Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Guy, Naamati"'
Autor:
Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones, Sarah Dyer
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-18 (2023)
Abstract Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a spe
Externí odkaz:
https://doaj.org/article/069a8982ca94413aba69f7a9e0d5fa0c
Autor:
Baron Koylass, Richard Finkers, Cyril Pommier, Guy Naamati, Timothee Cezard, Bruno Contreras-Moreira, Isuru Liyanage, Anne Fiebig, Stephan Weise, Paul J. Kersey, Sebastian Beier, Uwe Scholz, Matthias Lange, Mélanie Courtot, Sarah Dyer
Publikováno v:
F1000Research, Vol 11 (2022)
In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic
Externí odkaz:
https://doaj.org/article/cc87b8bf1c5e411fa65c2623879b4760
Autor:
Bruno Contreras‐Moreira, Carla V Filippi, Guy Naamati, Carlos García Girón, James E Allen, Paul Flicek
Publikováno v:
The Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
Abstract The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole‐genome alignment, promoter analysis, or pangenome exploration.
Externí odkaz:
https://doaj.org/article/b532ac8f92da477eab4920c1f846cd9b
Autor:
Nikolai M Adamski, Philippa Borrill, Jemima Brinton, Sophie A Harrington, Clémence Marchal, Alison R Bentley, William D Bovill, Luigi Cattivelli, James Cockram, Bruno Contreras-Moreira, Brett Ford, Sreya Ghosh, Wendy Harwood, Keywan Hassani-Pak, Sadiye Hayta, Lee T Hickey, Kostya Kanyuka, Julie King, Marco Maccaferrri, Guy Naamati, Curtis J Pozniak, Ricardo H Ramirez-Gonzalez, Carolina Sansaloni, Ben Trevaskis, Luzie U Wingen, Brande BH Wulff, Cristobal Uauy
Publikováno v:
eLife, Vol 9 (2020)
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of g
Externí odkaz:
https://doaj.org/article/109e6ba31f8a424f886686b500930153
Autor:
Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones, Sarah Dyer
Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of higher qua
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::06c69fff838af4bc55ee60cea2eaedf7
https://doi.org/10.1101/2023.01.03.520531
https://doi.org/10.1101/2023.01.03.520531
Autor:
Jennifer Regala, Lincoln Stein, Vivek Kumar, Irene Papatheodorou, Andrew Olson, Amit Gupta, Justin Cook, Bruno Contreras-Moreira, Justin Preece, Weijia Xu, Nancy George, Parul Gupta, Dan Bolser, Crispin B. Taylor, Peter D'Eustachio, Marcela K. Tello-Ruiz, Doreen Ware, Paul J. Kersey, Paul Flicek, Sharon Wei, Yinping Jiao, Justin Elser, Bo Wang, Sushma Naithani, Priyanka Garg, Guy Naamati, Sunita Kumari, Kapeel Chougule, Pankaj Jaiswal
Publikováno v:
Nucleic Acids Res
Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and repro
Autor:
Bruno, Contreras-Moreira, Guy, Naamati, Marc, Rosello, James E, Allen, Sarah E, Hunt, Matthieu, Muffato, Astrid, Gall, Paul, Flicek
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2443
Ensembl Plants ( http://plants.ensembl.org ) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparati
Autor:
Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, Paul Flicek
Publikováno v:
Plant Bioinformatics ISBN: 9781071620663
Ensembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::01596a2511978019bfcfcd35ad14b9bb
https://doi.org/10.1007/978-1-0716-2067-0_2
https://doi.org/10.1007/978-1-0716-2067-0_2
Autor:
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul J. Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
Publikováno v:
F1000Research 11 (2022)
F1000Research 11, 231-(2022). doi:10.12688/f1000research.109080.2
F1000Research, 11
F1000Research 11, 231-(2022). doi:10.12688/f1000research.109080.2
F1000Research, 11
In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5500ba52295a8c1663cf54603dfdf3e8
https://research.wur.nl/en/publications/recommendations-for-the-formatting-of-variant-call-format-vcf-fil
https://research.wur.nl/en/publications/recommendations-for-the-formatting-of-variant-call-format-vcf-fil
Autor:
Bruno Contreras-Moreira, Laurent Gil, Uma Maheswari, Erin Haskell, Paul Flicek, Kim E. Hammond-Kosack, Stephen J. Trevanion, Matthieu Barba, Sushma Naithani, Matthew Russell, Mark D. McDowall, Nancy George, Andrew D. Yates, Emily Perry, Vasily Sitnik, Dan Bolser, Michael Paulini, Paul J. Kersey, Pankaj Jaiswal, Mikkel B. Christensen, Helder Pedro, Gareth Maslen, Lahcen Cambell, Sophie Helen Janacek, Daniel M. Staines, Gary Williams, Matthieu Muffato, Carla Cummins, Wasiu Akanni, Marc Rosello, James E. Allen, Irene Papatheodorou, Astrid Gall, Nick Langridge, Marc Chakiachvili, Joshua C. Stein, Mateus Patricio, Silvie Fexova, Nishadi De Silva, Sarah E. Hunt, Benjamin Moore, Martin Urban, Justin Preece, Marcela K. Tello-Ruiz, Guy Naamati, Andrew Olson, Parul Gupta, Thomas Maurel, Jorge Alvarez-Jarreta, Doreen Ware, Paul Davis, Manuel Carbajo, Alayne Cuzick, Kevin L. Howe, Sharon Wei
Publikováno v:
Nucleic Acids Research
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org)