Research

The UCD AGG, led by Professor David MacHugh, applies advanced genomic technologies to key challenges in animal health, production, and conservation. Our research focuses on understanding the genetic basis of important traits in livestock and exploring the evolutionary history of domesticated animals.

Our Research Focus

• Host-Pathogen Interactions: In collaboration with Professor Stephen Gordon, we investigate the functional genomics of infectious diseases in livestock, with a specific focus on bovine tuberculosis caused by infection with Mycobacterium bovis. Our goal is to identify genetic markers for disease resistance and develop next-generation diagnostics to control and eradicate this disease from livestock populations.

• Population & Evolutionary Genomics: We study the genetic diversity and historical origins of modern and ancient livestock populations. Our work includes sequencing the genome of the extinct aurochs to understand its contribution to contemporary cattle breeds.

• Equine Genomics: In collaboration with Professor Emmeline Hill, we use genomics to identify genes related to athletic performance in thoroughbred horses, providing insights that can inform breeding decisions.

Highlighted

Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations

James A. Ward, Gillian P. McHugo, Michael J. Dover, Thomas J. Hall, Said Ismael Ng’ang’a, Tad S. Sonstegard, Daniel G. Bradley, Laurent A.F. Frantz, Michael Salter-Townshend, David E. MacHugh

iScience  ·  01 Jul 2022  ·  doi:10.1016/j.isci.2022.104672

All

2025

Functional genomics of trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense across multiple time points and tissues

Gillian P. McHugo, James A. Ward, John A. Browne, Grace M. O’Gorman, Kieran G. Meade, Emmeline W. Hill, Thomas J. Hall, David E. MacHugh

PLOS Neglected Tropical Diseases  ·  04 Aug 2025  ·  doi:10.1371/journal.pntd.0012882

Genetic control of the transcriptional response to active tuberculosis disease and treatment

John F. O’Grady, Alexander S. Leonard, Houcheng Li, Lingzhao Fang, Hubert Pausch, Isobel C. Gormley, Stephen. V. Gordon, David E. MacHugh

Cold Spring Harbor Laboratory  ·  14 Apr 2025  ·  doi:10.1101/2025.04.11.648383

Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle

John F. O’Grady, Gillian P. McHugo, James A. Ward, Thomas J. Hall, Sarah L. Faherty O’Donnell, …, Hubert Pausch, Kieran G. Meade, Isobel C. Gormley, Stephen V. Gordon, David E. MacHugh

Communications Biology  ·  24 Mar 2025  ·  doi:10.1038/s42003-025-07846-x

The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project

Lingzhao Fang, Jinyan Teng, Qing Lin, Zhonghao Bai, Shuli Liu, …, Laurent Frantz, Huaijun Zhou, Zhe Zhang, George E. Liu, Curtis P. Van Tassell

Nature Genetics  ·  17 Mar 2025  ·  doi:10.1038/s41588-025-02121-5

Cattle Genomics: Aurochs Admixture in East Asia

James A. Ward, David E. MacHugh

Animal Research and One Health  ·  12 Feb 2025  ·  doi:10.1002/aro2.102

Short communication: Genomic prediction based on unbiased estimation of the genomic relationship matrix in pigs

M.Y. Li, L.Y. Shi, D.E. MacHugh, X.Q. Wang, J.J. Tian, L.G. Wang, Y.J. Deng, L.X. Wang, F.P. Zhao

animal  ·  01 Feb 2025  ·  doi:10.1016/j.animal.2024.101402

Functional genomics of trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense across multiple time points and tissues

Gillian P. McHugo, James A. Ward, John A. Browne, Grace M. O’Gorman, Kieran G. Meade, Emmeline W. Hill, Thomas J. Hall, David E. MacHugh

Cold Spring Harbor Laboratory  ·  31 Jan 2025  ·  doi:10.1101/2025.01.31.635858

A genome‐wide association study for recurrent laryngeal neuropathy in the Thoroughbred horse identifies a candidate gene that regulates myelin structure

Charlotte L. McGivney, Beatrice A. McGivney, Gabriella Farries, Katie F. Gough, Haige Han, Amy R. Holtby, David E. MacHugh, Lisa Michelle Katz, Emmeline W. Hill

Equine Veterinary Journal  ·  10 Jan 2025  ·  doi:10.1111/evj.14461

2024

Genome-edited livestock to secure sustainability

Tad Sonstegard, Jon Bostrom, Kyra Martins, Eui-Soo Kim, Carolina Correia, David MacHugh, Sabreena Larson, Daniel Carlson

Reproduction, Fertility and Development  ·  13 Dec 2024  ·  doi:10.1071/rd24145

KPRR: a novel machine learning approach for effectively capturing nonadditive effects in genomic prediction

Mianyan Li, Thomas Hall, David E MacHugh, Liang Chen, Dorian Garrick, Lixian Wang, Fuping Zhao

Briefings in Bioinformatics  ·  22 Nov 2024  ·  doi:10.1093/bib/bbae683

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Gillian P. McHugo, James A. Ward, Said Ismael Ng’ang’a, Laurent A. F. Frantz, Michael Salter-Townshend, Emmeline W. Hill, Grace M. O’Gorman, Kieran G. Meade, Thomas J. Hall, David E. MacHugh

Heredity  ·  08 Nov 2024  ·  doi:10.1038/s41437-024-00734-w

Recent selection and introgression facilitated high-altitude adaptation in cattle

Yang Lyu, Fuwen Wang, Haijian Cheng, Jing Han, Ruihua Dang, …, Yu Wang, Yuanpeng Gao, Wenfa Lu, Chuzhao Lei, Ningbo Chen

Science Bulletin  ·  01 Nov 2024  ·  doi:10.1016/j.scib.2024.05.030

Functional analysis of the Mycobacterium bovis AF2122/97 PhoPR system

Jose Maria Urtasun-Elizari, Ruoyao Ma, Hayleah Pickford, Damien Farrell, Gabriel Gonzalez, …, Chie Nakajima, Yasuhiko Suzuki, David E. MacHugh, Apoorva Bhatt, Stephen V. Gordon

Tuberculosis  ·  01 Sep 2024  ·  doi:10.1016/j.tube.2024.102544

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

David MacHugh, Gillian McHugo, James Ward, Said Ng’ang’a, Laurent Frantz, Michael Salter-Townshend, Emmeline Hill, Grace O’Gorman, Kieran Meade, Thomas Hall

Springer Science and Business Media LLC  ·  31 Jul 2024  ·  doi:10.21203/rs.3.rs-4622059/v1

Integrative and comparative genomic analyses of mammalian macrophage responses to intracellular mycobacterial pathogens

Thomas J. Hall, Gillian P. McHugo, Michael P. Mullen, James A. Ward, Kate E. Killick, John A. Browne, Stephen V. Gordon, David E. MacHugh

Tuberculosis  ·  01 Jul 2024  ·  doi:10.1016/j.tube.2023.102453

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Gillian P. McHugo, James A. Ward, Said Ismael Ng’ang’a, Laurent A.F. Frantz, Michael Salter-Townshend, Emmeline W. Hill, Grace M. O’Gorman, Kieran G. Meade, Thomas J. Hall, David E. MacHugh

Cold Spring Harbor Laboratory  ·  20 Jun 2024  ·  doi:10.1101/2024.06.20.599852

Unveiling the Role of Endoplasmic Reticulum Stress Pathways in Canine Demodicosis

Pamela A. Kelly, Gillian P. McHugo, Caitriona Scaife, Susan Peters, M. Lynn Stevenson, Jennifer S. McKay, David E. MacHugh, Irene Lara Saez, Rory Breathnach

Parasite Immunology  ·  01 Apr 2024  ·  doi:10.1111/pim.13033

Genome-wide Association Studies of Novel Resilience Traits Identify Important Immune QTL Regions and Candidate Genes in Duroc Pigs

Mianyan Li, Lei Pu, David E. MacHugh, Jingjing Tian, Xiaoqing Wang, …, Lijun Shi, Hongmei Gao, Ying Yu, Lixian Wang, Fuping Zhao

Journal of Integrative Agriculture  ·  01 Apr 2024  ·  doi:10.1016/j.jia.2024.04.017

Genomic insights into the population history and adaptive traits of Latin American Criollo cattle

James A. Ward, Said I. Ng’ang’a, Imtiaz A. S. Randhawa, Gillian P. McHugo, John F. O’Grady, …, Jóse F. Garcia, Tad S. Sonstegard, Laurent A. F. Frantz, Michael Salter-Townshend, David E. MacHugh

Royal Society Open Science  ·  01 Mar 2024  ·  doi:10.1098/rsos.231388

2023

Unveiling the Role of Endoplasmic Reticulum Stress Pathways in Canine Demodicosis

Pamela A Kelly, Gillian P. McHugo, Caitriona Scaife, Susan Peters, M. Lynn Stevenson, Jennifer S McKay, David E. MacHugh, Irene Lara Saez, Rory Breathnach

Cold Spring Harbor Laboratory  ·  14 Aug 2023  ·  doi:10.1101/2023.08.11.552979

Preferential differential gene expression within the WC1.1⁺γδ T cell compartment in cattle naturally infected withMycobacterium bovis

Sajad A. Bhat, Mahmoud Elnaggar, Thomas J. Hall, Gillian P. McHugo, Cian Reid, David E. MacHugh, Kieran G. Meade

Cold Spring Harbor Laboratory  ·  25 Jul 2023  ·  doi:10.1101/2023.07.21.550071

Integrative and comparative genomic analyses of mammalian macrophage responses to intracellular mycobacterial pathogens

Thomas J. Hall, Gillian P. McHugo, Michael P. Mullen, James A. Ward, Kate E. Killick, John A. Browne, Stephen V. Gordon, David E. MacHugh

Cold Spring Harbor Laboratory  ·  15 Jul 2023  ·  doi:10.1101/2023.07.14.549042

Integrative genomics analysis highlights functionally relevant genes for equine behaviour

Amy R. Holtby, Thomas J. Hall, Beatrice A. McGivney, Haige Han, Keith J. Murphy, David E. MacHugh, Lisa M. Katz, Emmeline W. Hill

Animal Genetics  ·  27 Mar 2023  ·  doi:10.1111/age.13320

Inbreeding depression and durability in the North American Thoroughbred horse

Emmeline W. Hill, Beatrice A. McGivney, David E. MacHugh

Animal Genetics  ·  26 Feb 2023  ·  doi:10.1111/age.13309

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

Haige Han, Imtiaz A. S. Randhawa, David E. MacHugh, Beatrice A. McGivney, Lisa M. Katz, Manglai Dugarjaviin, Emmeline W. Hill

BMC Genomics  ·  19 Jan 2023  ·  doi:10.1186/s12864-023-09116-8

2022

Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Haige Han, Beatrice A. McGivney, Lucy Allen, Dongyi Bai, Leanne R. Corduff, …, Hubert Pausch, Carol Readhead, David Warburton, Manglai Dugarjaviin, Emmeline W. Hill

Communications Biology  ·  13 Dec 2022  ·  doi:10.1038/s42003-022-04206-x

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

Haige Han, Imtiaz A. S. Randhawa, David E. MacHugh, Beatrice A. McGivney, Lisa M. Katz, Manglai Dugarjaviin, Emmeline W. Hill

Research Square Platform LLC  ·  06 Sep 2022  ·  doi:10.21203/rs.3.rs-1810897/v1

High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course

Carolina N. Correia, Gillian P. McHugo, John A. Browne, Kirsten E. McLoughlin, Nicolas C. Nalpas, …, Bernardo Villarreal-Ramos, H. Martin Vordermeier, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh

Tuberculosis  ·  01 Sep 2022  ·  doi:10.1016/j.tube.2022.102235

Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations

James A. Ward, Gillian P. McHugo, Michael J. Dover, Thomas J. Hall, Said Ismael Ng’ang’a, Tad S. Sonstegard, Daniel G. Bradley, Laurent A.F. Frantz, Michael Salter-Townshend, David E. MacHugh

iScience  ·  01 Jul 2022  ·  doi:10.1016/j.isci.2022.104672

Inbreeding depression and the probability of racing in the Thoroughbred horse

Emmeline W. Hill, Martin A. Stoffel, Beatrice A. McGivney, David E. MacHugh, Josephine M. Pemberton

Proceedings of the Royal Society B: Biological Sciences  ·  29 Jun 2022  ·  doi:10.1098/rspb.2022.0487

High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected withMycobacterium bovisacross an experimental time course

Carolina N. Correia, Gillian P. McHugo, John A. Browne, Kirsten E. McLoughlin, Nicolas C. Nalpas, …, Bernardo Villarreal-Ramos, H. Martin Vordermeier, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh

Cold Spring Harbor Laboratory  ·  19 Apr 2022  ·  doi:10.1101/2022.04.19.488769

Transcriptome Profiling of Developing Ovine Fat Tail Tissue Reveals an Important Role for MTFP1 in Regulation of Adipogenesis

Jiangang Han, Sijia Ma, Benmeng Liang, Tianyou Bai, Yuhetian Zhao, Yuehui Ma, David E. MacHugh, Lina Ma, Lin Jiang

Frontiers in Cell and Developmental Biology  ·  08 Mar 2022  ·  doi:10.3389/fcell.2022.839731

2021

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes

Dagmara A. Niedziela, Amalia Naranjo-Lucena, Verónica Molina-Hernández, John A. Browne, Álvaro Martínez-Moreno, José Pérez, David E. MacHugh, Grace Mulcahy

Frontiers in Immunology  ·  20 Sep 2021  ·  doi:10.3389/fimmu.2021.729217

Genome-wide local ancestry and direct evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus)

James A. Ward, Gillian P. McHugo, Michael J. Dover, Thomas J. Hall, Said Ismael Ng’ang’a, Tad S. Sonstegard, Daniel G. Bradley, Laurent A. F. Frantz, Michael Salter-Townshend, David E. MacHugh

Cold Spring Harbor Laboratory  ·  27 Aug 2021  ·  doi:10.1101/2021.08.26.457829

Timing of transcriptomic peripheral blood mononuclear cell responses of sheep to Fasciola hepatica infection differs from those of cattle, reflecting different disease phenotypes

Dagmara A. Niedziela, Amalia Naranjo-Lucena, Verónica Molina-Hernández, John A. Browne, Álvaro Martínez-Moreno, José Pérez, David E. MacHugh, Grace Mulcahy

Cold Spring Harbor Laboratory  ·  22 Jun 2021  ·  doi:10.1101/2021.06.21.449266

Transcriptomic Analysis of Ovine Hepatic Lymph Node Following Fasciola hepatica Infection – Inhibition of NK Cell and IgE-Mediated Signaling

Amalia Naranjo-Lucena, Carolina N. Correia, Verónica Molina-Hernández, Álvaro Martínez-Moreno, John A. Browne, José Pérez, David E. MacHugh, Grace Mulcahy

Frontiers in Immunology  ·  28 May 2021  ·  doi:10.3389/fimmu.2021.687579

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

Kirsten E. McLoughlin, Carolina N. Correia, John A. Browne, David A. Magee, Nicolas C. Nalpas, …, Bernardo Villarreal-Ramos, H. Martin Vordermeier, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh

Frontiers in Veterinary Science  ·  28 May 2021  ·  doi:10.3389/fvets.2021.662002

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria

Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon, David E. MacHugh

BMC Genomics  ·  12 May 2021  ·  doi:10.1186/s12864-021-07643-w

2020

Integrative Genomics of the Mammalian Alveolar Macrophage Response to Intracellular Mycobacteria

Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon, David E. MacHugh

Springer Science and Business Media LLC  ·  10 Dec 2020  ·  doi:10.21203/rs.3.rs-121955/v1

Identification of novel molecular markers of mastitis caused by

Di Wang, Lei Liu, Serafino M A Augustino, Tao Duan, Thomas J Hall, David E MacHugh, Jinhuan Dou, Yi Zhang, Yachun Wang, Ying Yu

Journal of animal science and biotechnology  ·  11 Sep 2020  ·  pmid:32944235

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria

Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon, David E. MacHugh

Cold Spring Harbor Laboratory  ·  26 Aug 2020  ·  doi:10.1101/2020.08.25.266668

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

Haige Han, Beatrice A. McGivney, Gabriella Farries, Lisa M. Katz, David E. MacHugh, Imtiaz A. S. Randhawa, Emmeline W. Hill

PLOS ONE  ·  12 Feb 2020  ·  doi:10.1371/journal.pone.0227212

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

Beatrice A. McGivney, Haige Han, Leanne R. Corduff, Lisa M. Katz, Teruaki Tozaki, David E. MacHugh, Emmeline W. Hill

Scientific Reports  ·  16 Jan 2020  ·  doi:10.1038/s41598-019-57389-5

2019

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

Gillian P. McHugo, Michael J. Dover, David E. MacHugh

BMC Biology  ·  01 Dec 2019  ·  doi:10.1186/s12915-019-0724-7

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

Gabriella Farries, Kenneth Bryan, Charlotte L. McGivney, Paul A. McGettigan, Katie F. Gough, John A. Browne, David E. MacHugh, Lisa Michelle Katz, Emmeline W. Hill

Frontiers in Genetics  ·  26 Nov 2019  ·  doi:10.3389/fgene.2019.01215

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

Haige Han, Kenneth Bryan, Wunierfu Shiraigol, Dongyi Bai, Yiping Zhao, …, Siqin Yang, Wengang Zhang, David E MacHugh, Manglai Dugarjaviin, Emmeline W Hill

Journal of Heredity  ·  19 Oct 2019  ·  doi:10.1093/jhered/esz032

A Population Genomics Analysis of the Native Irish Galway Sheep Breed

Gillian P. McHugo, Sam Browett, Imtiaz A. S. Randhawa, Dawn J. Howard, Michael P. Mullen, …, Erik Scraggs, Michael J. Dover, Carolina N. Correia, James P. Hanrahan, David E. MacHugh

Frontiers in Genetics  ·  08 Oct 2019  ·  doi:10.3389/fgene.2019.00927

Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

Beatrice A. McGivney, Haige Han, Leanne R. Corduff, Lisa M Katz, Teruaki Tozaki, David E. MacHugh, Emmeline W. Hill

Cold Spring Harbor Laboratory  ·  16 Sep 2019  ·  doi:10.1101/770545

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

G. Farries, K. F. Gough, A. C. Parnell, B. A. McGivney, C. L. McGivney, P. A. McGettigan, D. E. MacHugh, L. M. Katz, E. W. Hill

Animal Genetics  ·  11 Sep 2019  ·  doi:10.1111/age.12848

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

Andres Garcia-Campos, Carolina N. Correia, Amalia Naranjo-Lucena, Laura Garza-Cuartero, Gabriella Farries, John A. Browne, David E. MacHugh, Grace Mulcahy

Frontiers in Immunology  ·  29 Aug 2019  ·  doi:10.3389/fimmu.2019.02081

Identification of expression quantitative trait loci in the skeletal muscle of Thoroughbreds reveals heritable variation in expression of genes relevant to cofactor metabolism

G. Farries, K. Bryan, C. L. McGivney, P. A. McGettigan, K. F. Gough, J.A. Browne, D. E. MacHugh, L. M. Katz, E. W. Hill

Cold Spring Harbor Laboratory  ·  24 Jul 2019  ·  doi:10.1101/713669

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

Marta Pereira Verdugo, Victoria E Mullin, Amelie Scheu, Valeria Mattiangeli, Kevin G Daly, …, Marjan Mashkour, David Orton, Liora Kolska Horwitz, Matthew D Teasdale, Daniel G Bradley

Science (New York, N.Y.)  ·  12 Jul 2019  ·  pmid:31296769

A genomic prediction model for racecourse starts in the Thoroughbred horse

B. A. McGivney, B. Hernandez, L. M. Katz, D. E. MacHugh, S. P. McGovern, A. C. Parnell, H. L. Wiencko, E. W. Hill

Animal Genetics  ·  01 Jul 2019  ·  doi:10.1111/age.12798

A Population Genomics Analysis of the Native Irish Galway Sheep Breed

Gillian P. McHugo, Sam Browett, Imtiaz A. S. Randhawa, Dawn J. Howard, Michael P. Mullen, …, Erik Scraggs, Michael Dover, Carolina N. Correia, James P. Hanrahan, David E. MacHugh

Cold Spring Harbor Laboratory  ·  23 May 2019  ·  doi:10.1101/645754

Genome to Phenome: Improving Animal Health, Production, and Well-Being – A New USDA Blueprint for Animal Genome Research 2018–2027

Caird Rexroad, Jeffrey Vallet, Lakshmi Kumar Matukumalli, James Reecy, Derek Bickhart, …, Jerry Taylor, Bhanu Telugu, Alison Van Eenennaam, Curtis P. Van Tassell, Kevin Wells

Frontiers in Genetics  ·  16 May 2019  ·  doi:10.3389/fgene.2019.00327

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

H. Han, B. Wallner, D. Rigler, D. E. MacHugh, D. Manglai, E. W. Hill

Animal Genetics  ·  09 May 2019  ·  doi:10.1111/age.12780

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

Alan Mark O’Doherty, Kevin Christophe Rue-Albrecht, David Andrew Magee, Simone Ahting, Rachelle Elizabeth Irwin, …, Nicolas Claude Nalpas, Colum Patrick Walsh, Stephen Vincent Gordon, Marcin Włodzimierz Wojewodzic, David Evan MacHugh

Scientific Reports  ·  06 Feb 2019  ·  doi:10.1038/s41598-018-37618-z

Alveolar macrophage chromatin is modified to orchestrate host response toMycobacterium bovisinfection

Thomas Jonathan Hall, Douglas Vernimmen, John Andrew Browne, Michael P. Mullen, Stephen Vincent Gordon, David Evan MacHugh, Alan Mark O’Doherty

Cold Spring Harbor Laboratory  ·  14 Jan 2019  ·  doi:10.1101/520098

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

E W Hill, B A McGivney, M F Rooney, L M Katz, A Parnell, D E MacHugh

Equine veterinary journal  ·  05 Jan 2019  ·  pmid:30604488

CHAPTER 4. MicroRNAs and Mycobacterial Infections in Humans and Domestic Animals

Sarah L. Faherty O’Donnell, Carolina N. Correia, David E. MacHugh

Drug Discovery  ·  01 Jan 2019  ·  doi:10.1039/9781788016421-00105

2018

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap.

Elisabetta Giuffra, Christopher K Tuggle

Annual review of animal biosciences  ·  14 Nov 2018  ·  pmid:30427726

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)

Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kevin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh

Frontiers in Genetics  ·  14 Aug 2018  ·  doi:10.3389/fgene.2018.00278

Domestication of cattle: Two or three events?

Daniel Pitt, Natalia Sevane, Ezequiel L Nicolazzi, David E MacHugh, Stephen D E Park, Licia Colli, Rodrigo Martinez, Michael W Bruford, Pablo Orozco-terWengel

Evolutionary applications  ·  23 Jul 2018  ·  pmid:30622640

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)

Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kevin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh

Cold Spring Harbor Laboratory  ·  04 Apr 2018  ·  doi:10.1101/294330

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

Kerri M Malone, Kévin Rue-Albrecht, David A Magee, Kevin Conlon, Olga T Schubert, …, Alicia Smyth, Eamonn Gormley, Ruedi Aebersold, David E MacHugh, Stephen V Gordon

Microbial genomics  ·  20 Mar 2018  ·  pmid:29557774

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed.

Sam Browett, Gillian McHugo, Ian W Richardson, David A Magee, Stephen D E Park, Alan G Fahey, John F Kearney, Carolina N Correia, Imtiaz A S Randhawa, David E MacHugh

Frontiers in genetics  ·  19 Feb 2018  ·  pmid:29520297

2017

Genetic contributions to precocity traits in racing Thoroughbreds.

G Farries, P A McGettigan, K F Gough, B A McGivney, D E MacHugh, L M Katz, E W Hill

Animal genetics  ·  12 Dec 2017  ·  pmid:29230835

Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

Sam Browett, Gillian McHugo, Ian W. Richardson, David A. Magee, Stephen D. E. Park, Alan G. Fahey, John F. Kearney, Carolina N. Correia, Imtiaz A. S. Randhawa, David E. MacHugh

Cold Spring Harbor Laboratory  ·  28 Oct 2017  ·  doi:10.1101/210229

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

M R Upadhyay, W Chen, J A Lenstra, C R J Goderie, D E MacHugh, …, D Matassino, F Ciani, H-J Megens, J A M van Arendonk, M A M Groenen

Heredity  ·  11 Oct 2017  ·  pmid:29019469

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

Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, Charlotte L. McGivney, Katie F. Gough, David E. MacHugh, Lisa M. Katz, Emmeline W. Hill

BMC Genomics  ·  09 Aug 2017  ·  doi:10.1186/s12864-017-4007-9

Circulating microRNAs as Potential Biomarkers of Infectious Disease

Carolina N. Correia, Nicolas C. Nalpas, Kirsten E. McLoughlin, John A. Browne, Stephen V. Gordon, David E. MacHugh, Ronan G. Shaughnessy

Frontiers in Immunology  ·  16 Feb 2017  ·  doi:10.3389/fimmu.2017.00118

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

David E. MacHugh, Greger Larson, Ludovic Orlando

Annual Review of Animal Biosciences  ·  08 Feb 2017  ·  doi:10.1146/annurev-animal-022516-022747

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

Martin Braud, David A. Magee, Stephen D. E. Park, Tad S. Sonstegard, Sinead M. Waters, David E. MacHugh, Charles Spillane

Frontiers in Genetics  ·  31 Jan 2017  ·  doi:10.3389/fgene.2017.00003

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

Bruce Moran, Stephen T. Butler, Stephen G. Moore, David E. MacHugh, Christopher J. Creevey

Reproduction, Fertility and Development  ·  01 Jan 2017  ·  doi:10.1071/RD15128

2016

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

M R Upadhyay, W Chen, J A Lenstra, C R J Goderie, D E MacHugh, …, D Matassino, F Ciani, H-J Megens, J A M van Arendonk, M A M Groenen

Heredity  ·  28 Sep 2016  ·  doi:10.1038/hdy.2016.79

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

Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew C. Parnell, Stephen V. Gordon, David E. MacHugh

BMC Bioinformatics  ·  11 Mar 2016  ·  doi:10.1186/s12859-016-0971-3

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

Claire Healy, Paul Golby, David E. MacHugh, Stephen V. Gordon

Tuberculosis  ·  01 Mar 2016  ·  doi:10.1016/j.tube.2015.10.003

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

F.M. McGovern, D.A. Magee, J.A. Browne, D.E. MacHugh, T.M. Boland

animal  ·  01 Jan 2016  ·  doi:10.1017/S1751731115002505

2015

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

Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus

BMC Genomics  ·  01 Dec 2015  ·  doi:10.1186/s12864-015-2246-1

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

Stephen D E Park, David A. Magee, Paul A. McGettigan, Matthew D. Teasdale, Ceiridwen J. Edwards, …, Shuaishuai Tai, Daniel G. Bradley, Tad S. Sonstegard, Brendan J. Loftus, David E. MacHugh

Genome Biology  ·  26 Oct 2015  ·  doi:10.1186/s13059-015-0790-2

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

Nicolas C. Nalpas, David A. Magee, Kevin M. Conlon, John A. Browne, Claire Healy, …, Paul A. McGettigan, Kate E. Killick, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh

Scientific Reports  ·  08 Sep 2015  ·  doi:10.1038/srep13629

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

Damien Farrell, Ronan G. Shaughnessy, Louise Britton, David E. MacHugh, Bryan Markey, Stephen V. Gordon

PLOS ONE  ·  28 Jul 2015  ·  doi:10.1371/journal.pone.0134310

Genomic imprinting effects on complex traits in domesticated animal species

Alan M. O’Doherty, David E. MacHugh, Charles Spillane, David A. Magee

Frontiers in Genetics  ·  24 Apr 2015  ·  doi:10.3389/fgene.2015.00156

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

Maura E. Casey, Kieran G. Meade, Nicolas C. Nalpas, Maria Taraktsoglou, John A. Browne, …, Stephen D. E. Park, Eamonn Gormley, Karsten Hokamp, David A. Magee, David E. MacHugh

Frontiers in Immunology  ·  04 Feb 2015  ·  doi:10.3389/fimmu.2015.00023

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

Peter Vegh, David A. Magee, Nicolas C. Nalpas, Kenneth Bryan, Matthew S. McCabe, …, Kevin M. Conlon, Stephen V. Gordon, Daniel G. Bradley, David E. MacHugh, David J. Lynn

Tuberculosis  ·  01 Jan 2015  ·  doi:10.1016/j.tube.2014.10.011

2014

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Mikkel Schubert, Hákon Jónsson, Dan Chang, Clio Der Sarkissian, Luca Ermini, …, Rasmus Nielsen, Laurent Excoffier, Eske Willerslev, Beth Shapiro, Ludovic Orlando

Proceedings of the National Academy of Sciences  ·  15 Dec 2014  ·  doi:10.1073/pnas.1416991111

Definition of the Cattle Killer Cell Ig–like Receptor Gene Family: Comparison with Aurochs and Human Counterparts

Nicholas D Sanderson, Paul J Norman, Lisbeth A Guethlein, Shirley A Ellis, Christina Williams, …, Mick Watson, Daniel G Bradley, David E MacHugh, Peter Parham, John A Hammond

The Journal of Immunology  ·  01 Dec 2014  ·  doi:10.4049/jimmunol.1401980

Comparative Functional Genomics and the Bovine Macrophage Response to Strains of the Mycobacterium Genus

Kévin Rue-Albrecht, David A. Magee, Kate E. Killick, Nicolas C. Nalpas, Stephen V. Gordon, David E. MacHugh

Frontiers in Immunology  ·  05 Nov 2014  ·  doi:10.3389/fimmu.2014.00536

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

Kate E. Killick, David A. Magee, Stephen D. E. Park, Maria Taraktsoglou, John A. Browne, …, Nicolas C. Nalpas, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh, Karsten Hokamp

Frontiers in Immunology  ·  01 Oct 2014  ·  doi:10.3389/fimmu.2014.00422

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

Kirsten E. McLoughlin, Nicolas C. Nalpas, Kévin Rue-Albrecht, John A. Browne, David A. Magee, …, Kieran G. Meade, Cliona O’Farrelly, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh

Frontiers in Immunology  ·  26 Aug 2014  ·  doi:10.3389/fimmu.2014.00396

Selection Signatures in Worldwide Sheep Populations

Maria-Ines Fariello, Bertrand Servin, Gwenola Tosser-Klopp, Rachel Rupp, Carole Moreno, Magali San Cristobal, Simon Boitard

PLoS ONE  ·  15 Aug 2014  ·  doi:10.1371/journal.pone.0103813

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

D A Magee, C Spillane, E W Berkowicz, K M Sikora, D E MacHugh

Animal genetics  ·  02 Jul 2014  ·  pmid:24990393

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

David A. Magee, David E. MacHugh, Ceiridwen J. Edwards

Animal Frontiers  ·  01 Jul 2014  ·  doi:10.2527/af.2014-0017

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

David A Magee, Kevin M Conlon, Nicolas C Nalpas, John A Browne, Chris Pirson, …, Jing Chen, H Martin Vordermeier, Eamonn Gormley, David E MacHugh, Stephen V Gordon

Tuberculosis (Edinburgh, Scotland)  ·  05 May 2014  ·  pmid:24882682

SNPs for parentage testing and traceability in globally diverse breeds of sheep.

Michael P Heaton, Kreg A Leymaster, Theodore S Kalbfleisch, James W Kijas, Shannon M Clarke, …, Veronica Basnayake, Dustin T Petrik, Barry Simpson, Timothy P L Smith, Carol G Chitko-McKown

PloS one  ·  16 Apr 2014  ·  pmid:24740156

2013

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

Peter Vegh, Amir B K Foroushani, David A Magee, Matthew S McCabe, John A Browne, …, Kevin M Conlon, Stephen V Gordon, Daniel G Bradley, David E MacHugh, David J Lynn

Veterinary immunology and immunopathology  ·  24 Aug 2013  ·  pmid:24021155

Receptor-mediated recognition of mycobacterial pathogens.

Kate E Killick, Clíona Ní Cheallaigh, Cliona O’Farrelly, Karsten Hokamp, David E MacHugh, James Harris

Cellular microbiology  ·  29 Jul 2013  ·  pmid:23795683

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

Nicolas C Nalpas, Stephen D E Park, David A Magee, Maria Taraktsoglou, John A Browne, …, Amanda J Lohan, Brendan J Loftus, Eamonn Gormley, Stephen V Gordon, David E MacHugh

BMC genomics  ·  08 Apr 2013  ·  pmid:23565803

Genomics of Performance

Emmeline W. Hill, Lisa M. Katz, David E. MacHugh

Equine Genomics  ·  04 Feb 2013  ·  doi:10.1002/9781118522158.ch17

2012

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

N Orr, E W Hill, J Gu, P Govindarajan, J Conroy, …, J H Knaap, P R van Weeren, D E Machugh, S Ennis, P A J Brama

Animal genetics  ·  25 Dec 2012  ·  pmid:23278111

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

Emmeline W Hill, Donal P Ryan, David E MacHugh

Recent patents on DNA & gene sequences  ·  01 Dec 2012  ·  pmid:22845060

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

Sinéad M Waters, Gerard S Coyne, David A Kenny, David E MacHugh, Dermot G Morris

Physiological genomics  ·  31 Jul 2012  ·  pmid:22851761

Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis.

David E Machugh, Maria Taraktsoglou, Kate E Killick, Nicolas C Nalpas, John A Browne, Stephen DE Park, Karsten Hokamp, Eamonn Gormley, David A Magee

Veterinary research  ·  28 Mar 2012  ·  pmid:22455317

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

Beatrice A McGivney, John A Browne, Rita G Fonseca, Lisa M Katz, David E Machugh, Ronan Whiston, Emmeline W Hill

Animal genetics  ·  27 Feb 2012  ·  pmid:22497477

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis.

David A Magee, Maria Taraktsoglou, Kate E Killick, Nicolas C Nalpas, John A Browne, …, David J Lynn, Karsten Hokamp, Stephen V Gordon, Eamonn Gormley, David E MacHugh

PloS one  ·  22 Feb 2012  ·  pmid:22384131

Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection.

James W Kijas, Johannes A Lenstra, Ben Hayes, Simon Boitard, Laercio R Porto Neto, …, William Barendse, Elena Ciani, Herman Raadsma, John McEwan, Brian Dalrymple

PLoS biology  ·  07 Feb 2012  ·  pmid:22346734

The genetic origin and history of speed in the Thoroughbred racehorse.

Mim A Bower, Beatrice A McGivney, Michael G Campana, Jingjing Gu, Lisa S Andersson, …, Alan G Fahey, Gabriella Lindgren, David E MacHugh, Galina Sulimova, Emmeline W Hill

Nature communications  ·  24 Jan 2012  ·  pmid:22273681

Functional characterisation of bovine interleukin 8 promoter haplotypes in vitro.

Kieran G Meade, Grace M O’Gorman, Fernando Narciandi, David E Machugh, Cliona O’Farrelly

Molecular immunology  ·  12 Jan 2012  ·  pmid:22244152

Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples.

Michael P Mullen, Christopher J Creevey, Donagh P Berry, Matt S McCabe, David A Magee, …, Stephen D Park, Paul A McGettigan, Matt C Lucy, David E Machugh, Sinead M Waters

BMC genomics  ·  11 Jan 2012  ·  pmid:22235840

2011

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes.

Kate E Killick, John A Browne, Stephen D E Park, David A Magee, Irene Martin, …, Stephen V Gordon, Eamonn Gormley, Cliona O’Farrelly, Karsten Hokamp, David E MacHugh

BMC genomics  ·  19 Dec 2011  ·  pmid:22182502

PHLDA2 is an imprinted gene in cattle.

K M Sikora, D A Magee, E W Berkowicz, P Lonergan, A C O Evans, F Carter, A Comte, S M Waters, D E MacHugh, C Spillane

Animal genetics  ·  02 Dec 2011  ·  pmid:22497461

Impact of delayed processing of bovine peripheral blood on differential gene expression.

Michael P Sheridan, John A Browne, David E MacHugh, Eamon Costello, Eamonn Gormley

Veterinary immunology and immunopathology  ·  17 Nov 2011  ·  pmid:22138316

On the Breeds of Cattle—Historic and Current Classifications

Marleen Felius, Peter A. Koolmees, Bert Theunissen, European Cattle Genetic Diversity Consortium, Johannes A. Lenstra

Diversity  ·  09 Nov 2011  ·  doi:10.3390/d3040660

MSTN genotype (g.66493737C/T) association with speed indices in Thoroughbred racehorses.

Emmeline W Hill, Rita G Fonseca, Beatrice A McGivney, Jingjing Gu, David E MacHugh, Lisa M Katz

Journal of applied physiology (Bethesda, Md. : 1985)  ·  20 Oct 2011  ·  pmid:22016373

PGC-1α encoded by the PPARGC1A gene regulates oxidative energy metabolism in equine skeletal muscle during exercise.

S S Eivers, B A McGivney, J Gu, D E MacHugh, L M Katz, E W Hill

Animal genetics  ·  21 Sep 2011  ·  pmid:22404351

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.

E W Berkowicz, D A Magee, D P Berry, K M Sikora, D J Howard, M P Mullen, R D Evans, C Spillane, D E MacHugh

Animal genetics  ·  23 May 2011  ·  pmid:22221028

Erratum to “Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle” (J. Dairy Sci. 93:5959–5969)

M.P. Mullen, D.P. Berry, D.J. Howard, M.G. Diskin, C.O. Lynch, E.W. Berkowicz, D.A. Magee, D.E. MacHugh, S.M. Waters

Journal of Dairy Science  ·  01 Feb 2011  ·  doi:10.3168/jds.2011-94-2-1069

Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle.

S M Waters, M S McCabe, D J Howard, L Giblin, D A Magee, D E MacHugh, D P Berry

Animal genetics  ·  01 Feb 2011  ·  pmid:20528848

DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic imprinting domain are associated with performance traits.

Klaudia M Sikora, David A Magee, Erik W Berkowicz, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, David E Machugh, Charles Spillane

BMC genetics  ·  07 Jan 2011  ·  pmid:21214909

2010

Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens.

Maria Taraktsoglou, Urszula Szalabska, David A Magee, John A Browne, Torres Sweeney, Eamonn Gormley, David E MacHugh

Veterinary immunology and immunopathology  ·  10 Dec 2010  ·  pmid:21242003

Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance.

E W Hill, J Gu, B A McGivney, D E MacHugh

Animal genetics  ·  01 Dec 2010  ·  pmid:21070277

Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses.

N Orr, W Back, J Gu, P Leegwater, P Govindarajan, …, J A M Van Arendonk, D E MacHugh, S Ennis, E W Hill, P A J Brama

Animal genetics  ·  01 Dec 2010  ·  pmid:21070269

Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle.

M P Mullen, D P Berry, D J Howard, M G Diskin, C O Lynch, E W Berkowicz, D A Magee, D E MacHugh, S M Waters

Journal of dairy science  ·  01 Dec 2010  ·  pmid:21094770

A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits.

D A Magee, E W Berkowicz, K M Sikora, D P Berry, S D E Park, …, D A Kenny, R D Evans, B W Wickham, C Spillane, D E Machugh

Animal : an international journal of animal bioscience  ·  01 Dec 2010  ·  pmid:22445369

Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle.

E W Hill, S S Eivers, B A McGivney, R G Fonseca, J Gu, N A Smith, J A Browne, D E MacHugh, L M Katz

Equine veterinary journal. Supplement  ·  01 Nov 2010  ·  pmid:21059063

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.

J Gu, D E MacHugh, B A McGivney, S D E Park, L M Katz, E W Hill

Equine veterinary journal. Supplement  ·  01 Nov 2010  ·  pmid:21059062

DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle.

David A Magee, Klaudia M Sikora, Erik W Berkowicz, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, Charles Spillane, David E MacHugh

BMC genetics  ·  13 Oct 2010  ·  pmid:20942903

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.

Emmeline W Hill, Beatrice A McGivney, Jingjing Gu, Ronan Whiston, David E Machugh

BMC genomics  ·  11 Oct 2010  ·  pmid:20932346

High concordance of bovine single nucleotide polymorphism genotypes generated using two independent genotyping strategies.

D A Magee, E W Berkowicz, K M Sikora, T Sweeney, D A Kenny, …, R D Evans, B W Wickham, D G Bradley, C Spillane, D E MacHugh

Animal biotechnology  ·  01 Oct 2010  ·  pmid:20967645

Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle.

Erik W Berkowicz, David A Magee, Klaudia M Sikora, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, Charles Spillane, David E MacHugh

The Journal of dairy research  ·  08 Sep 2010  ·  pmid:20822563

Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle.

David A Magee, Donagh P Berry, Erik W Berkowicz, Klaudia M Sikora, Dawn J Howard, Michael P Mullen, Ross D Evans, Charles Spillane, David E MacHugh

The Journal of heredity  ·  03 Sep 2010  ·  pmid:20817761

Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training.

Beatrice A McGivney, Paul A McGettigan, John A Browne, Alexander C O Evans, Rita G Fonseca, …, Amanda Lohan, David E MacHugh, Barbara A Murphy, Lisa M Katz, Emmeline W Hill

BMC genomics  ·  23 Jun 2010  ·  pmid:20573200

Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform.

D A Magee, S D E Park, E Scraggs, A M Murphy, M L Doherty, J W Kijas, D E MacHugh

Journal of animal science  ·  18 Jun 2010  ·  pmid:20562352

Spatial Trends of Genetic Variation of Domestic Ruminants in Europe

Denis Laloë, Katayoun Moazami-Goudarzi, Johannes A. Lenstra, Paolo Ajmone Marsan, Pedro Azor, …, Ingrid Olsaker, Clemen Rodellar, Alessio Valentini, Pamela Wiener, ECGDCEC

Diversity  ·  17 Jun 2010  ·  doi:10.3390/d2060932

Corrigendum

Physiological Genomics  ·  01 Apr 2010  ·  doi:10.1152/physiolgenomics.zh7-3458-corr.2010

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

Ceiridwen J Edwards, David A Magee, Stephen D E Park, Paul A McGettigan, Amanda J Lohan, …, Andrew T Chamberlain, Martin B Richards, Daniel G Bradley, Brendan J Loftus, David E MacHugh

PloS one  ·  17 Feb 2010  ·  pmid:20174668

Correction: A Sequence Polymorphism in MSTN Predicts Sprinting Ability and Racing Stamina in Thoroughbred Horses

Emmeline W. Hill, Jingjing Gu, Suzanne S. Eivers, Rita G. Fonseca, Beatrice A. McGivney, Preethi Govindarajan, Nick Orr, Lisa M. Katz, David E. MacHugh

PLoS ONE  ·  26 Jan 2010  ·  pmc:PMC2812075

A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in thoroughbred horses.

Emmeline W Hill, Jingjing Gu, Suzanne S Eivers, Rita G Fonseca, Beatrice A McGivney, Preethi Govindarajan, Nick Orr, Lisa M Katz, David E MacHugh

PloS one  ·  20 Jan 2010  ·  pmid:20098749

2009

Transcriptional adaptations following exercise in thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy.

Beatrice A McGivney, Suzanne S Eivers, David E MacHugh, James N MacLeod, Grace M O’Gorman, Stephen D E Park, Lisa M Katz, Emmeline W Hill

BMC genomics  ·  30 Dec 2009  ·  pmid:20042072

Divergent antimicrobial peptide (AMP) and acute phase protein (APP) responses to Trypanosoma congolense infection in trypanotolerant and trypanosusceptible cattle.

Kieran G Meade, Grace M O’Gorman, Emmeline W Hill, Fernando Narciandi, Morris Agaba, Stephen J Kemp, Cliona O’Farrelly, David E MacHugh

Molecular immunology  ·  03 Nov 2009  ·  pmid:19889461

Alterations in oxidative gene expression in equine skeletal muscle following exercise and training.

Suzanne S Eivers, Beatrice A McGivney, Rita G Fonseca, David E MacHugh, Katie Menson, Stephen D Park, Jose-Luis L Rivero, Cormac T Taylor, Lisa M Katz, Emmeline W Hill

Physiological genomics  ·  27 Oct 2009  ·  pmid:19861432

A genome scan for positive selection in thoroughbred horses.

Jingjing Gu, Nick Orr, Stephen D Park, Lisa M Katz, Galina Sulimova, David E MacHugh, Emmeline W Hill

PloS one  ·  02 Jun 2009  ·  pmid:19503617

Gene expression profiling of the host response to Mycobacterium bovis infection in cattle.

D E MacHugh, E Gormley, S D E Park, J A Browne, M Taraktsoglou, C O’Farrelly, K G Meade

Transboundary and emerging diseases  ·  26 May 2009  ·  pmid:19486308

Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility.

Grace M O’Gorman, Stephen D E Park, Emmeline W Hill, Kieran G Meade, Paul M Coussens, Morris Agaba, Jan Naessens, Stephen J Kemp, David E MacHugh

BMC genomics  ·  01 May 2009  ·  pmid:19409086

2008

Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program.

Kieran G Meade, Eamonn Gormley, Cliona O’Farrelly, Stephen D Park, Eamon Costello, Joseph Keane, Yingdong Zhao, David E MacHugh

BMC genomics  ·  29 Sep 2008  ·  pmid:18823559

Inbreeding effects on postweaning production traits, conformation, and calving performance in Irish beef cattle.

S McParland, J F Kearney, D E MacHugh, D P Berry

Journal of animal science  ·  01 Aug 2008  ·  pmid:18676727

Transmission ratio distortion at the growth hormone gene (GH1) in bovine preimplantation embryos: An in vitro culture-induced phenomenon?

Angela M Murphy, Kieran G Meade, Patricia A Hayes, Stephen D E Park, Alex C O Evans, Patrick Lonergan, David E MacHugh

Molecular reproduction and development  ·  01 May 2008  ·  pmid:17948248

2007

Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues.

Bojlul Bahar, Frank J Monahan, Aidan P Moloney, Olaf Schmidt, David E MacHugh, Torres Sweeney

BMC molecular biology  ·  29 Nov 2007  ·  pmid:18047648

Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease.

Kieran G Meade, Eamonn Gormley, Mairéad B Doyle, Tara Fitzsimons, Cliona O’Farrelly, Eamon Costello, Joseph Keane, Yingdong Zhao, David E MacHugh

BMC genomics  ·  31 Oct 2007  ·  pmid:17974019

Taurine and zebu admixture in Near Eastern cattle: a comparison of mitochondrial, autosomal and Y-chromosomal data.

C J Edwards, J F Baird, D E MacHugh

Animal genetics  ·  24 Aug 2007  ·  pmid:17725685

Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep chromosome 5.

Angela M Murphy, David E MacHugh, Stephen D E Park, Erik Scraggs, Chris S Haley, David J Lynn, Maurice P Boland, Michael L Doherty

Mammalian genome : official journal of the International Mammalian Genome Society  ·  22 Jan 2007  ·  pmid:17242863

Tumour necrosis factor-alpha (TNF-alpha) increases nuclear factor kappaB (NFkappaB) activity in and interleukin-8 (IL-8) release from bovine mammary epithelial cells.

D C Fitzgerald, K G Meade, A N McEvoy, L Lillis, E P Murphy, D E MacHugh, A W Baird

Veterinary immunology and immunopathology  ·  09 Jan 2007  ·  pmid:17276517

2006

Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses.

A M McGahern, C J Edwards, M A Bower, A Heffernan, S D E Park, P O Brophy, D G Bradley, D E MacHugh, E W Hill

Animal genetics  ·  01 Oct 2006  ·  pmid:16978181

Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations.

A McGahern, M A M Bower, C J Edwards, P O Brophy, G Sulimova, …, M Vizuete-Forster, M Levine, S Li, D E MacHugh, E W Hill

Animal genetics  ·  01 Oct 2006  ·  pmid:16978180

Cytokine mRNA profiling of peripheral blood mononuclear cells from trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense.

Grace M O’Gorman, Stephen D E Park, Emmeline W Hill, Kieran G Meade, Laura C Mitchell, …, John P Gibson, Olivier Hanotte, Jan Naessens, Stephen J Kemp, David E MacHugh

Physiological genomics  ·  19 Sep 2006  ·  pmid:16985010

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).

Kieran G Meade, Eamonn Gormley, Stephen D E Park, Tara Fitzsimons, Guilherme J M Rosa, Eamon Costello, Joseph Keane, Paul M Coussens, David E MacHugh

Veterinary immunology and immunopathology  ·  19 Jun 2006  ·  pmid:16784781

2005

Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics.

Emmeline W Hill, Grace M O’Gorman, Morris Agaba, John P Gibson, Olivier Hanotte, Stephen J Kemp, Jan Naessens, Paul M Coussens, David E MacHugh

Veterinary immunology and immunopathology  ·  15 May 2005  ·  pmid:15808304

Convenient detection of single nucleotide polymorphism haplotypes in the bovine growth hormone gene using amplification-created restriction sites.

K G Meade, E W Hill, F Buckley, D E MacHugh

Animal genetics  ·  01 Apr 2005  ·  pmid:15771738

2004

Admixture and diversity in West African cattle populations.

A R Freeman, C M Meghen, D E MacHugh, R T Loftus, M D Achukwi, A Bado, B Sauveroche, D G Bradley

Molecular ecology  ·  01 Nov 2004  ·  pmid:15488005

Ancient DNA analysis of 101 cattle remains: limits and prospects

Ceiridwen J Edwards, David E MacHugh, Keith M Dobney, Louise Martin, Nerissa Russell, …, Kevin C MacDonald, Daniel Helmer, Anne Tresset, Jean-Denis Vigne, Daniel G Bradley

Journal of Archaeological Science  ·  01 Jun 2004  ·  doi:10.1016/j.jas.2003.11.001

2003

Feasibility and utility of microsatellite markers in archaeological cattle remains from a Viking Age settlement in Dublin.

C J Edwards, J Connellan, P F Wallace, S D E Park, F M McCormick, I Olsaker, E Eythórsdóttir, D E MacHugh, J F Bailey, D G Bradley

Animal genetics  ·  01 Dec 2003  ·  pmid:14687070

2001

Livestock genetic origins: goats buck the trend.

D E MacHugh, D G Bradley

Proceedings of the National Academy of Sciences of the United States of America  ·  08 May 2001  ·  pmid:11344280

Genetic evidence for Near-Eastern origins of European cattle.

C S Troy, D E MacHugh, J F Bailey, D A Magee, R T Loftus, P Cunningham, A T Chamberlain, B C Sykes, D G Bradley

Nature  ·  26 Apr 2001  ·  pmid:11323670

Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus).

A R Freeman, D E MacHugh, S McKeown, C Walzer, D J McConnell, D G Bradley

Heredity  ·  01 Mar 2001  ·  pmid:11488972

2000

Phylogenetic analysis of the tribe Bovini using microsatellites.

L R Ritz, M L Glowatzki-Mullis, D E MacHugh, C Gaillard

Animal genetics  ·  01 Jun 2000  ·  pmid:10895308

Y-specific microsatellite polymorphisms in a range of bovid species.

C J Edwards, C Gaillard, D G Bradley, D E MacHugh

Animal genetics  ·  01 Apr 2000  ·  pmid:10782212

1999

A microsatellite survey of cattle from a centre of origin: the Near East.

R T Loftus, O Ertugrul, A H Harba, M A El-Barody, D E MacHugh, S D Park, D G Bradley

Molecular ecology  ·  01 Dec 1999  ·  pmid:10632853

Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds.

D E MacHugh, C S Troy, F McCormick, I Olsaker, E Eythórsdóttir, D G Bradley

Philosophical transactions of the Royal Society of London. Series B, Biological sciences  ·  29 Jan 1999  ·  pmid:10091250

1998

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers.

D E MacHugh, R T Loftus, P Cunningham, D G Bradley

Animal genetics  ·  01 Oct 1998  ·  pmid:9800321

1997

Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus).

D E MacHugh, M D Shriver, R T Loftus, P Cunningham, D G Bradley

Genetics  ·  01 Jul 1997  ·  pmid:9215909

1996

Mitochondrial diversity and the origins of African and European cattle.

D G Bradley, D E MacHugh, P Cunningham, R T Loftus

Proceedings of the National Academy of Sciences of the United States of America  ·  14 May 1996  ·  pmid:8643540

1994

Mitochondrial genetic variation in European, African and Indian cattle populations.

R T Loftus, D E MacHugh, L O Ngere, D S Balain, A M Badi, D G Bradley, E P Cunningham

Animal genetics  ·  01 Aug 1994  ·  pmid:7985843

Microsatellite DNA variation within and among European cattle breeds.

D E Machugh, R T Loftus, D G Bradley, P M Sharp, P Cunningham

Proceedings. Biological sciences  ·  22 Apr 1994  ·  pmid:8008754

Evidence for two independent domestications of cattle.

R T Loftus, D E MacHugh, D G Bradley, P M Sharp, P Cunningham

Proceedings of the National Academy of Sciences of the United States of America  ·  29 Mar 1994  ·  pmid:8146187

Zebu‐taurine variation in Y chromosomal DNA: a sensitive assay for genetic introgression in West African trypanotolerant cattle populations

D G Bradley, D E MacHugh, R T Loftus, R S Sow, C H Hoste, E P Cunningham

Animal Genetics  ·  01 Feb 1994  ·  doi:10.1111/j.1365-2052.1994.tb00048.x

Zebu-taurine variation in Y chromosomal DNA: a sensitive assay for genetic introgression in west African trypanotolerant cattle populations.

D G Bradley, D E MacHugh, R T Loftus, R S Sow, C H Hoste, E P Cunningham

Animal genetics  ·  01 Feb 1994  ·  pmid:7909219

ISSN 1664-8021 (Online) | Frontiers in genetics | The ISSN Portal

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