Recent Key References
Cabrera CP, Dunn IC, Fell M, Wilson PW, Burt DW, Waddington D, Talbot R, Hocking PM, Law A, Knott S, Haley, CS, de Koning DJ. (2012). Complex traits analysis of chicken growth using targeted genetical genomics. Animal Genetics, 43(2): 163-171
Everitt, A.R., Clare, S., Pertel, T., John, S.P., Wash, R.S., Smith, S.E., Chin, C.R., Feeley, E.M., Sims, J.S., Adams, D.J., Wise, H.M., Kane, L., Goulding, D., Digard, P., Anttila, V., Baillie, J.K., Walsh, T.S., Hume, D.A., Palotie, A., Xue, Y., Colonna, V., Tyler-Smith, C., Dunning, J., Gordon, S.B., The GenISIS Investigators, The MOSAIC Investigators, Smyth, R.L., Openshaw, P.J., Dougan, G., Brass, A.L. & Kellam, P. (2012). IFITM3 restricts the morbidity and mortality associated with influenza. Nature, 484(7395): 519-U146
Powell JE, Kranis A, Floyd J, Dekkers JCM, Knott S, Haley CS (2012). Optimal use of regression models in genome-wide association studies. Animal Genetics, 43(2): 133-143.
Wei WH, Hemani G, Gyenesei A, Vitart V, Navarro P, Hayward C, Cabrera CP, Huffman, JE, Knott SA, Hicks AA, Rudan I, Pramstaller PP, Wild SH, Wilson JF, Campbell H, Hastie ND, Wright AF, Haley CS. (2012). Genome-wide analysis of epistasis in body mass index using multiple human populations. European Journal of Human Genetics, E-pub 15 February.
Boulton K, Massault C, Houston RD, de Koning DJ, Haley CS, Bovenhuis H, Batargias C,
Canario AVM, Kotoulas G, Tsigenopoulos CS (2011). QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata). Aquaculture 319(1-2): 58-66.
Haley C. (2011). A cornucopia of maize genes. Nature Genetics 43(2): 87-88.
Hemani G, Theocharidis A, Wei W, Haley C. (2011). EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics 27(11): 1462-1465.
Karacaoren B, Silander T, Alvarez-Castro JM, Haley CS, de Koning DJ. (2011). Association analyses of the MAS-QTL data set using grammar, principal components and Bayesian network methodologies. BMC Proceedings 5 (Suppl 3): S8.
Massault C, Franch R, Haley C, de Koning DJ, Bovenhuis H, Pellizzari C, Patarnello T,
Bargelloni L. (2011). Quantitative trait loci for resistance to fish pasteurellosis in gilthead sea bream (Sparus aurata). Animal Genetics 42(2): 191-203.
Wei WH, Hemani, G, Hicks AA, Vitart V, Cabrera-Cardenas C, Navarro P, Huffman J,
Hayward C, Knott SA, Rudan I, Pramstaller PP, Wild SH, Wilson JF, Campbell H, Dunlop, MG, Hastie N, Wright AF, Haley CS. (2011). Characterisation of Genome-Wide Association Epistasis Signals for Serum Uric Acid in Human Population Isolates. PLoS One 6(8): e23836.
Wei WH, Duan Y, Haley CS, Ren J, de Koning DJ, Huang LS. (2011). High throughput analyses of epistasis for swine body dimensions and organ weights. Animal Genetics 42(1): 15-21.
Wei WH, Skinner TM, Anderson JA, Southwood OI, Plastow G, Archibald AL, Haley CS. (2011). Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/Large White composite population. Animal Genetics 42(1): 83-85.
Wilkinson S, Haley CS, Alderson L, Weiner P. (2011). An empirical assessment of individual-based population genetic statistical techniques: Application to British pig breeds. Heredity 106(2): 261-269.
Wilkinson S, Wiener P, Teverson D, Haley C, Hocking P. M. (2011). Characterisation of the genetic diversity, structure and admixture of British chicken breeds. Animal Genetics In Press.
Basheer A, Wilson PW, Talbot RT, Sharp PJ, Law A, Windsor D, Haley CS, Dunn, IC. (2010). Detection of genetic loci for incubation behaviour in chickens. British Poultry Abstracts 6(1): 43-44.
Calus MPL, de Koning DJ, Haley CS. (2010). Including copy number variation in association studies to predict genotypic values. Genetics Research 92(2): 115-125.
Gheyas AA, Haley CS, Guy DR, Hamilton A, Tinch AE, Mota-Velasco JC, Woolliams JA (2010). Effect of a major QTL affecting the IPN resistance on production traits in Atlantic salmon. Animal Genetics 41(6): 666-668.
Gheyas AA, Houston RD, Mota-Velasco JC, Guy DR, Tinch AE, Haley CS, Woolliams JA. (2010). Segregation of infectious pancreatic necrosis resistance QTL in the early life cycle of Atlantic Salmon (Salmo salar). Animal Genetics 41(5): 531-536.
Houston RD, Haley CS, Gheyas A, Guy DR, Hamilton A, Mota-Velasco JC, Tinch AE, Bron JE, Ireland J H McAndrew BJ, Starkey WG, Taggart JB, Paley R, Rimmer G, Tew I,
Verner-Jeffreys D Bishop SC. (2010). The susceptibility of Atlantic salmon fry to freshwater Infectious Pancreatic Necrosis is largely explained by a major QTL. Heredity 105(3): 318-327.
Massault C, Hellemans B, Louro B, Batargias C, Van Houdt JKJ, Canario A, Volckaert FAM,
Bovenhuis H, Haley C, de Koning DJ. (2010). QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax. Animal Genetics 41(4): 337-345.
Moreno CR, Moazami-Goudarzi K, Briand S, Robert-Granie C, Weisbecker JL, Laurent P,
Cribiu EP, Haley CS, Andreoletti O, Bishop SC, Pong-Wong R. (2010). Mapping of quantitative trait loci affecting classical scrapie incubation time in a population comprising several generations of scrapie-infected sheep. J Gen Virol 91(Pt 2): 575-579.
Navarro P, Vitart V, Hayward C, Tenesa A, Zgaga L, Juricic D, Polasek O, Hastie ND, Rudan I, Campbell H, Wright AF, Haley CS, Knott SA. (2010). Genetic comparison of a Croatian isolate and CEPH European founders. Genet Epidemiol 34(2): 140-145.
Sauvage C, Boudry P, de Koning DJ, Haley CS, Heurtebise S, Lapegue, S. (2010). QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas). Anim Genet 41(4): 390-399.
Wei WH, Knott S, Haley CS, de Koning, D. J. (2010). Controlling false positives in the mapping of epistatic QTL. Heredity 104(4): 401-409.
Antonello J, Massault C, Franch R, Haley C, Pellizzari C. Bovo G, Patarnello T, de Koning DJ, Bargelloni L. (2009). Estimates of heritability and genetic correlation for body length and resistance to fish pasteurellosis in the gilthead sea bream (Sparus aurata L.). Aquaculture 298(1-2): 29-35.
Baxter R, Craigmile SC ,Haley CS, Douglas AJ, Williams JL, Glass EJ (2009). BoLA-DR peptide binding pockets are fundamental for foot-and-mouth disease virus vaccine design on cattle. Vaccine 28(1): 28-37.
Ding NS, Guo YM, Knorr C, Ma JW, Mao HR, Lan LT, Xiao SJ, Ai HS, Haley CS, Brenig B,
Huang LS. (2009). Genome-wide QTL mapping for three traits related to teat number in a White Duroc x Erhualian pig resource population. BMC Genetics 10(6): 8pp.
Guo Y, Mao H, Ren J, Yan X, Duan Y, Yang G, Ren D, Zhang Z, Yang B, Ouyang J, Brenig B, Haley C, Huang L. (2009). A linkage map of the porcine genome from a large-scale White Duroc x Erhualian resource population and evaluation of factors affecting recombination rates."Anim Genet 40(1): 47-52.
Guo YM, Ai HS, Ren J, Wang GJ, Wen Y, Mao HR, Lan LT, Ma JW, Brenig B, Rothschild MF, Haley CS, Huang LS. (2009). A whole genome scan for quantitative trait loci for leg weakness and its related traits in a large F-2 intercross population between White Duroc and Erhualian. Journal of Animal Science 87(5): 1569-1575.
Gutierrez-Gil B, Williams JL, Homer D, Burton D, Haley CS, Wiener P. (2009). Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle. J Anim Sci. 87(1): 24-36
Haley C. (2009). "Human and livestock genetics: parallel evolution and horizontal exchange." J Anim Breed Genet 126(6): 413-414.
Hernandez SC, Finlayson HA, Ashworth CJ, Haley CS, Archibald AL.(2009). Mapping quantitative trait loci for reproduction in pigs."Soc Reprod Fertil Suppl 66: 117-118.
Houston RD, Bishop SC, Hamilton A. Guy DR, Tinch AE, Taggart JB, Derayat A, McAndrew BJ, Haley CS. (2009). Detection of QTL affecting harvest traits in a commercial Atlantic salmon population. Anim Genet 40(5): 753-755.
Kearney JF, Navarro P, Haley CS, Villanueva B. (2009). Consequences of selection for improving production traits on the frequency of deleterious alleles for fitness. J Anim Sci. 87(3): 850-859
Lallias D, Gomez-Raya L, Haley CS, Arzul I, Heurtebise S, Beaumont AR, Boudry P, Lapegue S. (2009). Combining two-stage testing and interval mapping strategies to detect QTL for resistance to bonamiosis in the European flat oyster Ostrea edulis Marine Biotechnology 11(5): 570-584.
Lam AC, Powell J, Wei WH, de Koning DJ, Haley CS. (2009). A combined strategy for quantitative trait loci detection by genome-wide association. BMC Proc 3 Suppl 1: S6.
Nagamine Y, Pong-Wong R, Visscher PM, Haley CS. (2009). Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations. Genet Sel Evol 41: 44.
Palermo S, Capra E, Torremorell M, Dolzan M, Davoli R, Haley CS, Giuffra E. (2009). Toll-like receptor 4 genetic diversity among pig populations. Anim Genet 40(3): 289-299.
Rowe SJ, Pong-Wong R, Haley CS, Knott, SA, De Koning DJ. (2009). Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology. Genet Sel Evol 41: 6.
Massault C, Bovenhuis H, Haley C, de Koning DJ, (2008). QTL mapping designs for aquaculture. Aquaculture 285(1-4): 23-29.
Rowe SJ, Pong-Wong R, Haley CS, Knott SA, De Koning DJ. 2008. Detecting dominant QTL with variance component analysis in simulated pedigrees. Genet Res. 90(4):363-74.
Chistiakov DA, Tsigenopoulos CS, Lagnel J, Guo YM, Hellemans B, Haley CS, Volckaert FA, Kotoulas G. 2008. A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Anim Genet. 39(6):623-34.
Houston RD, Gheyas A, Hamilton A, Guy DR, Tinch AE, Taggart JB, McAndrew BJ, Haley CS, Bishop SC. 2008. Detection and confirmation of a major QTL affecting resistance to infectious pancreatic necrosis (IPN) in Atlantic salmon (Salmo salar). Dev Biol (Basel). 2008;132:199-204.
Lam AC, Fu J, Jansen RC, Haley CS, de Koning DJ. 2008. Optimal design of genetic studies of gene expression with two-color microarrays in outbred crosses. Genetics. 180(3):1691-8.
Guo YM, Lee GJ, Archibald AL, Haley CS. 2008. Quantitative trait loci for production traits in pigs: a combined analysis of two Meishan x Large White populations. Anim Genet. 39(5):486-95. Epub 2008 Jul 21.
Hadjiconstantouras C, Sargent CA, Skinner TM, Archibald AL, Haley CS, Plastow GS. 2008. Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits. Anim Genet. 39(3):217-24.
Houston RD, Rance KA, Sutcliffe E, Archibald AL, Haley CS. 2008. The cholecystokinin type A receptor g.179A>G polymorphism affects feeding rate. Anim Genet. 39(2):187-8.
Houston RD, Haley CS, Hamilton A, Guy DR, Tinch AE, Taggart JB, McAndrew BJ, Bishop SC. 2008. Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). Genetics. 178(2):1109-15.
Lam AC, Schouten M, Aulchenko YS, Haley CS, de Koning DJ. 2007. Rapid and robust association mapping of expression quantitative trait loci. BMC Proc.1 Suppl 1:S144.
Brockmann GA, Karatayli E, Neuschl C, Stylianou IM, Aksu S, Ludwig A, Renne U, Haley CS, Knott S. 2007. Genetic control of lipids in the mouse cross DU6i x DBA/2. Mamm Genome. 18(11):757-66.
Lallias D, Beaumont AR, Haley CS, Boudry P, Heurtebise S, Lapègue S. 2007. A first-generation genetic linkage map of the European flat oyster Ostrea edulis (L.) based on AFLP and microsatellite markers. Anim Genet. 38(6):560-8.
Huang Y, Haley CS, Hu S, Hao J, Wu C, Li N. 2007. Detection of quantitative trait loci for body weights and conformation traits in Beijing ducks. Anim Genet. 38(5):525-6.
de Koning DJ, Cabrera CP, Haley CS. 2007. Genetical genomics: combining gene expression with marker genotypes in poultry. Poult Sci. 86(7):1501-9.
Wei WH, de Koning DJ, Penman JC, Finlayson HA, Archibald AL, Haley CS. 2007. QTL modulating ear size and erectness in pigs. Anim Genet. 38(3):222-6.
Huang Y, Haley CS, Wu F, Hu S, Hao J, Wu C, Li N. 2007. Genetic mapping of quantitative trait loci affecting carcass and meat quality traits in Beijing ducks (Anas platyrhynchos). Anim Genet. 38(2):114-9.
Murphy AM, MacHugh DE, Park SD, Scraggs E, Haley CS, Lynn DJ, Boland MP, Doherty ML. 2007. Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep chromosome 5. Mamm Genome. 18(1):43-52.
Haley, C. S., and D. J. de Koning, 2007 Towards in vitro genetics. Trends in Genetics 23: 382-386.
de Koning, D. J., A. Archibald, and C. S. Haley, 2007 Livestock genomics: bridging the gap between mice and men. Trends in Biotechnology 25: 483-489.
Aulchenko, Y. S., D. J. de Koning, and C. Haley, 2007 Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177: 577-585.
Carlborg, O., D. J. de Koning, K. F. Manly, E. Chesler, R. W. Williams and C. S. Haley 2005 Methodological aspects of the genetic dissection of gene expression. Bioinformatics. 21: 2383-2393.
Schouten, M. T., Williams, C. K. I. & Haley, C. S. (2005) The impact of using related individuals for haplotype reconstruction in population studies. Genetics 171: 1321-1330.
Carlborg, O., Brockmann, G. A. & Haley, C. S. (2005) Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice. Mammalian Genome 16: 481-494
Lee, G. J., Archibald, A. L., Law, A. S., Lloyd, S., Wood, J. & Haley, C. S. (2005) Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs. Animal Genetics 36: 14-22.