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Ancient nuclear genomes enable repatriation of Indigenous human remains.
Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J, Kennedy R, Winch P, Pappin M Sr, Wales T, Bates WB, Hamilton S, Whyman N, van Holst Pellekaan S, McAllister PJ, Taçon PSC, Curnoe D, Li R, Millar C, Subramanian S, Willerslev E, Malaspinas AS, Sikora M, Lambert DM. Wright JL, et al. Among authors: li r. Sci Adv. 2018 Dec 19;4(12):eaau5064. doi: 10.1126/sciadv.aau5064. eCollection 2018 Dec. Sci Adv. 2018. PMID: 30585290 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Conrad DF, et al. Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862. Nat Genet. 2011. PMID: 21666693 Free PMC article.
Genomic data for 78 chickens from 14 populations.
Li D, Che T, Chen B, Tian S, Zhou X, Zhang G, Li M, Gaur U, Li Y, Luo M, Zhang L, Xu Z, Zhao X, Yin H, Wang Y, Jin L, Tang Q, Xu H, Yang M, Zhou R, Li R, Zhu Q, Li M. Li D, et al. Among authors: li y, li m, li r. Gigascience. 2017 Jun 1;6(6):1-5. doi: 10.1093/gigascience/gix026. Gigascience. 2017. PMID: 28431039 Free PMC article.
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.
Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H, Ma H, Zhang F, Feng S, Zhang W, Du H, Tian G, Li J, Zhang X, Li S, Bolund L, Kristiansen K, de Smith AJ, Blakemore AI, Coin LJ, Yang H, Wang J, Wang J. Li Y, et al. Among authors: li s, li j, li r. Nat Biotechnol. 2011 Jul 24;29(8):723-30. doi: 10.1038/nbt.1904. Nat Biotechnol. 2011. PMID: 21785424
Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
Li M, Chen L, Tian S, Lin Y, Tang Q, Zhou X, Li D, Yeung CKL, Che T, Jin L, Fu Y, Ma J, Wang X, Jiang A, Lan J, Pan Q, Liu Y, Luo Z, Guo Z, Liu H, Zhu L, Shuai S, Tang G, Zhao J, Jiang Y, Bai L, Zhang S, Mai M, Li C, Wang D, Gu Y, Wang G, Lu H, Li Y, Zhu H, Li Z, Li M, Gladyshev VN, Jiang Z, Zhao S, Wang J, Li R, Li X. Li M, et al. Among authors: li c, li d, li y, li z, li x, li r. Genome Res. 2017 May;27(5):865-874. doi: 10.1101/gr.207456.116. Epub 2016 Sep 19. Genome Res. 2017. PMID: 27646534 Free PMC article.
TreeFam: a curated database of phylogenetic trees of animal gene families.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R. Li H, et al. Among authors: li r. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80. doi: 10.1093/nar/gkj118. Nucleic Acids Res. 2006. PMID: 16381935 Free PMC article.
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