The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
The UCSC Genome Browser database: 2023 update
Open accessAbstract
The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
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Cites
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,200
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Self-citationIntegrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
<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-citationdbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
The GTEx Consortium atlas of genetic regulatory effects across human tissues
The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science · doi:10.1126/science.aaz1776 · Cited by 5,547
Self-citationBenson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1195 · Cited by 3,261
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Self-citationSingle-cell transcriptomics of 20 mouse organs creates a Tabula Muris
The Tabula Muris Consortium, coordination, O., coordination, L., processing, O. C. A., sequencing, L. P. A., analysis, C. D., annotation, C. T., Writing group, Supplemental text writing group, & Principal investigators (2018) · Nature · doi:10.1038/s41586-018-0590-4 · Cited by 2,842 · cited 1×
“There are also two aggregate tracks: Tabula Sapiens (19), which contains data from the Tabula Sapiens Consortium providing an atlas of nearly 500 000 cells from 24 organs of 15 normal humans, and a Merged Cells track, which is an aggregate track created by the Genome Browser containing data from 12 papers covering 14…”
Cited by
Zhang, J., Dutta, D., Köttgen, A., Tin, A., Schlosser, P., Grams, M. E., Harvey, B., CKDGen Consortium, Yu, B., Boerwinkle, E., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01051-w · Cited by 373
Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots
Tian, L., Peel, G. J., Lei, Z., Aziz, N., Dai, X., He, J., Watson, B., Zhao, P. X., Sumner, L. W., & Dixon, R. A. (2009) · BMC Plant Biology · doi:10.1186/1471-2229-9-1 · Cited by 314
dmrff: identifying differentially methylated regions efficiently with power and control
Suderman, M., Staley, J. R., French, R., Arathimos, R., Simpkin, A., & Tilling, K. (2018) · doi:10.1101/508556 · Cited by 120
Oxidation of retromer complex controls mitochondrial translation
Zhang, J., Ali, M. Y., Chong, H. B., Tien, P.-C., Woods, J., Noble, C., Vornbäumen, T., Ordulu, Z., Possemato, A. P., Harry, S., et al. (2025) · Nature · doi:10.1038/s41586-025-08756-y · Cited by 38
State of the interactomes: an evaluation of molecular networks for generating biological insights
Wright, S. N., Colton, S., Schaffer, L. V., Pillich, R. T., Churas, C., Pratt, D., & Ideker, T. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00077-y · Cited by 32
Metadata
- Authors
- Nassar, L. R., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Lee, C. M., Muthuraman, P., Nguy, B., Pereira, T., Nejad, P., Perez, G., Raney, B. J., Schmelter, D., Speir, M. L., Wick, B. D., Zweig, A. S., Haussler, D., Kuhn, R. M., Haeussler, M., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-11-24
- Volume
- 51
- Issue
- D1
- Pages
- D1188-D1195
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4309999671
- Cited by
- 600
- References
- 36
- FWCI
- 34.87
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: The UCSC Genome Browser database: 2023 update. https://app.cochat.ai/papers/10.1093/nar/gkac1072
- The paper
- Nassar, L. R., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Lee, C. M., Muthuraman, P., Nguy, B., Pereira, T., Nejad, P., Perez, G., Raney, B. J., Schmelter, D., Speir, M. L., . . . Kent, W. J. (2023). The UCSC Genome Browser database: 2023 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac1072
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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.
