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The European Nucleotide Archive
Open accessAbstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe major changes and improvements introduced during 2010. These include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.
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“Tools such as DIGIT and Abysis source their data from the European Nucleotide Archive (ENA) [60] and the National Center for Biotechnology Information (NCBI) [61]; their sequence volumes are of the order of 105 and contain multiple artificially engineered sequences.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [60]
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Cites
The Sequence Alignment/Map format and SAMtools
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Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
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“Experimental search support for a limited number of raw reads is provided through De-Bruijn servers based on Velvet (9), using the Exonerate client-server protocol and being fully integrated with our search service.”
MethodAutomated generation of heuristics for biological sequence comparison
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The International Nucleotide Sequence Database Collaboration
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The International Nucleotide Sequence Database Collaboration
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DDBJ launches a new archive database with analytical tools for next-generation sequence data
Kaminuma, E., Mashima, J., Kodama, Y., Gojobori, T., Ogasawara, O., Okubo, K., Takagi, T., & Nakamura, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp847 · Cited by 99 · cited 1×
“The ENA works closely together with NCBI (1) and DDBJ (2) as partners in the International Nucleotide Sequence Database Collaboration (3).”
MethodImprovements to services at the European Nucleotide Archive
Leinonen, R., Akhtar, R. A., Birney, E., Bonfield, J., Bower, L., Corbett, M., Cheng, Y., Demiralp, F., Faruque, N., Goodgame, N., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp998 · Cited by 66 · cited 1×
“It contains a large diversity of data from patent, expressed sequence tag, whole genome shotgun and other high-throughput sequences, through genomic assemblies and richly annotated sequence fragments to whole replicons (5).”
BackgroundFast and efficient searching of biological data resources--using EB-eye
Valentin, F., Squizzato, S., Goujon, M., McWilliam, H., Paern, J., & López, R. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp065 · Cited by 37 · cited 1×
“Data can be queried using the EB-Eye free text search functionality available in the header section of all EBI web pages (7).”
Method
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Carvalho, M. B., Molina, F., & Felicori, L. F. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz387 · Cited by 6
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Oxidative pentose phosphate pathway is required for T cell activation and antitumor immunity
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MethodInfluentialGBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing
Pronozin, А. Y., Salina, E. A., & Afonnikov, D. A. (2023) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vjgb-23-86 · Cited by 5
A minimal Fanconi Anemia complex in early diverging fungi
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BackgroundIntegrative ‘Omic’ Approach Towards Understanding the Nature of Human Diseases
Peterlin, B., & Maver, A. (2012) · Balkan Journal of Medical Genetics · doi:10.2478/v10034-012-0018-7 · Cited by 5
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Wilms, S. N. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.692538 · Cited by 5
CyVerse for Reproducible Research: RNA-Seq Analysis
Williams, J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2067-0_3 · Cited by 5
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“We downloaded Genomes and/or Transcriptomes of 146 diverse marine phytoplankton (S3 Table) from the National Center for Biotechnology Information (NCBI) [92]; Joint Genome Institute (JGI) [93, 94]; iMicrobe [95], European Nucleotide Archive (ENA) [96]; pico-PLAZA [97], 1000 Plants (1KP) [98]; and the Reef Genomics Dat…”
MethodRNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis
Khan, N. S., Rahaman, M. M., Islam, S., & Zhang, S. (2023) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad040 · Cited by 5
“Rfam collects RNA sequences from the European Nucleotide Archive (ENA) database (33) and not all RNA chain sequences present in PDB exists in the ENA database.”
CENP-A associated lncRNAs influence chromosome segregation in human cellsPreprint
Quénet, D., Sturgill, D. M., Olson, M. K., & Dalal, Y. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/097956 · Cited by 5
“It has recently been reported in Xenopus (17), that centromeric RNAs appear to be spliced before they function to assist in CENP-A/CENP-C loading.”
BackgroundInfluentialINGOT-DR: An Interpretable Classifier for Predicting Drug Resistance in M. Tuberculosis
Zabeti, H., Dexter, N., Safari, A. H., Sedaghat, N., Libbrecht, M. W., & Chindelevitch, L. (n.d.) · Summit (Simon Fraser University) · Cited by 5
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“The raw FASTQ files corresponding to the identifiers in Supplementary Table 1 were obtained from the Sequence Read Archive (SRA) and European Nucleotide Archive (ENA) [35] using the SRA toolkit (v.2.9.1).”
InfluentialCausal network analysis of omics data using prior knowledge databases
Svinin, G. Е., & Glaab, E. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf654 · Cited by 4
Microsatellites explorer: A database of short tandem repeats across genomes
Provatas, K., Chantzi, N., Patsakis, M., Nayak, A., Mouratidis, I., & Georgakopoulos‐Soares, I. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.10.041 · Cited by 4
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Identification of ZNF384 as a regulator of epigenome in leukemia
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“The sample identifiers and associated metadata were acquired from the ENA database 53 .”
X-CRISP: domain-adaptable and interpretable CRISPR repair outcome prediction
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“We used sequence data from two template-free CRISPR targeting screens: FORECasT (European Nucleotide Archive project PRJEB29746, Allen et al. 2018) and inDelphi (NCBI Sequence Read Archive accession code SRP141144, Shen et al. 2018).”
Xu, Y. G., Wang, C., Xu, K., Ding, Y., Lü, A., & Zhang, L. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf469 · Cited by 4
“The rapid development of these technologies has contributed to large-scale publicly available datasets that have yet to be fully utilized (Leinonen et al. 2011, The ENCODE Project Consortium 2012, Luo et al. 2020).”
Plasmodium knowlesi Ligand-receptor Process in Baboon (Papio anubis) Placenta
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“fascicularis genome used in this study is available through the ENA [69] database via accession numbers from FR874244 to FR874264 [5].”
Molecular and associated approaches for studying soil biota and their functioning
Karaöz, U., Emerson, J., & Brodie, E. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-822941-5.00006-5 · Cited by 4
HSCGD: a comprehensive database of single-cell whole-genome data and metadata
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Epigenetics and Control of RNAs
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“These samples were downloaded from the European Nucleotide Archive (Leinonen et al., 2010) and are referred to hereafter as the “ companion data ” (Appendix S1).”
Advancing discovery in hearing research via biologist-friendly access to multi-omic data
Hertzano, R. P., & Mahurkar, A. (2022) · Human Genetics · doi:10.1007/s00439-022-02445-w · Cited by 4
“…deposited in repositories, such as the NCBI’s Sequence Read Archive (SRA) (Leinonen et al. 2011b) and EMBL–EBI’s European Nucleotide Archive (ENA) (Leinonen et al. 2011a) for raw sequence data, and NCBI’s Gene Expression Omnibus (GEO) (Clough and Barrett 2016) and EMBL–EBI’s ArrayExpress (Athar…”
BackgroundMethodInfluentialMLgsc: A Maximum-Likelihood General Sequence Classifier
Junier, T., Hervé, V., Wunderlin, T., & Junier, P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129384 · Cited by 4
“We downloaded all sequences from the European Nucleotide Archive (ENA) [23] that met the following criteria: “Coding” section, prokaryote (PRO) division, “nifH” gene name, and sequence length no greater than 1000 bp.”
MethodLeow, S.-S., Lee, W.-K., Khoo, J.-S., Teoh, S., Hoh, C.-C., Fairus, S., Sambanthamurthi, R., & Hayes, K. C. (2020) · Molecular Biology Reports · doi:10.1007/s11033-020-06003-3 · Cited by 4
Raes, N., Casino, A., Goodson, H., Islam, S., Koureas, D., Schiller, E., Schulman, L., Tilley, L., & Robertson, T. (2020) · Research Ideas and Outcomes · doi:10.3897/rio.6.e62361 · Cited by 4
The changes in the p53 protein across the animal kingdom pointing to its involvement in longevityPreprint
Bartas, M., Brázda, V., Volná, A., Červeň, J., Pečínka, P., & Zawacka‐Pankau, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.06.080200 · Cited by 4
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosisPreprint
Zabeti, H., Dexter, N., Safari, A. H., Sedaghat, N., Libbrecht, M. W., & Chindelevitch, L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.31.115741 · Cited by 4
EXPERT: Transfer Learning-enabled context-aware microbial source trackingPreprint
Chong, H., Yu, Q., Zha, Y., Xiong, G., Wang, N., Huang, X., Huang, S., Sun, C., Wu, S., Chen, W., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.29.428751 · Cited by 4
Abrudan, M. I., Matimba, A., Nikolic, D., Hughes, D., Argimón, S., Kekre, M., Underwood, A. P., & Aanensen, D. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.18.448940 · Cited by 4
Lamperti, L., François, O., Mouillot, D., Mathon, L., Sanchez, T., Albouy, C. P., Pellissier, L., & Manel, S. (2024) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.14430 · Cited by 3
Yadav, A. J., Bhagat, K., Sharma, A., & Padhi, A. K. (2025) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2024.10.011 · Cited by 3
Fifteen millennia of human mitogenome evolution in Sicily
Tommasi, A., Agostini, R. B., Villani, G., Migliore, N. R., Vizzari, M. T., Cardinali, I., Gerlando, R. D., Nicolini, V., Sorasio, G., Santos, P., et al. (2025) · Science Advances · doi:10.1126/sciadv.ady1674 · Cited by 6
“However, it remains a rare haplogroup, accounting for only 0.04 % of the total in online available datasets ( 31 – 33 ).”
InfluentialGeydirici, I., Martínez‐Cuesta, R., Bibinger, S., Espíndola‐Hernández, P., Gschwendtner, S., Rodríguez-Berbel, N., Schulz, S., Wicht, A.-C., & Schloter, M. (2026) · Biology and Fertility of Soils · doi:10.1007/s00374-026-02004-9 · Cited by 3
Karaji, R., & Peña‐Castillo, L. (2025) · PLoS ONE · doi:10.1371/journal.pone.0329355 · Cited by 3
The Era of Integrative Genomics: More Data or Better Methods?
Koestler, D. C., Jones, M. J., & Kobor, M. S. (2014) · Epigenomics · doi:10.2217/epi.14.44 · Cited by 3
“, cost constraints, insufficient biological material), allowing researchers to turn to the wealth of publicly available genomic data deposited in repositories such as: the Gene Expression Omnibus [9], ArrayExpress [10], European Genome-phenome archive [11] and The Cancer Genome Atlas [1].”
BackgroundAn Adapter Architecture for Heterogeneous Data Processing in Bioinformatics Pipelines
Lenadora, D., Wickramarachchi, A., Meedeniya, D., Mallawaarachchi, V., & Perera, I. (2019) · Moratuwa Engineering Research Conference (MERCon) · doi:10.1109/mercon.2019.8818781 · Cited by 3
“Another example of a service provider for bioinformatics processes would be the EMBL-EBI [3].”
BackgroundInfluentialBioinformatics Database Resources
Khandelwal, I., Sharma, A., Agrawal, P. K., & Shrivastava, R. (2019) · IGI Global eBooks · doi:10.4018/978-1-5225-8903-7.ch004 · Cited by 3
Gene co-expression analyses of health(span) across multiple species
Möller, S., Saul, N., Projahn, E., Barrantes, I., Gézsi, A., Walter, M., Antal, P., & Fuellen, G. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac083 · Cited by 3
“All target RNA-seq datasets were retrieved from the European Nucleotide Archive (Leinonen et al. , 2011), and the corresponding FASTQ files were filtered for Illumina adapters, phage PhiX sequences and quality (Phred score over 25) using BBTools version 38.49 (Bushnell et al. , 2017).”
MethodInfluentialIdentification of CoDREB Genes for Drought and Cold Tolerance in Camellia oleifera
Wang, Y., Guo, P., Sheng, S., Li, J., & Yan, J. (2023) · International Journal of Plant Biology · doi:10.3390/ijpb14010019 · Cited by 3
Expósito, R. R., & González‐Domínguez, J. (2024) · Future Generation Computer Systems · doi:10.1016/j.future.2024.01.011 · Cited by 4
Vochteloo, M., Deelen, P., Vink, B., Tsai, E. A., Runz, H., Andreu‐Sánchez, S., Fu, J., Zhernakova, A., Westra, H.-J., & Franke, L. (2024) · Genome biology · doi:10.1186/s13059-023-03151-0 · Cited by 4
Genome Informatics Pipelines and Genome Browsers
Barba, E., Tsermpini, E. E., Patrinos, G. P., & Koromina, M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813695-9.00008-x · Cited by 3
Gene Fusion Markup Language: a prototype for exchanging gene fusion data
Sundaram, S. K., Achiraman, S., & Chinnaiyan, A. M. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-269 · Cited by 3
“Similarly, several sequencing-based standardization formats have been developed by openaccess and international working bodies such as Genomic Standards Consortium (MIGS\MIMS\MIENS\MIMARKS\ MIxS) and European Nucleotide Archive (ENA\SRA) that describe genomic, meta-genomic, and environmental sequences [32-36].”
MethodBioDB extractor: customized data extraction system for commonly used bioinformatics databases
Karbhal, R., Sawant, S., & Kulkarni‐Kale, U. (2015) · BioData Mining · doi:10.1186/s13040-015-0067-z · Cited by 3
Classification and assessment tools for structural motif discovery algorithms
Badr, G. H., Al-Turaiki, I. M., & Mathkour, H. I. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s9-s4 · Cited by 3
“For each accession number, the subsequence corresponding to the motif with 200 nucleotides of flanking regions was retrieved directly from the European Nucleotide Archive at the European Bioinformatics Institute [38].”
MethodPavloudi, C., Oulas, A., Vasileiadou, K., Kotoulas, G., Troch, M. D., Friedrich, M. W., & Arvanitidis, C. (2017) · Aquatic Microbial Ecology · doi:10.3354/ame01829 · Cited by 3
Muhammed, M. K., Olsen, M. L., Kot, W., Neve, H., Castro-Mejía, J. L., Janzen, T., Hansen, L. H., Nielsen, D. S., Sørensen, S. J., Heller, K. J., et al. (2018) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2018.02.012 · Cited by 3
Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins
(2022) · doi:10.1371/journal.pcbi.1010016 · Cited by 3
“First, we downloaded all genomes from the European Nucleotide Archive (ENA) belonging to taxon 41665 (Actinopterygii).”
MethodGenomic Resources for Functional Genomics in Aquaculture Species
Zhang, J., Jiang, Y., Sun, F., Zhang, Y., Wang, R., Li, C., Liu, S., & Liu, Z. (2012) · doi:10.1002/9781118350041.ch2 · Cited by 3
Next-generation nematode genomes
Kumar, S. (2013) · ERA · Cited by 3
Role of Bioinformatic Tools and Databases in Cotton Research
Yu, J., & Main, D. (2015) · Agronomy monograph/Agronomy · doi:10.2134/agronmonogr57.2013.0043 · Cited by 3
Global distribution of mcr gene variants in 214,095 metagenomic samplesPreprint
Martiny, H.-M., Munk, P., Brinch, C., Szarvas, J., Aarestrup, F. M., & Petersen, T. (2022) · Research Square · doi:10.21203/rs.3.rs-640935/v2 · Cited by 3
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Floch, E. L., Adam‐Blondon, A., Alaux, M., Bardet, E., Bas, N., Bassi, F. M., Boczkowska, M., Bolc, P., Brouwer, M., Chalhoub, B., et al. (2026) · Scientific Data · doi:10.1038/s41597-026-06908-x · Cited by 3
Diurnal.plant.tools in 2024: Expanding to Marchantia polymorpha and Four Angiosperms
Tan, Q. W., Tan, E., & Mutwil, M. (2024) · Plant and Cell Physiology · doi:10.1093/pcp/pcae099 · Cited by 2
Kapoor, M., Ventura, E. S., Walsh, A. T., Sokolov, A., George, N., Kumari, S., Provart, N. J., Cole, B., Libault, M., Tickle, T. L., et al. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1460351 · Cited by 2
MiMyCS: A Processing-in-Memory Read Mapper for Compressing Next-Gen Sequencing Datasets
Moor, F. D., Mognol, M., Deltel, C., Drézen, E., Legriel, J., & Lavenier, D. D. (2024) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm62325.2024.10821790 · Cited by 2
“Both are paired-end datasets available for download on the European Nucleotide Archive browser [18].”
invertiaDB: a database of inverted repeats across organismal genomes
Provatas, K., Chantzi, N., Amptazi, N., Patsakis, M., Nayak, A., Mouratidis, I., Zaravinos, A., Pavlopoulos, G. A., & Georgakopoulos‐Soares, I. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf329 · Cited by 2
“The metadata include links to the established publicly available databases of the ENA Browser [ 55 ] and the NCBI Genome Browser [ 56 ].”
Chen, Y.-A., Kawashima, H., Park, J., Mohsen, A. S., Hosomi, K., Nakagata, T., Murakami, H., Nanri, H., Miyachi, M., Kunisawa, J., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-04339-z · Cited by 2
Tonon, E., Cecchetto, R., Carrera, M., Sorrentino, A., Zeni, G., Turri, G., Mantoan, M., Palmisano, A., Lagni, A., Lotti, V., et al. (2025) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkaf201 · Cited by 2
“The original Illumina-based FASTQ files of 18 sequences from Vaux et al. (2014) were downloaded from the European Nucleotide Archive (ENA) (Leinonen et al. 2011), together with 27 Illumina-based FASTQ files from the 2020 study by Menu et al. (2020).”
Exploring differences in the human gut microbiome between Han Chinese and non-Chinese populations
Wang, J., Zhang, Z., Chen, Y., Zhou, X., Xiang, J., Yang, C., Rodionov, D. A., Osterman, A. L., Qiu, Q., Deng, Y., et al. (2026) · Genome biology · doi:10.1186/s13059-026-03932-3 · Cited by 3
“We collected short-read metagenomic sequencing data from 9,320 human fecal samples available in the European Nucleotide Archive (ENA) [47], sourced from 39 distinct studies (Additional file 1: Table S1).”
Introduction to artificial intelligence in multi-omics analysis
Saha, A., Pal, R. K., & Saha, S. (2026) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2026.01.022 · Cited by 2
Mondal, R., Chaudhuri, R. S., Sheik, T. A., Gangadharaiah, L., Vijayan, D., Nishitha Naik, V., & Manthira Moorthy, S. (2026) · National Academy Science Letters · doi:10.1007/s40009-026-02073-2 · Cited by 2
Enabling Hardware Affinity in JVM-Based Applications: A Case Study for Big Data
Expósito, R. R., Veiga, J., & Touriño, J. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-50371-0_3 · Cited by 2
“MarDRe removes duplicate reads using the SRR377645 dataset, named after its accession number in the European Nucleotide Archive (ENA) [12], which contains 241 million reads of 100 base pairs each (67 GB in total).”
MethodGomes, J. D. A., Sgarioni, E., Kowalski, T. W., Giudicelli, G. C., Recamonde‐Mendoza, M., Fraga, L. R., Schüler‐Faccini, L., & Vianna, F. S. L. (2023) · Journal of Molecular Neuroscience · doi:10.1007/s12031-023-02126-x · Cited by 2
“The raw data from RNA-Seq studies retrieved from GEO databases were downloaded from the European Nucleotide Archive (ENA) in .fastq format and pre-processed (Leinonen et al. 2011).”
MethodGhedira, K., Dallali, H., Ardhaoui, M., Bouslama, Z., Hamdi, Y., Ben-Salah, S. F., Chelbi, H., Atri, C., Chaouch, M., Dekhil, N., et al. (2023) · BioMed Research International · doi:10.1155/2023/6638714 · Cited by 2
“Bayesian coalescent analyses were performed on BioMed Research International major lineages of the Nextstrain build in which (number of sequences of isolates from Africa as well as references from all over the world) sequences fell.”
MethodKyritsis, K., Pechlivanis, N., & Psomopoulos, F. E. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1275593 · Cited by 2
“Many of these biological datasets are accessible to the scienti fi c community through databases, such as the European Nucleotide Archive (ENA) (Leinonen et al., 2011a) and the Sequence Read Archive (SRA) (Leinonen et al., 2011b), or large consortia, such as the 1,000 Genomes (Auton et al., 2015)…”
BackgroundGonzález-Orozco, J. C., Escobedo-Ávila, I., & Velasco, I. (2023) · Genes · doi:10.3390/genes14122189 · Cited by 2
“Datasets were collected from the European Nucleotide Archive (ENA) [14] under the following accession numbers: axolotl [PRJNA378982] [15], rat [PRJNA760277] [16], and mouse [PRJNA193596] [17].”
MethodSunila, B. G., Dhanushkumar, T., Dasegowda, K. R., Vasudevan, K., & Rambabu, M. (2024) · Neuroscience Letters · doi:10.1016/j.neulet.2024.137764 · Cited by 2
Roy, A., Chaurasia, H., Kumar, B., Kumari, N., Jaiswal, S., Srivastava, M., Iquebal, M. A., Angadi, U. B., & Kumar, D. (2024) · BMC Plant Biology · doi:10.1186/s12870-024-05595-3 · Cited by 2
“…collected in FASTQ format both for single and paired end libraries for avocados, bananas, guavas, dates, figs, mangoes, papayas, and pineapples, from various public domain repositories, namely , Sequence Read Archive (SRA) [43], the European Nucleotide Archive (ENA) [44], and Ensembl Plants [45].”
BackgroundMulti-omics/genomics in predictive and personalized medicine
Ahmed, Z. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-91819-0.00005-1 · Cited by 2
Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure
Xu, R., Li, D., Yang, W., Wang, G., & Li, Y. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae640 · Cited by 2
“ENA (The European Nucleotide Archive), administered by the European Bioinformatics Institute, is a prominent database for nucleotide sequences.”
Liu, Y., Tang, T., Zhu, Z., Zeng, X., Zou, Q., & Li, K. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3539629 · Cited by 2
“Forinstance,theNationalIn-stitutesofHealth’sSequenceReadArchive[5]andtheEuropean NucleotideArchive(ENA)[6]haveaccumulatedapproximately tenquadrillionbasesoverthepastyears.”
Islakoğlu, Y. Ö., Korhan, P., Binokay, L., Keleş, B., Bağırsakçı, E., Taşçıoğlu, M. U., Şamdancı, E., Karakülah, G., & Atabey, N. (2025) · RNA Biology · doi:10.1080/15476286.2025.2529036 · Cited by 2
Chai, Y., Zhang, R., Jia, S., Zhu, D., Chen, S.-Y., Liu, S., Kong, N., Fu, X., & Sheng, X. (2025) · Stem Cell Reports · doi:10.1016/j.stemcr.2025.102605 · Cited by 2
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins
Li, C., Nagel, J., Androulakis, S., Song, J., & Buckle, A. M. (2016) · Database · doi:10.1093/database/baw021 · Cited by 2
“Annotations were extracted and reviewed from a variety of different publicly available resources, including ENA (27), 1000 Genome Project database (28), UniProt (29), Protein Data Bank (30), BioGrid (31), KEGG (32), SUPERFAMILY (33), Pfam (Version 27.”
BackgroundInfluentialMartín-Galiano, A. J. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.02.002 · Cited by 2
The search for Schizosaccharomyces fission yeasts in environmental metatranscriptomes
Shraim, R., & Nieuwenhuis, B. P. S. (2021) · Yeast · doi:10.1002/yea.3689 · Cited by 3
“A perl script by Michael Gerth was used to download data from the European Nucleotide Archive (Leinonen et al., 2011), using SRR/ERR/DRR accessions numbers as FASTQ files with ascp from Aspera (aspera/3.7.2; sra_download.pl, Gerth, 2018).”
MethodInfluentialMolecular Evolution & Phylogeny: What, When, Why & How?
Kolekar, P. S., Kale, M. M., & Kulkarni‐Kale, U. (2011) · InTech eBooks · doi:10.5772/20225 · Cited by 2
Nakazato, T., Bono, H. U., & Takagi, T. (2011) · InTech eBooks · doi:10.5772/18805 · Cited by 2
“Thus, the NGS data are also archived in public databases; the Sequence Read Archive (SRA) (Leinonen et al. 2011 b) at NCBI, European Nucleotide Archive (ENA) (Leinonen et al. 2011 a) at EBI, and DNA Data Bank of Japan (DDBJ) Sequence Read Archive (DRA) (Kaminuma et al. 2010) at DDBJ.”
InfluentialCatching Inconsistencies with the Semantic Web: A Biocuration Case Study.
Bolleman, J. T., Géhant, S., & Redaschi, N. (2012) · Cited by 2
Whole-Genome Sequencing Recommendations
Gabaldón, T., & Alioto, T. (2016) · Springer eBooks · doi:10.1007/978-3-319-31350-4_2 · Cited by 2
Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes
Abbas, M. M., & EL‐Manzalawy, Y. (2017) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3107411.3107472 · Cited by 2
“EMG is partnering with the European Nucleotide Archive (ENA) [18] in order to provide a permanent metagenomics data repository.”
BackgroundLeone, M., Galeota, E., Masseroli, M., & Pelizzola, M. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab815 · Cited by 2
Putra, A. M., Nugrahapraja, H., & Dwivany, F. M. (2023) · Indonesian Journal of Biotechnology · doi:10.22146/ijbiotech.49368 · Cited by 2
Metadata
- Authors
- Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R., Hoad, G., Jang, M., Pakseresht, N., Plaister, S., Radhakrishnan, R., Reddy, K., Sobhany, S., Ten Hoopen, P., Vaughan, R., Zalunin, V., & Cochrane, G.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Leinonen, R.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-23
- Volume
- 39
- Issue
- Database
- Pages
- D28-D31
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3013801
- OpenAlex
- W2120358246
- Cited by
- 690
- References
- 10
- Citations by year
- 2026: 37 · 2025: 49 · 2024: 74 · 2023: 52 · 2022: 44 · 2021: 64 · 2020: 37 · 2019: 42 · 2018: 41 · 2017: 47 · 2016: 39 · 2015: 48 · 2014: 33 · 2013: 31 · 2012: 23
- FWCI
- 10.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (085532)
- European Molecular Biology Laboratory
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- European Nucleotide Archive, Sequence Read Archive, DNA sequence databases, sequence similarity search, European Genome-phenome Archive
- MeSH terms
- Base Sequence, Europe, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing
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