Orphan gene (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Orphan gene" in English language version.

refsWebsite

Global rank English rank

80nih.gov

4^th place

50doi.org

2^nd place

11harvard.edu

18^th place

17^th place

6worldcat.org

5^th place

4semanticscholar.org

11^th place

8^th place

1books.google.com

3^rd place

1arxiv.org

69^th place

59^th place

1psu.edu

207^th place

136^th place

arxiv.org

Palmieri N, Kosiol C, Schlötterer C (February 2014). "The life cycle of Drosophila orphan genes". eLife. 3: e01311. arXiv:1401.4956. doi:10.7554/eLife.01311. PMC 3927632. PMID 24554240.

books.google.com

Ohno S (11 December 2013). Evolution by Gene Duplication. Springer Science & Business Media. ISBN 978-3-642-86659-3.

doi.org

Fischer D, Eisenberg D (September 1999). "Finding families for genomic ORFans". Bioinformatics. 15 (9): 759–762. doi:10.1093/bioinformatics/15.9.759. PMID 10498776.
Tautz D, Domazet-Lošo T (August 2011). "The evolutionary origin of orphan genes". Nature Reviews. Genetics. 12 (10): 692–702. doi:10.1038/nrg3053. PMID 21878963. S2CID 31738556.
Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC (September 2009). "More than just orphans: are taxonomically-restricted genes important in evolution?". Trends in Genetics. 25 (9): 404–413. doi:10.1016/j.tig.2009.07.006. PMID 19716618.
Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, et al. (September 2008). "On the origin of new genes in Drosophila". Genome Research. 18 (9): 1446–1455. doi:10.1101/gr.076588.108. PMC 2527705. PMID 18550802.
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM (March 2009). "Origin of primate orphan genes: a comparative genomics approach". Molecular Biology and Evolution. 26 (3): 603–612. doi:10.1093/molbev/msn281. PMID 19064677.
Cortez, Diego; Forterre, Patrick; Gribaldo, Simonetta (2009). "A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes". Genome Biology. 10 (6): R65. doi:10.1186/gb-2009-10-6-r65. ISSN 1465-6906. PMC 2718499. PMID 19531232.
Weisman CM, Murray AW, Eddy SR (November 2020). "Many, but not all, lineage-specific genes can be explained by homology detection failure". PLOS Biology. 18 (11): e3000862. doi:10.1371/journal.pbio.3000862. PMC 7660931. PMID 33137085.
Vakirlis N, Carvunis AR, McLysaght A (February 2020). "Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes". eLife. 9. doi:10.7554/eLife.53500. PMC 7028367. PMID 32066524.
Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E (2013). "Mechanisms and dynamics of orphan gene emergence in insect genomes". Genome Biology and Evolution. 5 (2): 439–455. doi:10.1093/gbe/evt009. PMC 3590893. PMID 23348040.
Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD (17 October 2013). "De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences". PLOS Genetics. 9 (10): e1003860. doi:10.1371/journal.pgen.1003860. PMC 3798262. PMID 24146629.
Suenaga Y, Islam SM, Alagu J, Kaneko Y, Kato M, Tanaka Y, et al. (January 2014). "NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas". PLOS Genetics. 10 (1): e1003996. doi:10.1371/journal.pgen.1003996. PMC 3879166. PMID 24391509.
Yu G, Stoltzfus A (2012). "Population diversity of ORFan genes in Escherichia coli". Genome Biology and Evolution. 4 (11): 1176–87. doi:10.1093/gbe/evs081. PMC 3514957. PMID 23034216.
Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV (November 2016). "Two fundamentally different classes of microbial genes". Nature Microbiology. 2 (3): 16208. doi:10.1038/nmicrobiol.2016.208. PMID 27819663. S2CID 21799266.
Koonin EV, Makarova KS, Wolf YI (July 2021). "Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century". Trends in Microbiology. 29 (7): 582–592. doi:10.1016/j.tim.2021.01.005. PMC 9404256. PMID 33541841. S2CID 231820647.
Domazet-Loso, Tomislav (13 October 2003). "An Evolutionary Analysis of Orphan Genes in Drosophila". Genome Research. 13 (10): 2213–2219. doi:10.1101/gr.1311003. PMC 403679. PMID 14525923.
Tautz, Diethard (31 August 2011). "The evolutionary origin of orphan genes". Nature Reviews Genetics. 12 (10): 692–702. doi:10.1038/nrg3053. PMID 21878963. Retrieved 26 April 2024.
Jacob F (June 1977). "Evolution and tinkering". Science. 196 (4295): 1161–1166. Bibcode:1977Sci...196.1161J. doi:10.1126/science.860134. PMID 860134.
Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, Field D (August 2005). "Orphans as taxonomically restricted and ecologically important genes". Microbiology. 151 (Pt 8): 2499–2501. doi:10.1099/mic.0.28146-0. PMID 16079329.
Cai J, Zhao R, Jiang H, Wang W (May 2008). "De novo origination of a new protein-coding gene in Saccharomyces cerevisiae". Genetics. 179 (1): 487–496. doi:10.1534/genetics.107.084491. PMC 2390625. PMID 18493065.
Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES (May 2009). "Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves". The Plant Journal. 58 (3): 485–498. doi:10.1111/j.1365-313X.2009.03793.x. PMID 19154206.
Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, et al. (November 2015). "QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions". Proceedings of the National Academy of Sciences of the United States of America. 112 (47): 14734–14739. Bibcode:2015PNAS..11214734L. doi:10.1073/pnas.1514670112. PMC 4664325. PMID 26554020.
Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C (February 2011). "Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana". BMC Evolutionary Biology. 11 (1): 47. Bibcode:2011BMCEE..11...47D. doi:10.1186/1471-2148-11-47. PMC 3049755. PMID 21332978.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–3402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
Albà MM, Castresana J (April 2007). "On homology searches by protein Blast and the characterization of the age of genes". BMC Evolutionary Biology. 7 (1): 53. Bibcode:2007BMCEE...7...53A. doi:10.1186/1471-2148-7-53. PMC 1855329. PMID 17408474.
Moyers BA, Zhang J (January 2015). "Phylostratigraphic bias creates spurious patterns of genome evolution". Molecular Biology and Evolution. 32 (1): 258–267. doi:10.1093/molbev/msu286. PMC 4271527. PMID 25312911.
Domazet-Loso T, Brajković J, Tautz D (November 2007). "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages". Trends in Genetics. 23 (11): 533–539. doi:10.1016/j.tig.2007.08.014. PMID 18029048.
Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC (2015). "Remote homology and the functions of metagenomic dark matter". Frontiers in Genetics. 6: 234. doi:10.3389/fgene.2015.00234. PMC 4508852. PMID 26257768.
McLysaght A, Guerzoni D (September 2015). "New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370 (1678): 20140332. doi:10.1098/rstb.2014.0332. PMC 4571571. PMID 26323763.
Palmieri N, Kosiol C, Schlötterer C (February 2014). "The life cycle of Drosophila orphan genes". eLife. 3: e01311. arXiv:1401.4956. doi:10.7554/eLife.01311. PMC 3927632. PMID 24554240.
Zhao L, Saelao P, Jones CD, Begun DJ (February 2014). "Origin and spread of de novo genes in Drosophila melanogaster populations". Science. 343 (6172): 769–772. Bibcode:2014Sci...343..769Z. doi:10.1126/science.1248286. PMC 4391638. PMID 24457212.
Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ (June 2006). "Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression". Proceedings of the National Academy of Sciences of the United States of America. 103 (26): 9935–9939. Bibcode:2006PNAS..103.9935L. doi:10.1073/pnas.0509809103. PMC 1502557. PMID 16777968.
Heinen TJ, Staubach F, Häming D, Tautz D (September 2009). "Emergence of a new gene from an intergenic region". Current Biology. 19 (18): 1527–1531. Bibcode:2009CBio...19.1527H. doi:10.1016/j.cub.2009.07.049. PMID 19733073.
Chen S, Zhang YE, Long M (December 2010). "New genes in Drosophila quickly become essential". Science. 330 (6011): 1682–1685. Bibcode:2010Sci...330.1682C. doi:10.1126/science.1196380. PMC 7211344. PMID 21164016.
Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LE, Loudet O, et al. (April 2013). "Extensive natural epigenetic variation at a de novo originated gene". PLOS Genetics. 9 (4): e1003437. doi:10.1371/journal.pgen.1003437. PMC 3623765. PMID 23593031.
Neme R, Tautz D (March 2014). "Evolution: dynamics of de novo gene emergence". Current Biology. 24 (6): R238–R240. Bibcode:2014CBio...24.R238N. doi:10.1016/j.cub.2014.02.016. PMID 24650912.
Moyers BA, Zhang J (May 2016). "Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution". Molecular Biology and Evolution. 33 (5): 1245–1256. doi:10.1093/molbev/msw008. PMC 5010002. PMID 26758516.
Hunter R. Johnson; Jessica A. Blandino; Beatriz C. Mercado; José A. Galván; William J. Higgins; Nathan H. Lents (June 2022). "The evolution of de novo human-specific microRNA genes on chromosome 21". American Journal of Biological Anthropology. 178 (2): 223–243. doi:10.1002/ajpa.24504. S2CID 247240062.
Lynch M, Katju V (November 2004). "The altered evolutionary trajectories of gene duplicates". Trends in Genetics. 20 (11): 544–549. CiteSeerX 10.1.1.335.7718. doi:10.1016/j.tig.2004.09.001. PMID 15475113.
Arendsee ZW, Li L, Wurtele ES (November 2014). "Coming of age: orphan genes in plants". Trends in Plant Science. 19 (11): 698–708. doi:10.1016/j.tplants.2014.07.003. PMID 25151064.
Mukherjee S, Panda A, Ghosh TC (June 2015). "Elucidating evolutionary features and functional implications of orphan genes in Leishmania major". Infection, Genetics and Evolution. 32: 330–337. doi:10.1016/j.meegid.2015.03.031. PMID 25843649.
Wilson BA, Foy SG, Neme R, Masel J (June 2017). "Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth". Nature Ecology & Evolution. 1 (6): 0146–146. Bibcode:2017NatEE...1..146W. doi:10.1038/s41559-017-0146. PMC 5476217. PMID 28642936.
Willis S, Masel J (September 2018). "Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes". Genetics. 210 (1): 303–313. doi:10.1534/genetics.118.301249. PMC 6116962. PMID 30026186.
Bungard D, Copple JS, Yan J, Chhun JJ, Kumirov VK, Foy SG, et al. (November 2017). "Foldability of a Natural De Novo Evolved Protein". Structure. 25 (11): 1687–1696.e4. doi:10.1016/j.str.2017.09.006. PMC 5677532. PMID 29033289.
Zhang, Wenyu; Gao, Yuanxiao; Long, Manyuan; Shen, Bairong (April 2019). "Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans". Science China. Life Sciences. 62 (4): 579–593. doi:10.1007/s11427-019-9482-0. ISSN 1869-1889. PMID 30919281.
Fellner, Lea; Simon, Svenja; Scherling, Christian; Witting, Michael; Schober, Steffen; Polte, Christine; Schmitt-Kopplin, Philippe; Keim, Daniel A.; Scherer, Siegfried; Neuhaus, Klaus (18 December 2015). "Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting". BMC Evolutionary Biology. 15 (1): 283. Bibcode:2015BMCEE..15..283F. doi:10.1186/s12862-015-0558-z. ISSN 1471-2148. PMC 4683798. PMID 26677845.
Arendsee, Zebulun W.; Li, Ling; Wurtele, Eve Syrkin (November 2014). "Coming of age: orphan genes in plants". Trends in Plant Science. 19 (11): 698–708. doi:10.1016/j.tplants.2014.07.003. ISSN 1878-4372. PMID 25151064.
Guerra-Almeida, Diego; Nunes-da-Fonseca, Rodrigo (20 October 2020). "Small Open Reading Frames: How Important Are They for Molecular Evolution?". Frontiers in Genetics. 11. doi:10.3389/fgene.2020.574737. PMC 7606980. PMID 33193682.
Lehmann, M.; Siegmund, T.; Lintermann, K. G.; Korge, G. (23 October 1998). "The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain". The Journal of Biological Chemistry. 273 (43): 28504–28509. doi:10.1074/jbc.273.43.28504. ISSN 0021-9258. PMID 9774480.
Tanvir, Rezwan; Ping, Wenli; Sun, Jiping; Cain, Morgan; Li, Xuejun; Li, Ling (April 2022). "AtQQS orphan gene and NtNF-YC4 boost protein accumulation and pest resistance in tobacco (Nicotiana tabacum)". Plant Science. 317: 111198. doi:10.1016/j.plantsci.2022.111198. ISSN 1873-2259. PMID 35193747.
Nautiyal, Katherine M.; Hen, René (2017). "Serotonin receptors in depression: From a to B". F1000Research. 6: 123. doi:10.12688/f1000research.9736.1. PMC 5302148. PMID 28232871.

harvard.edu

ui.adsabs.harvard.edu

Jacob F (June 1977). "Evolution and tinkering". Science. 196 (4295): 1161–1166. Bibcode:1977Sci...196.1161J. doi:10.1126/science.860134. PMID 860134.
Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, et al. (November 2015). "QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions". Proceedings of the National Academy of Sciences of the United States of America. 112 (47): 14734–14739. Bibcode:2015PNAS..11214734L. doi:10.1073/pnas.1514670112. PMC 4664325. PMID 26554020.
Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C (February 2011). "Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana". BMC Evolutionary Biology. 11 (1): 47. Bibcode:2011BMCEE..11...47D. doi:10.1186/1471-2148-11-47. PMC 3049755. PMID 21332978.
Albà MM, Castresana J (April 2007). "On homology searches by protein Blast and the characterization of the age of genes". BMC Evolutionary Biology. 7 (1): 53. Bibcode:2007BMCEE...7...53A. doi:10.1186/1471-2148-7-53. PMC 1855329. PMID 17408474.
Zhao L, Saelao P, Jones CD, Begun DJ (February 2014). "Origin and spread of de novo genes in Drosophila melanogaster populations". Science. 343 (6172): 769–772. Bibcode:2014Sci...343..769Z. doi:10.1126/science.1248286. PMC 4391638. PMID 24457212.
Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ (June 2006). "Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression". Proceedings of the National Academy of Sciences of the United States of America. 103 (26): 9935–9939. Bibcode:2006PNAS..103.9935L. doi:10.1073/pnas.0509809103. PMC 1502557. PMID 16777968.
Heinen TJ, Staubach F, Häming D, Tautz D (September 2009). "Emergence of a new gene from an intergenic region". Current Biology. 19 (18): 1527–1531. Bibcode:2009CBio...19.1527H. doi:10.1016/j.cub.2009.07.049. PMID 19733073.
Chen S, Zhang YE, Long M (December 2010). "New genes in Drosophila quickly become essential". Science. 330 (6011): 1682–1685. Bibcode:2010Sci...330.1682C. doi:10.1126/science.1196380. PMC 7211344. PMID 21164016.
Neme R, Tautz D (March 2014). "Evolution: dynamics of de novo gene emergence". Current Biology. 24 (6): R238–R240. Bibcode:2014CBio...24.R238N. doi:10.1016/j.cub.2014.02.016. PMID 24650912.
Wilson BA, Foy SG, Neme R, Masel J (June 2017). "Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth". Nature Ecology & Evolution. 1 (6): 0146–146. Bibcode:2017NatEE...1..146W. doi:10.1038/s41559-017-0146. PMC 5476217. PMID 28642936.
Fellner, Lea; Simon, Svenja; Scherling, Christian; Witting, Michael; Schober, Steffen; Polte, Christine; Schmitt-Kopplin, Philippe; Keim, Daniel A.; Scherer, Siegfried; Neuhaus, Klaus (18 December 2015). "Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting". BMC Evolutionary Biology. 15 (1): 283. Bibcode:2015BMCEE..15..283F. doi:10.1186/s12862-015-0558-z. ISSN 1471-2148. PMC 4683798. PMID 26677845.

nih.gov

pubmed.ncbi.nlm.nih.gov

Fischer D, Eisenberg D (September 1999). "Finding families for genomic ORFans". Bioinformatics. 15 (9): 759–762. doi:10.1093/bioinformatics/15.9.759. PMID 10498776.
Tautz D, Domazet-Lošo T (August 2011). "The evolutionary origin of orphan genes". Nature Reviews. Genetics. 12 (10): 692–702. doi:10.1038/nrg3053. PMID 21878963. S2CID 31738556.
Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC (September 2009). "More than just orphans: are taxonomically-restricted genes important in evolution?". Trends in Genetics. 25 (9): 404–413. doi:10.1016/j.tig.2009.07.006. PMID 19716618.
Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, et al. (September 2008). "On the origin of new genes in Drosophila". Genome Research. 18 (9): 1446–1455. doi:10.1101/gr.076588.108. PMC 2527705. PMID 18550802.
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM (March 2009). "Origin of primate orphan genes: a comparative genomics approach". Molecular Biology and Evolution. 26 (3): 603–612. doi:10.1093/molbev/msn281. PMID 19064677.
Cortez, Diego; Forterre, Patrick; Gribaldo, Simonetta (2009). "A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes". Genome Biology. 10 (6): R65. doi:10.1186/gb-2009-10-6-r65. ISSN 1465-6906. PMC 2718499. PMID 19531232.
Weisman CM, Murray AW, Eddy SR (November 2020). "Many, but not all, lineage-specific genes can be explained by homology detection failure". PLOS Biology. 18 (11): e3000862. doi:10.1371/journal.pbio.3000862. PMC 7660931. PMID 33137085.
Vakirlis N, Carvunis AR, McLysaght A (February 2020). "Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes". eLife. 9. doi:10.7554/eLife.53500. PMC 7028367. PMID 32066524.
Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E (2013). "Mechanisms and dynamics of orphan gene emergence in insect genomes". Genome Biology and Evolution. 5 (2): 439–455. doi:10.1093/gbe/evt009. PMC 3590893. PMID 23348040.
Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD (17 October 2013). "De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences". PLOS Genetics. 9 (10): e1003860. doi:10.1371/journal.pgen.1003860. PMC 3798262. PMID 24146629.
Suenaga Y, Islam SM, Alagu J, Kaneko Y, Kato M, Tanaka Y, et al. (January 2014). "NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas". PLOS Genetics. 10 (1): e1003996. doi:10.1371/journal.pgen.1003996. PMC 3879166. PMID 24391509.
Yu G, Stoltzfus A (2012). "Population diversity of ORFan genes in Escherichia coli". Genome Biology and Evolution. 4 (11): 1176–87. doi:10.1093/gbe/evs081. PMC 3514957. PMID 23034216.
Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV (November 2016). "Two fundamentally different classes of microbial genes". Nature Microbiology. 2 (3): 16208. doi:10.1038/nmicrobiol.2016.208. PMID 27819663. S2CID 21799266.
Koonin EV, Makarova KS, Wolf YI (July 2021). "Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century". Trends in Microbiology. 29 (7): 582–592. doi:10.1016/j.tim.2021.01.005. PMC 9404256. PMID 33541841. S2CID 231820647.
Domazet-Loso, Tomislav (13 October 2003). "An Evolutionary Analysis of Orphan Genes in Drosophila". Genome Research. 13 (10): 2213–2219. doi:10.1101/gr.1311003. PMC 403679. PMID 14525923.
Tautz, Diethard (31 August 2011). "The evolutionary origin of orphan genes". Nature Reviews Genetics. 12 (10): 692–702. doi:10.1038/nrg3053. PMID 21878963. Retrieved 26 April 2024.
Jacob F (June 1977). "Evolution and tinkering". Science. 196 (4295): 1161–1166. Bibcode:1977Sci...196.1161J. doi:10.1126/science.860134. PMID 860134.
Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, Field D (August 2005). "Orphans as taxonomically restricted and ecologically important genes". Microbiology. 151 (Pt 8): 2499–2501. doi:10.1099/mic.0.28146-0. PMID 16079329.
Cai J, Zhao R, Jiang H, Wang W (May 2008). "De novo origination of a new protein-coding gene in Saccharomyces cerevisiae". Genetics. 179 (1): 487–496. doi:10.1534/genetics.107.084491. PMC 2390625. PMID 18493065.
Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES (May 2009). "Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves". The Plant Journal. 58 (3): 485–498. doi:10.1111/j.1365-313X.2009.03793.x. PMID 19154206.
Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, et al. (November 2015). "QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions". Proceedings of the National Academy of Sciences of the United States of America. 112 (47): 14734–14739. Bibcode:2015PNAS..11214734L. doi:10.1073/pnas.1514670112. PMC 4664325. PMID 26554020.
Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C (February 2011). "Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana". BMC Evolutionary Biology. 11 (1): 47. Bibcode:2011BMCEE..11...47D. doi:10.1186/1471-2148-11-47. PMC 3049755. PMID 21332978.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–3402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
Albà MM, Castresana J (April 2007). "On homology searches by protein Blast and the characterization of the age of genes". BMC Evolutionary Biology. 7 (1): 53. Bibcode:2007BMCEE...7...53A. doi:10.1186/1471-2148-7-53. PMC 1855329. PMID 17408474.
Moyers BA, Zhang J (January 2015). "Phylostratigraphic bias creates spurious patterns of genome evolution". Molecular Biology and Evolution. 32 (1): 258–267. doi:10.1093/molbev/msu286. PMC 4271527. PMID 25312911.
Domazet-Loso T, Brajković J, Tautz D (November 2007). "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages". Trends in Genetics. 23 (11): 533–539. doi:10.1016/j.tig.2007.08.014. PMID 18029048.
Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC (2015). "Remote homology and the functions of metagenomic dark matter". Frontiers in Genetics. 6: 234. doi:10.3389/fgene.2015.00234. PMC 4508852. PMID 26257768.
McLysaght A, Guerzoni D (September 2015). "New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370 (1678): 20140332. doi:10.1098/rstb.2014.0332. PMC 4571571. PMID 26323763.
Palmieri N, Kosiol C, Schlötterer C (February 2014). "The life cycle of Drosophila orphan genes". eLife. 3: e01311. arXiv:1401.4956. doi:10.7554/eLife.01311. PMC 3927632. PMID 24554240.
Zhao L, Saelao P, Jones CD, Begun DJ (February 2014). "Origin and spread of de novo genes in Drosophila melanogaster populations". Science. 343 (6172): 769–772. Bibcode:2014Sci...343..769Z. doi:10.1126/science.1248286. PMC 4391638. PMID 24457212.
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Cortez, Diego; Forterre, Patrick; Gribaldo, Simonetta (2009). "A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes". Genome Biology. 10 (6): R65. doi:10.1186/gb-2009-10-6-r65. ISSN 1465-6906. PMC 2718499. PMID 19531232.
Zhang, Wenyu; Gao, Yuanxiao; Long, Manyuan; Shen, Bairong (April 2019). "Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans". Science China. Life Sciences. 62 (4): 579–593. doi:10.1007/s11427-019-9482-0. ISSN 1869-1889. PMID 30919281.
Fellner, Lea; Simon, Svenja; Scherling, Christian; Witting, Michael; Schober, Steffen; Polte, Christine; Schmitt-Kopplin, Philippe; Keim, Daniel A.; Scherer, Siegfried; Neuhaus, Klaus (18 December 2015). "Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting". BMC Evolutionary Biology. 15 (1): 283. Bibcode:2015BMCEE..15..283F. doi:10.1186/s12862-015-0558-z. ISSN 1471-2148. PMC 4683798. PMID 26677845.
Arendsee, Zebulun W.; Li, Ling; Wurtele, Eve Syrkin (November 2014). "Coming of age: orphan genes in plants". Trends in Plant Science. 19 (11): 698–708. doi:10.1016/j.tplants.2014.07.003. ISSN 1878-4372. PMID 25151064.
Lehmann, M.; Siegmund, T.; Lintermann, K. G.; Korge, G. (23 October 1998). "The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain". The Journal of Biological Chemistry. 273 (43): 28504–28509. doi:10.1074/jbc.273.43.28504. ISSN 0021-9258. PMID 9774480.
Tanvir, Rezwan; Ping, Wenli; Sun, Jiping; Cain, Morgan; Li, Xuejun; Li, Ling (April 2022). "AtQQS orphan gene and NtNF-YC4 boost protein accumulation and pest resistance in tobacco (Nicotiana tabacum)". Plant Science. 317: 111198. doi:10.1016/j.plantsci.2022.111198. ISSN 1873-2259. PMID 35193747.