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Ensembl 2013
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The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
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Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
International network of cancer genome projects
The International Cancer Genome Consortium (2010) · Nature · doi:10.1038/nature08987 · Cited by 2,299
CAFE: a computational tool for the study of gene family evolution
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl097 · Cited by 1,790
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
Pruitt, K. D., Tatusova, T., Brown, G. R., & Maglott, D. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1079 · Cited by 1,149 · cited 1×
“For example, we provide up to date external database references to gene names from the HUGO Gene Nomenclature Committee (HGNC) (1), the Universal Protein Resource (UniProt) (2), Orphanet portal for rare diseases and orphan drugs (3), the Online Mendelian Inheritance in Man (OMIM) database (4), the RefSeq collection of…”
BackgroundVISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080
Cited by
Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O'Keeffe, S., Phatnani, H. P., Guarnieri, P., Caneda, C., Ruderisch, N., et al. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.1860-14.2014 · Cited by 4,875
Fagerberg, L., Hallström, B. M., Oksvold, P., Kampf, C., Djureinovic, D., Odeberg, J., Habuka, M., Tahmasebpoor, S., Danielsson, A., Edlund, K., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.035600 · Cited by 3,665
A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells
Carreno, B. M., Magrini, V., Becker-Hapak, M., Kaabinejadian, S., Hundal, J., Petti, A. A., Ly, A., Lie, W.-R., Hildebrand, W. H., Mardis, E. R., et al. (2015) · Science · doi:10.1126/science.aaa3828 · Cited by 1,285
Gateways to the FANTOM5 promoter level mammalian expression atlas
Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology · doi:10.1186/s13059-014-0560-6 · Cited by 871
Large-scale whole-genome sequencing of the Icelandic population
Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3247 · Cited by 791
Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways
The Network and Pathway Analysis Subgroup of the Psychiatric Genomics Consortium (2015) · Nature Neuroscience · doi:10.1038/nn.3922 · Cited by 755
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
The UCSC Genome Browser database: 2014 update
Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1168 · Cited by 670
Patro, R., Mount, S. M., & Kingsford, C. (2014) · Nature Biotechnology · doi:10.1038/nbt.2862 · Cited by 586
Widespread intron retention in mammals functionally tunes transcriptomes
Braunschweig, U., Barbosa-Morais, N. L., Pan, Q., Nachman, E. N., Alipanahi, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., & Blencowe, B. J. (2014) · Genome Research · doi:10.1101/gr.177790.114 · Cited by 664
DISEASES: Text mining and data integration of disease–gene associations
Pletscher-Frankild, S., Pallejà, A., Tsafou, K., Binder, J. X., & Jensen, L. J. (2015) · Methods · doi:10.1016/j.ymeth.2014.11.020 · Cited by 591
RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
Wolfe, A. L., Singh, K., Zhong, Y., Drewe, P., Rajasekhar, V. K., Sanghvi, V. R., Mavrakis, K. J., Jiang, M., Roderick, J. E., Van der Meulen, J., et al. (2014) · Nature · doi:10.1038/nature13485 · Cited by 635
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease
Gjoneska, E., Pfenning, A. R., Mathys, H., Quon, G., Kundaje, A., Tsai, L.-H., & Kellis, M. (2015) · Nature · doi:10.1038/nature14252 · Cited by 576
Zerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429
Self-citationAbundant contribution of short tandem repeats to gene expression variation in humans
Gymrek, M., Willems, T., Guilmatre, A., Zeng, H., Markus, B., Georgiev, S., Daly, M. J., Price, A. L., Pritchard, J. K., Sharp, A. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3461 · Cited by 410
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Pefanis, E., Wang, J., Rothschild, G., Lim, J., Kazadi, D., Sun, J., Federation, A., Chao, J., Elliott, O., Liu, Z.-P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.034 · Cited by 464
Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy
Chandler, R. J., LaFave, M. C., Varshney, G. K., Trivedi, N. S., Carrillo-Carrasco, N., Senac, J. S., Wu, W., Hoffmann, V., Elkahloun, A. G., Burgess, S. M., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci79213 · Cited by 403
Insights into the evolution of longevity from the bowhead whale genome
Keane, M., Semeiks, J., Webb, A. E., Li, Y. I., Quesada, V., Craig, T., Madsen, L. B., van Dam, S., Brawand, D., Marques, P. I., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2014.12.008 · Cited by 375
Heritability and genomics of gene expression in peripheral blood
Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362
Seitan, V. C., Faure, A. J., Zhan, Y., McCord, R. P., Lajoie, B. R., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A. G., et al. (2013) · Genome Research · doi:10.1101/gr.161620.113 · Cited by 318
Self-citationPrehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324
Woo, D., Falcone, G. J., Devan, W. J., Brown, W. M., Biffi, A., Howard, T. D., Anderson, C. D., Brouwers, H. B., Valant, V., Battey, T. W. K., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.02.012 · Cited by 290
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Shirai, C. L., Ley, J. N., White, B. S., Kim, S., Tibbitts, J., Shao, J., Ndonwi, M., Wadugu, B., Duncavage, E. J., Okeyo-Owuor, T., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.04.008 · Cited by 287
Veloso, A., Kirkconnell, K. S., Magnuson, B., Biewen, B., Paulsen, M. T., Wilson, T. E., & Ljungman, M. (2014) · Genome Research · doi:10.1101/gr.171405.113 · Cited by 281
Tan, G., Muffato, M., Ledergerber, C., Herrero, J., Goldman, N., Gil, M., & Dessimoz, C. (2015) · Systematic Biology · doi:10.1093/sysbio/syv033 · Cited by 261
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Grissa, D., Junge, A., Oprea, T. I., & Jensen, L. J. (2022) · Database · doi:10.1093/database/baac019 · Cited by 144
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Lynch, V. J., Bedoya-Reina, O. C., Ratan, A., Sulak, M., Drautz-Moses, D. I., Perry, G. H., Miller, W., & Schuster, S. C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.06.027 · Cited by 130
Nepal, C., Hadzhiev, Y., Previti, C., Haberle, V., Li, N., Takahashi, H., Suzuki, A. M. M., Sheng, Y., Abdelhamid, R. F., Anand, S., et al. (2013) · Genome Research · doi:10.1101/gr.153692.112 · Cited by 127
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van Dam, S., Craig, T., & de Magalhães, J. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1042 · Cited by 115
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Hoss, A. G., Kartha, V. K., Dong, X., Latourelle, J. C., Dumitriu, A., Hadzi, T. C., MacDonald, M. E., Gusella, J. F., Akbarian, S., Chen, J.-F., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004188 · Cited by 111
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Inoue, D., Polaski, J. T., Taylor, J., Castel, P., Chen, S., Kobayashi, S., Hogg, S. J., Hayashi, Y., Pineda, J. M. B., El Marabti, E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00828-9 · Cited by 108
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Seki, R., Li, C., Fang, Q., Hayashi, S., Egawa, S., Hu, J., Xu, L., Pan, H., Kondo, M., Sato, T., et al. (2017) · Nature Communications · doi:10.1038/ncomms14229 · Cited by 84
Granneman, J. G., Kimler, V. A., Zhang, H., Ye, X., Luo, X., Postlethwait, J. H., & Thummel, R. (2017) · eLife · doi:10.7554/elife.21771 · Cited by 77
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Smith, C. M., Finger, J. H., Hayamizu, T. F., McCright, I. J., Xu, J., Berghout, J., Campbell, J., Corbani, L. E., Forthofer, K. L., Frost, P. J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt954 · Cited by 75
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Rissone, A., Weinacht, K. G., la Marca, G., Bishop, K., Giocaliere, E., Jagadeesh, J., Felgentreff, K., Dobbs, K., Al-Herz, W., Jones, M., et al. (2015) · Journal of Experimental Medicine · doi:10.1084/jem.20141286 · Cited by 63
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Golden, M. S., Cote, S. M., Sayeg, M., Zerbe, B. S., Villar, E. A., Beglov, D., Sazinsky, S. L., Georgiadis, R. M., Vajda, S., Kozakov, D., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja400914z · Cited by 47
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Strøm, T. B., Tveten, K., Laerdahl, J. K., & Leren, T. P. (2014) · FEBS Open Bio · doi:10.1016/j.fob.2014.03.007 · Cited by 38
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Lee, H.-J., Park, H.-S., Kim, W., Yoon, D., & Seo, S. (2014) · International Journal of Genomics · doi:10.1155/2014/679437 · Cited by 24
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Metadata
- Authors
- Flicek, P., Ahmed, I., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., García-Girón, C., Gordon, L., Hourlier, T., Hunt, S., Juettemann, T., Kähäri, A. K., Keenan, S., Komorowska, M., Kulesha, E., Longden, I., Maurel, T., McLaren, W. M., Muffato, M., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sheppard, D., Sobral, D., Taylor, K., Thormann, A., Trevanion, S., White, S., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Harrow, J., Herrero, J., Hubbard, T. J. P., Johnson, N., Kinsella, R., Parker, A., Spudich, G., Yates, A., Zadissa, A., & Searle, S. M. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-30
- Volume
- 41
- Issue
- D1
- Pages
- D48-D55
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4210290733
- Cited by
- 869
- References
- 11
- FWCI
- 64.01
- Type
- journal article
- Language
- en
- Open access
- gold
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