Ensembl 2024

Authors: HARRISON, PETER - European Bioinformatics Institute; AMODE, RIDWAN - European Bioinformatics Institute; AUSTINE-ORIMOLOYE, OLANREWAJU - European Bioinformatics Institute; AZIV, ANDREY - European Bioinformatics Institute; BARBA, MATTHIEU - European Bioinformatics Institute; BARNES, IF - European Bioinformatics Institute; BECKER, ARNE - European Bioinformatics Institute; BENNETT, RUTH - European Bioinformatics Institute; BERRY, ANDREW - European Bioinformatics Institute; YATES, ANDREW - European Bioinformatics Institute; BHAI, JYOTHISH - European Bioinformatics Institute; BHURJI, SIMARPREET KAUR - European Bioinformatics Institute; BODDU, SANJAY - European Bioinformatics Institute; BRANCO LINS, PAULO - European Bioinformatics Institute; BROOKS, LUCY - European Bioinformatics Institute; BUDHANURU RAMARAJU, SHASHANK - European Bioinformatics Institute; CAMPBELL, LAHCEN - European Bioinformatics Institute; CARBAJO MARTINEZ, MANUEL - European Bioinformatics Institute; CHARKHCHI, MAHRNAZ - European Bioinformatics Institute; CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; COCKBURN, ALEXANDER - European Bioinformatics Institute; DAVIDSON, CLAIRE - European Bioinformatics Institute; DE SILVA, NISHADI - European Bioinformatics Institute; DODIYA, KAMALKUMAR - European Bioinformatics Institute; DONALDSON, SARAH - European Bioinformatics Institute; EL HOUDAIGUI, BILAL - European Bioinformatics Institute; EL NABOULSI, TAMARA - European Bioinformatics Institute; FATIMA, REHAM - European Bioinformatics Institute; GARCIA GIRON, CARLOS - European Bioinformatics Institute; GENEZ, THIAGO - European Bioinformatics Institute; GRIGORIADIS, DIONYSIOS - European Bioinformatics Institute; GHATTAORAYA, GURPREET - European Bioinformatics Institute; GONZALEZ MARTINEZ, JOSE - European Bioinformatics Institute; GURBICH, TATIANA - European Bioinformatics Institute; HARDY, MATTHEW - European Bioinformatics Institute; HOLLIS, ZOE - European Bioinformatics Institute; HOURLIER, THIBAUT - European Bioinformatics Institute; HUNT, TOBY - European Bioinformatics Institute; KAY, MIKE - European Bioinformatics Institute; KAYKALA, VINAY - European Bioinformatics Institute; LE, TUAN - European Bioinformatics Institute; LELMOS, DIANA - European Bioinformatics Institute; LODHA, DISHA - European Bioinformatics Institute; MARQUES-COELHO, DIEGO - European Bioinformatics Institute; MASLEN, GARETH - European Bioinformatics Institute; MERINO, GABRIELA - European Bioinformatics Institute; MIRABUENO, LOUISSE PAOLA - European Bioinformatics Institute; MUSHTAQ, ALEENA - European Bioinformatics Institute; NAKIB HOSSAIN, SYED - European Bioinformatics Institute; OGEH, DENYE - European Bioinformatics Institute; PANDIAN SAKTHIVEL, MANOJ - European Bioinformatics Institute; PARKER, ANNE - European Bioinformatics Institute; PERRY, MALCOLM - European Bioinformatics Institute; PILIZOTA, IVANA - European Bioinformatics Institute; POPPLETON, DANIEL - European Bioinformatics Institute; PROSOVETSKAIA, IRINA - European Bioinformatics Institute; RAJ, SHRIYA - European Bioinformatics Institute; PEREZ-SILVA, JOSE - European Bioinformatics Institute; SALAM, AHAMED IMRAN - European Bioinformatics Institute; SARAF, SHRADHA - European Bioinformatics Institute; SARAIVA-AGOSTINHO, NUNO - European Bioinformatics Institute; SHEPPARD, DAN - European Bioinformatics Institute; SINHA, SWATI - European Bioinformatics Institute; SIPOS, BOTOND - European Bioinformatics Institute; SITNIK, VASILY - European Bioinformatics Institute; STARK, WILLIAM - European Bioinformatics Institute; STEED, EMILY - European Bioinformatics Institute; SUNER, MARIE-MARTHE - European Bioinformatics Institute; SURAPANENI, LIKHITHA - European Bioinformatics Institute; SUTINEN, KYOSTI - European Bioinformatics Institute; TRICOMI, FRANCESCA - European Bioinformatics Institute; URBINA-GOMEZ, DAVID - European Bioinformatics Institute; VEIDENBERG, ANDRES - European Bioinformatics Institute; WALSH, THOMAS - European Bioinformatics Institute; Ware, Doreen; WASS, ELIZABETH - European Bioinformatics Institute; WILLHOFT, NATALIE - European Bioinformatics Institute; ALLEN, JAMIE - European Bioinformatics Institute; ALVAREZ-JARRETA, JORGE - European Bioinformatics Institute; CHAKIACHVILI, MARC - European Bioinformatics Institute; FLINT, BETHANY - European Bioinformatics Institute; GIORGETTI, STEFANO - European Bioinformatics Institute; HAGGERTY, LEANNE - European Bioinformatics Institute; ILSLEY, GARTH - European Bioinformatics Institute; KEATLEY, JON - European Bioinformatics Institute; LOVELAND, JANE - European Bioinformatics Institute; MOORE, BENJAMIN - European Bioinformatics Institute; MUDGE, JONATHAN - European Bioinformatics Institute; NAAMATI, GUY - European Bioinformatics Institute; TATE, JOHN - European Bioinformatics Institute; TREVANION, STEPHEN - European Bioinformatics Institute; WINTERBOTTOM, ANDREA - European Bioinformatics Institute; FRANKISH, ADAM - European Bioinformatics Institute; HUNT, SARAH - European Bioinformatics Institute; CUNNINGHAM, FIONA - European Bioinformatics Institute; DYSER, SARAH - European Bioinformatics Institute; FINN, ROBERT - European Bioinformatics Institute; MARTIN, FERGAL - European Bioinformatics Institute

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2023
Publication Date: 11/11/2023
Citation: Harrison, P.W., Amode, R., Austine-Orimoloye, O., Aziv, A.G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., Yates, A.D., Bhai, J., Bhurji, S., Boddu, S., Branco Lins, P.R., Brooks, L., Budhanuru Ramaraju, S., Campbell, L.I., Carbajo Martinez, M., Charkhchi, M., Chougule, K., Cockburn, A., Davidson, C.E., De Silva, N.H., Dodiya, K., Donaldson, S., El Houdaigui, B., El Naboulsi, T., Fatima, R., Garcia Giron, C., Genez, T., Grigoriadis, D., Ghattaoraya, G., Gonzalez Martinez, J., Gurbich, T.A., Hardy, M.E., Hollis, Z., Hourlier, T.E., Hunt, T., Kay, M., Kaykala, V., Le, T., Lelmos, D., Lodha, D., Marques-Coelho, D., Maslen, G., Merino, G.A., Mirabueno, L., Mushtaq, A.E., Nakib Hossain, S., Ogeh, D.N., Pandian Sakthivel, M., Parker, A., Perry, M., Pilizota, I., Poppleton, D., Prosovetskaia, I., Raj, S., Perez-Silva, J.G., Salam, A.A., Saraf, S., Saraiva-Agostinho, N., Sheppard, D., Sinha, S., Sipos, B., Sitnik, V., Stark, W., Steed, E., Suner, M., Surapaneni, L., Sutinen, K., Tricomi, F.F., Urbina-Gomez, D., Veidenberg, A.E., Walsh, T.A., Ware, D., Wass, E., Willhoft, N.L., Allen, J., Alvarez-Jarreta, J., Chakiachvili, M., Flint, B., Giorgetti, S., Haggerty, L., Ilsley, G.R., Keatley, J., Loveland, J.E., Moore, B., Mudge, J.M., Naamati, G., Tate, J., Trevanion, S.J., Winterbottom, A., Frankish, A., Hunt, S.E., Cunningham, F.E., Dyser, S., Finn, R.D., Martin, F. 2023. Ensembl 2024. Nucleic Acids Research. Vol.52, p. D891-899. https://doi.org/10.1093/nar/gkad1049.
DOI: https://doi.org/10.1093/nar/gkad1049

Interpretive Summary: Ensembl is a massive online library where scientists can find detailed information about the DNA of many different animals, including humans and other important species. For over 20 years, Ensembl has been providing high-quality information and tools that help researchers understand the genetic makeup of these creatures. Recently, there has been a large increase in the number and variety of detailed genetic maps (genomes) available. These new maps cover a wide range of species and provide more complete pictures of their DNA. Ensembl is working hard to keep up with these advancements by speeding up the process of adding new genomes, creating better ways to compare different genomes, and improving the accuracy of the information they provide. In 2024, Ensembl has made huge strides to support research on global biodiversity. They have doubled the number of genomes available on their Rapid Release site to over 1700, thanks to partnerships with biodiversity projects like Darwin Tree of Life. This helps scientists study a wide variety of species more easily. Ensembl has also focused on important farm animals, providing new detailed maps of their DNA that help improve farming and agriculture. Additionally, they have updated key tools like the Ensembl Variant Effect Predictor, which helps scientists understand how changes in DNA might affect an organism. All the data, software, and tools provided by Ensembl are free for anyone to use, making it a valuable resource for the global scientific community.

Technical Abstract: Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.