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3 results on '"Thybert D"'

1. The Quest for Orthologs orthology benchmark service in 2022.

Author

Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C, Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, and Altenhoff A

Subjects
Phylogeny, Proteome, Benchmarking, Genomics methods
Abstract

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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2. Ensembl 2021.

Author

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, and Flicek P

Subjects
Animals, COVID-19 epidemiology, COVID-19 virology, Humans, Internet, Molecular Sequence Annotation methods, Pandemics, Vertebrates classification, Computational Biology methods, Databases, Nucleic Acid, Genomics methods, SARS-CoV-2 genetics, Vertebrates genetics
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., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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3. Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Author

Dent Earl, Monica Abrudan, Benedict Paten, Adam Frankish, Lesley Shirley, Cristina Sisu, Ian T. Fiddes, Mark Gerstein, James G. R. Gilbert, Mark G. Thomas, Anne Czechanski, Duncan T. Odom, William Chow, Stephan C. Collins, Clayton E. Mathews, Mark Diekhans, Ruth Bennett, Jane E. Loveland, David J. Adams, Jingtao Lilue, Beiyuan Fu, Dirk-Dominic Dolle, Fengtang Yang, Laura G. Reinholdt, Glen Threadgold, Anne C. Ferguson-Smith, Jonathan Wood, Kim Wong, Leo Goodstadt, Paul R. Muir, Thomas M. Keane, Phan Sk, Jonathan Flint, Naomi R Park, Richard Mott, Joel Armstrong, Thybert D, Jen Harrow, Petr Danecek, Marcela K. Sjoberg-Herrera, Sarah Pelan, Anthony G. Doran, Kerstin Howe, Charles A. Steward, Mario Stanke, Binnaz Yalcin, Joanna Collins, Lelliott C, Matthew Dunn, Fabio C. P. Navarro, Michael A. Quail, Paul Flicek, James Torrance, Richard Durbin, Köenig S, Lars Romoth, and Mikhail Kolmogorov

Subjects
Genetics, 0303 health sciences, Strain (biology), Haplotype, Genomics, Retrotransposon, Biology, Genome, 03 medical and health sciences, 0302 clinical medicine, Genome Reference Consortium, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Reference genome
Abstract

The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most widely used inbred strains and reveal for the first time extensive strain-specific haplotype variation. We identify and characterise 2,567 regions on the current Genome Reference Consortium mouse reference genome exhibiting the greatest sequence diversity between strains. These regions are enriched for genes involved in defence and immunity, and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. Several immune related loci, some in previously identified QTLs for disease response have novel haplotypes not present in the reference that may explain the phenotype. We used these genomes to improve the mouse reference genome resulting in the completion of 10 new gene structures, and 62 new coding loci were added to the reference genome annotation. Notably this high quality collection of genomes revealed a previously unannotated gene (Efcab3-like) encoding 5,874 amino acids, one of the largest known in the rodent lineage. Interestingly, Efcab3-like−/− mice exhibit severe size anomalies in four regions of the brain suggesting a mechanism of Efcab3-like regulating brain development.

Published
2018

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