References analysis of the Wikipedia article "Conserved sequence" in the English version

doi.org

Sanger, F. (24 September 1949). "Species Differences in Insulins". Nature. 164 (4169): 529. Bibcode:1949Natur.164..529S. doi:10.1038/164529a0. PMID 18141620. S2CID 4067991.

Marmur, J; Falkow, S; Mandel, M (October 1963). "New Approaches to Bacterial Taxonomy". Annual Review of Microbiology. 17 (1): 329–372. doi:10.1146/annurev.mi.17.100163.001553. PMID 14147455.

Pace, N. R.; Sapp, J.; Goldenfeld, N. (17 January 2012). "Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life". Proceedings of the National Academy of Sciences. 109 (4): 1011–1018. Bibcode:2012PNAS..109.1011P. doi:10.1073/pnas.1109716109. PMC 3268332. PMID 22308526.

Margoliash, E (October 1963). "Primary Structure and Evolution of Cytochrome C". Proceedings of the National Academy of Sciences. 50 (4): 672–679. Bibcode:1963PNAS...50..672M. doi:10.1073/pnas.50.4.672. PMC 221244. PMID 14077496.

Zuckerkandl, E; Pauling, LB (1965). "Evolutionary Divergence and Convergence in Proteins". Evolving Genes and And Proteins: 96–166. doi:10.1016/B978-1-4832-2734-4.50017-6. ISBN 9781483227344.

Eck, R. V.; Dayhoff, M. O. (15 April 1966). "Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences". Science. 152 (3720): 363–366. Bibcode:1966Sci...152..363E. doi:10.1126/science.152.3720.363. PMID 17775169. S2CID 23208558.

Kimura, M (17 February 1968). "Evolutionary Rate at the Molecular Level". Nature. 217 (5129): 624–626. Bibcode:1968Natur.217..624K. doi:10.1038/217624a0. PMID 5637732. S2CID 4161261.

King, J. L.; Jukes, T. H. (16 May 1969). "Non-Darwinian Evolution". Science. 164 (3881): 788–798. Bibcode:1969Sci...164..788L. doi:10.1126/science.164.3881.788. PMID 5767777.

Kimura, M; Ohta, T (1974). "On Some Principles Governing Molecular Evolution". Proc Natl Acad Sci USA. 71 (7): 2848–2852. Bibcode:1974PNAS...71.2848K. doi:10.1073/pnas.71.7.2848. PMC 388569. PMID 4527913.

Asthana, Saurabh; Roytberg, Mikhail; Stamatoyannopoulos, John; Sunyaev, Shamil (28 December 2007). Brudno, Michael (ed.). "Analysis of Sequence Conservation at Nucleotide Resolution". PLOS Computational Biology. 3 (12): e254. Bibcode:2007PLSCB...3..254A. doi:10.1371/journal.pcbi.0030254. ISSN 1553-7358. PMC 2230682. PMID 18166073.

Cooper, G. M.; Brown, C. D. (1 February 2008). "Qualifying the relationship between sequence conservation and molecular function". Genome Research. 18 (2): 201–205. doi:10.1101/gr.7205808. ISSN 1088-9051. PMID 18245453.

Gilson, Amy I.; Marshall-Christensen, Ahmee; Choi, Jeong-Mo; Shakhnovich, Eugene I. (2017). "The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution". Biophysical Journal. 112 (7): 1350–1365. arXiv:1606.05802. Bibcode:2017BpJ...112.1350G. doi:10.1016/j.bpj.2017.02.029. PMC 5390048. PMID 28402878.

Hunt, Ryan C.; Simhadri, Vijaya L.; Iandoli, Matthew; Sauna, Zuben E.; Kimchi-Sarfaty, Chava (2014). "Exposing synonymous mutations". Trends in Genetics. 30 (7): 308–321. doi:10.1016/j.tig.2014.04.006. PMID 24954581.

Zhang, Jianzhi (2000). "Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes". Journal of Molecular Evolution. 50 (1): 56–68. Bibcode:2000JMolE..50...56Z. doi:10.1007/s002399910007. ISSN 0022-2844. PMID 10654260. S2CID 15248867.

Sousounis, Konstantinos; Haney, Carl E; Cao, Jin; Sunchu, Bharath; Tsonis, Panagiotis A (2012). "Conservation of the three-dimensional structure in non-homologous or unrelated proteins". Human Genomics. 6 (1): 10. doi:10.1186/1479-7364-6-10. ISSN 1479-7364. PMC 3500211. PMID 23244440.

Kairys, Visvaldas; Fernandes, Miguel X. (2007). "SitCon: Binding site residue conservation visualization and protein sequence-to-function tool". International Journal of Quantum Chemistry. 107 (11): 2100–2110. Bibcode:2007IJQC..107.2100K. doi:10.1002/qua.21396. hdl:10400.13/5004. ISSN 0020-7608.

Chamary, JV; Hurst, Laurence D (2005). "Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals". Genome Biology. 6 (9): R75. doi:10.1186/gb-2005-6-9-r75. PMC 1242210. PMID 16168082.

Wadler, C. S.; Vanderpool, C. K. (27 November 2007). "A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide". Proceedings of the National Academy of Sciences. 104 (51): 20454–20459. Bibcode:2007PNAS..10420454W. doi:10.1073/pnas.0708102104. PMC 2154452. PMID 18042713.

Johnsson, Per; Lipovich, Leonard; Grandér, Dan; Morris, Kevin V. (March 2014). "Evolutionary conservation of long non-coding RNAs; sequence, structure, function". Biochimica et Biophysica Acta (BBA) - General Subjects. 1840 (3): 1063–1071. doi:10.1016/j.bbagen.2013.10.035. PMC 3909678. PMID 24184936.

Freyhult, E. K.; Bollback, J. P.; Gardner, P. P. (6 December 2006). "Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA". Genome Research. 17 (1): 117–125. doi:10.1101/gr.5890907. PMC 1716261. PMID 17151342.

Margulies, E. H. (1 December 2003). "Identification and Characterization of Multi-Species Conserved Sequences". Genome Research. 13 (12): 2507–2518. doi:10.1101/gr.1602203. ISSN 1088-9051. PMC 403793. PMID 14656959.

Edwards, John R.; Ruparel, Hameer; Ju, Jingyue (2005). "Mass-spectrometry DNA sequencing". Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 573 (1–2): 3–12. Bibcode:2005MRFMM.573....3E. doi:10.1016/j.mrfmmm.2004.07.021. PMID 15829234.

Drost, Hajk-Georg; Gabel, Alexander; Grosse, Ivo; Quint, Marcel (1 May 2015). "Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis". Molecular Biology and Evolution. 32 (5): 1221–1231. doi:10.1093/molbev/msv012. ISSN 0737-4038. PMC 4408408. PMID 25631928.

Nawrocki, E. P.; Eddy, S. R. (4 September 2013). "Infernal 1.1: 100-fold faster RNA homology searches". Bioinformatics. 29 (22): 2933–2935. doi:10.1093/bioinformatics/btt509. PMC 3810854. PMID 24008419.

Eddy, SR; Durbin, R (11 June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079–88. doi:10.1093/nar/22.11.2079. PMC 308124. PMID 8029015.

Trivedi, Rakesh; Nagarajaram, Hampapathalu Adimurthy (2020). "Substitution scoring matrices for proteins - An overview". Protein Science. 29 (11): 2150–2163. doi:10.1002/pro.3954. ISSN 0961-8368. PMC 7586916. PMID 32954566.

Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S.; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J.; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E.; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict (December 2014). "Alignathon: a competitive assessment of whole-genome alignment methods". Genome Research. 24 (12): 2077–2089. doi:10.1101/gr.174920.114. PMC 4248324. PMID 25273068.

Rouli, L.; Merhej, V.; Fournier, P.-E.; Raoult, D. (September 2015). "The bacterial pangenome as a new tool for analysing pathogenic bacteria". New Microbes and New Infections. 7: 72–85. doi:10.1016/j.nmni.2015.06.005. PMC 4552756. PMID 26442149.

Méric, Guillaume; Yahara, Koji; Mageiros, Leonardos; Pascoe, Ben; Maiden, Martin C. J.; Jolley, Keith A.; Sheppard, Samuel K.; Bereswill, Stefan (27 March 2014). "A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter". PLOS ONE. 9 (3): e92798. Bibcode:2014PLoSO...992798M. doi:10.1371/journal.pone.0092798. PMC 3968026. PMID 24676150.

Cooper, G. M. (17 June 2005). "Distribution and intensity of constraint in mammalian genomic sequence". Genome Research. 15 (7): 901–913. doi:10.1101/gr.3577405. PMC 1172034. PMID 15965027.

Nawar Malhis; Steven J. M. Jones; Jörg Gsponer (2019). "Improved measures for evolutionary conservation that exploit taxonomy distances". Nature Communications. 10 (1): 1556. Bibcode:2019NatCo..10.1556M. doi:10.1038/s41467-019-09583-2. PMC 6450959. PMID 30952844.

Nawar Malhis; Matthew Jacobson; Steven J. M. Jones; Jörg Gsponer (2020). "LIST-S2: Taxonomy Based Sorting of Deleterious Missense Mutations Across Species". Nucleic Acids Research. 48 (W1): W154–W161. doi:10.1093/nar/gkaa288. PMC 7319545. PMID 32352516.

Chang KT, Guo J, di Ronza A, Sardiello M (January 2018). "Aminode: Identification of Evolutionary Constraints in the Human Proteome". Sci. Rep. 8 (1): 1357. Bibcode:2018NatSR...8.1357C. doi:10.1038/s41598-018-19744-w. PMC 5778061. PMID 29358731.

Pollard, K. S.; Hubisz, M. J.; Rosenbloom, K. R.; Siepel, A. (26 October 2009). "Detection of nonneutral substitution rates on mammalian phylogenies". Genome Research. 20 (1): 110–121. doi:10.1101/gr.097857.109. PMC 2798823. PMID 19858363.

Fan, Xiaodan; Zhu, Jun; Schadt, Eric E; Liu, Jun S (2007). "Statistical power of phylo-HMM for evolutionarily conserved element detection". BMC Bioinformatics. 8 (1): 374. doi:10.1186/1471-2105-8-374. PMC 2194792. PMID 17919331.

Bejerano, G. (28 May 2004). "Ultraconserved Elements in the Human Genome". Science. 304 (5675): 1321–1325. Bibcode:2004Sci...304.1321B. CiteSeerX 10.1.1.380.9305. doi:10.1126/science.1098119. PMID 15131266. S2CID 2790337.

Siepel, A. (1 August 2005). "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes". Genome Research. 15 (8): 1034–1050. doi:10.1101/gr.3715005. PMC 1182216. PMID 16024819.

Harmston, N.; Baresic, A.; Lenhard, B. (11 November 2013). "The mystery of extreme non-coding conservation". Philosophical Transactions of the Royal Society B: Biological Sciences. 368 (1632): 20130021. doi:10.1098/rstb.2013.0021. PMC 3826495. PMID 24218634.

Faircloth, B. C.; McCormack, J. E.; Crawford, N. G.; Harvey, M. G.; Brumfield, R. T.; Glenn, T. C. (9 January 2012). "Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales". Systematic Biology. 61 (5): 717–726. doi:10.1093/sysbio/sys004. PMID 22232343.

Faircloth, Brant C.; Branstetter, Michael G.; White, Noor D.; Brady, Seán G. (May 2015). "Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera". Molecular Ecology Resources. 15 (3): 489–501. doi:10.1111/1755-0998.12328. PMC 4407909. PMID 25207863.

Reneker, J.; Lyons, E.; Conant, G. C.; Pires, J. C.; Freeling, M.; Shyu, C.-R.; Korkin, D. (10 April 2012). "Long identical multispecies elements in plant and animal genomes". Proceedings of the National Academy of Sciences. 109 (19): E1183–E1191. doi:10.1073/pnas.1121356109. PMC 3358895. PMID 22496592.

Isenbarger, Thomas A.; Carr, Christopher E.; Johnson, Sarah Stewart; Finney, Michael; Church, George M.; Gilbert, Walter; Zuber, Maria T.; Ruvkun, Gary (14 October 2008). "The Most Conserved Genome Segments for Life Detection on Earth and Other Planets". Origins of Life and Evolution of Biospheres. 38 (6): 517–533. Bibcode:2008OLEB...38..517I. doi:10.1007/s11084-008-9148-z. PMID 18853276. S2CID 15707806.

Harris, J. K. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803. PMC 430263. PMID 12618371.

Ban, Nenad; Beckmann, Roland; Cate, Jamie HD; Dinman, Jonathan D; Dragon, François; Ellis, Steven R; Lafontaine, Denis LJ; Lindahl, Lasse; Liljas, Anders; Lipton, Jeffrey M; McAlear, Michael A; Moore, Peter B; Noller, Harry F; Ortega, Joaquin; Panse, Vikram Govind; Ramakrishnan, V; Spahn, Christian MT; Steitz, Thomas A; Tchorzewski, Marek; Tollervey, David; Warren, Alan J; Williamson, James R; Wilson, Daniel; Yonath, Ada; Yusupov, Marat (February 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology. 24: 165–169. doi:10.1016/j.sbi.2014.01.002. PMC 4358319. PMID 24524803.

Gadagkar, Sudhindra R.; Rosenberg, Michael S.; Kumar, Sudhir (15 January 2005). "Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 304B (1): 64–74. Bibcode:2005JEZB..304...64G. doi:10.1002/jez.b.21026. PMID 15593277.

Ludwig, W; Schleifer, KH (October 1994). "Bacterial phylogeny based on 16S and 23S rRNA sequence analysis". FEMS Microbiology Reviews. 15 (2–3): 155–73. doi:10.1111/j.1574-6976.1994.tb00132.x. PMID 7524576.

Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C.; Banfield, Jillian F. (11 April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.

Zhang, Liqing; Li, Wen-Hsiung (February 2004). "Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes". Molecular Biology and Evolution. 21 (2): 236–239. doi:10.1093/molbev/msh010. PMID 14595094.

Clermont, O.; Bonacorsi, S.; Bingen, E. (1 October 2000). "Rapid and Simple Determination of the Escherichia coli Phylogenetic Group". Applied and Environmental Microbiology. 66 (10): 4555–4558. Bibcode:2000ApEnM..66.4555C. doi:10.1128/AEM.66.10.4555-4558.2000. PMC 92342. PMID 11010916.

Kullberg, Morgan; Nilsson, Maria A.; Arnason, Ulfur; Harley, Eric H.; Janke, Axel (August 2006). "Housekeeping Genes for Phylogenetic Analysis of Eutherian Relationships". Molecular Biology and Evolution. 23 (8): 1493–1503. doi:10.1093/molbev/msl027. PMID 16751257.

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dx.doi.org

ebi.ac.uk

"Clustal FAQ #Symbols". Clustal. Archived from the original on 24 October 2016. Retrieved 8 December 2014.

nih.gov

pubmed.ncbi.nlm.nih.gov

Sanger, F. (24 September 1949). "Species Differences in Insulins". Nature. 164 (4169): 529. Bibcode:1949Natur.164..529S. doi:10.1038/164529a0. PMID 18141620. S2CID 4067991.

Marmur, J; Falkow, S; Mandel, M (October 1963). "New Approaches to Bacterial Taxonomy". Annual Review of Microbiology. 17 (1): 329–372. doi:10.1146/annurev.mi.17.100163.001553. PMID 14147455.

Kimura, M (17 February 1968). "Evolutionary Rate at the Molecular Level". Nature. 217 (5129): 624–626. Bibcode:1968Natur.217..624K. doi:10.1038/217624a0. PMID 5637732. S2CID 4161261.

King, J. L.; Jukes, T. H. (16 May 1969). "Non-Darwinian Evolution". Science. 164 (3881): 788–798. Bibcode:1969Sci...164..788L. doi:10.1126/science.164.3881.788. PMID 5767777.

Eddy, SR; Durbin, R (11 June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079–88. doi:10.1093/nar/22.11.2079. PMC 308124. PMID 8029015.

Cooper, G. M. (17 June 2005). "Distribution and intensity of constraint in mammalian genomic sequence". Genome Research. 15 (7): 901–913. doi:10.1101/gr.3577405. PMC 1172034. PMID 15965027.

Harris, J. K. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803. PMC 430263. PMID 12618371.

Bertram, L. (2009). "Genome-wide association studies in Alzheimer's disease". Human Molecular Genetics. 18 (R2): R137–R145. doi:10.1093/hmg/ddp406. PMC 2758713. PMID 19808789.

ncbi.nlm.nih.gov

Eddy, SR; Durbin, R (11 June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079–88. doi:10.1093/nar/22.11.2079. PMC 308124. PMID 8029015.

Cooper, G. M. (17 June 2005). "Distribution and intensity of constraint in mammalian genomic sequence". Genome Research. 15 (7): 901–913. doi:10.1101/gr.3577405. PMC 1172034. PMID 15965027.

Harris, J. K. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803. PMC 430263. PMID 12618371.

Bertram, L. (2009). "Genome-wide association studies in Alzheimer's disease". Human Molecular Genetics. 18 (R2): R137–R145. doi:10.1093/hmg/ddp406. PMC 2758713. PMID 19808789.

semanticscholar.org

api.semanticscholar.org

Sanger, F. (24 September 1949). "Species Differences in Insulins". Nature. 164 (4169): 529. Bibcode:1949Natur.164..529S. doi:10.1038/164529a0. PMID 18141620. S2CID 4067991.

Kimura, M (17 February 1968). "Evolutionary Rate at the Molecular Level". Nature. 217 (5129): 624–626. Bibcode:1968Natur.217..624K. doi:10.1038/217624a0. PMID 5637732. S2CID 4161261.

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