The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
Open accessAbstract
The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets.
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Citations
Cites
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
The NIH Roadmap Epigenomics Mapping Consortium
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1045 · Cited by 1,892
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×
“Details pages for the annotated elements show evidence used to build the annotation such as UniProt (13), CCDS (14), RefSeq (15) and GenBank (16) sequences, and PubMed IDs for published experimental evidence.”
Method
Cited by
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
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Identification of seven loci affecting mean telomere length and their association with disease
CARDIoGRAM consortium, Codd, V., Nelson, C. P., Albrecht, E., Mangino, M., Deelen, J., Buxton, J. L., Hottenga, J. J., Fischer, K., Esko, T., et al. (2013) · Nature Genetics · doi:10.1038/ng.2528 · Cited by 933
Metadata
- Authors
- Rosenbloom, K. R., Dreszer, T. R., Long, J. C., Malladi, V. S., Sloan, C. A., Raney, B. J., Cline, M. S., Karolchik, D., Barber, G. P., Clawson, H., Diekhans, M., Fujita, P. A., Goldman, M., Gravell, R. C., Harte, R. A., Hinrichs, A. S., Kirkup, V. M., Kuhn, R. M., Learned, K., Maddren, M., Meyer, L. R., Pohl, A., Rhead, B., Wong, M. C., Zweig, A. S., Haussler, D., & Kent, W. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-09
- Volume
- 40
- Issue
- D1
- Pages
- D912-D917
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2009935171
- Cited by
- 257
- References
- 4
- FWCI
- 15.16
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: ENCODE whole-genome data in the UCSC Genome Browser: update 2012. https://app.cochat.ai/papers/10.1093/nar/gkr1012
- The paper
- Rosenbloom, K. R., Dreszer, T. R., Long, J. C., Malladi, V. S., Sloan, C. A., Raney, B. J., Cline, M. S., Karolchik, D., Barber, G. P., Clawson, H., Diekhans, M., Fujita, P. A., Goldman, M., Gravell, R. C., Harte, R. A., Hinrichs, A. S., Kirkup, V. M., Kuhn, R. M., Learned, K., . . . Kent, W. J. (2012). ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr1012
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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.
