Ensembl 2023

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ID: 302663
2022
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Ranked #351 of 1,306 articles by views in Nucleic Acids Research

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Abstract
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
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Authors Fergal J. Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García Girón, Thiago A. L. Genez, Gurpreet S Ghattaoraya, José M. González, Cristina Guijarro-Clarke, Matthew P. Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Anh Tuấn Lê, Diana Lemos, Diego Marques‐Coelho, José Carlos Marugán, Gabriela Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie‐Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michał Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas Walsh, Brandon Walts, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Álvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane Loveland, Benjamin Moore, Jonathan M. Mudge, John Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert Finn, Kevin Howe, Peter W. Harrison, Andrew Yates, Paul Flicek
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Journal Nucleic Acids Research
Year 2022
DOI
10.1093/nar/gkac958
URL
https://academic.oup.com/nar/article-pdf/51/D1/D933/48440737/gkac958.pdf
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