The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
The UCSC Genome Browser database: 2016 update
Open accessPublished version of a preprint
Abstract
For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
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-citationTandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
<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-citationAn integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
dbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
Cited by
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
Lowe, T. M., & Chan, P. P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw413 · Cited by 2,709
Manzoni, C., Kia, D. A., Vandrovcova, J., Hardy, J., Wood, N. W., Lewis, P. A., & Ferrari, R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bbw114 · Cited by 804
Inflammatory memory sensitizes skin epithelial stem cells to tissue damage
Naik, S., Larsen, S. B., Gomez, N. C., Alaverdyan, K., Sendoel, A., Yuan, S., Polak, L., Kulukian, A., Chai, S., & Fuchs, E. (2017) · Nature · doi:10.1038/nature24271 · Cited by 745
Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3774 · Cited by 628
Metadata
- Authors
- Speir, M. L., Zweig, A. S., Rosenbloom, K. R., Raney, B. J., Paten, B., Nejad, P., Lee, B. T., Learned, K., Karolchik, D., Hinrichs, A. S., Heitner, S., Harte, R. A., Haeussler, M., Guruvadoo, L., Fujita, P. A., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G. P., Haussler, D., Kuhn, R. M., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-20
- Volume
- 44
- Issue
- D1
- Pages
- D717-D725
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2176686025
- Cited by
- 451
- References
- 63
- FWCI
- 34.99
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The UCSC Genome Browser database: 2016 update. https://app.cochat.ai/papers/10.1093/nar/gkv1275
- The paper
- Speir, M. L., Zweig, A. S., Rosenbloom, K. R., Raney, B. J., Paten, B., Nejad, P., Lee, B. T., Learned, K., Karolchik, D., Hinrichs, A. S., Heitner, S., Harte, R. A., Haeussler, M., Guruvadoo, L., Fujita, P. A., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., . . . Kent, W. J. (2016). The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkv1275
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.
