The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
The UCSC Genome Browser Database: update 2009
Open accessAbstract
The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.
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Cites
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Self-citationThe International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“This track, which displays the results of a multiz alignment and phastCons computation (25), is useful for viewing the evolutionary relatedness of sequences across a wide range of animals.”
BackgroundSelf-citationDetection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Yang, Z., & Nielsen, R. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004148 · Cited by 1,374
Mapping and sequencing of structural variation from eight human genomes
Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119
Patterns of Positive Selection in Six Mammalian Genomes
Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000144 · Cited by 576
Cited by
Li, J.-H., Liu, S., Zhou, H., Qu, L.-H., & Yang, J.-H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1248 · Cited by 4,686
Detection of nonneutral substitution rates on mammalian phylogenies
Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research · doi:10.1101/gr.097857.109 · Cited by 2,353
Self-citationCircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs
Dudekula, D. B., Panda, A. C., Grammatikakis, I., De, S., Abdelmohsen, K., & Gorospe, M. (2016) · RNA Biology · doi:10.1080/15476286.2015.1128065 · Cited by 1,255
Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232
Common genetic variants on 5p14.1 associate with autism spectrum disorders
Wang, K., Zhang, H., Ma, D., Bucan, M., Glessner, J. T., Abrahams, B. S., Salyakina, D., Imielinski, M., Bradfield, J. P., Sleiman, P. M. A., et al. (2009) · Nature · doi:10.1038/nature07999 · Cited by 989
Metadata
- Authors
- Kuhn, R. M., Karolchik, D., Zweig, A. S., Wang, T., Smith, K. E., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pheasant, M., Meyer, L., Hsu, F., Hinrichs, A. S., Harte, R. A., Giardine, B., Fujita, P., Diekhans, M., Dreszer, T., Clawson, H., Barber, G. P., Haussler, D., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D755-D761
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2916408032
- Cited by
- 385
- References
- 7
- FWCI
- 30.65
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: The UCSC Genome Browser Database: update 2009. https://app.cochat.ai/papers/10.1093/nar/gkn875
- The paper
- Kuhn, R. M., Karolchik, D., Zweig, A. S., Wang, T., Smith, K. E., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pheasant, M., Meyer, L., Hsu, F., Hinrichs, A. S., Harte, R. A., Giardine, B., Fujita, P., Diekhans, M., Dreszer, T., Clawson, H., . . . Kent, W. J. (2009). The UCSC Genome Browser Database: update 2009. Nucleic Acids Research. https://doi.org/10.1093/nar/gkn875
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
