Canovas, A., Rincon, G., Islas-Trejo, A., Wickramasinghe, S., and Medrano, J. (2010). SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mammalian Genome. 21: 592-598.
Djari, A., Esquerre, D., Weiss, B., Martins, F., Meersseman, C., Boussaha, M., et al. (2013). Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics. 14: 307.
Do, D.N., Janss, L.L. G., Jensen, J., and Kadarmideen, H.N. (2015). SNP annotation-based whole genomic prediction and selection: An application to feed efficiency and its component traits in pigs. Journal of Animal Science. 93: 2056-2063.
Druet, T., Macleod, I.M., and Hayes, B.J. (2014). Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity. 112: 39-47.
Erbe, M., Hayes, B.J., Matukumalli, L.K., Goswami, S., Bowman, P.J., Reich, C.M., et al. (2012). Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. Journal of Dairy Science. 95: 4114-4129.
Flintoft, L. (2008). Transcriptomics: Digging deep with RNA-Seq. Nature Reviews Genetics, 9: 568-568.
Haas, B.J. and Zody, M.C. (2010). Advancing RNA-seq analysis. Nature Biotechnolog, 28: 421-423.
Hayes, B., Bowman, P., Chamberlain, A., and Goddard, M. (2009). Invited review: genomic selection in dairy cattle: progress and challenge. Journal of Dairy Science, 92: 433 - 443.
Huang, W., Nadeem, A., Zhang, B., Babar, M., Soller, M., and Khatib, H. (2012). Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds. PLoS ONE, 7: e30244.
Khansefid, M., Pryce, J.E., Bolormaa, S., Miller, S.P., Wang, Z., Li, C., and Goddard, M. E. (2014). Estimation of genomic breeding values for residual feed intake in a multibreed cattle population. Journal of Animal Science. 92: 3270-3283.
Koufariotis, L., Chen, Y.-P., Bolormaa, S., and Hayes, B. (2014). Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics. 15: 436.
Levin, J., Adiconis, X., Yassour, M., Thompson, D., Guttman, M., Berger, M., et al. (2010).
[v1] Development and evaluation of RNA-seq methods.
Genome Biology. 11(Suppl 1): P26.
Marguerat, S. and Bahler, J. (2010). RNA-seq: from technology to biology. Cellular and Molecular Life Sciences. 67: 569-579.
Meuwissen, T., Hayes, B. and Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics. 157: 1819 - 1829.
Morota, G., Abdollahi-Arpanahi, R., Kranis, A., and Gianola, D. (2014). Genome-enabled prediction of quantitative traits in chickens using genomic annotation. BMC Genomics. 15: 109.
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods. 5: 621-628.
Nicolazzi, E.L., Caprera, A., Nazzicari, N., Cozzi, P., Strozzi, F., Lawley, C., et al. (2015).
SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
BMC genomics, 16: 283.
Park, K.-D., Park, J., Ko, J., Kim, B., Kim, H.-S., Ahn, K., et al. (2012). Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics. 13: 473.
Pennisi, E. (2012). ENCODE Project Writes Eulogy for Junk DNA. Science. 337: 1159-1161.
Ponting, C.P., Oliver, P.L. and Reik, W. (2009). Evolution and functions of long noncoding RNAs. Cell. 136: 629-641.
Pryce, J., Arias, J., Bowman, P., Davis, S., Macdonald, K., Waghorn, G. et al. (2012). Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers. Journal of Dairy Science. 95: 2108 - 2119.
Schaeffer, L. (2006). Strategy for applying genome-wide selection in dairy cattle. Journal of Animal Breeding and Genetics. 123: 218-223.
Sharma, U., Banerjee, P., Joshi, J. and Vijh R.K. (2012). Identification of SNPs in Goats (Capra hircus) using RNA-Seq Analysis. International Journal of Animal and Veterinary Advances, 4: 272-283.
Wang, K.C. and Chang, H.Y. (2011). Molecular mechanisms of long noncoding RNAs. Molecular Cell. 43: 904-914.
Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics. 10: 57- 63.
Wilhelm, B.T. and Landry, J.R. (2009). RNA-seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods. 48: 249-257.
Zhang, C., Wang, G., Wang, J., Ji, Z., Liu, Z., Pi, X., and Chen, C. (2013). Characterization and Comparative Analyses of Muscle Transcriptomes in Dorper and Small-Tailed Han Sheep Using RNA-Seq Technique. PLoS ONE, 8: e72686.