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Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection.

Hall TJ, Vernimmen D, Browne JA, Mullen MP, Gordon SV, MacHugh DE, O'Doherty AM.

Front Genet. 2020 Feb 7;10:1386. doi: 10.3389/fgene.2019.01386. eCollection 2019.


Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed.

Han H, McGivney BA, Farries G, Katz LM, MacHugh DE, Randhawa IAS, Hill EW.

PLoS One. 2020 Feb 12;15(2):e0227212. doi: 10.1371/journal.pone.0227212. eCollection 2020.


Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population.

McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW.

Sci Rep. 2020 Jan 16;10(1):466. doi: 10.1038/s41598-019-57389-5.


Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome.

Farries G, Bryan K, McGivney CL, McGettigan PA, Gough KF, Browne JA, MacHugh DE, Katz LM, Hill EW.

Front Genet. 2019 Nov 26;10:1215. doi: 10.3389/fgene.2019.01215. eCollection 2019.


Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.

McHugo GP, Dover MJ, MacHugh DE.

BMC Biol. 2019 Dec 2;17(1):98. doi: 10.1186/s12915-019-0724-7. Review.


A Population Genomics Analysis of the Native Irish Galway Sheep Breed.

McHugo GP, Browett S, Randhawa IAS, Howard DJ, Mullen MP, Richardson IW, Park SDE, Magee DA, Scraggs E, Dover MJ, Correia CN, Hanrahan JP, MacHugh DE.

Front Genet. 2019 Oct 8;10:927. doi: 10.3389/fgene.2019.00927. eCollection 2019.


Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations.

Han H, Bryan K, Shiraigol W, Bai D, Zhao Y, Bao W, Yang S, Zhang W, MacHugh DE, Dugarjaviin M, Hill EW.

J Hered. 2019 Dec 17;110(7):769-781. doi: 10.1093/jhered/esz032.


Fasciola hepatica Infection in Cattle: Analyzing Responses of Peripheral Blood Mononuclear Cells (PBMC) Using a Transcriptomics Approach.

Garcia-Campos A, Correia CN, Naranjo-Lucena A, Garza-Cuartero L, Farries G, Browne JA, MacHugh DE, Mulcahy G.

Front Immunol. 2019 Aug 29;10:2081. doi: 10.3389/fimmu.2019.02081. eCollection 2019.


Analysis of genetic variation contributing to measured speed in Thoroughbreds identifies genomic regions involved in the transcriptional response to exercise.

Farries G, Gough KF, Parnell AC, McGivney BA, McGivney CL, McGettigan PA, MacHugh DE, Katz LM, Hill EW.

Anim Genet. 2019 Dec;50(6):670-685. doi: 10.1111/age.12848. Epub 2019 Sep 11.


Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent.

Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertuğrul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanović I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG.

Science. 2019 Jul 12;365(6449):173-176. doi: 10.1126/science.aav1002.


A genomic prediction model for racecourse starts in the Thoroughbred horse.

McGivney BA, Hernandez B, Katz LM, MacHugh DE, McGovern SP, Parnell AC, Wiencko HL, Hill EW.

Anim Genet. 2019 Aug;50(4):347-357. doi: 10.1111/age.12798. Epub 2019 Jul 1.


Chinese Mongolian horses may retain early domestic male genetic lineages yet to be discovered.

Han H, Wallner B, Rigler D, MacHugh DE, Manglai D, Hill EW.

Anim Genet. 2019 Aug;50(4):399-402. doi: 10.1111/age.12780. Epub 2019 May 9.


The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis.

O'Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S, Irwin RE, Hall TJ, Browne JA, Nalpas NC, Walsh CP, Gordon SV, Wojewodzic MW, MacHugh DE.

Sci Rep. 2019 Feb 6;9(1):1510. doi: 10.1038/s41598-018-37618-z.


Domestication of cattle: Two or three events?

Pitt D, Sevane N, Nicolazzi EL, MacHugh DE, Park SDE, Colli L, Martinez R, Bruford MW, Orozco-terWengel P.

Evol Appl. 2018 Jul 23;12(1):123-136. doi: 10.1111/eva.12674. eCollection 2019 Jan.


The contribution of myostatin (MSTN) and additional modifying genetic loci to race distance aptitude in Thoroughbred horses racing in different geographic regions.

Hill EW, McGivney BA, Rooney MF, Katz LM, Parnell A, MacHugh DE.

Equine Vet J. 2019 Sep;51(5):625-633. doi: 10.1111/evj.13058. Epub 2019 Jan 5.


RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus).

Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, Gordon SV, MacHugh DE.

Front Genet. 2018 Aug 14;9:278. doi: 10.3389/fgene.2018.00278. eCollection 2018.


Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli.

Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000163. Epub 2018 Mar 20.


Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed.

Browett S, McHugo G, Richardson IW, Magee DA, Park SDE, Fahey AG, Kearney JF, Correia CN, Randhawa IAS, MacHugh DE.

Front Genet. 2018 Feb 19;9:51. doi: 10.3389/fgene.2018.00051. eCollection 2018.


Genetic contributions to precocity traits in racing Thoroughbreds.

Farries G, McGettigan PA, Gough KF, McGivney BA, MacHugh DE, Katz LM, Hill EW.

Anim Genet. 2018 Jun;49(3):193-204. doi: 10.1111/age.12622. Epub 2017 Dec 12.


Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, MacHugh DE, Park SDE, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JAM, Groenen MAM; European Cattle Genetic Diversity Consortium; RPMA Crooijmans.

Heredity (Edinb). 2017 Dec;119(6):469. doi: 10.1038/hdy.2017.59. Epub 2017 Oct 11.


Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components.

Bryan K, McGivney BA, Farries G, McGettigan PA, McGivney CL, Gough KF, MacHugh DE, Katz LM, Hill EW.

BMC Genomics. 2017 Aug 9;18(1):595. doi: 10.1186/s12864-017-4007-9.


Circulating microRNAs as Potential Biomarkers of Infectious Disease.

Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, Shaughnessy RG.

Front Immunol. 2017 Feb 16;8:118. doi: 10.3389/fimmu.2017.00118. eCollection 2017. Review.


Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes.

Braud M, Magee DA, Park SD, Sonstegard TS, Waters SM, MacHugh DE, Spillane C.

Front Genet. 2017 Jan 31;8:3. doi: 10.3389/fgene.2017.00003. eCollection 2017.


Taming the Past: Ancient DNA and the Study of Animal Domestication.

MacHugh DE, Larson G, Orlando L.

Annu Rev Anim Biosci. 2017 Feb 8;5:329-351. doi: 10.1146/annurev-animal-022516-022747. Epub 2016 Oct 28. Review.


Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

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; European Cattle Genetic Diversity Consortium; RPMA Crooijmans.

Heredity (Edinb). 2017 Feb;118(2):169-176. doi: 10.1038/hdy.2016.79. Epub 2016 Sep 28. Erratum in: Heredity (Edinb). 2017 Oct 11;:.


GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.

Rue-Albrecht K, McGettigan PA, Hernández B, Nalpas NC, Magee DA, Parnell AC, Gordon SV, MacHugh DE.

BMC Bioinformatics. 2016 Mar 11;17:126. doi: 10.1186/s12859-016-0971-3.


High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.

Aulicino A, Dinan AM, Miranda-CasoLuengo AA, Browne JA, Rue-Albrecht K, MacHugh DE, Loftus BJ.

BMC Genomics. 2015 Dec 9;16:1046. doi: 10.1186/s12864-015-2246-1.


The MarR family transcription factor Rv1404 coordinates adaptation of Mycobacterium tuberculosis to acid stress via controlled expression of Rv1405c, a virulence-associated methyltransferase.

Healy C, Golby P, MacHugh DE, Gordon SV.

Tuberculosis (Edinb). 2016 Mar;97:154-62. doi: 10.1016/ Epub 2015 Nov 10.


Iodine supplementation of the pregnant dam alters intestinal gene expression and immunoglobulin uptake in the newborn lamb.

McGovern FM, Magee DA, Browne JA, MacHugh DE, Boland TM.

Animal. 2016 Apr;10(4):598-606. doi: 10.1017/S1751731115002505. Epub 2015 Nov 20.


Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.

Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE.

Genome Biol. 2015 Oct 26;16:234. doi: 10.1186/s13059-015-0790-2.


RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli.

Nalpas NC, Magee DA, Conlon KM, Browne JA, Healy C, McLoughlin KE, Rue-Albrecht K, McGettigan PA, Killick KE, Gormley E, Gordon SV, MacHugh DE.

Sci Rep. 2015 Sep 8;5:13629. doi: 10.1038/srep13629.


Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits.

Moran B, Butler ST, Moore SG, MacHugh DE, Creevey CJ.

Reprod Fertil Dev. 2017 Feb;29(2):274-282. doi: 10.1071/RD15128.


The Identification of Circulating MiRNA in Bovine Serum and Their Potential as Novel Biomarkers of Early Mycobacterium avium subsp paratuberculosis Infection.

Farrell D, Shaughnessy RG, Britton L, MacHugh DE, Markey B, Gordon SV.

PLoS One. 2015 Jul 28;10(7):e0134310. doi: 10.1371/journal.pone.0134310. eCollection 2015.


Genomic imprinting effects on complex traits in domesticated animal species.

O'Doherty AM, MacHugh DE, Spillane C, Magee DA.

Front Genet. 2015 Apr 24;6:156. doi: 10.3389/fgene.2015.00156. eCollection 2015. Review.


Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.

Casey ME, Meade KG, Nalpas NC, Taraktsoglou M, Browne JA, Killick KE, Park SD, Gormley E, Hokamp K, Magee DA, MacHugh DE.

Front Immunol. 2015 Feb 4;6:23. doi: 10.3389/fimmu.2015.00023. eCollection 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.

Vegh P, Magee DA, Nalpas NC, Bryan K, McCabe MS, Browne JA, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ.

Tuberculosis (Edinb). 2015 Jan;95(1):60-7.


Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

Schubert M, Jónsson 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 TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5661-9. doi: 10.1073/pnas.1416991111. Epub 2014 Dec 15.


Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus.

Rue-Albrecht K, Magee DA, Killick KE, Nalpas NC, Gordon SV, MacHugh DE.

Front Immunol. 2014 Nov 5;5:536. doi: 10.3389/fimmu.2014.00536. eCollection 2014. Review.


Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts.

Sanderson ND, Norman PJ, Guethlein LA, Ellis SA, Williams C, Breen M, Park SD, Magee DA, Babrzadeh F, Warry A, Watson M, Bradley DG, MacHugh DE, Parham P, Hammond JA.

J Immunol. 2014 Dec 15;193(12):6016-30. doi: 10.4049/jimmunol.1401980. Epub 2014 Nov 14.


Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.

Killick KE, Magee DA, Park SD, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K.

Front Immunol. 2014 Oct 1;5:422. doi: 10.3389/fimmu.2014.00422. eCollection 2014.


RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.

McLoughlin KE, Nalpas NC, Rue-Albrecht K, Browne JA, Magee DA, Killick KE, Park SD, Hokamp K, Meade KG, O'Farrelly C, Gormley E, Gordon SV, MacHugh DE.

Front Immunol. 2014 Aug 26;5:396. doi: 10.3389/fimmu.2014.00396. eCollection 2014.


Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits.

Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE.

Anim Genet. 2014 Aug;45 Suppl 1:25-39. doi: 10.1111/age.12168. Epub 2014 Jul 2. Review.


Innate cytokine profiling of bovine alveolar macrophages reveals commonalities and divergence in the response to Mycobacterium bovis and Mycobacterium tuberculosis infection.

Magee DA, Conlon KM, Nalpas NC, Browne JA, Pirson C, Healy C, McLoughlin KE, Chen J, Vordermeier HM, Gormley E, MacHugh DE, Gordon SV.

Tuberculosis (Edinb). 2014 Jul;94(4):441-50. doi: 10.1016/ Epub 2014 May 5.


Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.

Vegh P, Foroushani AB, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ.

Vet Immunol Immunopathol. 2013 Oct 1;155(4):238-44. doi: 10.1016/j.vetimm.2013.08.004. Epub 2013 Aug 24.


Receptor-mediated recognition of mycobacterial pathogens.

Killick KE, Ní Cheallaigh C, O'Farrelly C, Hokamp K, MacHugh DE, Harris J.

Cell Microbiol. 2013 Sep;15(9):1484-95. doi: 10.1111/cmi.12161. Epub 2013 Jul 29. Review.


Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.

Nalpas NC, Park SD, Magee DA, Taraktsoglou M, Browne JA, Conlon KM, Rue-Albrecht K, Killick KE, Hokamp K, Lohan AJ, Loftus BJ, Gormley E, Gordon SV, MacHugh DE.

BMC Genomics. 2013 Apr 8;14:230. doi: 10.1186/1471-2164-14-230.


Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10.

Orr N, Hill EW, Gu J, Govindarajan P, Conroy J, van Grevenhof EM, Ducro BJ, van Arendonk JA, Knaap JH, van Weeren PR, Machugh DE, Ennis S, Brama PA.

Anim Genet. 2013 Aug;44(4):408-12. doi: 10.1111/age.12016. Epub 2012 Dec 25.


Dietary n-3 polyunsaturated fatty acid supplementation alters the expression of genes involved in the control of fertility in the bovine uterine endometrium.

Waters SM, Coyne GS, Kenny DA, MacHugh DE, Morris DG.

Physiol Genomics. 2012 Sep 18;44(18):878-88. Epub 2012 Jul 31.


Horses for courses: a DNA-based test for race distance aptitude in thoroughbred racehorses.

Hill EW, Ryan DP, MacHugh DE.

Recent Pat DNA Gene Seq. 2012 Dec;6(3):203-8.


MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance.

McGivney BA, Browne JA, Fonseca RG, Katz LM, Machugh DE, Whiston R, Hill EW.

Anim Genet. 2012 Dec;43(6):810-2. doi: 10.1111/j.1365-2052.2012.02329.x. Epub 2012 Feb 27.


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