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Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits.
Published in:
Genetics Selection Evolution, 2023, v. 55, n. 1, p. 1, doi. 10.1186/s12711-023-00822-1
By:
- Hess, Melanie K.;
- Zetouni, Larissa;
- Hess, Andrew S.;
- Budel, Juliana;
- Dodds, Ken G.;
- Henry, Hannah M.;
- Brauning, Rudiger;
- McCulloch, Alan F.;
- Hickey, Sharon M.;
- Johnson, Patricia L.;
- Elmes, Sara;
- Wing, Janine;
- Bryson, Brooke;
- Knowler, Kevin;
- Hyndman, Dianne;
- Baird, Hayley;
- McRae, Kathryn M.;
- Jonker, Arjan;
- Janssen, Peter H.;
- McEwan, John C.
Publication type:
Article
Beyond the genome: a perspective on the use of DNA methylation profiles as a tool for the livestock industry.
Published in:
Animal Frontiers, 2021, v. 11, n. 6, p. 90, doi. 10.1093/af/vfab060
By:
- Clarke, Shannon;
- Caulton, Alex;
- McRae, Kathryn;
- Brauning, Rudiger;
- Couldrey, Christine;
- Dodds, Ken
Publication type:
Article
The effects of transcription and recombination on mutational dynamics of short tandem repeats.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 3, p. 1321, doi. 10.1093/nar/gkx1253
By:
- Zavodna, Monika;
- Bagshaw, Andrew;
- Brauning, Rudiger;
- Gemmell, Neil J
Publication type:
Article
Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing.
Published in:
Animal Bioscience, 2023, v. 36, n. 7, p. 1010, doi. 10.5713/ab.22.0181
By:
- Sabahat, Sajida;
- Nadeem, Asif;
- Brauning, Rudiger;
- Thomson, Peter C.;
- Khatkar, Mehar S.
Publication type:
Article
Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep.
Published in:
Animal Genetics, 2023, v. 54, n. 3, p. 389, doi. 10.1111/age.13296
By:
- Bedhiaf‐Romdhani, Sonia;
- Baazaoui, Imen;
- Dodds, Ken G.;
- Brauning, Rudiger;
- Anderson, Rayna M.;
- Van Stijn, Tracey C.;
- McCulloch, Alan F.;
- McEwan, John Colin
Publication type:
Article
Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip.
Published in:
Animal Genetics, 2014, v. 45, n. 5, p. 754, doi. 10.1111/age.12197
By:
- Kijas, James W.;
- Porto‐Neto, Laercio;
- Dominik, Sonja;
- Reverter, Antonio;
- Bunch, Rowan;
- McCulloch, Russell;
- Hayes, Ben J.;
- Brauning, Rudiger;
- McEwan, John
Publication type:
Article
The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms.
Published in:
PLoS ONE, 2014, v. 9, n. 12, p. 1, doi. 10.1371/journal.pone.0113862
By:
- Zavodna, Monika;
- Bagshaw, Andrew;
- Brauning, Rudiger;
- Gemmell, Neil J.
Publication type:
Article
Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle.
Published in:
PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0101853
By:
- Couldrey, Christine;
- Brauning, Rudiger;
- Bracegirdle, Jeremy;
- Maclean, Paul;
- Henderson, Harold V.;
- McEwan, John C.
Publication type:
Article
Copy number variants in the sheep genome detected using multiple approaches.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2754-7
By:
- Jenkins, Gemma M.;
- Goddard, Michael E.;
- Black, Michael A.;
- Brauning, Rudiger;
- Auvray, Benoit;
- Dodds, Ken G.;
- Kijas, James W.;
- Cockett, Noelle;
- McEwan, John C.
Publication type:
Article
Construction of relatedness matrices using genotyping-by-sequencing data.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2252-3
By:
- Dodds, Ken G.;
- McEwan, John C.;
- Brauning, Rudiger;
- Anderson, Rayna M.;
- van Stijn, Tracey C.;
- Kristjánsson, Theodor;
- Clarke, Shannon M.
Publication type:
Article
An entropy-reducing data representation approach for bioinformatic data.
Published in:
Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay029
By:
- McCulloch, Alan F;
- Jauregui, Ruy;
- Maclean, Paul H;
- Ashby, Rachael L;
- Moraga, Roger A;
- Laugraud, Aurelie;
- Brauning, Rudiger;
- Dodds, Ken G;
- McEwan, John C
Publication type:
Article
A multiway analysis for identifying high integrity bovine BACs.
Published in:
BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-46
By:
- Ratnakumar, Abhirami;
- Barris, Wesley;
- McWilliam, Sean;
- Brauning, Rudiger;
- McEwan, John C.;
- Snelling, Warren M.;
- Dalrymple, Brian P.
Publication type:
Article
Genomic signatures of inbreeding in a critically endangered parrot, the kākāpo.
Published in:
G3: Genes | Genomes | Genetics, 2021, v. 11, n. 11, p. 1, doi. 10.1093/g3journal/jkab307
By:
- Foster, Yasmin;
- Dutoit, Ludovic;
- Grosser, Stefanie;
- Dussex, Nicolas;
- Foster, Brodie J.;
- Dodds, Ken G.;
- Brauning, Rudiger;
- Stijn, Tracey Van;
- Robertson, Fiona;
- McEwan, John C.;
- Jacobs, Jeanne M. E.;
- Robertson, Bruce C.
Publication type:
Article
Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus).
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 6, p. 2069, doi. 10.1534/g3.120.401295
By:
- Palaiokostas, Christos;
- Clarke, Shannon M.;
- Jeuthe, Henrik;
- Brauning, Rudiger;
- Bilton, Timothy P.;
- Dodds, Ken G.;
- McEwan, John C.;
- De Koning, Dirk-Jan
Publication type:
Article
Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data.
Published in:
G3: Genes | Genomes | Genetics, 2019, v. 9, n. 10, p. 3239, doi. 10.1534/g3.119.400501
By:
- Dodds, Ken G.;
- McEwan, John C.;
- Brauning, Rudiger;
- van Stijn, Tracey C.;
- Rowe, Suzanne J.;
- McEwan, K. Mary;
- Clarke, Shannon M.
Publication type:
Article
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling.
Published in:
PLoS ONE, 2020, v. 15, n. 4, p. 1, doi. 10.1371/journal.pone.0219882
By:
- Hess, Melanie K.;
- Rowe, Suzanne J.;
- Van Stijn, Tracey C.;
- Henry, Hannah M.;
- Hickey, Sharon M.;
- Brauning, Rudiger;
- McCulloch, Alan F.;
- Hess, Andrew S.;
- Kirk, Michelle R.;
- Kumar, Sandeep;
- Pinares-Patiño, Cesar;
- Kittelmann, Sandra;
- Wood, Graham R.;
- Janssen, Peter H.;
- McEwan, John C.
Publication type:
Article
Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.
Published in:
BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09660-3
By:
- Hess, Melanie K.;
- Hodgkinson, Hannah E.;
- Hess, Andrew S.;
- Zetouni, Larissa;
- Budel, Juliana C. C.;
- Henry, Hannah;
- Donaldson, Alistair;
- Bilton, Timothy P.;
- van Stijn, Tracey C.;
- Kirk, Michelle R.;
- Dodds, Ken G.;
- Brauning, Rudiger;
- McCulloch, Alan F.;
- Hickey, Sharon M.;
- Johnson, Patricia L.;
- Jonker, Arjan;
- Morton, Nickolas;
- Hendy, Shaun;
- Oddy, V. Hutton;
- Janssen, Peter H.
Publication type:
Article
Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps.
Published in:
BMC Genetics, 2017, v. 18, p. 1, doi. 10.1186/s12863-017-0534-2
By:
- Prieur, Vincent;
- Clarke, Shannon M.;
- Brito, Luiz F.;
- McEwan, John C.;
- Lee, Michael A.;
- Brauning, Rudiger;
- Dodds, Ken G.;
- Auvray, Benoît
Publication type:
Article
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 57, doi. 10.1186/s13059-015-0622-4
By:
- Andersson, Leif;
- Archibald, Alan L;
- Bottema, Cynthia D;
- Brauning, Rudiger;
- Burgess, Shane C;
- Burt, Dave W;
- Casas, Eduardo;
- Cheng, Hans H;
- Clarke, Laura;
- Couldrey, Christine;
- Dalrymple, Brian P;
- Elsik, Christine G;
- Foissac, Sylvain;
- Giuffra, Elisabetta;
- Groenen, Martien A;
- Hayes, Ben J;
- Huang, LuSheng S;
- Khatib, Hassan;
- Kijas, James W;
- Heebal Kim
Publication type:
Article
Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data.
Published in:
Genetics, 2018, v. 209, n. 2, p. 389, doi. 10.1534/genetics.118.300831
By:
- Bilton, Timothy P.;
- McEwan, John C.;
- Clarke, Shannon M.;
- Brauning, Rudiger;
- van Stijn, Tracey C.;
- Rowe, Suzanne J.;
- Dodds, Ken G.
Publication type:
Article
Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02809-1
By:
- Naval-Sanchez, Marina;
- Nguyen, Quan;
- McWilliam, Sean;
- Porto-Neto, Laercio R.;
- Tellam, Ross;
- Vuocolo, Tony;
- Reverter, Antonio;
- Perez-Enciso, Miguel;
- Brauning, Rudiger;
- Clarke, Shannon;
- McCulloch, Alan;
- Zamani, Wahid;
- Naderi, Saeid;
- Rezaei, Hamid Reza;
- Pompanon, Francois;
- Taberlet, Pierre;
- Worley, Kim C.;
- Gibbs, Richard A.;
- Muzny, Donna M.;
- Jhangiani, Shalini N.
Publication type:
Article
Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome.
Published in:
2022
By:
- Murdoch, Brenda M.;
- Davenport, Kimberly M.;
- Xie, Shangqian;
- Salavati, Mazdak;
- Clark, Emily;
- Archibald, Alan;
- White, Stephen N.;
- Mousel, Michelle R.;
- Worley, Kim;
- Bhattarai, Suraj;
- McKay, Stephanie D.;
- Caulton, Alex;
- Clarke, Shannon;
- Brauning, Rudiger;
- Hadfield, Tracy;
- Rosen, Benjamin D.;
- Smith, Timothy P. L.;
- Cockett, Noelle
Publication type:
Abstract
Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail.
Published in:
Genes, 2024, v. 15, n. 3, p. 294, doi. 10.3390/genes15030294
By:
- Volkova, Natalia A.;
- Romanov, Michael N.;
- Abdelmanova, Alexandra S.;
- Larionova, Polina V.;
- German, Nadezhda Yu.;
- Vetokh, Anastasia N.;
- Shakhin, Alexey V.;
- Volkova, Ludmila A.;
- Sermyagin, Alexander A.;
- Anshakov, Dmitry V.;
- Fisinin, Vladimir I.;
- Griffin, Darren K.;
- Sölkner, Johann;
- Brem, Gottfried;
- McEwan, John C.;
- Brauning, Rudiger;
- Zinovieva, Natalia A.
Publication type:
Article
Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep.
Published in:
Genes, 2021, v. 12, n. 10, p. 1560, doi. 10.3390/genes12101560
By:
- McRae, Kathryn M.;
- Rowe, Suzanne J.;
- Johnson, Patricia L.;
- Baird, Hayley J.;
- Cullen, Neil G.;
- Bixley, Matthew J.;
- Plowman, Jeffrey E.;
- Deb-Choudhury, Santanu;
- Brauning, Rudiger;
- Amyes, Neville C.;
- Dodds, Ken G.;
- Newman, Sheryl-Anne N.;
- McEwan, John C.;
- Clarke, Shannon M.
Publication type:
Article
Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri).
Published in:
Genes, 2018, v. 9, n. 11, p. 544, doi. 10.3390/genes9110544
By:
- Mischler, Claudia;
- Veale, Andrew;
- van Stijn, Tracey;
- Brauning, Rudiger;
- McEwan, John C.;
- Maloney, Richard;
- Robertson, Bruce C.
Publication type:
Article
Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora.
Published in:
Molecular Ecology Resources, 2011, v. 11, n. 3, p. 503, doi. 10.1111/j.1755-0998.2010.02962.x
By:
- OSBORNE, AMY J.;
- BRAUNING, RUDIGER;
- SCHULTZ, JENNIFER K.;
- KENNEDY, MARTIN A.;
- SLATE, JON;
- GEMMELL, NEIL J.
Publication type:
Article
SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 283, doi. 10.1186/s12864-015-1497-1
By:
- Nicolazzi, Ezequiel L;
- Caprera, Andrea;
- Nazzicari, Nelson;
- Cozzi, Paolo;
- Strozzi, Francesco;
- Lawley, Cindy;
- Pirani, Ali;
- Soans, Chandrasen;
- Brew, Fiona;
- Jorjani, Hossein;
- Evans, Gary;
- Simpson, Barry;
- Tosser-Klopp, Gwenola;
- Brauning, Rudiger;
- Williams, John L;
- Stella, Alessandra
Publication type:
Article
Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds.
Published in:
Animals (2076-2615), 2023, v. 13, n. 22, p. 3439, doi. 10.3390/ani13223439
By:
- Volkova, Natalia A.;
- Romanov, Michael N.;
- Abdelmanova, Alexandra S.;
- Larionova, Polina V.;
- German, Nadezhda Yu.;
- Vetokh, Anastasia N.;
- Shakhin, Alexey V.;
- Volkova, Ludmila A.;
- Anshakov, Dmitry V.;
- Fisinin, Vladimir I.;
- Narushin, Valeriy G.;
- Griffin, Darren K.;
- Sölkner, Johann;
- Brem, Gottfried;
- McEwan, John C.;
- Brauning, Rudiger;
- Zinovieva, Natalia A.
Publication type:
Article
Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations.
Published in:
Animals (2076-2615), 2023, v. 13, n. 15, p. 2525, doi. 10.3390/ani13152525
By:
- Moravčíková, Nina;
- Kasarda, Radovan;
- Židek, Radoslav;
- McEwan, John Colin;
- Brauning, Rudiger;
- Landete-Castillejos, Tomás;
- Chonco, Louis;
- Ciberej, Juraj;
- Pokorádi, Jaroslav
Publication type:
Article
Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection.
Published in:
Animals (2076-2615), 2022, v. 12, n. 11, p. 1423, doi. 10.3390/ani12111423
By:
- Moradi, Mohammad Hossein;
- Nejati-Javaremi, Ardeshir;
- Moradi-Shahrbabak, Mohammad;
- Dodds, Ken G.;
- Brauning, Rudiger;
- McEwan, John C.
Publication type:
Article
GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds.
Published in:
Animals (2076-2615), 2020, v. 10, n. 1, p. 5, doi. 10.3390/ani10010005
By:
- Baazaoui, Imen;
- McEwan, John;
- Anderson, Rayna;
- Brauning, Rudiger;
- McCulloch, Alan;
- Van Stijn, Tracey;
- Bedhiaf-Romdhani, Sonia
Publication type:
Article
The Use of "Genotyping-by-Sequencing" to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations.
Published in:
Forests (19994907), 2021, v. 12, n. 7, p. 904, doi. 10.3390/f12070904
By:
- Klápště, Jaroslav;
- Ashby, Rachael L.;
- Telfer, Emily J.;
- Graham, Natalie J.;
- Dungey, Heidi S.;
- Brauning, Rudiger;
- Clarke, Shannon M.;
- Dodds, Ken G.
Publication type:
Article

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