References analysis of the Wikipedia article "假基因" in the Chinese version

doi.org

Vanin EF. Processed pseudogenes: characteristics and evolution. Annual Review of Genetics. 1985, 19: 253–72. PMID 3909943. doi:10.1146/annurev.ge.19.120185.001345.

Chang Y, Stuart A, et al. Antigen presenting genes and genomic copy number variations in the Tasmanian devil MHC. BMC Genomics. 2012, 13:87. doi:10.1186/1471-2164-13-87.

Jacq C, Miller JR, Brownlee GG. A pseudogene structure in 5S DNA of Xenopus laevis. Cell. September 1977, 12 (1): 109–20. PMID 561661. doi:10.1016/0092-8674(77)90189-1.

Xiao-Jie L, Ai-Mei G, Li-Juan J, Jiang X. Pseudogene in cancer: real functions and promising signature. Journal of Medical Genetics. January 2015, 52 (1): 17–24. PMID 25391452. doi:10.1136/jmedgenet-2014-102785.

van Baren MJ, Brent MR. Iterative gene prediction and pseudogene removal improves genome annotation. Genome Research. May 2006, 16 (5): 678–85. PMC 1457044 

. PMID 16651666. doi:10.1101/gr.4766206.

Kim, MS; et al. A draft map of the human proteome.. Nature. 2014, 509: 575–581. PMC 4403737 

. PMID 24870542. doi:10.1038/nature13302.

Jurka J. Evolutionary impact of human Alu repetitive elements. Current Opinion in Genetics & Development. December 2004, 14 (6): 603–8. PMID 15531153. doi:10.1016/j.gde.2004.08.008.

Dewannieux M, Heidmann T. LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling. Cytogenetic and Genome Research. 2005, 110 (1–4): 35–48. PMID 16093656. doi:10.1159/000084936.

Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nature Genetics. September 2003, 35 (1): 41–8. PMID 12897783. doi:10.1038/ng1223.

Graur D, Shuali Y, Li WH. Deletions in processed pseudogenes accumulate faster in rodents than in humans. Journal of Molecular Evolution. April 1989, 28 (4): 279–85. PMID 2499684. doi:10.1007/BF02103423.

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. October 2008, 9: 466. PMC 2584115 

. PMID 18842134. doi:10.1186/1471-2164-9-466.

Pavlícek A, Paces J, Zíka R, Hejnar J. Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. Gene. October 2002, 300 (1–2): 189–94. PMID 12468100. doi:10.1016/S0378-1119(02)01047-8.

Navarro FC, Galante PA. A Genome-Wide Landscape of Retrocopies in Primate Genomes. Genome Biology and Evolution. July 2015, 7 (8): 2265–75. PMC 4558860 

. PMID 26224704. doi:10.1093/gbe/evv142.

Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ. Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genetics. 2013-01-24, 9 (1): e1003242. PMC 3554589 

. PMID 23359205. doi:10.1371/journal.pgen.1003242.

Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. November 2000, 290 (5494): 1151–5. Bibcode:2000Sci...290.1151L. PMID 11073452. doi:10.1126/science.290.5494.1151.

Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Research. February 2002, 12 (2): 272–80. PMC 155275 

. PMID 11827946. doi:10.1101/gr.207102.

Zhang J. Evolution by gene duplication: an update.. Trends in Ecology and Evolution. 2003, 18 (6): 292–298. doi:10.1016/S0169-5347(03)00033-8.

Xue Y, Daly A, Yngvadottir B, Liu M, Coop G, Kim Y, Sabeti P, Chen Y, Stalker J, Huckle E, Burton J, Leonard S, Rogers J, Tyler-Smith C. Spread of an inactive form of caspase-12 in humans is due to recent positive selection. American Journal of Human Genetics. April 2006, 78 (4): 659–70. PMC 1424700 

. PMID 16532395. doi:10.1086/503116.

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. June 2007, 17 (6): 839–51. PMC 1891343 

. PMID 17568002. doi:10.1101/gr.5586307.

Prieto-Godino LL, Rytz R, Bargeton B, Abuin L, Arguello JR, Peraro MD, Benton R. Olfactory receptor pseudo-pseudogenes. Nature. November 2016, 539 (7627): 93–97. PMC 5164928 

. PMID 27776356. doi:10.1038/nature19824.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biology. September 2012, 13 (9): R51. PMC 3491395 

. PMID 22951037. doi:10.1186/gb-2012-13-9-r51.

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science. February 2012, 335 (6070): 823–8. PMC 3299548 

. PMID 22344438. doi:10.1126/science.1215040.

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. Nature Communications. June 2016, 7: 11778. PMC 4895710 

. PMID 27250503. doi:10.1038/ncomms11778.

Long M, Langley CH. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science. April 1993, 260 (5104): 91–5. Bibcode:1993Sci...260...91L. PMID 7682012. doi:10.1126/science.7682012.

Jeffs P, Ashburner M. Processed pseudogenes in Drosophila. Proceedings. Biological Sciences. May 1991, 244 (1310): 151–9. PMID 1679549. doi:10.1098/rspb.1991.0064.

Wang W, Zhang J, Alvarez C, Llopart A, Long M. The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Molecular Biology and Evolution. September 2000, 17 (9): 1294–301. PMID 10958846. doi:10.1093/oxfordjournals.molbev.a026413.

Dierick HA, Mercer JF, Glover TW. A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7 A). Gene. October 1997, 198 (1–2): 37–41. PMID 9370262. doi:10.1016/s0378-1119(97)00289-8.

Betrán E, Wang W, Jin L, Long M. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Molecular Biology and Evolution. May 2002, 19 (5): 654–63. PMID 11961099. doi:10.1093/oxfordjournals.molbev.a004124.

Okuda H, Tsujimura A, Irie S, Yamamoto K, Fukuhara S, Matsuoka Y, Takao T, Miyagawa Y, Nonomura N, Wada M, Tanaka H. A single nucleotide polymorphism within the novel sex-linked testis-specific retrotransposed PGAM4 gene influences human male fertility. PloS One. 2012, 7 (5): e35195. PMC 3348931 

. PMID 22590500. doi:10.1371/journal.pone.0035195.

Chan WL, Chang JG. Pseudogene-derived endogenous siRNAs and their function. Methods in Molecular Biology. 2014, 1167: 227–39. PMID 24823781. doi:10.1007/978-1-4939-0835-6_15.

Chan WL, Yuo CY, Yang WK, Hung SY, Chang YS, Chiu CC, Yeh KT, Huang HD, Chang JG. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma. Nucleic Acids Research. April 2013, 41 (6): 3734–47. PMC 3616710 

. PMID 23376929. doi:10.1093/nar/gkt047.

Roberts TC, Morris KV. Not so pseudo anymore: pseudogenes as therapeutic targets. Pharmacogenomics. December 2013, 14 (16): 2023–34. PMC 4068744 

. PMID 24279857. doi:10.2217/pgs.13.172.

Olovnikov I, Le Thomas A, Aravin AA. A framework for piRNA cluster manipulation. Methods in Molecular Biology. 2014, 1093: 47–58. PMID 24178556. doi:10.1007/978-1-62703-694-8_5.

Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nature Reviews Molecular Cell Biology. April 2011, 12 (4): 246–58. PMID 21427766. doi:10.1038/nrm3089.

Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera Mdel C, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. April 2015, 161 (2): 319–32. PMID 25843629. doi:10.1016/j.cell.2015.02.043.

Dahia PL, FitzGerald MG, Zhang X, Marsh DJ, Zheng Z, Pietsch T, von Deimling A, Haluska FG, Haber DA, Eng C. A highly conserved processed PTEN pseudogene is located on chromosome band 9p21. Oncogene. May 1998, 16 (18): 2403–6. PMID 9620558. doi:10.1038/sj.onc.1201762.

Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. June 2010, 465 (7301): 1033–8. PMC 3206313 

. PMID 20577206. doi:10.1038/nature09144.

Balakirev ES, Ayala FJ. Pseudogenes: are they "junk" or functional DNA?. Annual Review of Genetics. 2003, 37: 123–51. PMID 14616058. doi:10.1146/annurev.genet.37.040103.103949.

Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Current Opinion in Microbiology. February 2015, 23: 102–9. PMID 25461580. doi:10.1016/j.mib.2014.11.012.

Williams DL, Slayden RA, Amin A, Martinez AN, Pittman TL, Mira A, Mitra A, Nagaraja V, Morrison NE, Moraes M, Gillis TP. Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics. August 2009, 10: 397. PMC 2753549 

. PMID 19706172. doi:10.1186/1471-2164-10-397.

harvard.edu

ui.adsabs.harvard.edu

nih.gov

ncbi.nlm.nih.gov

Vanin EF. Processed pseudogenes: characteristics and evolution. Annual Review of Genetics. 1985, 19: 253–72. PMID 3909943. doi:10.1146/annurev.ge.19.120185.001345.

Jacq C, Miller JR, Brownlee GG. A pseudogene structure in 5S DNA of Xenopus laevis. Cell. September 1977, 12 (1): 109–20. PMID 561661. doi:10.1016/0092-8674(77)90189-1.

van Baren MJ, Brent MR. Iterative gene prediction and pseudogene removal improves genome annotation. Genome Research. May 2006, 16 (5): 678–85. PMC 1457044 

. PMID 16651666. doi:10.1101/gr.4766206.

Kim, MS; et al. A draft map of the human proteome.. Nature. 2014, 509: 575–581. PMC 4403737 

. PMID 24870542. doi:10.1038/nature13302.

Jurka J. Evolutionary impact of human Alu repetitive elements. Current Opinion in Genetics & Development. December 2004, 14 (6): 603–8. PMID 15531153. doi:10.1016/j.gde.2004.08.008.

Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nature Genetics. September 2003, 35 (1): 41–8. PMID 12897783. doi:10.1038/ng1223.

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. October 2008, 9: 466. PMC 2584115 

. PMID 18842134. doi:10.1186/1471-2164-9-466.

Navarro FC, Galante PA. A Genome-Wide Landscape of Retrocopies in Primate Genomes. Genome Biology and Evolution. July 2015, 7 (8): 2265–75. PMC 4558860 

. PMID 26224704. doi:10.1093/gbe/evv142.

. PMID 23359205. doi:10.1371/journal.pgen.1003242.

Walsh JB. How often do duplicated genes evolve new functions?. Genetics. January 1995, 139 (1): 421–8. PMC 1206338 

. PMID 7705642.

Lynch M, O'Hely M, Walsh B, Force A. The probability of preservation of a newly arisen gene duplicate. Genetics. December 2001, 159 (4): 1789–804. PMC 1461922 

. PMID 11779815.

. PMID 11827946. doi:10.1101/gr.207102.

Nishikimi M, Kawai T, Yagi K. Guinea pigs possess a highly mutated gene for L-gulono-gamma-lactone oxidase, the key enzyme for L-ascorbic acid biosynthesis missing in this species. The Journal of Biological Chemistry. October 1992, 267 (30): 21967–72. PMID 1400507.

Nishikimi M, Fukuyama R, Minoshima S, Shimizu N, Yagi K. Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man. The Journal of Biological Chemistry. May 1994, 269 (18): 13685–8. PMID 8175804.

. PMID 16532395. doi:10.1086/503116.

. PMID 17568002. doi:10.1101/gr.5586307.

Prieto-Godino LL, Rytz R, Bargeton B, Abuin L, Arguello JR, Peraro MD, Benton R. Olfactory receptor pseudo-pseudogenes. Nature. November 2016, 539 (7627): 93–97. PMC 5164928 

. PMID 27776356. doi:10.1038/nature19824.

. PMID 22951037. doi:10.1186/gb-2012-13-9-r51.

. PMID 22344438. doi:10.1126/science.1215040.

. PMID 27250503. doi:10.1038/ncomms11778.

Jeffs P, Ashburner M. Processed pseudogenes in Drosophila. Proceedings. Biological Sciences. May 1991, 244 (1310): 151–9. PMID 1679549. doi:10.1098/rspb.1991.0064.

. PMID 22590500. doi:10.1371/journal.pone.0035195.

Chan WL, Chang JG. Pseudogene-derived endogenous siRNAs and their function. Methods in Molecular Biology. 2014, 1167: 227–39. PMID 24823781. doi:10.1007/978-1-4939-0835-6_15.

. PMID 23376929. doi:10.1093/nar/gkt047.

Roberts TC, Morris KV. Not so pseudo anymore: pseudogenes as therapeutic targets. Pharmacogenomics. December 2013, 14 (16): 2023–34. PMC 4068744 

. PMID 24279857. doi:10.2217/pgs.13.172.

Olovnikov I, Le Thomas A, Aravin AA. A framework for piRNA cluster manipulation. Methods in Molecular Biology. 2014, 1093: 47–58. PMID 24178556. doi:10.1007/978-1-62703-694-8_5.

. PMID 20577206. doi:10.1038/nature09144.

Balakirev ES, Ayala FJ. Pseudogenes: are they "junk" or functional DNA?. Annual Review of Genetics. 2003, 37: 123–51. PMID 14616058. doi:10.1146/annurev.genet.37.040103.103949.

Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Current Opinion in Microbiology. February 2015, 23: 102–9. PMID 25461580. doi:10.1016/j.mib.2014.11.012.

. PMID 19706172. doi:10.1186/1471-2164-10-397.

web.archive.org

Max EE. Plagiarized Errors and Molecular Genetics. Creation Evolution Journal. 1986, 6 (3): 34–46 [2017-10-19]. （原始内容存档于2019-03-01）.

Chandrasekaran C, Betrán E. Origins of new genes and pseudogenes.. Nature Education. 2008, 1 (1): 181 [2017-10-19]. （原始内容存档于2020-11-22）.

Max EE. Plagiarized Errors and Molecular Genetics. TalkOrigins Archive. 2003-05-05 [2008-07-22]. （原始内容存档于2020-11-12）.

假基因 (Chinese Wikipedia)

archive.org

doi.org

harvard.edu

ui.adsabs.harvard.edu

nature.com

ncse.com

nih.gov

ncbi.nlm.nih.gov

talkorigins.org

web.archive.org