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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
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587 · cited 1×
“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
Slater, G., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,959
The International Nucleotide Sequence Database Collaboration
Karsch‐Mizrachi, I., Nakamura, Y., & Cochrane, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1006 · Cited by 717
Benson, D. A., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1024 · Cited by 348
Krause, J., Unger, T., Noçon, A., Malaspinas, A., Kolokotronis, S., Stiller, M., Soibelzon, L. H., Spriggs, H. F., Dear, P. H., Briggs, A. W., et al. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-220 · Cited by 288
The International Nucleotide Sequence Database Collaboration
Cochrane, G., Karsch‐Mizrachi, I., & Nakamura, Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1150 · Cited by 113
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).”
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Koncz, M., Stirling, T., Mehdi, H. H., Méhi, O., Eszenyi, B., Asbóth, A., Apjok, G., Tóth, Á., Orosz, L. I., Vásárhelyi, B. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.009 · Cited by 69
“For ISAba1, 117,118 we compiled a list of ISAba1 sequences using the European Nucleotide Archive 119 and ISMapper.”
Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model
van Tonder, A. J., Mistry, S., Bray, J. E., Hill, D. M. C., Cody, A. J., Farmer, C. L., Klugman, K. P., von Gottberg, A., Bentley, S. D., Parkhill, J., et al. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003788 · Cited by 65
“The advent of next-generation sequencing (NGS) has greatly increased the number of bacterial genomes sequenced and made available for study in public databases such as GenBank, the Sequence Read Archive and European Nucleotide Archive (ENA) [1–3].”
BackgroundGenome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe
Marques, C. A., Dickens, N. J., Paape, D., Campbell, S. J., & McCulloch, R. (2015) · Genome biology · doi:10.1186/s13059-015-0788-9 · Cited by 65
Vitsios, D., Kentepozidou, E., Quintais, L. T., Benito‐Gutiérrez, È., van Dongen, S., Davis, M. P. A., & Enright, A. J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx836 · Cited by 66
“In order to finetune our model we tested its performance independently for various numbers of randomly selected predictors (mtry) and numbers of trees (ntrees) on 65 mouse samples downloaded from ENA (31).”
MethodSieber, P. A., Voigt, K., Kämmer, P., Brunke, S., Schuster, S., & Linde, J. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02313 · Cited by 67
“We based our analyses on RNA-Seq data from public available sources [Gene Expression Omnibus (GEO) (Edgar, 2002) and European Nucleotide Archive (Leinonen et al., 2011)] with data sets connected to response to the host (ex vivo interaction with human or murine cells, mostly immune cells) and other isolated stress cond…”
MethodMarques, V., Guérin, P., Rocle, M., Valentini, A., Manel, S., Mouillot, D., & Déjean, T. (2020) · Ecography · doi:10.1111/ecog.05049 · Cited by 65
BioSamples database: FAIRer samples metadata to accelerate research data management
Courtot, M., Gupta, D., Liyanage, I. U., Xu, F., & Burdett, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1046 · Cited by 64
“For example, the PHA4GE consortium’s SARS-CoV-2 checklist (27) has been added to the JSON schema store, and can be used in conjunction with the ERC000033 checklist (https://www. ebi.ac.uk/ena/browser/view/ERC000033) required by ENA and the COVID portal for pathogen sequence submission.”
BackgroundInfluentialAssessing the global phylum level diversity within the bacterial domain: A review
Youssef, N. H., Couger, M. B., McCully, A. L., Criado, A. E. G., & Elshahed, M. S. (2014) · Journal of Advanced Research · doi:10.1016/j.jare.2014.10.005 · Cited by 65
“As a proof of principle, we queried one of such database depositories, the European Nucleotide Archive (ENA) [92], for novel 16S rRNA sequences.”
BackgroundMethodInfluentialGhaye, A. P., Bergemann, D., Tarifeño-Saldivia, E., Flasse, L. C., Berg, V. V., Peers, B., Voz, M. L., & Manfroid, I. (2015) · BMC Biology · doi:10.1186/s12915-015-0179-4 · Cited by 64
Use of environmental DNA in assessment of fish functional and phylogenetic diversity
Marques, V., Castagné, P., Polanco, A., Borrero‐Pérez, G. H., Hocdé, R., Guérin, P., Juhel, J., Velez, L., Loiseau, N., Letessier, T. B., et al. (2021) · Conservation Biology · doi:10.1111/cobi.13802 · Cited by 63
[FeFe]-Hydrogenase Maturation: Insights into the Role HydE Plays in Dithiomethylamine Biosynthesis
Betz, J. N., Boswell, N. W., Fugate, C. J., Holliday, G. L., Akiva, E., Scott, A. G., Babbitt, P. C., Peters, J. W., Shepard, E. M., & Broderick, J. B. (2015) · Biochemistry · doi:10.1021/bi501205e · Cited by 63
“(34) Each of the 563 HydE family enzymes was mapped onto its corresponding genome, and the ten proteins encoded upstream and downstream were gathered (as established in the ENA database(35)) creating a set of ~7,000 gene neighbors.”
A deep learning approach to pattern recognition for short DNA sequencesPreprint
Busia, A., Dahl, G. E., Fannjiang, C., Alexander, D. H., Dorfman, E. H., Poplin, R. E., McLean, C. Y., Chang, P.-C., & DePristo, M. A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/353474 · Cited by 68
“To evaluate our trained classifiers, we used 16S mock community sequencing data from Nelson et al., 22 Schirmer et al., 29 and D’Amore et al. 23 (PRJEB4688 and PRJEB6244 in the European Nucleotide Archive 24 ).”
MethodFrankl‐Vilches, C., Kuhl, H., Werber, M., Klages, S., Kerick, M., Bakker, A., de Oliveira, E. H. C., Reusch, C., Capuano, F., Vowinckel, J., et al. (2015) · Genome biology · doi:10.1186/s13059-014-0578-9 · Cited by 66
Ntountoumi, C., Vlastaridis, P., Mossialos, D., Stathopoulos, C., Iliopoulos, I., Promponas, V. J., Oliver, S. G., & Amoutzias, G. D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz730 · Cited by 62
“For the codon frequency analysis of LCRs, the DNA sequences (CDSs) of their proteins were retrieved from EMBL-Bank (50) by mapping Uniprot IDs to EMBL-bank IDs.”
MethodPlasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism
Pinheiro, M. M., Ahmed, M. A., Millar, S. B., Sanderson, T., Otto, T. D., Woon, L. C., Krishna, S., Rayner, J. C., & Cox‐Singh, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0121303 · Cited by 61
“uk)[19].”
Avershina, E., Sharma, P., Taxt, A. M., Singh, H., Frye, S. A., Paul, K., Kapil, A., Naseer, U., Kaur, P., & Ahmad, R. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.027 · Cited by 62
“All our isolates were colistin-sensitive, so we downloaded publicly available data for colistin-resistant isolates of E. coli and K. pneumoniae from the EMBL-EBI European Nucleotide [31] and Macesic et al. [9].”
MethodAssessing and managing risk when sharing aggregate genetic variant data
Craig, D. W., Goor, R. M., Wang, Z., Paschall, J. E., Ostell, J., Feolo, M., Sherry, S. T., & Manolio, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3067 · Cited by 56
Polymerase specific error rates and profiles identified by single molecule sequencing
Hestand, M. S., Houdt, J. V., Cristofoli, F., & Vermeesch, J. R. (2016) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2016.01.003 · Cited by 58
Big Data: the challenge for small research groups in the era of cancer genomics
Noor, A. M., Holmberg, L., Gillett, C., & Grigoriadis, A. E. (2015) · British Journal of Cancer · doi:10.1038/bjc.2015.341 · Cited by 59
“…the Database of Genotypes and Phenotypes (NIH, 2007), the European Genome Archive (Lappalainen et al, 2015) and the European Nucleotide Archive (Leinonen et al, 2011), allow users to access, query and download regions of interest from raw large-scale sequencing data sets, whereas databases…”
BackgroundSEED: efficient clustering of next-generation sequences
Bao, E., Jiang, T., Kaloshian, I., & Girke, T. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr447 · Cited by 59
Rail-RNA: scalable analysis of RNA-seq splicing and coverage
Nellore, A., Collado‐Torres, L., Jaffe, A. E., Alquicira-Hernández, J., Wilks, C., Pritt, J., Morton, J. T., Leek, J. T., & Langmead, B. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw575 · Cited by 54
“Each cluster downloaded source data from a European Nucleotide Archive FTP server [34, 35].”
MethodPrecision medicine with multi-omics strategies, deep phenotyping, and predictive analysis
Ahmed, Z. (2022) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2022.02.002 · Cited by 61
Attwood, T. K., Gisel, A., Eriksson, N.-E., & Bongcam‐Rudloff, E. (2011) · InTech eBooks · doi:10.5772/23535 · Cited by 58
“Together, EMBL-Bank and the ETA became known as ENA, the European Nucleotide Archive, Europe’s primary nucleotide-sequence repository (Cochrane et al., 2008).”
BackgroundInfluentialA Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective
Khan, A. R., Pervez, M. T., Babar, M. E., Naveed, N., & Shoaib, M. (2018) · Evolutionary Bioinformatics · doi:10.1177/1176934318758650 · Cited by 56
pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Baran, J., Gerner, M., Haeussler, M., Nenadić, G., & Bergman, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024716 · Cited by 55
“We automatically generated genePMID links from the EMBL nucleotide databank [20] by extracting EMBL records that contain a PMID and using the corresponding DNA sequences in a BLAST search against a database of transcripts from Ensembl genes, with subsequent filtering for promiscuous BLAST matches.”
MethodExploring biogeographic patterns of bacterioplankton communities across global estuaries
Ghosh, A., & Bhadury, P. (2018) · MicrobiologyOpen · doi:10.1002/mbo3.741 · Cited by 53
Bioinformatics: new tools and applications in life science and personalized medicine
Branco, I., & Choupina, A. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-11056-2 · Cited by 60
Kohl, S., Hollmann, J., Blattner, F. R., Radchuk, V. V., Andersch, F., Steuernagel, B., Schmutzer, T., Scholz, U., Krupinska, K., Weber, H. H., et al. (2012) · BMC Plant Biology · doi:10.1186/1471-2229-12-154 · Cited by 53
HADEG: A curated hydrocarbon aerobic degradation enzymes and genes database
Rojas-Vargas, J., Castelán-Sánchez, H. G., & Pardo‐López, L. (2023) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2023.107966 · Cited by 51
Ehrlich, K. C., & Mack, B. M. (2014) · Toxins · doi:10.3390/toxins6061916 · Cited by 51
Chartier, M., Gaudreault, F., & Najmanovich, R. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts149 · Cited by 51
“…of tRNAs (Duret, 2000; Ikemura, 1985; Moriyama and Powell, 1997; Percudani et al., 1997) thus causing ribosomes to pause at rare codons until the scarce activated tRNA brings the next amino acid to the growing polypeptide (Sørensen et al., 1989; ∗To whom correspondence should be addressed.”
BackgroundGenomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh
Monir, M. M., Islam, M. T., Mazumder, R., Mondal, D., Nahar, K. S., Sultana, M., Morita, M., Ohnishi, M., Huq, A., Watanabe, H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36687-7 · Cited by 50
McAdam, P. R., Broek, C. W. V., Lindsay, D., Ward, M. J., Hanson, M., Gillies, M., Watson, M., Stevens, J. M., Edwards, G. F., & Fitzgerald, J. R. (2014) · Genome biology · doi:10.1186/preaccept-1675723368141690 · Cited by 52
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
Ambrosino, L., Tangherlini, M., Colantuono, C., Esposito, A., Sangiovanni, M., Miralto, M., Sansone, C., & Chiusano, M. L. (2019) · Marine Drugs · doi:10.3390/md17100576 · Cited by 53
“In addition, due to the generation and release of huge numbers of sequences (raw reads) produced and released by next-generation sequencing efforts, the INSDC system built specialized archives to store data either as raw or processed, such as the Sequence Read Archive (SRA) [92] and Gene Expression Omnibus (GEO) [93]…”
BackgroundComparative analysis of metagenomic classifiers for long-read sequencing datasets
Marić, J., Križanović, K., Riondet, S., Nagarajan, N., & Šikić, M. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05634-8 · Cited by 63
“Data was downloaded from multiple sources (details in Additional file 1: Table S7), including the European Nucleotide Archive (ENA [41]) and the National Center for Biotechnology Information (NCBI [42]).”
MethodDetecting unknown sequences with DNA microarrays: explorative probe design strategies
Dugat‐Bony, É., Peyretaillade, É., Parisot, N., Biderre‐Petit, C., Jaziri, F., Hill, D. R. C., Rimour, S., & Peyret, P. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02559.x · Cited by 49
“, 2011), European Nucleotide Archive (ENA) (Leinonen et al., 2011) and the DNA Data Bank of Japan (DDBJ) (Kaminuma et al.”
BackgroundRosenberg, A. A., Marx, A., & Bronstein, A. M. (2022) · Nature Communications · doi:10.1038/s41467-022-30390-9 · Cited by 48
Golob, J. L., Oskotsky, T., Tang, A., Roldan, A., Chung, V., Ha, C. W. Y., Wong, R. J., Flynn, K. J., Chai, R., Dubin, C., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101350 · Cited by 53
Somboonna, N., Assawamakin, A., Wilantho, A., Tangphatsornruang, S., & Tongsima, S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s7-s29 · Cited by 48
“All the sequences were compared with NCBI non-redundant [11], EMBL [14,15] and SILVA [16] databases using BLASTN [10].”
Doğan, T., MacDougall, A., Saidi, R., Poggioli, D., Bateman, A. G., O’Donovan, C., & Martin, M. J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw114 · Cited by 48
Functional sequencing read annotation for high precision microbiome analysis
Zhu, C., Miller, M. J., Marpaka, S., Vaysberg, P., Rühlemann, M. C., Wu, G. G., Heinsen, F., Tempel, M., Zhao, L., Lieb, W., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1209 · Cited by 48
“For each protein of the PE1-set and GS-set, we extracted the corresponding gene from ENA (European Nucleotide Archive) (16) (including 5′ UTR and 3′ UTR) and randomly generated 10 DNA reads (50–250 nucleotides) that overlap by at least one nucleotide of the coding region.”
MethodAhmed, Z. (2022) · Emerging Topics in Life Sciences · doi:10.1042/etls20210244 · Cited by 52
Quek, C. Y. J., Bellingham, S. A., Jung, C., Scicluna, B. J., Shambrook, M., Sharples, R. A., Cheng, L., & Hill, A. F. (2016) · RNA Biology · doi:10.1080/15476286.2016.1270005 · Cited by 47
Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels
Hlevnjak, M., Polyansky, A. A., & Žagrović, B. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks679 · Cited by 44
“The coding sequences of their corresponding mRNAs were extracted using the ‘Cross-references’ section of each UniProtKB entry, where out of several possible translated RNA or DNA sequences the first one satisfying the length criterion (RNA length=3 protein length+3) was selected and its sequence downloaded from The Eu…”
MethodGuerzoni, D., & McLysaght, A. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw074 · Cited by 47
Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7
Leegwater, P. A. J., Vos‐Loohuis, M., Ducro, B. J., Boegheim, I. J. M., van Steenbeek, F. G., Nijman, I. J., Monroe, G. R., Bastiaansen, J. W. M., Dibbits, B. W., Goor, L., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-3186-0 · Cited by 46
Nakazato, T., Ohta, T., & Bono, H. U. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077910 · Cited by 45
“The SRA database is maintained by the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ) as NCBI SRA [3], the European Nucleotide Archive (ENA) [4], and DDBJ SRA (DRA) [5], respectively.”
MethodDetailed comparison of two popular variant calling packages for exome and targeted exon studies
Warden, C., Adamson, A. W., Neuhausen, S. L., & Wu, X. (2014) · PeerJ · doi:10.7717/peerj.600 · Cited by 47
“All datasets were downloaded as .fastq files from the European Nucleotide Archive (Leinonen et al., 2011).”
BackgroundBirger, C., Hanna, M., Salinas, E. A., Neff, J., Saksena, G., Livitz, D. G., Rosebrock, D., Stewart, C., Leshchiner, I., Baumann, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/209494 · Cited by 45
“The maturation and availability of large public data sets [2-5] from projects such as The Cancer Genome Atlas (TCGA) (http://cancergenome.”
BackgroundScaling Unlocks Broader Generation and Deeper Functional Understanding of Proteins
Bhatnagar, A., Jain, S., Beazer, J., Curran, S. C., Hoffnagle, A. M., Ching, K., Martyn, M., Nayfach, S., Ruffolo, J. A., & Madani, A. (2025) · neural information processing systems · doi:10.52202/085713-1536 · Cited by 55
Sketching and Sublinear Data Structures in Genomics
Marçais, G., Solomon, B., Patro, R., & Kingsford, C. (2019) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-072018-021156 · Cited by 45
“Public repositories of genomics data (7–9) have seen an exponential growth for over two 9).”
BackgroundGlobal Distribution of mcr Gene Variants in 214K Metagenomic Samples
Martiny, H.-M., Munk, P., Brinch, C., Szarvas, J., Aarestrup, F. M., & Petersen, T. N. (2022) · mSystems · doi:10.1128/msystems.00105-22 · Cited by 43
“We queried the ENA API for samples uploaded between 1 January 2010 and 1 January 2020 that were shotgun sequenced and had at least 100,000 sequencing reads.”
MethodInfluentialSchrörs, B., Riesgo-Ferreiro, P., Sorn, P., Gudimella, R., Bukur, T., Rösler, T., Löwer, M., & Şahin, U. (2021) · PLoS ONE · doi:10.1371/journal.pone.0249254 · Cited by 41
Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing
Auburn, S., Marfurt, J., Maslen, G., Campino, S., Ruano-Rubio, V., Manske, M., Machunter, B., Kenangalem, E., Noviyanti, R., Trianty, L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053160 · Cited by 44
“uk/ena/data/search?query = plasmodium) [33].”
Whole-Genome Sequencing in Personalized Therapeutics
Cordero, P., & Ashley, E. A. (2012) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2012.51 · Cited by 45
Dowall, S., Matthews, D. A., García-Dorival, I., Taylor, I., Kenny, J. G., Hertz‐Fowler, C., Hall, N., Corbin-Lickfett, K. A., Empig, C. J., Schlunegger, K., et al. (2014) · Genome biology · doi:10.1186/preaccept-1724277741482641 · Cited by 49
Ardui, S., Race, V., Zablotskaya, A., Hestand, M. S., Esch, H. V., Devriendt, K., Matthijs, G., & Vermeesch, J. R. (2016) · Human Mutation · doi:10.1002/humu.23150 · Cited by 42
“Data access: The raw data is available at the European Nucleotide Archive (ENA) (Leinonen et al. 2011) under study accession number PRJEB15075 (http://www.”
MethodJingleBells: A Repository of Immune-Related Single-Cell RNA–Sequencing Datasets
Ner‐Gaon, H., Melchior, A., Golan, N., Ben-Haim, Y., & Shay, T. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700272 · Cited by 42
“PubMed (11), GEO (6), ArrayExpress (7), and the European Nucleotide Archive (8) were searched with the term “single-cell RNA-seq.””
MethodReducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA
Boivin, V., Reulet, G., Boisvert, O., Couture, S., Elela, S. A., & Scott, M. S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa028 · Cited by 41
“RNA in RNAcentral obtained from sources that do not provide genomic coordinates such as ENA (46), or that are only present in a single specialized database with little experimental validation such as snoRNA Atlas (47) and piRNABank (48) entries were considered previously nonannotated.”
BackgroundDriessche, L. V., Vanneste, K., Bogaerts, B., Keersmaecker, S. C. J. D., Roosens, N. H. C., Haesebrouck, F., Cremer, L. D., Deprez, P. R., Pardon, B., & Boyen, F. (2020) · Emerging infectious diseases · doi:10.3201/eid2604.190962 · Cited by 42
“We have deposited all generated WGS data in the National Center for Biotechnology Information Sequence Read Archive (20) under accession number PRJNA541488.”
MethodDDBJ progress report: a new submission system for leading to a correct annotation
Kosuge, T., Mashima, J., Kodama, Y., Fujisawa, T., Kaminuma, E., Ogasawara, O., Okubo, K., Takagi, T., & Nakamura, Y. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1066 · Cited by 41
“This database content is shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC).”
MethodGonzalez-Beltran, A. N., Li, P., Zhao, J., Ávila-García, M. S., Roos, M., Thompson, M., van der Horst, E., Kaliyaperumal, R., Luo, R., Lee, T., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127612 · Cited by 45
“This ensures meeting annotation requirements covering key steps of specific experimental processes, enabling direct deposition to the European Nucleotide Archive [34] or to the Short Read Archive repository [35] using ISAcreator format interconversion function.”
MethodBaricz, A., Chiriac, M., Andrei, A., Bulzu, P., Levei, E. A., Cadar, O., Battes, K. P., Cîmpean, M., Șenilă, M., Cristea, A., et al. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.14909 · Cited by 41
Mornico, D., Miché, L., Béna, G., Nouwen, N. P., Verméglio, A., Vallenet, D., Smith, A., Giraud, É., Médigue, C., & Moulin, L. (2011) · Genes · doi:10.3390/genes3010035 · Cited by 41
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
Trappe, K., Marschall, T., & Renard, B. Y. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw423 · Cited by 38
Muhammed, M. K., Kot, W., Neve, H., Mahony, J., Castro-Mejía, J. L., Krych, Ł., Hansen, L. H., Nielsen, D. S., Sørensen, S. J., Heller, K. J., et al. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.00888-17 · Cited by 39
Zhang, S., Zhang, L., Tai, Y., Wang, X., Ho, C., & Wan, X. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00480 · Cited by 40
Data-driven synthetic microbes for sustainable future
Mariam, I., Rova, U., Christakopoulos, P., Μάτσακας, Λ., & Patel, A. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00556-4 · Cited by 41
“EMBL data resources are well categorized into 54 data resources that span from the nucleotide sequences database (European Nucleotide Archive (ENA)) tothe large archive for mathematical models of biological and biomedical systems (BioModels) 21,22 .”
Plant protein-coding gene families: emerging bioinformatics approaches
Martínez, M. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.06.003 · Cited by 37
Albayrak, L., Khanipov, K., Pimenova, M., Golovko, G., Rojas, M., Pavlidis, I. T., Chumakov, S., Aguilar, G., Chávez, A., Widger, W. R., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-3375-x · Cited by 37
““Average” (yellow) represents the average length of the identified LCS or LSS that covers an individual nucleotide position in mtDNA low-abundance variation in mitochondrial population to large data collections such as NCBI Sequence Read Archive [40], European Nucleotide Archive [41], The Cancer Genome Atlas [42], and…”
Pavloudi, C., Oulas, A., Kristoffersen, J. B., Friedrich, M. W., & Arvanitidis, C. (2017) · PeerJ · doi:10.7717/peerj.3687 · Cited by 37
“All the raw sequence files of this study were submitted to the European Nucleotide Archive (ENA) (Leinonen et al., 2011) with the study accession number PRJEB20211 (available at http://www.”
MethodThe emerging role of bacterial regulatory RNAs in disease
Eichner, H., Karlsson, J., & Loh, E. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.03.007 · Cited by 35
Network approaches for modeling the effect of drugs and diseases
Rintala, T., Ghosh, A., & Fortino, V. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac229 · Cited by 39
“European Nucleotide Archive (ENA) √ √ √ [127]”
Open questions in the social lives of viruses
Leeks, A., Bono, L. M., Ampolini, E. A., Souza, L. S., Höfler, T., Mattson, C. L., Dye, A. E., & Díaz‐Muñoz, S. L. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14203 · Cited by 38
Maervoet, V. E. T., Maeseneire, S. L. D., Avcı, F. G., Beauprez, J. J., Soetaert, W., & Mey, M. D. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0421-y · Cited by 36
“Glycerol dehydrogenases belong to the family of iron-dependent alcohol dehydrogenases [28].”
BackgroundDeclaring a tuberculosis outbreak over with genomic epidemiology
Hatherell, H.-A., Didelot, X., Pollock, S., Tang, P., Crisan, A., Johnston, J. C., Colijn, C., & Gardy, J. L. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000060 · Cited by 36
A framework for improving microRNA prediction in non-human genomes
Peace, R. J., Biggar, K. K., Storey, K. B., & Green, J. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv698 · Cited by 35
“Coding region and ncRNA sequences were retrieved from the European Nucleotide Archive (56).”
MethodLeekitcharoenphon, P., Friis, C., Zankari, E., Svendsen, C. A., Price, L. B., Rahmani, M., Herrero-Fresno, A., Fashae, K., Vandenberg, O., Aarestrup, F. M., et al. (2013) · The Journal of Infection in Developing Countries · doi:10.3855/jidc.3328 · Cited by 34
García-Núñez, M., Martí, S., Puig, C., Pérez‐Brocal, V., Millares, L., Santos, S., Ardanuy, C., Moyá, A., Liñares, J., & Monsó, E. (2017) · Future Microbiology · doi:10.2217/fmb-2016-0127 · Cited by 37
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Bradley, P. H., Nayfach, S., & Pollard, K. S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006242 · Cited by 33
“Accession numbers were identified using the aid of SRAdb [73] and downloaded from the Sequence Read Archive (SRA) [74].”
MethodNovel nuclear barcode regions for the identification of flatfish species
Paracchini, V., Petrillo, M., Lievens, A., Gallardo, A. P., Martinsohn, J. T., Hofherr, J., Maquet, A., Silva, A. P. B., Kagkli, D. M., Querci, M., et al. (2017) · Food Control · doi:10.1016/j.foodcont.2017.04.009 · Cited by 34
Frans, G., Meert, W., ten Bosch, J. V. D. W., Meyts, I., Bossuyt, X., Vermeesch, J. R., & Hestand, M. S. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2017.10.005 · Cited by 34
Cyberbiosecurity Challenges of Pathogen Genome Databases
Vinatzer, B. A., Heath, L. S., Almohri, H. M. J., Stulberg, M. J., Lowe, C., & Li, S. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00106 · Cited by 33
“ENA also allows sequence-based searches.”
BackgroundInfluentialBloois, L. V. D. G., Duim, B., Miller, W. G., Forbes, K. J., Wagenaar, J. A., & Zomer, A. (2016) · BMC Genomics · doi:10.1186/s12864-016-3058-7 · Cited by 32
“Genome sequences are available from the European Nucleotide Archive (ENA) and from NCBI GenBank, with the accession numbers listed in Table 1.”
InfluentialCRUP: a comprehensive framework to predict condition-specific regulatory units
Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schöpflin, R., Li, N., Kinkley, S., Römer-Hillmann, A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1860-7 · Cited by 29
“Raw data generated by the DEEP consortium is available via ENA/EGA: mouse: study accession number: PRJEB25978 [98]; human: study accession number: EGAS00001001937 [99].”
MethodA review of COVID-19 biomarkers and drug targets: resources and tools
Caruso, F. P., Scala, G., Cerulo, L., & Ceccarelli, M. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa328 · Cited by 35
“Most of data are available on public databases, such as Gene Expression Omnibus (GEO) [33], Sequence Read Archive (SRA) [34], European Nucleotide Archive (ENA) [35], European Genome-phenome Archive (EGA) [36] and Genome Sequence Archive (GSA) [37].”
BackgroundA bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine
Xi, H., Nie, X., Gao, F., Liang, X., Hu, L. H., Zhou, H., Cai, Y., & Yang, C. (2023) · Science Advances · doi:10.1126/sciadv.adj9075 · Cited by 35
Pavloudi, C., Oulas, A., Vasileiadou, K., Sarropoulou, E., Kotoulas, G., & Arvanitidis, C. (2016) · Marine Genomics · doi:10.1016/j.margen.2016.01.005 · Cited by 31
“uk/ena/data/view/ PRJEB3370) (Leinonen et al., 2011) and to the MG-RAST Metagenomics Analysis Server (Meyer et al.”
MethodInfluentialGhosh, A., & Som, A. (2020) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2020.107239 · Cited by 30
Ecosystem-specific microbiota and microbiome databases in the era of big data
Lobanov, V. P., Gobet, A., & Joyce, A. (2022) · Environmental Microbiome · doi:10.1186/s40793-022-00433-1 · Cited by 33
Pitfalls of genotyping microbial communities with rapidly growing genome collections
Zhao, C., Shi, Z. J., & Pollard, K. S. (2023) · Cell Systems · doi:10.1016/j.cels.2022.12.007 · Cited by 33
Developing and implementing an institute-wide data sharing policy
Dyke, S. O. M., & Hubbard, T. (2011) · Genome Medicine · doi:10.1186/gm276 · Cited by 31
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni
Boroni, M., Sammeth, M., Gava, S. G., Jorge, N. A. N., Macedo, A. M., Machado, C. R., Mourão, M. D. M., & Franco, G. R. (2018) · Scientific Reports · doi:10.1038/s41598-018-22093-3 · Cited by 30
Dong, M., & Feng, H. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.879260 · Cited by 30
“The 38 seed sequences were mapped against the SILVA databases with EMBL-EBI/ENA, GTDB, RDP, LTP taxonomy, using the SILVA Alignment, Classification, and Tree Services (ACT) to small subunit (16S) and large subunit (23S), respectively (Leinonen et al., 2011; Pruesse et al., 2012; Quast et al., 2013; Cole et al., 2014;…”
MethodMetabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis
Dai, D., Wang, T., Wu, S., Gao, N., & Chen, W. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01205 · Cited by 29
“In total three metagenomic datasets, including two for IBD and one for CRC, were obtained from the European Nucleotide Archive (ENA; Leinonen et al., 2011)1 database.”
MethodRoselli, M., Devirgiliis, C., Zinno, P., Guantario, B., Finamore, A., Rami, R., & Perozzi, G. (2017) · Genes & Nutrition · doi:10.1186/s12263-017-0583-1 · Cited by 29
“Availability of data and materials Raw NGS data are available at the EMBL-EBI European Nucleotide Archive (ENA) [66], under the study accession number PRJEB20801.”
MethodSoul, J., Hardingham, T., Boot-Handford, R., & Schwartz, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty947 · Cited by 29
Ederveen, T. H. A., Smits, J. P. H., Hajo, K., van Schalkwijk, S., Kouwenhoven, T. A., Lukovac, S., Wels, M., van den Bogaard, E. H. J., Schalkwijk, J., Boekhorst, J., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-56065-y · Cited by 28
Clinical and genomic assessment of PD-L1 SP142 expression in triple-negative breast cancer
Ahn, S. G., Kim, S., Shepherd, J. H., Cha, Y. J., Bae, S. J., Kim, C., Jeong, J., & Perou, C. M. (2021) · Breast Cancer Research and Treatment · doi:10.1007/s10549-021-06193-9 · Cited by 29
“Finally, we tested the SP142 signature in the cohorts of other malignancies treated with immune-check point inhibitors (ICIs).”
MethodInfluentialInvestigating the impact of reference assembly choice on genomic analyses in a cattle breed
Lloret‐Villas, A., Bhati, M., Kadri, N. K., Fries, R., & Pausch, H. (2021) · BMC Genomics · doi:10.1186/s12864-021-07554-w · Cited by 31
“All raw sequencing data are publicly available at the Sequencing Read Archive of the NCBI [26] or the European Nucleotide Archive of the EMBL-EBI [27].”
Method
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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