elements in the human genome. Nature 489 (7414): 57–74.8 Frankish, A., Uszczynska, B., Ritchie, G.R. et al. (2015). Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics 16 (Suppl 8): S2.
9 Goffeau, A., Barrell, B.G., Bussey, H. et al. (1996). Life with 6000 genes. Science 274 (5287): 546, 563–567.
10 Green, E.D. (2001). Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2 (8): 573–583.
11 GTEx Consortium (2015). Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348 (6235): 648–660.
12 Haeussler, M., Zweig, A.S., Tyner, C. et al. (2019). The UCSC Genome Browser database: 2019 update. Nucleic Acids Res 47 (D1): D853–D858.
13 Harrow, J., Frankish, A., Gonzalez, J.M. et al. (2012). GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22 (9): 1760–1774.
14 Herrero, J., Muffato, M., Beal, K. et al. (2016). Ensembl comparative genomics resources. Database (Oxford) 2016: bav096.
15 Howald, C., Tanzer, A., Chrast, J. et al. (2012). Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 22 (9): 1698–1710.
16 Hubbard, T., Barker, D., Birney, E. et al. (2002). The Ensembl genome database project. Nucleic Acids Res. 30 (1): 38–41.
17 Kent, W.J. (2002). BLAT–the BLAST-like alignment tool. Genome Res. 12 (4): 656–664.
18 Kent, W.J. and Haussler, D. (2001). Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11 (9): 1541–1548.
19 Kent, W.J. and Zahler, A.M. (2000). The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res. 28 (1): 91–93.
20 Kinsella, R.J., Kähäri, A., Haider, S. et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030.
21 Kitts, P. (2003). Genome assembly and annotation process. In: The NCBI Handbook (eds. J. McEntyre and J. Ostell) ch. 14. Bethesda, MD: National Center for Biotechnology Information.
22 Lander, E.S., Linton, L.M., Birren, B. et al., and International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409 (6822): 860–921.
23 Lawrence, M., Daujat, S., and Schneider, R. (2016). Lateral thinking: how histone modifications regulate gene expression. Trends Genet. 32 (1): 42–56.
24 Li, R., Fan, W., Tian, G. et al. (2010). The sequence and de novo assembly of the giant panda genome. Nature 463 (7279): 311–317.
25 McLaren, W., Gil, L., Hunt, S.E. et al. (2016). The Ensembl variant effect predictor. Genome Biol. 17 (1): 122.
26 Moreland, R.T., Nguyen, A.D., Ryan, J.F. et al. (2014). A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 15: 316.
27 Mudge, J.M. and Harrow, J. (2015). Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26 (9–10): 366–378.
28 Ryan, J.F., Pang, K., Schnitzler, C.E. et al. (2013). The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342 (6164): 1242592.
29 Sayers, E.W., Agarwala, R., Bolton, E.E. et al. (2019). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 47 (D1): D23–D28.
30 Skinner, M.E. and Holmes, I.H. (2010). Setting up the JBrowse genome browser. Curr. Protoc. Bioinformatics. Chapter 9: Unit 9.13. https://doi.org/10.1002/0471250953.bi0913s32.
31 Trapnell, C., Williams, B.A., Pertea, G. et al. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28 (5): 511–515.
32 Wheeler, D.L., Church, D.M., Lash, A.E. et al. (2001). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 29 (1): 11–16.
33 Wolfsberg, T.G., Wetterstrand, K.A., Guyer, M.S. et al. (2002). A user's guide to the human genome. Nat. Genet. 32 (Suppl): 1–79.
34 Wu, P.Y., Phan, J.H., and Wang, M.D. (2013). Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinformatics 14 (Suppl 11): S8.
35 Zerbino, D.R., Johnson, N., Juetteman, T. et al. (2016). Ensembl regulation resources. Database (Oxford) 2016, pii: bav119.
This chapter was written by Dr. Tyra G. Wolfsberg in her private capacity. No official support or endorsement by the National Institutes of Health or the United States Department of Health and Human Services is intended or should be inferred.
Конец ознакомительного фрагмента.
Текст предоставлен ООО «ЛитРес».
Прочитайте эту книгу целиком, купив полную легальную версию на ЛитРес.
Безопасно оплатить книгу можно банковской картой Visa, MasterCard, Maestro, со счета мобильного телефона, с платежного терминала, в салоне МТС или Связной, через PayPal, WebMoney, Яндекс.Деньги, QIWI Кошелек, бонусными картами или другим удобным Вам способом.
