The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
GENCODE reference annotation for the human and mouse genomes
Open accessAbstract
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationAn integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
miRBase: annotating high confidence microRNAs using deep sequencing data
Kozomara, A., & Griffiths-Jones, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1181 · Cited by 5,073
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Self-citationGenetic effects on gene expression across human tissues
GTEx Consortium (2017) · Nature · doi:10.1038/nature24277 · Cited by 4,036
International network of cancer genome projects
The International Cancer Genome Consortium (2010) · Nature · doi:10.1038/nature08987 · Cited by 2,299
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232
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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-citationExpanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378
Self-citationSequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., Taliun, S. A. G., Corvelo, A., Gogarten, S. M., Kang, H. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03205-y · Cited by 2,213
Self-citationConserved pan-cancer microenvironment subtypes predict response to immunotherapy
Bagaev, A., Kotlov, N., Nomie, K., Svekolkin, V., Gafurov, A., Isaeva, O., Osokin, N., Kozlov, I., Frenkel, F., Gancharova, O., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.04.014 · Cited by 1,302
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Guilliams, M., Bonnardel, J., Haest, B., Vanderborght, B., Wagner, C., Remmerie, A., Bujko, A., Martens, L., Thoné, T., Browaeys, R., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.018 · Cited by 985
Metadata
- Authors
- Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J. M., Sisu, C., Wright, J., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Carbonell Sala, S., Chrast, J., Cunningham, F., Di Domenico, T., Donaldson, S., Fiddes, I. T., García Girón, C., Gonzalez, J. M., Grego, T., Hardy, M., Hourlier, T., Hunt, T., Izuogu, O. G., Lagarde, J., Martin, F. J., Martínez, L., Mohanan, S., Muir, P., Navarro, F. C. P., Parker, A., Pei, B., Pozo, F., Ruffier, M., Schmitt, B. M., Stapleton, E., Suner, M.-M., Sycheva, I., Uszczynska-Ratajczak, B., Xu, J., Yates, A., Zerbino, D., Zhang, Y., Aken, B., Choudhary, J. S., Gerstein, M., Guigó, R., Hubbard, T. J. P., Kellis, M., Paten, B., Reymond, A., Tress, M. L., & Flicek, P.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-24
- Volume
- 47
- Issue
- D1
- Pages
- D766-D773
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2898598946
- Cited by
- 3,040
- References
- 16
- FWCI
- 90.25
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: GENCODE reference annotation for the human and mouse genomes. https://app.cochat.ai/papers/10.1093/nar/gky955
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- Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J. M., Sisu, C., Wright, J., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Carbonell Sala, S., Chrast, J., Cunningham, F., Di Domenico, T., Donaldson, S., Fiddes, I. T., . . . Flicek, P. (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. https://doi.org/10.1093/nar/gky955
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