Ahmed, Z.M., Yousaf, R., Lee, B.C., Khan, S.N., Lee, S.,
Lee, K.,
Husnain, T.,
UrRehman, A.,
Bonneux, S.,
Ansar, M.,
Ahmad, W.,
Leal, S.M.,
Gladyshev, V.N,
Belyantseva, I.A.,
VanCamp, G.,
Riazuddin, S.,
Friedman, T.B &
Riazuddin, S. (2011). Functional null mutations of MSRB3 encoding methionine sulfoxide reductase are associated with human deafness DFNB74.
The American Journal of Human Genetics, 88: 19-29.
Anderson, S., Kusters, D.H., Clarke, I.J., Pow, D.V., & Curlewis, J.D. (2005). Expression of pituitary adenylate cyclase activating polypeptide type 1 receptor (PAC1R) in the ewe hypothalamus: distribution and colocalization with tyrosine hydroxylase immunoreactive neurones. Journal of Neuroendocrinology, 17: 298-305.
Aoki-Kinoshita, K., & Kanehisa, M. (2007). Gene annotation and pathway mapping in KEGG, Methods in Molecular Biology, 396: 71-91.
Aznar, N., Midde, K.K., Dunkel, Y., Lopez-Sanchez, I., Pavlova, Y., Marivin, A., Barbazán, J., Murray, F., Nitsche, U., Janssen, K.P., Willert, K., Goel, A., Abal, M., Garcia-Marcos, M., &
Ghosh, P. (2015). Daple is a novel non-receptor GEF required for trimeric G protein activation in Wnt signaling.
Elife, 4: e07091.
Bathke, J., & Lühken, G. 2021. OVarFlow: a resource optimized GATK 4 based open source variant calling work flow. BMC Bioinformatics, 22, 1-18.
Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A.,
Fridman, W.H.,
Pagès, F.,
Trajanoski, Z., & Galon, J. (2009). ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bioinformatics, 25(8): 1091-1093.
Closs, E.I., Gräf, P., Habermeier, A., Cunningham, J.M., & Förstermann, U. (1997). Human cationic amino acid transporters hCAT-1, hCAT-2A, and hCAT-2B: three related carriers with distinct transport properties. Biochemistry, 36: 6462-68.
Djari, A.D., Esquerre, B., Weiss, F., Martins, C., Meersseman, M., Boussaha, C., Klopp, A., & Rocha D., 2013. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics, 14(1): 307.
Eydivandi, S., Sahana, G., Momen, M., Moradi, M.H., & Schönherz, A.A. (2020). Genetic diversity in Iranian indigenous sheep vis‐à‐vis selected exogenous sheep breeds and wild mouflon. Animal Genetics, 51(5), 772-787.
Fan, B., Du, Z.Q., Gorbach, D.M. & Rothschild, M.F. (2010). Development and application of high-density SNP arrays in genomic studies of domestic animals. Asian-Australasian Journal of Animal Science, 23(7): 833-847.
Gao, H. Wu, G., Spencer, T.E., Johnson, G.A., & Bazer, F.W. (2009). Select nutrients in the ovine uterine lumen. III. Cationic amino acid transporters in the ovine uterus and peri-implantation conceptuses. Biology of Reproduction, 80: 602-09.
Gautier, M., Klassmann, A., & Vitalis, R. (2017). Rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Molecular Ecology Resources, 17(1): 78-90.
Goddard, M.E., & Hayes, B.J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programs. Nature Reviews Genetics, 10(6), 381-391.
Groenen, M.A.M., Megens, H.J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P.M. A.,Vereijken, A., Okimoto, R., Muir, W.M. & Cheng, H.H. (2011). The development and characterization of a 60K SNP chip for chicken. BMC Genomics, 12(1):1-9.
Hama, H. 2010. Fatty acid 2-Hydroxylation in mammalian sphingolipid biology. Biochimica et Biophysica Acta, 1801: 405–414.
Helyar, S. J., Hemmer‐Hansen, J., Bekkevold, D., Taylor, M.I., Ogden, R., Limborg, M.T., Cariani,
A.,
Maes, G. E.,
Diopere, E.,
Carvalho, G.R., &
Nielsen, E.E. (2011). Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges.
Molecular Ecology Resources, 11: 123-136.
Kawano,Y., Sahin, I., Moschetta, M., Wang, J., Manier, S., Glavey, S., Mishima, Y., Kokubun, K., Tsukamoto, S., Sacco, A., Anderson, K. Roccaro, A.M., Gray, N.S., & Ghobrial, I.M. (2014). Citron rho-interacting serine/threonine kinase (CIT) is a novel therapeutic target in multiple myeloma cells. Blood, 124: 3430.
McCulloch, R., & McWilliam, S. (2009). A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PloS ONE, 4: 46-68.
Kim, H.Y., & Gladyshev, V.N. (2004). Methionine sulfoxide reduction in mammals: characterization of methionine-R-sulfoxide reductases. Molecular Biology of the Cell, 15: 1055-64.
Koch, M., Murrell, J.R., Hunter, D.D., Olson, P.F., Jin, W.,
Keene, D.R.,
Brunken, W.J.,
& Burgeson, R.E. (2000). A novel member of the netrin family, β-netrin, shares homology with the β chain of laminin: identification, expression, and functional characterization.
The Journal of Cell Biology, 151: 221-34.
Kume, K., Iizumi,Y., Shimada, M., Ito, Y., Kishi, T.,
Yamaguchi,Y., &
Handa, H. (2010). Role of N‐end rule ubiquitin ligases UBR1 and UBR2 in regulating the leucine‐mTOR signaling pathway.
Genes to Cells,15: 339-49.
Kwak, K.S., Zhou, X., Solomon, V., Baracos, V.E., Davis, J.,
Bannon, A.W.,
Boyle, W.J.,
Lacey, D.L.,
& Han, H. Q. (2004). Regulation of protein catabolism by muscle-specific and cytokine-inducible ubiquitin ligase E3α-II during cancer cachexia.
Cancer Research, 64: 8193-98.
Lammers, G., Gilissen, C., Nillesen, S.T., Uijtdewilligen, P.J., Wismans, R.G., Veltman, J.A., Daamen, W.F. & Van Kuppevelt, T.H. (2010). High density gene expression microarrays and gene ontology analysis for identifying processes in implanted tissue engineering constructs. Biomaterials, 31(32): 8299-8312.
Larti, F., Kahrizi, K., Musante, L., Hu, H., Papari, E.,
Fattahi, Z., Bazazzadegan, N.,
Liu, Z.,
Banan, M.,
Garshasbi, M.,
Wienker, T.F.,
Ropers, H.,
Galjart, N.,
& Najmabadi, H. (2015). A defect in the CLIP1 gene (CLIP-170) can cause autosomal recessive intellectual disability.
European Journal of Human Genetics, 23: 331-36.
Matta-Camacho, E., Kozlov, G., Li, F.F, & Gehring, K. (2010). Structural basis of substrate recognition and specificity in the N-end rule pathway. Nature Structural & Molecular Biology, 17: 1182-87.
Mahal, G.S., Johnston, A., & Burns, R.H. (1951). Types and dimensions of fiber scales from the wool types of domestic sheep and wild life. Textile Research Journal, 21(2), 83-93.
Matukumalli, L., Lawley, C., Schnabel, R., Taylor, J., Allan, M., Heaton, M., O'Connell, J., Moore, S., Smith, T., Sonstegard, T. & Van Tassell, C. (2009). Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE, 4: 4:e5350.
Meuwissen, T.H., Hayes, B.J., & Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819-1829.
Mohammadi, H., Rafat, S.A., Moradi Shahrebabak, H., Shodja, J. & Moradi, M.A. (2017). Genome-wide analysis for detection of loci under positive selection in Zandi sheep breed. Iranian Journal of Animal Science, 48(4): 533-548. (In Persian).
Moradi, M.H., Farahani, A.H. & Nejati-Javaremi, A. (2017). Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information. Iranian Journal of Animal Science, 48(1), 39-49. (In Persian).
Nenadic, I., Maitra, R., Scherpiet, S., Gaser, C., Schultz, C.C., Schachtzabel, C., Smesny, S., Reichenbach, J.R., Treutlein, J., Mühleisen, T.W.,
Deufel, T.,
Cichon, S.,
Rietschel, M., Nöthen, M.M., Sauer, H., & Schlösser, R. G. (2012). Glutamate receptor delta 1 (GRID1) genetic variation and brain structure in schizophrenia.
Journal of Psychiatric Research, 46(12), 1531-1539.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P. de Bakker, P.I.W., Daly, M.J., & Sham, P.C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3): 559-575.
Ryder, M. L. (1964). The history of sheep breeds in Britain. The Agricultural History Review, 12(1), 1-12.
Ryder, M. L. (1983). Sheep and man. London: Duckworth, 846 pp.
Rupp, R., Mucha, S., Larroque, H., McEwan, J., & Conington, J. (2016). Genomic application in sheep and goat breeding. Animal Frontiers, 6(1):39-44.
Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., & et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164): 913-918.
Sachajko, M., Herudzińska, M., Jaskowski, J.M., Szczepanek, J., Buszewska-Forajta, M., Feng, Y. Kumar D., & Pareek, C.S. (2019). Data set for transcriptome analysis of liver in cattle breeds. Translational Research in Veterinary Science, 2(2), 51-56.
Sewe, S.O., Silva, G., Sicat, P., Seal, S.E., and Visendi, P. (2022). Trimming and validation of Illumina short reads using trimmomatic, trinity assembly, and assessment of RNA-seq data. Methods in Molecular Biology, 2443: 211-232.
Tayara, H., and Chong, K.T. (2019). Improving the quantification of DNA sequences using evolutionary information based on deep learning. Cells, 8(12), 1635.
Tang, K., Thornton, K.R., & Stoneking, M. (2007). A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology, 5: 171.
Tosser-Klopp, G., Bardou, P., Bouchez, O., Cabau, C., Crooijmans, R., Dong, Y., & et al. 2014. Design and characterization of a 52K SNP chip for goats. PLoS ONE, 9(1): 86227.
VanRaden, P.M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414 - 4423.
Voight, B.F., Kudaravalli, S., Wen, X., & Pritchard, J.K. (2006). A map of recent positive selection in the human genome. PLoS Biology, 4: 72.
Wu, C., Li, J., Xu, X., Xu, Q., Qin, C.,
Liu,G.,
Wei, C.,
Zhang, G.,
Tian, K., &
Fu, X. (2022). Effect of the FA2H gene on cashmere fineness of Jiangnan cashmere goats based on transcriptome sequencing.
BMC Genomics, 23: 1-14.
Wu, X.L.,
Xu, J.,
Feng, G.,
Wiggans, G.R.,
Taylor, J.F.,
He, J.,
Qian, C.,
Qiu, J.,
Simpson, B.,
Walker, J., and
Bauck, S. (2016). Optimal design of low-density SNP arrays for genomic prediction: algorithm and applications.
PLoS ONE, 1;11(9): e0161719.
Xie, W., Chen, C., Han, Z., Huang, J., Liu, X.,
Chen, H.,
Zhang, T.,
Chen, S.,
Chen, C.,
Lu, M.,
Shen, X. &, X. (2020). CD2AP inhibits metastasis in gastric cancer by promoting cellular adhesion and cytoskeleton assembly.
Molecular carcinogenesis, 59: 339-352.
Yang, J., Li, W.R., Lv, F.H., He, S.G., Tian, S.L., Peng, W.F., & et al. (2016). Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments. Molecular Biology and Evolution, 33(10), 2576-2592.
Zenker, M., Mayerle, J., Lerch, M.M., Tagariello, A., Zerres, K.,
Durie, P.R. & et al. (2005). Deficiency of UBR1, a ubiquitin ligase of the N-end rule pathway, causes pancreatic dysfunction, malformations and mental retardation (Johanson-Blizzard syndrome).
Nature Genetics, 37: 1345-1350.