The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
The UCSC Genome Browser database: update 2011
Open accessAbstract
The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.
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Cites
The Sequence Alignment/Map format and SAMtools
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<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-citationGREAT improves functional interpretation of cis-regulatory regions
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Detection 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
Ancient human genome sequence of an extinct Palaeo-Eskimo
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NCBI Reference Sequences: current status, policy and new initiatives
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“Most organisms also have tracks containing alignments of RefSeq genes (3,4), mRNAs and ESTs from GenBank (5) as well as gene and gene prediction tracks such as Ensembl Genes (6).”
BackgroundThe Comprehensive Knockout Mouse Project Consortium (2004) · Nature Genetics · doi:10.1038/ng0904-921 · Cited by 608
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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Circular RNAs are a large class of animal RNAs with regulatory potency
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
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
Metadata
- Authors
- Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., Goldman, M., Barber, G. P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T. R., Giardine, B. M., Harte, R. A., Hillman-Jackson, J., Hsu, F., Kirkup, V., Kuhn, R. M., Learned, K., Li, C. H., Meyer, L. R., Pohl, A., Raney, B. J., Rosenbloom, K. R., Smith, K. E., Haussler, D., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-18
- Volume
- 39
- Issue
- Database
- Pages
- D876-D882
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2127640118
- Cited by
- 1,811
- References
- 8
- FWCI
- 126.18
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: The UCSC Genome Browser database: update 2011. https://app.cochat.ai/papers/10.1093/nar/gkq963
- The paper
- Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., Goldman, M., Barber, G. P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T. R., Giardine, B. M., Harte, R. A., Hillman-Jackson, J., Hsu, F., Kirkup, V., Kuhn, R. M., Learned, K., . . . Kent, W. J. (2011). The UCSC Genome Browser database: update 2011. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq963
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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.
