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Your search keyword '"Cristina, Guijarro-Clarke"' showing total 3 results
Start Over Author "Cristina, Guijarro-Clarke" Publisher oxford university press (oup)
3 results on '"Cristina, Guijarro-Clarke"'

1. Ensembl 2022

Author

Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, José G Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E Hunt, Garth R IIsley, Jane E Loveland, Fergal J Martin, Benjamin Moore, Jonathan M Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Sarah Dyer, Peter W Harrison, Kevin L Howe, Andrew D Yates, Daniel R Zerbino, and Paul Flicek

Subjects
Genome, ComputingMethodologies_PATTERNRECOGNITION, AcademicSubjects/SCI00010, Databases, Genetic, Genetics, Database Issue, Animals, Computational Biology, Humans, Molecular Sequence Annotation, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Software
Abstract

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Published
2021
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2. Ensembl 2021

Author

Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G Izuogu, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj P Sakthivel, Ahamed I Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth R IIsley, Nick Langridge, Jane E Loveland, Fergal J Martin, Jonathan M Mudge, Joanella Morales, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Fiona Cunningham, Andrew D Yates, Daniel R Zerbino, and Paul Flicek

Subjects
Internet, 0303 health sciences, SARS-CoV-2, AcademicSubjects/SCI00010, 030302 biochemistry & molecular biology, COVID-19, Computational Biology, Molecular Sequence Annotation, Genomics, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, Vertebrates, Genetics, Animals, Humans, Database Issue, Databases, Nucleic Acid, Pandemics, 030304 developmental biology
Abstract

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Published
2020
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3. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Author

Andrew D. Yates, Michael Paulini, Anne Parker, Kim E. Hammond-Kosack, Marcela K. Tello-Ruiz, Justin Elser, Jyothish Bhai, Manuel Luypaert, Faye H. Rodgers, Stavros Diamantakis, James Seager, Pankaj Jaiswal, Robert D. Finn, Thomas Maurel, Michal Szpak, Marc Rosello, James E. Allen, Parul Gupta, Matthieu Barba, Lahcen I. Campbell, Marc Chakiachvili, Vivek Kumar, Manuel Carbajo Martinez, Benjamin Moore, Nishadi De Silva, John Tate, Ridwan M Amode, Andrew Olson, Astrid Gall, Magali Ruffier, Paul Davis, Mikkel B. Christensen, Mark Quinton-Tulloch, Alayne Cuzick, Kevin L. Howe, Martin Urban, Justin Preece, Nick Langridge, Sunita Kumari, Kapeel Chougule, Emily Perry, Tuan Le, Gareth Maslen, Sharon Wei, Dionysios Grigoriadis, Carla Valeria Filippi, Andrea Winterbottom, Doreen Ware, Aleena Mushtaq, Vinay Kaikala, Andrey G Azov, Helder Pedro, Luca Da Rin Fioretto, Gary Williams, Magdalena Zarowiecki, Cristina Guijarro-Clarke, Guy Naamati, Sushma Naithani, Bruno Contreras-Moreira, Sarah Dyer, Andrés Becerra, Paul Flicek, Matthieu Muffato, Vasily Sitnik, and Stephen J. Trevanion

Subjects
Whole genome sequencing, Internet, AcademicSubjects/SCI00010, Computational Biology, Genomics, Genome project, Gene Annotation, Computational biology, Plants, Biology, Genome, Annotation, Resource (project management), ComputingMethodologies_PATTERNRECOGNITION, Ensembl Genomes, Databases, Genetic, Vertebrates, Genetics, Database Issue, Animals, Ensembl, Genome, Fungal, Genome, Bacterial, Genome, Plant, Software
Abstract

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.

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