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1. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Author

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

Published
2021
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2. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, DʼEustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, and Ware, Doreen

Published
2014
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3. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Author

Tello-Ruiz, Marcela K, primary, Naithani, Sushma, additional, Gupta, Parul, additional, Olson, Andrew, additional, Wei, Sharon, additional, Preece, Justin, additional, Jiao, Yinping, additional, Wang, Bo, additional, Chougule, Kapeel, additional, Garg, Priyanka, additional, Elser, Justin, additional, Kumari, Sunita, additional, Kumar, Vivek, additional, Contreras-Moreira, Bruno, additional, Naamati, Guy, additional, George, Nancy, additional, Cook, Justin, additional, Bolser, Daniel, additional, D’Eustachio, Peter, additional, Stein, Lincoln D, additional, Gupta, Amit, additional, Xu, Weijia, additional, Regala, Jennifer, additional, Papatheodorou, Irene, additional, Kersey, Paul J, additional, Flicek, Paul, additional, Taylor, Crispin, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2020
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4. Plant Reactome: a knowledgebase and resource for comparative pathway analysis

Author

Naithani, Sushma, primary, Gupta, Parul, additional, Preece, Justin, additional, D’Eustachio, Peter, additional, Elser, Justin L, additional, Garg, Priyanka, additional, Dikeman, Daemon A, additional, Kiff, Jason, additional, Cook, Justin, additional, Olson, Andrew, additional, Wei, Sharon, additional, Tello-Ruiz, Marcela K, additional, Mundo, Antonio Fabregat, additional, Munoz-Pomer, Alfonso, additional, Mohammed, Suhaib, additional, Cheng, Tiejun, additional, Bolton, Evan, additional, Papatheodorou, Irene, additional, Stein, Lincoln, additional, Ware, Doreen, additional, and Jaiswal, Pankaj, additional

Published
2019
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5. Ensembl Genomes 2020—enabling non-vertebrate genomic research

Author

Howe, Kevin L, primary, Contreras-Moreira, Bruno, additional, De Silva, Nishadi, additional, Maslen, Gareth, additional, Akanni, Wasiu, additional, Allen, James, additional, Alvarez-Jarreta, Jorge, additional, Barba, Matthieu, additional, Bolser, Dan M, additional, Cambell, Lahcen, additional, Carbajo, Manuel, additional, Chakiachvili, Marc, additional, Christensen, Mikkel, additional, Cummins, Carla, additional, Cuzick, Alayne, additional, Davis, Paul, additional, Fexova, Silvie, additional, Gall, Astrid, additional, George, Nancy, additional, Gil, Laurent, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Haskell, Erin, additional, Hunt, Sarah E, additional, Jaiswal, Pankaj, additional, Janacek, Sophie H, additional, Kersey, Paul J, additional, Langridge, Nick, additional, Maheswari, Uma, additional, Maurel, Thomas, additional, McDowall, Mark D, additional, Moore, Ben, additional, Muffato, Matthieu, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Papatheodorou, Irene, additional, Patricio, Mateus, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Rosello, Marc, additional, Russell, Matthew, additional, Sitnik, Vasily, additional, Staines, Daniel M, additional, Stein, Joshua, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Wei, Sharon, additional, Ware, Doreen, additional, Williams, Gary, additional, Yates, Andrew D, additional, and Flicek, Paul, additional

Published
2019
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6. Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Author

Naithani, Sushma, Gupta, Parul, Preece, Justin, D'Eustachio, Peter, Elser, Justin L, Garg, Priyanka, Dikeman, Daemon A, Kiff, Jason, Cook, Justin, Olson, Andrew, Wei, Sharon, Tello-Ruiz, Marcela K, Mundo, Antonio Fabregat, Munoz-Pomer, Alfonso, Mohammed, Suhaib, Cheng, Tiejun, Bolton, Evan, Papatheodorou, Irene, Stein, Lincoln, and Ware, Doreen

Published
2020
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7. Gramene 2018: unifying comparative genomics and pathway resources for plant research

Author

Tello-Ruiz, Marcela K, primary, Naithani, Sushma, additional, Stein, Joshua C, additional, Gupta, Parul, additional, Campbell, Michael, additional, Olson, Andrew, additional, Wei, Sharon, additional, Preece, Justin, additional, Geniza, Matthew J, additional, Jiao, Yinping, additional, Lee, Young Koung, additional, Wang, Bo, additional, Mulvaney, Joseph, additional, Chougule, Kapeel, additional, Elser, Justin, additional, Al-Bader, Noor, additional, Kumari, Sunita, additional, Thomason, James, additional, Kumar, Vivek, additional, Bolser, Daniel M, additional, Naamati, Guy, additional, Tapanari, Electra, additional, Fonseca, Nuno, additional, Huerta, Laura, additional, Iqbal, Haider, additional, Keays, Maria, additional, Munoz-Pomer Fuentes, Alfonso, additional, Tang, Amy, additional, Fabregat, Antonio, additional, D’Eustachio, Peter, additional, Weiser, Joel, additional, Stein, Lincoln D, additional, Petryszak, Robert, additional, Papatheodorou, Irene, additional, Kersey, Paul J, additional, Lockhart, Patti, additional, Taylor, Crispin, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2017
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8. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Author

Kersey, Paul Julian, primary, Allen, James E, additional, Allot, Alexis, additional, Barba, Matthieu, additional, Boddu, Sanjay, additional, Bolt, Bruce J, additional, Carvalho-Silva, Denise, additional, Christensen, Mikkel, additional, Davis, Paul, additional, Grabmueller, Christoph, additional, Kumar, Navin, additional, Liu, Zicheng, additional, Maurel, Thomas, additional, Moore, Ben, additional, McDowall, Mark D, additional, Maheswari, Uma, additional, Naamati, Guy, additional, Newman, Victoria, additional, Ong, Chuang Kee, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Russell, Matthew, additional, Sparrow, Helen, additional, Tapanari, Electra, additional, Taylor, Kieron, additional, Vullo, Alessandro, additional, Williams, Gareth, additional, Zadissia, Amonida, additional, Olson, Andrew, additional, Stein, Joshua, additional, Wei, Sharon, additional, Tello-Ruiz, Marcela, additional, Ware, Doreen, additional, Luciani, Aurelien, additional, Potter, Simon, additional, Finn, Robert D, additional, Urban, Martin, additional, Hammond-Kosack, Kim E, additional, Bolser, Dan M, additional, De Silva, Nishadi, additional, Howe, Kevin L, additional, Langridge, Nicholas, additional, Maslen, Gareth, additional, Staines, Daniel Michael, additional, and Yates, Andrew, additional

Published
2017
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9. Gramene 2016: comparative plant genomics and pathway resources

Author

Tello-Ruiz, Marcela K., primary, Stein, Joshua, additional, Wei, Sharon, additional, Preece, Justin, additional, Olson, Andrew, additional, Naithani, Sushma, additional, Amarasinghe, Vindhya, additional, Dharmawardhana, Palitha, additional, Jiao, Yinping, additional, Mulvaney, Joseph, additional, Kumari, Sunita, additional, Chougule, Kapeel, additional, Elser, Justin, additional, Wang, Bo, additional, Thomason, James, additional, Bolser, Daniel M., additional, Kerhornou, Arnaud, additional, Walts, Brandon, additional, Fonseca, Nuno A., additional, Huerta, Laura, additional, Keays, Maria, additional, Tang, Y. Amy, additional, Parkinson, Helen, additional, Fabregat, Antonio, additional, McKay, Sheldon, additional, Weiser, Joel, additional, D'Eustachio, Peter, additional, Stein, Lincoln, additional, Petryszak, Robert, additional, Kersey, Paul J., additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2015
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11. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., primary, Stein, Joshua, additional, Naithani, Sushma, additional, Wei, Sharon, additional, Dharmawardhana, Palitha, additional, Kumari, Sunita, additional, Amarasinghe, Vindhya, additional, Youens-Clark, Ken, additional, Thomason, James, additional, Preece, Justin, additional, Pasternak, Shiran, additional, Olson, Andrew, additional, Jiao, Yinping, additional, Lu, Zhenyuan, additional, Bolser, Dan, additional, Kerhornou, Arnaud, additional, Staines, Dan, additional, Walts, Brandon, additional, Wu, Guanming, additional, D’Eustachio, Peter, additional, Haw, Robin, additional, Croft, David, additional, Kersey, Paul J., additional, Stein, Lincoln, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2013
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12. Gramene 2016: comparative plant genomics and pathway resources.

Author

Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., and Huerta, Laura

Published
2016
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13. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Author

Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, and Flicek P

Subjects
Animals, Computational Biology, Genome, Bacterial genetics, Genome, Fungal genetics, Genome, Plant genetics, Plants classification, Plants genetics, Vertebrates classification, Vertebrates genetics, Databases, Genetic, Genomics, Internet, 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., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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14. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

Author

Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, and Ware D

Subjects
Crops, Agricultural, DNA Transposable Elements, Gene Duplication, Gene Ontology, Gene Regulatory Networks, Internet, Knowledge Bases, Metabolic Networks and Pathways, Molecular Sequence Annotation, Oryza genetics, Oryza metabolism, Plant Proteins metabolism, Plants classification, Plants metabolism, Polyploidy, Protein Interaction Mapping, Software, Zea mays genetics, Zea mays metabolism, Databases, Genetic, Gene Expression Regulation, Plant, Genome, Plant, Genomics methods, Plant Proteins genetics, Plants genetics
Abstract

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 reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome., (Published by Oxford University Press on behalf of Nucleic Acids Research 2020.)

Published
2021
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15. Ensembl Genomes 2020-enabling non-vertebrate genomic research.

Author

Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, and Flicek P

Subjects
Algorithms, Animals, Caenorhabditis elegans genetics, Genomics, Internet, Molecular Sequence Annotation, Phenotype, Plants genetics, Reference Values, Software, User-Computer Interface, Computational Biology methods, Databases, Genetic, Genetic Variation, Genome, Bacterial, Genome, Fungal, Genome, Plant
Abstract

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). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2020
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16. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Author

Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, and Yates A

Subjects
Amino Acid Sequence, Animals, Base Sequence, Data Mining, Forecasting, Genome, Molecular Sequence Annotation, RNA genetics, User-Computer Interface, Archaea genetics, Bacteria genetics, Databases, Genetic, Databases, Protein, Eukaryota genetics, Genomics
Abstract

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 Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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