References

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature 409: 860-921. [CrossRef] [Google Scholar] [PubMed]
2. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, et al. (2012) Systematic localization of common disease associated variation in regulatory DNA. Science 337: 1190-1195. [CrossRef] [Google Scholar] [PubMed]
3. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M, et al. (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22: 1748-2759. [CrossRef] [Google Scholar] [PubMed]
4. Martinez AF, Abe Y, Hong S, Molyneux K, Yarnell D, et al. (2016) An ultraconserved brain-specific enhancer within DGRL3 (LPHN3) underpins attention-deficit/hyperactivity disorder susceptibility. Biol Psychiatry 80: 943-954. [CrossRef] [Google Scholar] [PubMed]
5. Amiel J, Benko S, Gordon CT, Lyonnet S (2010) Disruption of long-distance higly conserved noncoding elements in neurocristopathies Ann N Y Acad Sci 1214: 34-46. [CrossRef] [Google Scholar] [PubMed]
6. Braconi C, Valeri N, Kogure T, Gasparini P, Huang N, et al. (2011) Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci USA 108: 786-791. [CrossRef] [Google Scholar] [PubMed]
7. Bao BY, Lin VC, Yu CC, Yin HL, Chang TY, et al. (2016) Genetic variants in ultraconserved regions associate with prostate cancer recurrence and survival. Scientific Reports 6: 22124. [CrossRef] [Google Scholar]
8. Zhang Fand, Lupsky JR (2015) Non-coding genetic variants in human disease. Hum Mol Genet 24: R102-R110. [CrossRef] [Google Scholar] [PubMed]
9. Eddy SR (2014) The C-value paradox, junk DNA and ENCODE. Curr Biol 22: R898-R899. [CrossRef] [Google Scholar] [PubMed]
10. Palazzo AF, Gregory TR (2014) The case for junk DNA. PLoS Genet 10: e1004351. [CrossRef] [Google Scholar] [PubMed]
11. Koonin EV (2005) Orthologs, Paralogs and Evolutionary Genomics. Annu Rev Genet 39: 309-338. [CrossRef] [Google Scholar] [PubMed]
12. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, et al. (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17: 839-851. [CrossRef] [Google Scholar] [PubMed]
13. Niimura Y, Nei M (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2: 860-921. [CrossRef] [Google Scholar] [PubMed]
14. Pink RC, Wicks K, Caley DP, Punch EK, Jacobs L, et al. (2011) Pseudogenes: pseudo-functional or key regulators in health and disease? RNA 17: 792-798. [CrossRef] [Google Scholar] [PubMed]
15. Korneev SA, Park JH, O’Shea M (1999) Neuronal Expression of Neural Nitrix Oxide Synthase (nNOS) Protein is suppressed by an Antisense RNA Transcribed from an NOS Pseudogene. J Neurosci 19: 7711-7720. [CrossRef] [Google Scholar] [PubMed]
16. Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M, et al. (2010) Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol 11: R26. [CrossRef] [Google Scholar] [PubMed]
17. Mighell AJ, Smith NR, Robinson PA, Markham AF (2000) Vertebrate pseudogenes. FEBS letters 468: 109-114. [CrossRef] [Google Scholar] [PubMed]
18. D’Errico I, Gadaleta G, Saccone C (2014) Pseudogenes in metazoa: origin and features. Brief Funct Genomic Proteomic 3: 157-167. [CrossRef] [Google Scholar] [PubMed]
19. Zhang Z, Harrison P, Gerstein M (2002) Identification and analysis of over 200 ribosomal protein pseudogenes in the human genome. Genome Res 12: 1466-1482. [CrossRef] [Google Scholar] [PubMed]
20. McDonell L, Drouin G (2012) The abundance of processed pseudogenes derived from glycolitic genes is correlated with their expression level. Genome 5: 147-151. [CrossRef] [Google Scholar] [PubMed]
21. Vinckenbosch N, Dupanloup I, Kaessmann H (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 103: 3220-3225. [CrossRef] [Google Scholar] [PubMed]
22. Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, et al. (2011) RNA-seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS Oone 6: e22356. [CrossRef] [Google Scholar] [PubMed]
23. Poliseno L, Salamena L, Zhang J, Carver B, Haveman WJ, et al. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumor biology. Nature 465: 1033-1038. [CrossRef] [Google Scholar] [PubMed]
24. Zhou M, Baitei EY, Alzahrani AS, Al-Mohanna F, Farid NR, et al. (2009) Oncogenic activation of MAP kinase by BRAF pseudogene in thyroid tumors. Neoplasia 11: 57-65. [CrossRef] [Google Scholar] [PubMed]
25. Chiefari E, Iiritano S, Paonessa F, Pra IL, Arcidiacono B, et al. (2010) Pseudogene-mediated pstrascriptional silencing of HMGA1 can result in insulin resistance and Type 2 diabetes. Nat Commun 1: 40. [CrossRef] [Google Scholar] [PubMed]
26. Khachane AN, Harrison PM (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 10: 435. [CrossRef] [Google Scholar] [PubMed]
27. Podlaha O, Zhang J (2004) Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol Biol Evol 21: 2202-2209. [CrossRef] [Google Scholar] [PubMed]
28. Ross J (1996) Control of messenger RNA stability in higher eukaryotes. Trends Genet 12: 171-175. [CrossRef] [Google Scholar] [PubMed]
29. Pink RC, Carter DRF (2013) Pseudogenes as regulators of biological function. Essays Biochem 54: 103-112. [CrossRef] [Google Scholar] [PubMed]
30. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biology 7: S4. [CrossRef] [Google Scholar]
31. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, et al. (2006) PseudoPipe: An automated pseudogene identification pipeline. Bioinformatics 22: 1437-1439. [CrossRef] [Google Scholar] [PubMed]
32. Das MK, Dai HK (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics 8: S21. [CrossRef] [Google Scholar] [PubMed]
33. Thompson W, Rouchka EC, Lawrence CE (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 31: 3580-3585. [CrossRef] [Google Scholar] [PubMed]
34. Mitrophanov AY, Borodovsky M (2005) Statistical significance in biological sequence analysis. Brief Bioinform 7: 2-24. [CrossRef] [Google Scholar] [PubMed]
35. Durbin R, Eddy SR, Krogh A, Mitchinson G (1998) Biological Sequence Analysis. Cambridge University Press.
36. Gropl C (2012) Markov Chains and Hidden Markov Models.
37. Isaev A (2004) Introduction to Mathematical Methods. Bioinformatics in Springer.
38. Haggstrom O (2002) Finite Markov Chains in Algorithmic Applications. Cambridge University Press.
39. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, et al. (1993) Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science 262: 208-214. [CrossRef] [Google Scholar] [PubMed]
40. Rouchka EC (2008) A brief Overview of Gibbs Sampling. University of Louisville Bioinformatics Laboratory Technical Report. [Google Scholar]
41. Bier A, Oviedo-Landaverde I, Zhao J, Mamane Y, Kandouz M, et al. (2009) Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target. Mol Cancer Ther 8: 786-793. [CrossRef] [Google Scholar] [PubMed]
42. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, et al. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 8: 534-538. [CrossRef] [Google Scholar] [PubMed]
43. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, et al. (2010) Orphan CpG islands identify numerous conserve promoters in the mammalian genome. PLoS Genet 6: 786-793. [CrossRef] [Google Scholar] [PubMed]
44. Zheng D, Gerstein MB (2006) A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol 7: S13. [CrossRef] [Google Scholar] [PubMed]
45. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 197 : 261-282. [CrossRef] [Google Scholar] [PubMed]
46. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99: 3740-3745. [CrossRef] [Google Scholar] [PubMed]
47. Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M, Rafeied F, Imumorin IG, et al. (2019) Whole genome comparative analysis of CpG islands in camelid and other mammalian genomes. Mammalian Biology 98: 73-79. [CrossRef] [Google Scholar]
48. Barazandeh A, Mohammadabadi MR, Ghaderi M, Nezamabadipour H (2016) Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features. Czech Journal of Animal Science 61: 487-495. [CrossRef] [Google Scholar]
49. Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M, Nezamabadipour H (2016) Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm. Iranian Journal of Applied Animal Science 6: 571-579. [Google Scholar]