Killick, K. E., Mullen, M. P., McLoughlin, K. E., Nalpas, N. C., Richardson, I. W., Magee, D. A., Correia, C. N., Browne, J. A., Vordermeier, H. M., Villarreal-Ramos , B., Berry, D. P., Bradley, D. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) Integrative network genomics of the bovine host response to infection with Mycobacterium bovis 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
Haige, H., Bryan, K., Shiraigol, W., MacHugh, D. E., Dugarjaviin, M., Hill, E. W. (2017) Genetic Diversity and Population Structure in Chinese Mongolian Horses 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
O'Doherty, A. M., Rue-Albrecht, K., Browne, J. A., Hall, T. J., Nalpas, N. C., Magee, D. A., Gordon, S. V., Vernimmen, D., MacHugh, D. E. (2017) Evaluating the role of epigenomic modifications in host-pathogen interaction for bovine alveolar macrophages infected with Mycobacterium bovis 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
MacHugh, D. E., O'Doherty, A. M., Hall, T. J., Rue-Albrecht, K., Ahting, S., Browne, J. A., Nalpas, N. C., Magee, D. A., Gordon, S. V., Vernimmen, D. (2017) Evaluating the role of epigenomic modifications in host-pathogen interaction for bovine alveolar macrophages infected with Mycobacterium bovis Animal Genetics and Diseases Cambridge, UK, [Details]
Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., Vordermeier, H. M., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2017) Globin mRNA depletion is an unnecessary step in RNA-seq transcriptomics studies of peripheral blood from cattle UCD Conway Festival of Research and Innovation Dublin, Ireland, [Details]
Hall, T. J., Killick, K. E., Mullen, M. P., McLoughlin, K. E., Nalpas, N. C., Richardson, I. W., Magee, D. A., Correia, C. N., Browne, J. A., Vordermeier, H. M., Villarreal-Ramos , B., Berry, D. P., Bradley, D. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) Integrative network genomics of the bovine host response to infection with Mycobacterium bovis UCD Conway Festival of Research and Innovation Dublin, Ireland, [Details]
Faherty O'Donnell, S. L., McLoughlin, K. E., Correia, C. N., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., Vordermeier, H. M., Villarreal-Ramos , B., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) RNA transcript biomarker development for bovine tuberculosis using the NanoString nCounter® Analysis System 36th International Society for Animal Genetics Conference Dublin, Ireland, [Details]
O'Doherty, A. M., Rue-Albrecht, K., Browne, J. A., Hall, T. J., Nalpas, N. C., Magee, D. A., Gordon, S. V., Vernimmen, D., MacHugh, D. E. (2017) Evaluating the role of epigenomic modifications in host-pathogen interaction for bovine alveolar macrophages infected with Mycobacterium bovis UCD Conway Festival of Research and Innovation Dublin, Ireland, [Details]
Haige, H., Bryan, K., Shiraigol, W., MacHugh, D. E., Dugarjaviin, M., Hill, E. W. (2017) Genetic Diversity and Population Structure in Chinese Mongolian Horses UCD Conway Festival of Research and Innovation Dublin, Ireland, [Details]
Killick, K. E., Mullen, M. P., Hall, T. J., Nalpas, N. C., Richardson, I. W., Magee, D. A., McLoughlin, K. E., Correia, C. N., Burkitt-Gray, L., Wiencko, H. L., Browne, J. A., Villarreal-Ramos , B., Vordermeier, H. M., Berry, D. P., Bradley, D. G., Naranbhai, V., Hill, A. V., Gormley, E., Gordon, S. V., MacHugh, D. E. (2017) Integrative genomics of human and bovine tuberculosis ASM Conference on Tuberculosis: Past, Present and Future New York, USA, [Details]
Hill, E. W., McGivney, B. A., Wiencko, H. L., Parnell, A. C., Farries, G., Bryan, K., Katz, L. M., MacHugh, D. E., Weiser, M. (2017) Predictive genetic markers for racing durability and the identification of an exercise-mediating behavioural response gene Cell Symposium on Exercise Metabolism Gothenburg, Sweden, [Details]
Shaughnessy R., Farrell D., Ripema K., Britton L., MacHugh D.E., Markey B., Bakker D. and Gordon S.V. (2015) Characterization of remarkably stable circulating miRNA in bovine serum and their potential as novel biomarkers of early Mycobacterium avium subsp paratuberculosis infection Association of Veterinary Teachers and Research Workers, 49th Annual Scientific Meeting [Details]
Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Killick, K. E., Vordermeier, H. M., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2016) RNA-seq transcriptional profiling of PPD-b-stimulated peripheral blood from cattle infected with Mycobacterium bovis UCD Conway Festival of Research and Innovation UCD Conway Institute of Biomolecular and Biomedical Research, , 13-SEP-16 - 15-SEP-16 [Details]
MacHugh, D. E. (2016) Integrative genomics of the bovine host response to Integrative genomics of the bovine host response to Mycobacterium bovis infection Microbiology Society Focused Meeting 2016: Irish Division Host-Pathogen Interactions Trinity College Dublin, Dublin, Ireland, , 30-JUN-16 - 01-JUL-16 [Details]
Killick, K. E., Mullen, M. P., Nalpas, N. C., Richardson, I. W., Magee, D. A., McLoughlin, K. E., Correia, C. N., Burkitt-Gray, L., Wiencko, H. L., Browne, J. A., Villarreal-Ramos , B., Vordermeier, H. M., Berry, D. P., Bradley, D. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2016) Network-based integration of gene expression and genome-wide association data to prioritize genomic variants associated with susceptibility/resistance to bovine tuberculosis EMBL-EBI Livestock Genomics Meeting Homerton College, Cambridge, United Kingdom, , 14-SEP-16 - 16-SEP-16 [Details]
Shaughnessy R., Farrell D., Ripema K., Britton L., MacHugh D.E., Markey B., Bakker D. and Gordon S.V. (2016) Circulating miRNA in bovine serum and their potential use as novel bio markers of early Mycobacterium avium subsp. paratuberculosis infection 13th International Colloquium on Paratuberculosis [Details]
Shaughnessy R., Farrell D., Ripema K., Britton L., MacHugh D.E., Markey B., Bakker D. and Gordon S.V. (2016) Circulating miRNA in bovine serum and their potential use as novel biomarkers of early Mycobacterium avium subsp. paratuberculosis infection 29th World Buiatrics Congress [Details]
Killick, K. E., Mullen, M. P., Nalpas, N. C., Richardson, I. W., Magee, D. A., McLoughlin, K. E., Correia, C. N., Burkitt-Gray, L., Wiencko, H. L., Browne, J. A., Villarreal-Ramos , B., Vordermeier, H. M., Berry, D. P., Bradley, D. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2016) Network-based integration of gene expression and genome-wide association data to prioritize genomic variants associated with susceptibility/resistance to bovine tuberculosis UCD Conway Festival of Research and Innovation UCD Conway Institute of Biomolecular and Biomedical Research, , 13-SEP-16 - 15-SEP-16 [Details]
Malone, K. M., Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., Smyth, A., Gormley, E., MacHugh, D. E., Gordon, S. V. (2016) Human and bovine tubercle bacilli elicit distinct innate responses during early stage infection of bovine alveolar macrophages EMBO Conference Tuberculosis 2016: Interdisciplinary research on tuberculosis and pathogenic mycobacteria Pasteur Institute, Paris France, , 19-SEP-16 - 23-SEP-16 [Details]
Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Killick, K. E., Vordermeier, H. M., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2016) RNA-seq transcriptional profiling of PPD-b-stimulated peripheral blood from cattle infected with Mycobacterium bovis EMBO Conference Tuberculosis 2016: Interdisciplinary research on tuberculosis and pathogenic mycobacteria Pasteur Institute, Paris France, , 19-SEP-16 - 23-SEP-16 [Details]
Correia, C. N., Nalpas, N. C., McLoughlin, K. E., Magee, D. A., Shaughnessy, R. G., Browne, J. A., Whelan, A. O., Vordermeier, H. M., Gormley, E., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2016) Circulating serum microRNAs as novel biomarkers for bovine tuberculosis The Acid Fast Club Winter Meeting The London School of Hygiene and Tropical Medicine, London, UK, , 08-JAN-16 - 08-JAN-16 [Details]
Killick, K. E., McLoughlin, K. E., Burkitt-Gray, L., Browne, J. A., Richardson, I. W., Hokamp, K., Berry, D. P., Bradley, D. G., Gordon, S. V., MacHugh, D. E. (2016) Network-based Integration of Gene Expression and Genome-wide Association Data to Prioritize Genomic Variants Associated with Susceptibility/Resistance to Bovine Tuberculosis The Acid Fast Club Summer Meeting Public Health England, Porton Down, Salisbury, United Kingdom, , 07-JUL-16 - 08-JUL-16 [Details]
Killick, K. E., McLoughlin, K. E., Nalpas, N. C., Burkitt-Gray, L., Richardson, I. W., Wiencko, H. L., Magee, D. A., Browne, J. A., Villarreal-Ramos , B., Vordermeier, H. M., Berry, D. P., Bradley, D. G., Gordon, S. V., MacHugh, D. E. (2016) Network-based integration of gene expression and genome-wide association data to prioritize genomic variants associated with susceptibility/resistance to bovine tuberculosis 35th International Society for Animal Genetics Conference Salt Lake City, Utah, USA, , 23-JUL-16 - 27-JUL-16 [Details]
Burkitt-Gray, L., McLoughlin, K. E., Richardson, I., Nalpas, N. C., Magee, D. A., Browne, J. A., Killick, K. E., Whelan, A. O., Villarreal-Ramos , B., Vordermeier, H. M., Berry, D. P., Gormley, E., Bradley, D. G., Gordon, S. V., MacHugh, D. E. (2015) Integration of in vivo host infection gene expression data with results from a genome-wide association study to prioritise genomic variants associated with susceptibility or resistance to bovine tuberculosis Proceedings of the PhD Symposium in Computational Biology & Innovation UCD, Dublin 4., Ireland, [Details]
Correia, C. N., Nalpas, N. C., McLoughlin, K. E., Magee, D. A., Shaughnessy, R. G., Browne, J. A., Whelan, A. O., Vordermeier, H. M., Gormley, E., Villarreal-Ramos , B., Gordon, S. V., MacHugh, D. E. (2015) Circulating serum microRNAs as novel biomarkers for bovine tuberculosis 6th International Symposium on Animal Functional Genomics Universita Cattolica del Sacre Cuore, Piacenza, Italy, [Details]
Correia, C. N., Nalpas, N. C., McLoughlin, K. E., Magee, D. A., Shaughnessy, R. G., Browne, J. A., Whelan, A. O., Vordermeier, H. M., Gormley, E., Villarreal-Ramos, B., Gordon, S. V., MacHugh, D. E. (2015) Circulating serum microRNAs as novel biomarkers for bovine tuberculosis Proceedings of the Virtual Institute of Bioinformatics and Evolution Meeting Dublin City University, Dublin, Ireland, [Details]
Hill, E. W., McGettigan, P. A., Parnell, A. C., Ryan, D., MacHugh, D. E. (2015) Development of genomic prediction methods for elite racing performance in Thoroughbred racehorses 11th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Leonardo Hotel, Hannover, Germany, [Details]
McGettigan, P. A., Farries, G., Browne, J. A., McGivney, B. A., Herdan, C., Gough, K., Katz, L. M., MacHugh, D. E., Hill, E. W. (2015) Field Study of Thoroughbred racehorse skeletal muscle gene expression response to exercise pre- and post-training using RNA-seq 11th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Leonardo Hotel, Hannover, Germany, [Details]
Rue-Albrecht, K., McGettigan, P. A., Hernandez, B., Magee, D. A., Nalpas, N. C., Parnell, A. C., Gordon, S. V., MacHugh, D. E. (2015) GOexpress: An R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data 6th International Symposium on Animal Functional Genomics Universita Cattolica del Sacre Cuore, Piacenza, Italy, [Details]
Rue-Albrecht, K., McGettigan, P. A., Hernandez, B., Parnell, A. C., Gordon, S. V., Hill, E. W., MacHugh, D. E. (2015) GOexpress: analysis and visualisation of gene expression data using gene ontology annotations 11th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Leonardo Hotel, Hannover, Germany, [Details]
Braud, M., Morris, D., MacHugh, D. E., Sonstegard, T. S., Spillane, C. (2014) Identification and ranking of microRNA binding sites of seven cattle breeds for miRNA-association studies for genomic selection in domestic cattle Proceedings of the Agricultural Research Forum Tullamore, Ireland, [Details]
McGettigan, P. A., Farries, G., Browne, J. A., McGivney, B. A., Herdan, C., Gough, K., Katz, L. M., MacHugh, D. E., Hill, E. W. (2014) Field study of Thoroughbred racehorse muscle transcriptomic response to exercise pre- and post-training using RNA-seq Proceedings of the EMBL-EBI Livestock Genomics Meeting Homerton College, Cambridge, UK, [Details]
Nalpas, N. C., Magee, D. A., Conlon, K. M., Browne, J. A., Healy, C., McLoughlin, K. E., Killick, K. E., Rue-Albrecht, K., McGettigan, P. A., Gormley, E., Gordon, S. V., MacHugh, D. E. (2014) Innate immunomodulatory mechanisms underlying Mycobacterium bovis infection are reflected in the bovine alveolar macrophage transcriptome Proceedings of the VI International M. bovis Conference City Hall, Cardiff, Wales, United Kingdom, [Details]
Nalpas, N. C., Magee, D. A., Conlon, K. M., Browne, J. A., Healy, C., McLoughlin, K. E., Rue-Albrecht, K., McGettigan, P. A., Killick, K. E., Gormley, E., Gordon, S. V., MacHugh, D. E. (2014) RNA-seq analysis provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli Proceedings of the PhD Symposium in Computational Biology & Innovation UCD, Dublin 4., Ireland, [Details]
Park, S. D. E., Magee, D. A., McGettigan, P. A., Teasdale, M. D., Edwards, C. J., Lohan, A. J., Murphy, A., Liu, Y., Finlay, E. K., Chamberlain, A. T., Schroeder, S., Bradley, D. G., Sonstegard, T. S., Loftus, B. J., MacHugh, D. E. (2014) A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius) Proceedings of the Cell Symposium: Evolution of Modern Humans - From Bones to Genomes Sitges, Spain, [Details]
Park, S. D. E., Magee, D. A., McGettigan, P. A., Teasdale, M. D., Edwards, C. J., Lohan, A. J., Murphy, A., Liu, Y., Finlay, E. K., Chamberlain, A. T., Schroeder, S., Bradley, D. G., Sonstegard, T. S., Loftus, B. J., MacHugh, D. E. (2014) A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius) Proceedings of the From Fossils to the Genome Symposium (The 150th anniversary of the naming of Homo neanderthalensis by William King) NUI Galway, Galway, Ireland, [Details]
Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Gormley, E., MacHugh, D. E., Gordon, S. V. (2014) Development of a software package for the visualisation of gene expression and gene ontologies, and application to the transcriptional analysis of bovine alveolar macrophage response to members of the Mycobacterium tuberculosis complex Proceedings of the UCD Conway Festival of Research and Innovation UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland, [Details]
Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Healy, C., McLoughlin, K. E., Gormley, E., Gordon, S. V., MacHugh, D. E. (2014) Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex Proceedings of the EMBL-EBI Livestock Genomics Meeting Homerton College, Cambridge, UK, [Details]
Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Healy, C., McLoughlin, K. E., Gormley, E., MacHugh, D. E., Gordon, S. V. (2014) Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex Proceedings of the EMBO Conference - Microbiology after the Genomics Revolution: Genomes 2014 Institut Pasteur, Paris, France, [Details]
Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Healy, C., McLoughlin, K. E., Gormley, E., MacHugh, D. E., Gordon, S. V. (2014) Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex Proceedings of the Virtual Institute of Bioinformatics and Evolution Meeting IT Carlow, Carlow, Ireland, [Details]
Rue-Albrecht, K., Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Healy, C., McLoughlin, K. E., Gormley, E., MacHugh, D. E., Gordon, S. V. (2014) Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex Proceedings of the Acid Fast Club Summer Meeting (60th Anniversary) Kaiserin Friedrich-Haus, Berlin, Germany, [Details]
Rue-Albrecht, K., Magee, D. A., Nalpas, N. C., McGettigan, P. A., MacHugh, D. E., Gordon, S. V. (2014) anovaGO: R package for semi-supervised clustering of samples based on gene expression Proceedings of the Virtual Institute of Bioinformatics and Evolution Meeting IT Carlow, Carlow, Ireland, [Details]
MacHugh, D. E., McGivney, B. A., Killick, K. E., McGettigan, P. A., Gu, J., Carberry, C., Hill, E. W. (2013) A pooled high-throughput sequencing approach to identify novel equine SNPs and associations with elite Thoroughbred racing performance Proceedings of the 10th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Furnas, Sao Miguel, Azores, Portugal, [Details]
Moran, B., Butler, S. T., Cummins, S. B., Moore, S., MacHugh, D. E., Creevey, C. J. (2013) Differential gene expression and alternative transcription in endometrial tissue of a lactating cow model of fertility Proceedings of the Agricultural Research Forum Tullamore, Ireland, [Details]
Hill, E. W., McGivney, B. A., Donovan, G., Gough, K., Carberry, C., MacHugh, D. E. (2013) SNP associations with height in the Thoroughbred (Flat) racehorseSNP associations with height in the Thoroughbred (Flat) racehorse Proceedings of the 10th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Furnas, Sao Miguel, Azores, Portugal, [Details]
Rue-Albrecht, K., Magee, D. A., Nalpas, N. C., Taraktsoglou, M., Conlon, K. M., Killick, K. E., Browne, J. A., Gormley, E., Gordon, S. V., MacHugh, D. E. (2013) Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guerin (BCG) and M. avium subspecies paratuberculosis Proceedings of the UCD Conway Festival of Research & Innovation UCD, Dublin 4., Ireland, [Details]
Magee, D. A., Berkowicz, E. W., Sikora, K. M., Spillane, C., MacHugh, D. E. (2013) Imprinted gene loci as candidate targets for performance traits in cattle Proceedings of the Plant and Animal Genome XVII Conference Town & Country Convention Center, San Diego, California, USA, [Details]
Magee, D. A., Conlon, K. M., Nalpas, N. C., Browne, J. A., McGettigan, P. A., Healy, C., McLoughlin, K. E., Chen, J., Rue-Albrecht, K., Gormley, E., MacHugh, D. E., Gordon, S. V. (2013) Transcriptome analysis reveals differential innate immune response in bovine macrophages to strains of the Mycobacterium tuberculosis complex Proceedings of Animal Health Ireland: Animal Health - A Cornerstone of Sustainable and Profitable Farming Rochestown Park Hotel, Cork, Ireland, [Details]
McLoughlin, K. E., Dinan, A., Magee, D. A., Browne, J. A., Whelan, A. O., Villarreal-Ramos , B., Vordermeier, M. H., Gormley, E., Gordon, S. V., MacHugh, D. E. (2013) An infection time course experiment to identify putative microRNA biomarkers of infection with Mycobacterium bovis, the causative agent of bovine tuberculosis Proceedings of the UCD Conway Festival of Research & Innovation UCD, Dublin 4., Ireland, [Details]
Switzenberg, J. A., Kabara, E., Rue-Albrecht, K., Magee, D. A., MacHugh, D. E., Coussens, P. M. (2013) Transcriptomic studies of Mycobacterium avium subsp. paratuberculosis infected monocyte-derived macrophages from individual dairy cows Proceedings of the T cell Function and Modulation Meeting Maui, Hawaii, USA, [Details]
Carberry, C., McGivney, B. A., McLoughlin, K., MacHugh, D. E., Hill, E. W. (2013) A genome wide association study to identify SNPs associated with precocity in the Thoroughbred (Flat) racehorse Proceedings of the 10th Dororthy Russell Havemeyer Foundation - International Equine Genome Mapping Workshop Furnas, Sao Miguel, Azores, Portugal, [Details]
Casey, M., Meade, K. G., Magee, D. A., Taraktsoglou, M., Nalpas, N. C., Browne, J. A., Lohan, A. J., MacHugh, D. E. (2013) Transcriptomic analysis using RNA-seq of the response to Mycobacterium avium subspecies paratuberculosis infection in bovine monocyte-derived macrophages (MDM) Proceedings of the UCD Conway Festival of Research & Innovation UCD, Dublin 4., Ireland, [Details]
Rue-Albrecht, K., Magee, D. A., Nalpas, N. C., Killick, K. E., Browne, J. A., Gormley, E., Gordon, S., MacHugh, D. E. (2013) Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guerin (BCG) and M. avium subspecies paratuberculosis Proceedings of the Irish Branch of the Association of Veterinary Teaching & Research Work (AVTRW), 47th Annual Scientific Meeting AFBI, Hillsborough, Co. Down, Northern Ireland, [Details]
Rue-Albrecht, K., Magee, D. A., Nalpas, N. C., Killick, K. E., Browne, J. A., Gormley, E., Gordon, S., MacHugh, D. E. (2013) Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guerin (BCG) and M. avium subspecies paratuberculosis Proceedings of Animal Health Ireland: Animal Health - A Cornerstone of Sustainable and Profitable Farming Rochestown Park Hotel, Cork, Ireland, [Details]
Park, S. D. E., Magee, D. A., McGettigan, P. A., Teasdale, M., Edwards, C. J., Lohan, A. J., Murphy, A., Liu, Y., Finlay, E. K., Schroeder, S. G., Bradley, D. G., Sonstegard T. S., Loftus, B. J., MacHugh, D. E. (2013) A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius) Proceedings of the Plant and Animal Genome XVII Conference Town & Country Convention Center, San Diego, California, USA, [Details]
Nalpas, N. C., Magee, D. A., Conlon, K. M., Browne, J. A., McLoughlin, K. E., Healy, C., Killick, K. E., McGettigan, P. A., Rue-Albrecht, K., Gormley, E., Gordon, S. V., MacHugh, D. E. (2013) Whole-transcriptome analysis of the bovine alveolar macrophage response to Mycobacterium bovis infection in vitro Proceedings of the PhD Symposium in Computational Biology & Innovation UCD, Dublin 4., Ireland, [Details]
Nalpas, N. C., Magee, D. A., Conlon, K. M., Browne, J. A., McLoughlin, K. E., Healy, C., Killick, K. E., McGettigan, P. A., Rue-Albrecht, K., Gormley, E., Gordon, S. V., MacHugh, D. E. (2013) Whole-transcriptome analysis of the bovine alveolar macrophage response to Mycobacterium bovis infection in vitro Proceedings of the UCD Conway Festival of Research & Innovation UCD, Dublin 4., Ireland, [Details]
MacHugh, D. E. (2013) Functional genomics and systems biology of the bovine macrophage response to pathogenic and non-pathogenic strains of Mycobacterium bovis Proceedings of the Acid Fast Club Meeting University College Dublin, Dublin, Ireland, [Details]
Killick, K. E., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Nalpas, N. C., Gormley, E., Gordon, S. V., MacHugh, D. E., Hokamp, K. (2012) Key hub and bottleneck genes differentiate the bovine macrophage response to virulent and avirulent strains of Mycobacterium bovis Proceedings of Virtual Institute of Bioinformatics and Evolution Meeting Dublin, Ireland, [Details]
Mullen, M. P., Creevey, C. J., McCabe, M. S., Berry, D. P., Magee, D. A., Killeen, A. P., Howard, D. J., MacHugh, D. E., Waters, S, M. (2012) Characterisation of the sequence variation in genes of the somatotrophic axis in DNA pools from cattle divergent for carcass weightCharacterisation of the sequence variation in genes of the somatotrophic axis in DNA pools from cattle divergent for carcass weight Proceedings of the Agricultural Research Forum Tullamore, Ireland, [Details]
Braud, M., Donoghue, M. T., MacHugh, D. E., Morris, D., Spillane, C. (2012) Genetic variation in pre-miRNAs and mature miRNAs in the genomes of domestic cattleGenetic variation in pre-miRNAs and mature miRNAs in the genomes of domestic cattle Proceedings of the Agricultural Research Forum Tullamore, Ireland, [Details]
Nalpas, N. C., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Lohan, A. J., Conlon, K., Gordon, S. V., Gormley, E., MacHugh, D. E. (2011) Whole-transcriptome high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitro Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Mullen, M. P., McCabe, M. S., Berry, D. P., Magee, D. A., Creevey, C. J., Killeen, A. P., Park, S. D., McGettigan, P. A., Lucy, M. C., MacHugh, D. E., Waters, S. M. (2011) Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McLoughlin, K. E., Magee, D. A., Nalpas, N. C., Browne, J. A., Killick, K. E., Park, S. D. E., Whelan, A. O., Vordermeier, H. M., Hewinson, R. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Technical assessment of bovine cytokine gene expression using compromised RNA samples from cattle experimentally infected with Mycobacterium bovisTechnical assessment of bovine cytokine gene expression using compromised RNA samples from cattle experimentally infected with Mycobacterium bovis Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McGivney, B. A., Whiston, R., Browne, J. A., Fonseca, R. G., Gu, J., Katz, L. M., MacHugh, D. E., Hill, E. W. (2011) Investigation of myostatin pathway gene expression in untrained and trained Thoroughbred horse skeletal muscleInvestigation of myostatin pathway gene expression in untrained and trained Thoroughbred horse skeletal muscle Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Magee, D. A., Nalpas, N. C., Conlon, K., Browne, J. A., McLoughlin, K. E., Healy, C., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Transcriptional profiling of key host genes using RNA from bovine alveolar macrophages co-cultured with Mycobacterium bovis and Mycobacterium tuberculosisTranscriptional profiling of key host genes using RNA from bovine alveolar macrophages co-cultured with Mycobacterium bovis and Mycobacterium tuberculosis Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin, K. E., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Vegh, P., McCabe, M., Magee, D. A., Conlon, K. M., Browne, J. A., Nalpas, N. C., Bradley, D. G., Gordon, S. V., MacHugh, D. E., Lynn, D. J. (2011) Profiling miRNA expression in bovine alveolar macrophagesProfiling miRNA expression in bovine alveolar macrophages Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Browne, J. A., Park, S. D. E., Magee, D. A., Martin, I., Meade, K. G., Gordon, S. V., Gormley, E., O'Farrelly, C., Hokamp, K., MacHugh, D. E. (2011) Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genesGenome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killeen, A. P., Mullen, M. P., Creevey, C. J., McCabe, M. S., Magee, D. A., Diskin, M. G., MacHugh, D. E., Waters, S. M. (2011) Polymorphism discovery and allele frequency estimation for 10 candidate genes in DNA pools from dairy cattle divergent for calving intervalPolymorphism discovery and allele frequency estimation for 10 candidate genes in DNA pools from dairy cattle divergent for calving interval Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Casey, M. E., Earley, B., McGee, M., Kennedy, E., Browne, J. A., MacHugh, D. E., Meade, K. G. (2011) Investigating the cellular and molecular mechanisms contributing to the development of bovine neonatal immunityInvestigating the cellular and molecular mechanisms contributing to the development of bovine neonatal immunity Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Carberry, C. A., Creevey, C. J., Kenny, D. A., MacHugh, D. E., Waters, S. M. (2011) Identification of rumen bacterial populations in cattle divergent for residual feed intake (RFI)Identification of rumen bacterial populations in cattle divergent for residual feed intake (RFI) Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Park, S. D. E., Magee, D. A., McGettigan, P. A., Teasdale, M., Edwards, C. J., Lohan, A. J., Murphy, A., Liu, Y., Finlay, E. K., Chamberlain, A. T., Schroeder, S., Bradley, D. G., Sonstegard, T. S., Loftus, B. J., MacHugh, D. E. (2011) A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius)A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius) Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin K. E., Lynn, D. J., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Berkowicz, E. W., Magee, D. A., Berry, D. P., Sikora, K. M., Howard, D. J., Mullen, M. P., Evans, R. D., Spillane, C., MacHugh, D. E. (2010) DNA sequence variation at the imprinted bovine IGF2 and IGF2R loci and associations with performance traits in dairy cattleDNA sequence variation at the imprinted bovine IGF2 and IGF2R loci and associations with performance traits in dairy cattle Proceedings of the 32nd Conference of the International Society of Animal Genetics Edinburgh, UK, [Details]
Hill, E. W., Gu, J., Eivers, S. S., Fonseca, R. G., McGivney, B. A., Govindarajan, P., Orr, N., Katz, L. M., MacHugh, D. E. (2010) A sequence polymorphism in the MSTN gene predicts sprinting ability and racing stamina in Thoroughbred horses Proceedings of the Annual General Meeting of the Irish Thoroughbred Breeder's Association Kill, Ireland, [Details]
Magee, D. A., Park, S. D. E., Edwards, C. J., McGettigan, P. A., Lohan, A. J., Finlay, E. K., Chamberlain, A. T., Schroeder, S., Bradley, D. G., Loftus, B. J., Sonstegard, T. S., MacHugh, D. E. (2010) Genome sequencing of the extinct wild aurochs (Bos primigenius)Genome sequencing of the extinct wild aurochs (Bos primigenius) Proceedings of the 32nd Conference of the International Society of Animal Genetics Edinburgh, UK, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP)Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP) Proceedings of Gene Expression and Signaling in the Immune System Cold Spring Harbor Laboratory, New York, USA, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP)Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP) Proceedings of the 32nd Conference of the International Society of Animal Genetics Edinburgh, UK, [Details]
Edwards, C. J., Magee, D. A., Park, S. D. E., McGettigan, P. A., Lohan, A. J., Murphy, A., Finlay, E. K., Shapiro, B., Chamberlain, A. T., Richards, M. B., Bradley, D. G., Loftus, B. J., MacHugh, D. E. (2009) Genomic analyses of a British Mesolithic aurochs (Bos primigenius) using conventional and second-generation DNA sequencing technologiesGenomic analyses of a British Mesolithic aurochs (Bos primigenius) using conventional and second-generation DNA sequencing technologies Proceedings of Irish Quaternary Association Annual Symposium 2009 Geological Survey, Dublin, Ireland, [Details]
Eivers, S. S., Gu, J., McGivney, B. A., Fonseca, R. G., MacHugh, D. E., Katz, L. M., Hill, E. W. (2009) Targets of selection in the Thoroughbred horse (Equus caballus) genome contain genes expressed in skeletal muscle following exercise Proceedings of 14th International Biochemistry of Exercise Conference University of Guelph, Ontario, Canada, [Details]
McGivney, B. A., McGettigan, P., Browne, J. A., Fonseca, R. G., Eivers, S. S., Evans, A. C., Loftus, B., Lohan, A., MacHugh, D. E., Katz, L. M., MacHugh, D. E. (2009) Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training The Physiological Society - Physiology 2009 University College Dublin, Ireland, [Details]
Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Sweeney, T., Gormley, E., MacHugh, D. E. (2009) Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to the causative agents of tuberculosis (M. bovis) and Johneâ¿¿s Disease (M. avium subsp. paratuberculosis)Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to the causative agents of tuberculosis (M. bovis) and Johneâ¿¿s Disease (M. avium subsp. paratuberculosis) Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Gormley, E., MacHugh, D. E. (2009) Functional genomics studies of bovine macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCGFunctional genomics studies of bovine macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Meade, K. G., O'Gorman, G. M., Narciandi, F., MacHugh, D. E., O'Farrelly, C. (2009) Functional implications of bovine interleukin 8 promoter haplotype for neutrophil recruitmentFunctional implications of bovine interleukin 8 promoter haplotype for neutrophil recruitment ISI Annual Meeting 2009 Institute of Molecular Medicine, St James Hospital, Dublin 8, Ireland, [Details]
Meade, K. G., O'Gorman, G. M., Hill, E. W., Narciandi, F., Agaba, M., Kemp, S. J., O'Farrelly, C., MacHugh, D. E. (2009) Divergent antimicrobial peptide and acute phase protein responses to Divergent antimicrobial peptide and acute phase protein responses to Trypanosoma congolense infection in tolerant and susceptible cattle ISI Annual Meeting 2009 Institute of Molecular Medicine, St James Hospital, Dublin 8, Ireland, [Details]
Meade, K. G., Oâ¿¿Gorman, G. M., Narciandi, F., MacHugh, D. E., O'Farrelly, C. (2009) Functional implications of bovine interleukin 8 promoter haplotype for neutrophil recruitmentFunctional implications of bovine interleukin 8 promoter haplotype for neutrophil recruitment Proceedings of the Irish Society for Immunology Annual General Meeting Institute of Molecular Medicine, St. James Hospital, Dublin, Ireland, [Details]
Meade, K. G., Oâ¿¿Gorman, G. M., Hill, E. W., Narciandi, F., Agaba, M., Kemp, S. J., O'Farrelly, C., MacHugh, D. E. (2009) Divergent antimicrobial peptide and acute phase protein responses to Trypanosoma congolense infection in tolerant and susceptible cattleDivergent antimicrobial peptide and acute phase protein responses to Trypanosoma congolense infection in tolerant and susceptible cattle Proceedings of the Irish Society for Immunology Annual General Meeting Institute of Molecular Medicine, St. James Hospital, Dublin, Ireland, [Details]
McGivney, B. A., McGettigan, P., Browne, J. A., Fonseca, R. G., Eivers, S. S., Evans, A. C., Loftus, B. J., Lohan, A., MacHugh, D. E., Katz, L. M., Hill, E. W. (2009) Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise trainingDigital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training Proceedings of The Physiological Society Meeting University College Dublin, Dublin, Ireland, [Details]
MacHugh, D. E., Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D. E., Szalabaska, U., Gormley, E. (2009) A functional genomics study of bovine monocyte-derived macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCGA functional genomics study of bovine monocyte-derived macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Edwards, C. J., Magee, D. A., McGettigan, P. A., Lohan, A. J., Murphy, A., Park, S. D., Finlay, E. K., Shapiro, B., Chamberlain, A. T., Richards, M. B., Bradley, D. G., Loftus, B. J., MacHugh, D. E. (2009) A complete mitochondrial genome sequence from the extinct wild aurochs (Bos primigenius)A complete mitochondrial genome sequence from the extinct wild aurochs (Bos primigenius) Proceedings of Cold Spring Harbor Bovine Genome Consortium Meeting Cold Spring Harbor Laboratory, New York, USA, [Details]
Browne, J. A., Park, S. D. E., McGettigan, P., Meade, K. G., O'Farrelly, C., Gormley, E., MacHugh, D. E. (2009) Identification of a gene signature associated with Mycobacterium bovis infection in cattleIdentification of a gene signature associated with Mycobacterium bovis infection in cattle Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Gu, J., MacHugh, D. E., Hill, E. W. (2008) A whole genome scan for regions of positive selection in thoroughbred racehorsesA whole genome scan for regions of positive selection in thoroughbred racehorses Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
Berkowicz, E.W., Magee, D. A., Spillane, C., Sikora, K., Sweeney, T., Kelly, A., Kenny, D., Evans, R., Park, S. D., MacHugh, D. E. (2008) SNP haplotype distributions for the imprinted bovine SNP haplotype distributions for the imprinted bovine IGF2 and IGF2R genes Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
McGivney, B., Eivers, S. S., Katz, L. M., MacLeod, J., MacHugh, D. E., O'Gorman, G. M., Park, S. D., Hill, E. W. (2008) Transcriptional profiling of thoroughbred skeletal muscle response to exercise using an equine cDNA microarrayTranscriptional profiling of thoroughbred skeletal muscle response to exercise using an equine cDNA microarray Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
MacHugh, D. E., Meade, K. G., Gormley, E. (2008) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattleTranscriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle Proceedings of: Genetics of Bovine TB Meeting Belfast, UK, [Details]
Taraktsoglou, M., Szalabaska, U., Sweeney, T., Gormley, E., MacHugh, D. E. (2008) Transcriptional responses of bovine monocyte-derived macrophage (MDM) to mycobacterial purified protein derivative (PPD) and to lipopolysaccharideTranscriptional responses of bovine monocyte-derived macrophage (MDM) to mycobacterial purified protein derivative (PPD) and to lipopolysaccharide Proceedings of the Joint Meeting of the Irish Society for Immunology (ISI) & the Ulster Immunology Group (UIG) Royal Dublin Society, Dublin, Ireland, [Details]
Taraktsoglou, M., Szalabaska, U., Gormley, E., Sweeney, T., MacHugh, D. E. (2008) Response of bovine monocyte derived macrophage (MDM) to purified protein derivative from Mycobacterium bovis and to Mycobacterium avium subspecies paratuberculosisResponse of bovine monocyte derived macrophage (MDM) to purified protein derivative from Mycobacterium bovis and to Mycobacterium avium subspecies paratuberculosis Proceedings of Agricultural Biotechnology International Conference University College Cork, Cork, Ireland, [Details]
Taraktsoglou, M., Szalabaska, U., Gormley, E., Sweeney, T., MacHugh, D. E. (2008) Response of bovine monocyte-derived macrophage (MDM) to purified protein derivative (PPD) from Response of bovine monocyte-derived macrophage (MDM) to purified protein derivative (PPD) from Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
Szalabaska, U., Taraktsoglou, M., Gormley, E., Sweeney, T., MacHugh, D. E. (2008) Gene expression profiles of immune-related genes in Mycobacterium bovis infected and healthy control cattle Gene expression profiles of immune-related genes in Mycobacterium bovis infected and healthy control cattle Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
Szalabaska, U., Meade, K., Taraktsoglou, M., Gormley, E., Sweeney, T., MacHugh, D. E. (2008) Gene expression profiles of immune genes in Gene expression profiles of immune genes in Mycobacterium bovis-infected and healthy cattle Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
Scraggs, Erik, Murphy, Angela M., Park, Stephen D. E., Doherty, Michael L., MacHugh, David E. (2008) Fine mapping of the ovine chromosomal region containing the inherited ovine arthrogryposis (IOA) geneFine mapping of the ovine chromosomal region containing the inherited ovine arthrogryposis (IOA) gene Proceedings of Plant and Animal Genome XVI Town and Country Hotel, San Diego, USA, [Details]
O'Gorman, G. M., Park, Stephen D. E., Hill, E. W., Agaba, M., Kemp, S. J., MacHugh, David E. (2008) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infectionTranscriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infection Proceedings of Plant and Animal Genome XVI Town and Country Hotel, San Diego, USA, [Details]
Oâ¿¿Gorman, G. M., Park, S. D., Hill, E. W., Agaba, M., Kemp, S. J., MacHugh, D. E. (2008) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infection Proceedings of: Plant and Animal Genome XVII Conference Town & Country Convention Center, San Diego, California, USA, [Details]
Meade, K. G., O'Gorman, G. M., Kemp, S. J., O'Farrelly, C., MacHugh, D. E. (2008) Antimicrobial Peptide (AMP) and Acute Phase Protein (APP) expression in two subspecies of cattle in response to bovine TrypanosomiasisAntimicrobial Peptide (AMP) and Acute Phase Protein (APP) expression in two subspecies of cattle in response to bovine Trypanosomiasis Proceedings of the Joint Meeting of the Irish Society for Immunology (ISI) & the Ulster Immunology Group (UIG) Royal Dublin Society, Dublin, Ireland, [Details]
McParland, S., Kearney, J.F., MacHugh, D.E., Berry, D. P. (2008) The effect of inbreeding on carcass quality and live conformation measures in Irish beef cattleThe effect of inbreeding on carcass quality and live conformation measures in Irish beef cattle Proceedings of the Agricultural Research Forum Tullamore, Co. Offaly, Ireland, , pp.95 [Details]
Berkowicz, E. W., Magee, D. A., Spillane, C., Sikora, K., Sweeney, T., Kenny, D., Evans, R., MacHugh, D. E. (2008) Identification, validation and genotyping of single nucleotide polymorphisms (SNPs) within bovine imprinted genesIdentification, validation and genotyping of single nucleotide polymorphisms (SNPs) within bovine imprinted genes Proceedings of: 3rd International Symposium on Animal Functional Genomics (ISAFG) Edinburgh International Conference Centre, Edinburgh, UK, [Details]
Eivers, S., McGivney, B., MacHugh, D. E., Taylor, C. T., Mason, K., MacLeod, J., Katz, L. M., Hill, E. W. (2008) Exercise-induced gene expression in equine skeletal muscleExercise-induced gene expression in equine skeletal muscle Proceedings of: International Society for Animal Genetics Conference (ISAG 2008) Amsterdam,The Netherlands, [Details]
Quinn, K.M., Hennessy, K.D., MacHugh, D.E., Feely, D., & Brophy, P.O.; (2007) Genetic parameters for showjumping ability in young horse competitions in Ireland European Association of Animal Production [Details]
Berkowicz, E.W., Magee, D. A., MacHugh, D. E. (2007) Identification and validation of single nucleotide polymorphisms (SNPs) within bovine imprinted genes.Identification and validation of single nucleotide polymorphisms (SNPs) within bovine imprinted genes Proceedings of: Irish Network of Developmental Biologists Meeting University College Cork, Ireland, [Details]
MacHugh, D. E., Gormley, E., Doyle, M. B., Fitzsimons, T., O'Farrelly, C., Costello, E., Keane, J., Zhao, Y., Coussens, P. M., Meade, K. (2007) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattleTranscriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle Proceedings of: International Symposium on Animal Genomics for Animal Health World Organisation for Animal Health, Paris, France, [Details]
Egan, A., MacHugh, D. E., Evans, A. C. (2007) Attention in the stand! Do students need to attend lectures to perform well in exams?Attention in the stand! Do students need to attend lectures to perform well in exams? Proceedings of: Inaugural International Colloquium on University Teaching and Learning University College Dublin, Ireland, [Details]
Quinn. K.M, Hennessy, K.D., MacHugh, D.E., Feely, D., & Brophy, P.O., ; (2007) Sport horse and pony breeding in Ireland European Association of Animal Production [Details]
Oâ¿¿Gorman, G. M., Park, S. D., MacHugh, D. E. (2006) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infection Proceedings of: 6th UK Farm Animal Functional Genomics Workshop Cambridge University Cambridge, UK, [Details]
Park, S. D., Oâ¿¿Gorman, G. M., MacHugh, D. E. (2006) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infection Proceedings of: 6th UK Farm Animal Functional Genomics Workshop Cambridge University Cambridge, UK, [Details]
Park, S. D., Oâ¿¿Gorman, G. M., MacHugh, D. E. (2006) Gene expression changes in Trypanotolerant and Trypanosusceptible African Cattle in response to Gene expression changes in Trypanotolerant and Trypanosusceptible African Cattle in response to Trypanosoma congolense Infection Proceedings of: 2nd International Symposium on Animal Functional Genomics (ISAFG) Michigan State University, USA, [Details]
Bahar, B., Monahan, F.J., Moloney, A.P., Schmidt, O., MacHugh, D.E. & Sweeney, T.; (2006) Stability of gene transcripts in post-mortem bovine skeletal muscle 2nd International Symposium on Animal Functional Genomics Michigan State University, East Lansing, U.S, , 16-MAY-06 - 19-MAY-06 , pp.13-* [Details]
Oâ¿¿Gorman, G. M., Park, S. D., Hill, E. W., MacHugh, D. E. (2006) A functional genomics study of trypanotolerant and trypanosusceptible African cattle during A functional genomics study of trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense Infection Proceedings of: 2nd International Symposium on Animal Functional Genomics (ISAFG) Michigan State University, USA, [Details]
Meade, K.G., Gormley, E., O'Farrelly, C., Costello, E., Keane, J., Zhao, Y., MacHugh, D. E. (2006) Distinct transcriptional profiles of bovine peripheral blood mononuclear cells (PBMC) stimulated with Distinct transcriptional profiles of bovine peripheral blood mononuclear cells (PBMC) stimulated with Mycobacterium bovis antigens in vitro Proceedings of: 6th UK Farm Animal Functional Genomics Workshop Cambridge University Cambridge, UK, [Details]
Meade, K., Gormley, E., O'Farrelly, C., Costello, E., Keane, J., Zhao, Y., MacHugh, D. E. (2006) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle: identification of a gene expression signature of infectionTranscriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle: identification of a gene expression signature of infection Proceedings of: 2nd International Symposium on Animal Functional Genomics (ISAFG) Michigan State University, USA, [Details]
Meade, K., Gormley, E., O'Farrelly, C., Costello, E., Keane, J., Zhao, Y., MacHugh, D. E. (2006) Distinct transcriptional profiles of bovine peripheral blood mononuclear cells (PBMC) stimulated with Distinct transcriptional profiles of bovine peripheral blood mononuclear cells (PBMC) stimulated with Mycobacterium bovis antigens in vitro Proceedings of: 16th European Congress of Immunology - ECI Paris, France, [Details]
MacHugh, D. E. (2006) Functional Genomics of the Immune Response in Cattle: A Tale of Pathogens and ParasitesFunctional Genomics of the Immune Response in Cattle: A Tale of Pathogens and Parasites Proceedings of: 2nd International Symposium on Animal Functional Genomics (ISAFG) Michigan State University, USA, [Details]
MacHugh, D. E. (2006) Genomic approach to animal breeding; thinking â¿¿inside the boxâ¿¿Genomic approach to animal breeding; thinking â¿¿inside the boxâ¿¿ Proceedings of Veterinary Conference - Functional Genomics: The New Route to Food Quality and Improved Animal Health William Jefferson Clinton Auditorium, University College Dublin, Belfield, Dublin 4, Ireland, [Details]
Bahar, B., Monahan, F. J., Moloney, A. P., Schmidt, O., MacHugh, D. E., Sweeney, T. (2006) Stability of gene transcripts in the post-mortem bovine skeletal muscleStability of gene transcripts in the post-mortem bovine skeletal muscle Proceedings of: 2nd International Symposium on Animal Functional Genomics (ISAFG) Michigan State University, USA, [Details]
Howard, D., Hanrahan, J.P., MacHugh, D. E. (2005) Genetic variation in the Galway sheep breed based on microsatellite markersGenetic variation in the Galway sheep breed based on microsatellite markers Proceedings of the Agricultural Research Forum Tullamore, Co. Offaly, Ireland, [Details]
Meade, K.G., Gormley, E., O'Farrelly, C., Costello, E., Keane, J., Coussens, P. M., MacHugh, D. E. (2005) Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle: identification of a gene expression signature of infection.Transcriptional profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and healthy control cattle: identification of a gene expression signature of infection Proceedings of: 4th International Conference on Mycobacterium bovis Dublin, Ireland, [Details]
McGahern, A., Hill, E.W., MacHugh, D.E., Brophy, P. O. (2005) A molecular genetic characterisation of the endangered Irish Draught horseA molecular genetic characterisation of the endangered Irish Draught horse Proceedings of the Agricultural Research Forum Tullamore, Co. Offaly, Ireland, , pp.9 [Details]
Meade, K.G., Coussens, P. M., Gormley, E., MacHugh, D. E. (2004) Gene expression profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and uninfected cattle using immunogenetic bovine cDNA microarrays.Gene expression profiling of peripheral blood mononuclear cells (PBMC) from tuberculosis-infected and uninfected cattle using immunogenetic bovine cDNA microarrays Proceedings of: 1st International Conference on Basic and Clinical Immunogenomics Budapest, Hungary, [Details]
Murphy, A. M., MacHugh, D. E., Boland, M. P., Doherty, M. L. (2004) Linkage mapping and identification of the causative gene for congenital ovine arthrogryposisLinkage mapping and identification of the causative gene for congenital ovine arthrogryposis 29th International Conference on Animal Genetics Meiji University, Surugadai Campus, Tokyo, , pp.79 [Details]
Meade, K.G., Coussens, P. M., Gormley, E., MacHugh, D. E. (2004) Exploring the host response to bovine tuberculosis using cDNA microarrays.Exploring the host response to bovine tuberculosis using cDNA microarrays Proceedings of: 4th UK Farm Animal Functional Genomics Workshop Manchester, UK, [Details]
MacHugh, D.E. (2004) Genomic approaches to animal breeding: thinking inside the boxGenomic approaches to animal breeding: thinking inside the box Proceedings of the International Food Conference, Thinking Beyond Tomorrow: A Safe and Nutritious Food Chain for the Consumer Dublin, Ireland, , pp.10-18 [Details]
Hill, E. W., O'Gorman, G. M., Agaba, M., Gibson, J. P., Hanotte, O., Kemp, S. J., Naessens, J., Coussens, P. M., MacHugh, D. E. (2004) Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics.Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics Proceedings of: 1st International Conference on Basic and Clinical Immunogenomics Budapest, Hungary, [Details]
Fitzpatrick, R., Casey, O., MacHugh, D. E. (2004) Bovine genomics: challenges and applicationsBovine genomics: challenges and applications Proceedings of the Agricultural Research Forum Tullamore, Co. Offaly, Ireland, , pp.109-115 [Details]
Meade, K.G., Gormley, E., Fitzsimons, T., Rosa, G J.M., Coussens, P. M., MacHugh, D. E. (2003) Analysis of host gene expression in tuberculosis-infected cattle using Analysis of host gene expression in tuberculosis-infected cattle using in vitro stimulation of peripheral blood mononuclear cells (PBMC) and cDNA microarrays Proceedings of: Science Foundation Ireland BIOT Meeting Killarney, Ireland, [Details]
Meade, K., Gormley, E., Fitzpatrick, T., Rosa, G.J.M., Coussens, P.M., MacHugh, D.E. (2003) Analysis of host gene expression in tuberculosis-infected cattle using Analysis of host gene expression in tuberculosis-infected cattle using in vitro stimulation of peripheral blood mononuclear cells (PBMC) and cDNA microarrays Proceedings of the International Symposium on Animal Functional Genomics Michigan State University, USA, [Details]
MacHugh, D. E., Meade, K.G., O'Gorman, G. M., Gormley, E., Rosa, G J.M., Coussens, P. M., Hill, E. W. (2003) Using gene expression technologies to analyse the bovine immune response to pathogens and parasitesUsing gene expression technologies to analyse the bovine immune response to pathogens and parasites Proceedings of: Science Foundation Ireland BIOT Meeting Killarney, Ireland, [Details]
MacHugh, D.E. (2003) Functional genomics of the bovine immune system and trypanosomiasis IIFunctional genomics of the bovine immune system and trypanosomiasis II Proceedings of Wellcome Trust Host/Pathogen Meeting Roslin Institute, Roslin, Midlothian, Scotland, [Details]
Hill, E.W., O'Gorman, G.M., Gormley, E., Fitzpatrick, T., Rosa, G J.M., Coussens P.M., MacHugh, D.E. (2003) Functional genomics analysis of the bovine immune response to Functional genomics analysis of the bovine immune response to in vitro co-culture with trypanosomes (Trypanosoma brucei) Proceedings of the International Symposium on Animal Functional Genomics Michigan State University, USA, [Details]
Hill, E. W., Oâ¿¿Gorman, G. M., Gormley, E., Fitzsimons, T., Rosa, G J.M., Coussens, P. M., MacHugh, D. E. (2003) Functional genomics analysis of the bovine immune response to Functional genomics analysis of the bovine immune response to in vitro co-culture with trypanosomes (Trypanosoma brucei) Proceedings of: Science Foundation Ireland BIOT Meeting Killarney, Ireland, [Details]
Murphy, A. M., MacHugh, D. E., Doherty, M. L. (2002) The molecular genetics of inherited ovine arthrogryposisThe molecular genetics of inherited ovine arthrogryposis UCD Conway Institute Festival of Research University College Dublin, Ireland, [Details]
Meade, K. G., Buckley, F., MacHugh, D. E. (2002) Reconstruction of haplotype configurations for key genes associated with milk production in selected cattle populationsReconstruction of haplotype configurations for key genes associated with milk production in selected cattle populations UCD Conway Institute Festival of Research University College Dublin, Ireland, [Details]
MacHugh, D.E. (2002) Functional genomics of the bovine immune system and trypanosomiasis IFunctional genomics of the bovine immune system and trypanosomiasis I Proceedings of Wellcome Trust Host/Pathogen Meeting Roslin Institute, Roslin, Midlothian, Scotland, [Details]
Freeman, A.R., MacHugh, D.E., McKeown, S., Walzer, C., McConnell, D.J., Bradley, D.G. (2000) Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus) Proceedings of the 27th International Conference on Animal Genetics Minneapolis, USA, [Details]
MacHugh, D.E. (1999) Genetic analysis of cattle faunal material from a range of archaeological contexts.Genetic analysis of cattle faunal material from a range of archaeological contexts Proceedings of Wellcome Trust Symposium on Bioarchaeology London, UK, [Details]
Meghen, C.N., Scott, C.S., Bradley, D.G., MacHugh, D.E., Loftus, R.T., Cunningham, E.P. (1998) DNA-based traceability for the meat industryDNA-based traceability for the meat industry Proceedings of the 8th World Conference on Animal Production Seoul, South Korea, , pp.774-775 [Details]
Loftus, R.T., Bradley, D.G., MacHugh, D.E., Troy, C.S., Meghen, C.N., Cunningham, E.P. (1998) Molecular genetics and the evolution of domesticated cattleMolecular genetics and the evolution of domesticated cattle Proceedings of the 8th World Conference on Animal Production Seoul, Korea, , pp.4144-4145 [Details]
Meghen, C., MacHugh, D. E., Loftus, R. T., Bradley, D. G. (1996) Genetic admixture and gene flow in West African cattle populationsGenetic admixture and gene flow in West African cattle populations Proceedings of the 25th International Conference on Animal Genetics Tours, France, [Details]
MacHugh, D.E., Loftus, R.T., Troy, C.S., Bradley, D.G. (1996) DNA Analysis and the Origins and History of Domesticated CattleDNA Analysis and the Origins and History of Domesticated Cattle Proceedings of the Conference on the Archaeozoology of Southwest Asia and Adjacent Areas Working Group Budapest, Hungary, [Details]
MacHugh, D.E., Meghen, C., Loftus, R.T., Cunningham P., Bradley, D.G. (1996) Molecular biogeography of domesticated cattle revealed with microsatellite DNA polymorphismsMolecular biogeography of domesticated cattle revealed with microsatellite DNA polymorphisms Proceedings of the 25th International Conference on Animal Genetics Tours, France, [Details]
Cunningham, E.P., Loftus, R.T., MacHugh, D.E., Bradley, D.G. (1994) Molecular evolution of African, European and Asian cattleMolecular evolution of African, European and Asian cattle Proceedings of the 5th World Congress on Genetics Applied to Livestock Production , pp.86-89 [Details]
Bradley, D.G., Sharp, P.M., Loftus, R.T., MacHugh, D.E., Cunningham, E.P. (1991) Bovine genome mapping and trypanotolerance.Bovine genome mapping and trypanotolerance Proceedings of a workshop held at ILRAD Nairobi, Kenya, [Details]
MacHugh, D.E., Loftus, R.T., Sharp, P.M., Cunningham, E.P. (1990) Bovine microsatellites for studies of genetic diversity in cattle.Bovine microsatellites for studies of genetic diversity in cattle Proceedings of the First Conference on DNA Fingerprinting Berne, Switzerland, [Details]
                                                                                                                                       

Research

Research Interests

1) Development of biomarkers for mycobacterial infections in livestock; in particular, bovine tuberculosis caused by Mycobacterium bovis and Johne's disease caused by M. avium subsp. paratuberculosis (in collaboration with Prof. Stephen Gordon, UCD).

2) Functional genomics of host-pathogen interactions in mammalian mycobacterial infections  (in collaboration with Prof. Stephen Gordon, UCD).

3) Identification of genes, cellular pathways and genetic variants underlying important health and production traits in domestic livestock.

4) Genetic diversity and evolutionary origins of domestic mammals, including analyses of ancient livestock genomes from archaeological material.

4) Identification of genes, cellular pathways and genetic variants underlying athletic performance, exercise and health traits in Thoroughbred horses (in collaboration with Dr. Emmeline Hill, UCD).

5) Computational biology, bioinformatics and biostatistics for large-scale high-dimensional genomics data: gene expression microarrays, genome sequencing, RNA-sequencing (RNA-seq), microRNA-seq, and proteomics.

This research work has contributed to the generation and exploitation of significant intellectual property and Prof. MacHugh is a co-founder and shareholder in IdentiGEN Ltd. (www.identigen.com), Equinome Ltd. (www.equinome.com) and Plusvital Ltd. (www.plusvital.com).

Research Projects

Sponsor : Science Foundation Ireland (SFI)
Title : Development and Validation of Novel Circulating microRNA Biomarkers for Bovine Tuberculosis.
Start Date / End Date : 01-JAN-14 / 30-APR-15
Sponsor : Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)
Title : Novel bovine tuberculosis diagnostics based on bovine circulating serum microRNAs
Start Date / End Date : 01-FEB-14 / 31-JAN-18
Sponsor : Irish Research Council (IRC)
Title : Comparative immunogenomics of the human and animal response to mycobacterial infection.
Start Date / End Date : 01-OCT-15 / 30-SEP-17
Sponsor : University College Dublin (UCD)
Title : Ciara Carberry 2012 Proposal: Analysis of the ruminant microbial methanogenic diversity in cattle divergent for residual feed intake using next generation sequencing technology
Start Date / End Date : 01-MAY-12 / 31-OCT-13
Sponsor : University College Dublin (UCD)
Title : 4th ISAFG 2011
Start Date / End Date : 01-OCT-11 / 31-MAR-12
Sponsor : Science Foundation Ireland (SFI)
Title : 4th International Symposium on Animal Functional Genomics (ISAFG)
Start Date / End Date : 01-AUG-11 / 31-MAR-12
Sponsor : Teagasc
Title : Uterine endometrial gene expression in cows of high and low fertility
Start Date / End Date : 01-OCT-08 / 30-SEP-11
Sponsor : EC Framework (FP7)
Title : MacroSys-Macrophage Systems Biology Applied to Disease Control
Start Date / End Date : 01-NOV-08 / 31-OCT-12
Sponsor : Science Foundation Ireland (SFI)
Title : Functional genomics and proteomics studies of bovine tuberculosis
Start Date / End Date : 01-SEP-09 / 31-AUG-15
Sponsor : Teagasc
Title : Bovine neonatal immunity
Start Date / End Date : 01-OCT-10 / 30-SEP-13
Sponsor : Dept. of Agriculture, Fisheries & Food (DAFF)
Title : A high-resolution survey of genome diversity in the Kerry cattle breed using high-throughput, pan-genomic 54K single nucleotide polymorphism (SNP) chips
Start Date / End Date : 01-APR-10 / 30-SEP-17
Sponsor : Teagasc
Title : Ruminal molecular microbiological analysis in cattle divergent for net feed efficiency
Start Date / End Date : 01-JAN-09 / 31-DEC-11
Sponsor : Teagasc
Title : Investigation of genetic basis of bovine fertility using gene expression and genome-wide association data
Start Date / End Date : 01-OCT-10 / 30-SEP-14
Sponsor : Dept. of Agriculture, Fisheries & Food (DAFF)
Title : A high-resolution survey of genome diversity in the Galway sheep breed using pan-genomic 60K single nucleotide polymorphism (SNP) chips
Start Date / End Date : 01-APR-09 / 31-MAR-10
Sponsor : Science Foundation Ireland (SFI)
Title : Aran O'Loughlin, UREKA supplement - Student summer placement 2007
Start Date / End Date : 11-JUN-07 / 31-AUG-07
Sponsor : Dept. of Agriculture, Fisheries & Food (DAFF)
Title : Development of high-throughout genetic markers for beef traits using variation in genes subject to genomic imprinting
Start Date / End Date : 01-OCT-06 / 30-SEP-09
Sponsor : Dept. of Agriculture, Fisheries & Food (DAFF)
Title : Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to three economically important animal pathogens
Start Date / End Date : 01-OCT-06 / 31-MAR-09
Sponsor : University College Dublin (UCD)
Title : Award: Molecular Genetic Analysis of Bull Fertility via Mitochondrial DNA Sequencing and in vitro Fertilisation
Start Date / End Date : 01-APR-01 / 01-MAR-02
Sponsor : Science Foundation Ireland (SFI)
Title : Fine--mapping and identification of the mutation responsible for inherited ovine arthrogryposis multiplex congenita (AMC): development of an animal model for human AMC
Start Date / End Date : 01-OCT-05 / 31-JAN-09
Sponsor : Science Foundation Ireland (SFI)
Title : Microarray & qRT-PCR validation of gene expression in Trypanotolerant and Trypanosuscoptibus Cattle
Start Date / End Date : 13-JUN-05 / 02-SEP-05
Sponsor : Science Foundation Ireland (SFI)
Title : Study of gene expression in peripheral blood mononuclear cells (PBMC) from cattle infected with Bovine TB
Start Date / End Date : 13-JUN-05 / 02-SEP-05
Sponsor : Science Foundation Ireland (SFI)
Title : Irish Population Genomics: A foundation for pharmacogenomic and complex disease research
Start Date / End Date : 01-FEB-06 / 31-JAN-07
Sponsor : Teagasc
Title : Analysis of Lengtic Diversity in the Galway Sheep Breed
Start Date / End Date : 01-OCT-03 / 30-SEP-05
Sponsor : Science Foundation Ireland (SFI)
Title : Analysis of Mammalian Physiological and genetic regulatory networks using cDNA microarrams
Start Date / End Date : 01-OCT-02 / 31-MAR-08
Sponsor : Teagasc
Title : Genomic analysis of genes influencing fertility and milk production in dairy cattle and a range of other populations and species
Start Date / End Date : 01-SEP-00 / 31-AUG-02

Recent Postgraduates

2005
Dr. Angela M. Murphy:
Genetic linkage mapping of inherited ovine arthrogryposis and identification of a candidate region on sheep chromosome five (PhD thesis).
Ms. Angela McGahern: Masters thesis.
2006
Dr. Kieran G. Meade:
Structural and functional genomics studies in domestic cattle (PhD thesis).
2007
Dr. Grace M. O'Gorman:
Transcriptional profiling studies of trypanotolerant and trypanosusceptible African cattle during Trypanosoma congolense infection (PhD thesis).
2009
Dr. Sinead McParland: Inbreeding in Irish Dairy and Beef Cattle (PhD thesis).
2010
Dr. Dawn Howard: A comparative study of molecular genetic variation in three Irish sheep breeds; the Galway, Texel and Suffolk (PhD thesis).

2011
Dr. Gerard Coyne: Affect of n-3 PUFA on endometrial gene expression (PhD thesis).
Dr. Ciara Carberry: 
An examination of the microbial population in the rumen of beef cattle divergent for feed efficiency (PhD thesis).
Dr. Aideen Killeen: Studies on the molecular control of uterine function and fertility in cattle (PhD thesis).
Dr. Erik Scraggs: High-resolution genomic analyses of inherited ovine arthrogryposis (PhD thesis).

2012
Dr. Erik Berkowicz: Bovine candidate imprinted gene polymorphisms and associations with production, health and fertility traits in Irish beef and dairy cattle (PhD thesis).

2013
Dr. Kate Killick: Functional genomics and systems biology of the bovine host response to mycobacterial pathogens (PhD thesis).

2014
Dr. Nicolas Nalpas: Functional genomics of mycobacteria-macrophage interactions in cattle (PhD thesis).
Dr. Bruce Moran: Next generation sequencing and bioinformatic analysis of a dairy cow fertility model (PhD thesis).
Ms. Maura Casey: Functional genomics and systems biology of the bovine macrophage response to Mycobacterium avium subspecies paratuberculosis (MAP) (MAnSci thesis).

2015
Dr. Kirsten McLoughlin: Biomarker development and functional genomics of the bovine host response to infection with Mycobacterium bovis (PhD thesis).
Dr. Kévin Rue-Albrecht: Comparative functional genomics of the bovine innate immune response to mycobacterial infections (PhD thesis).

 

Teaching

Teaching Philosophy

Introduction to Animal Science (ANSC10010)
Genetics and Biotechnology (ANSC20010)
Animal Genomics (ANSC30030)
Applied Biotechnology (ANSC30100)
Applied Biotechnology (ANSC4115)

 

Postgraduate Education Coordinator, UCD School of Agriculture, Food Science and Veterinary Medicine.
Conway induction lectures for 1st Year Ph.D. students.


 

Enhancement of Teaching

Review and Enhancement of Curriculum

Developing as a Teacher

Innovation & Leadership

Collaborators

Internal Collaborators

Dr. David Magee, UCD School of Agriculture and Food Science.
Dr. Stephen Park, UCD School of Agriculture and Food Science.
Dr. Eamonn Gormley, UCD School of Veterinary Medicine.
Prof. Steve Gordon, UCD School of Veterinary Medicine.
Prof. Michael Doherty, UCD School of Veterinary Medicine.
Dr. Emmeline Hill, UCD School of Agriculture and Food Science.
Dr. Torres Sweeney, UCD School of Veterinary Medicine.
Prof. Alex Evans, UCD School of Agriculture and Food Science.
Prof. Pat Lonergan, UCD School of Agriculture and Food Science.
 
Prof. Brendan Loftus, UCD Conway Institute of Biomolecular and Biomedical Science.
 
Dr. Giuliano Elia, UCD Conway Institute of Biomolecular and Biomedical Science.

Prof. Stephen Pennington, UCD Conway Institute of Biomolecular and Biomedical Science.

External Collaborators

Prof. Dan Bradley, Department of Genetics, Smurfit Institute, TCD.
Dr. Karsten Hokamp, Department of Genetics, Smurfit Institute, TCD.
Prof. Cliona O'Farrelly, School of Biochemistry and Immunology, TCD.
Dr. Noel Murphy, Department of Biology, NUI, Maynooth.
Dr. Morris Agaba, International Livestock Research Institute (ILRI), Kenya.
Prof. Paul Coussens, Michigan State University, USA.
Dr. Tad Sonstegard, Bovine Functional Genomics, Agricultural Research Service, USDA, USA.
Prof. Guilherme Rosa, University of Wisconsin, USA.
Prof. John Gibson, University of New England, Australia.
Prof. Chris Haley, Roslin Institute, Scotland.
Prof. Liz Glass, Roslin Institute, Scotland.
Prof. John Williams. Parco Tecnologico Padano, Italy.
Prof. Steve Kemp, Animal Genomics Laboratory, University of Liverpool.
Prof. Mark Shriver, Pennsylvania State University, USA.
Prof. Richard Simon and Dr. Yingdong Zhao, National Cancer Institute, USA.