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 2010
Open accessAbstract
The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
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Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
<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-citationEvolutionarily 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 7×
“Both phastCons (25) and phyloP (26) conservation scores have been computed separately for three groups of organisms: 8 primates alone, 31 placental mammals, and all 44 vertebrates.”
BackgroundInfluentialSelf-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
NCBI Reference Sequences: current status, policy and new initiatives
Pruitt, K. D., Tatusova, T., Klimke, W., & Maglott, D. R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn721 · Cited by 736 · cited 1×
“The minimal set of annotation ‘tracks’ on every browser generally includes assembly and gaps, the percentage of guanine and cytosine bases, alignments of RefSeq genes (3,4), mRNAs and ESTs obtained from GenBank (5) and repeat region annotations.”
BackgroundSignals of recent positive selection in a worldwide sample of human populations
Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W., et al. (2009) · Genome Research · doi:10.1101/gr.087577.108 · Cited by 717
The Comprehensive Knockout Mouse Project Consortium (2004) · Nature Genetics · doi:10.1038/ng0904-921 · Cited by 608
Cited by
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., & Jaffrey, S. R. (2012) · Cell · doi:10.1016/j.cell.2012.05.003 · Cited by 4,223
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072
High density DNA methylation array with single CpG site resolution
Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J. M., Delano, D., Zhang, L., Schroth, G. P., Gunderson, K. L., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.07.007 · Cited by 1,727
“Toward this end, both gene and CpG island regions were subdivided according to UCSC classifications [29,30] (Fig.”
BackgroundIdentifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., & Batzoglou, S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001025 · Cited by 1,757
Metadata
- Authors
- Rhead, B., Karolchik, D., Kuhn, R. M., Hinrichs, A. S., Zweig, A. S., Fujita, P. A., Diekhans, M., Smith, K. E., Rosenbloom, K. R., Raney, B. J., Pohl, A., Pheasant, M., Meyer, L. R., Learned, K., Hsu, F., Hillman-Jackson, J., Harte, R. A., Giardine, B., Dreszer, T. R., Clawson, H., Barber, G. P., Haussler, D., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-11
- Volume
- 38
- Issue
- Database
- Pages
- D613-D619
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2918025614
- Cited by
- 568
- References
- 7
- FWCI
- 46.69
- Type
- journal article
- Language
- en
- Open access
- gold
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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- CoChat. (2026). Citation check: The UCSC Genome Browser database: update 2010. https://app.cochat.ai/papers/10.1093/nar/gkp939
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- Rhead, B., Karolchik, D., Kuhn, R. M., Hinrichs, A. S., Zweig, A. S., Fujita, P. A., Diekhans, M., Smith, K. E., Rosenbloom, K. R., Raney, B. J., Pohl, A., Pheasant, M., Meyer, L. R., Learned, K., Hsu, F., Hillman-Jackson, J., Harte, R. A., Giardine, B., Dreszer, T. R., . . . Kent, W. J. (2010). The UCSC Genome Browser database: update 2010. Nucleic Acids Research. https://doi.org/10.1093/nar/gkp939
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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.
