MGnify
Names
More detailed information about this field from each metasource.
MGnify
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
EBI Metagenomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
formerly: EBI Metagenomics
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
ebi_metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
Names
More detailed information about this field from each metasource.
MGnify
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
EBI Metagenomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
formerly: EBI Metagenomics
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
ebi_metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:06.735983
Other names: EBI Metagenomics, formerly: EBI Metagenomics, ebi_metagenomics
Names
More detailed information about this field from each metasource.
MGnify
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
EBI Metagenomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
formerly: EBI Metagenomics
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
ebi_metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:06.735983
EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
Description
More detailed information about this field from each metasource.
EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
Web resource targeted at metagenomic researchers.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:06.735983
Webpage:
https://www.ebi.ac.uk/metagenomics/Webpage
More detailed information about this field from each metasource.
https://www.ebi.ac.uk/metagenomics/
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
http://www.ebi.ac.uk/metagenomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: EMBL-EBI Terms of UseLicence name
More detailed information about this field from each metasource.
EMBL-EBI Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
other
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/about/terms-of-use
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://www.ebi.ac.uk/about/terms-of-use
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
MGnify: the microbiome analysis resource in 2020
PMID: 31696235
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
PMID: 29069476
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data
PMID: 24165880
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkx967
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1195
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
Publications
More detailed information about this field from each metasource.
MGnify: the microbiome analysis resource in 2020
PMID: 31696235
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
PMID: 29069476
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data
PMID: 24165880
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkx967
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1195
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:06.735983
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MGnify: the microbiome analysis resource in 2020
PubMed citations: 101.
101 articles citing: MGnify: the microbiome analysis resource in 2020
Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples. PMID:35902093
New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? PMID:35887492
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
Bioinformatics approaches and applications in plant biotechnology. PMID:35838847
Fast-HBR: Fast hash based duplicate read remover. PMID:35815196
Functional metagenomic screening identifies an unexpected β-glucuronidase. PMID:35799064
Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide. PMID:35721890
Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream. PMID:35701635
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. PMID:35687095
Deep learning geometrical potential for high-accuracy ab initio protein structure prediction. PMID:35663033
ColabFold: making protein folding accessible to all. PMID:35637307
The Search for Cryptic L-Rhamnosyltransferases on the Sporothrix schenckii Genome. PMID:35628784
Large-Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families. PMID:35608365
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. PMID:35576001
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches. PMID:35473941
B-Cell Epitope Mapping of TprC and TprD Variants of Treponema pallidum Subspecies Informs Vaccine Development for Human Treponematoses. PMID:35422800
Metagenomics-enabled microbial surveillance. PMID:35365786
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. PMID:35365655
Unifying the known and unknown microbial coding sequence space. PMID:35356891
Improved prediction of protein-protein interactions using AlphaFold2. PMID:35273146
Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. PMID:35258340
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants. PMID:35198984
Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide. PMID:35178038
Ontology-aware neural network: a general framework for pattern mining from microbiome data. PMID:35091743
Petabase-scale sequence alignment catalyses viral discovery. PMID:35082445
ExTaxsI: an exploration tool of biodiversity molecular data. PMID:35077538
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity. PMID:35069509
Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases. PMID:35059858
Protein structure predictions to atomic accuracy with AlphaFold. PMID:35017726
Synthetic antibacterial discovery of symbah-1, a macrocyclic β-hairpin peptide antibiotic. PMID:35005555
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial. PMID:34904950
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. PMID:34873061
Metagenomic discovery of CRISPR-associated transposons. PMID:34845024
Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites. PMID:34831464
A roadmap for metagenomic enzyme discovery. PMID:34821235
Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. PMID:34817235
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. PMID:34788838
A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure. PMID:34762696
AMDB: a database of animal gut microbial communities with manually curated metadata. PMID:34747470
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. PMID:34723319
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome. PMID:34669476
Advancing Equity and Inclusion in Microbiome Research and Training. PMID:34636663
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010
Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. PMID:34588691
Persistence of functional microbiota composition across generations. PMID:34561474
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PMID:34529671
FALCON2: a web server for high-quality prediction of protein tertiary structures. PMID:34525939
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. PMID:34520557
Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome. PMID:34490420
Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. PMID:34382712
Improved protein structure prediction by deep learning irrespective of co-evolution information. PMID:34368623
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14). PMID:34350630
Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. PMID:34331351
Highly accurate protein structure prediction with AlphaFold. PMID:34265844
PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes. PMID:34240105
HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis. PMID:34225648
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. PMID:34168315
MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction. PMID:34162922
Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. PMID:34108585
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. PMID:34046429
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. PMID:34041266
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. PMID:34012005
DOE JGI Metagenome Workflow. PMID:34006627
Microbiome and oral squamous cell carcinoma: a possible interplay on iron metabolism and its impact on tumor microenvironment. PMID:34002353
Microbiome Sample Comparison and Search: From Pair-Wise Calculations to Model-Based Matching. PMID:33897651
Taxonomic composition and variation in the gut microbiota of laboratory mice. PMID:33893864
Reduced metagenome sequencing for strain-resolution taxonomic profiles. PMID:33781324
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. PMID:33766108
Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings. PMID:33759266
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. PMID:33737920
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog. PMID:33709074
Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. PMID:33692771
Balrog: A universal protein model for prokaryotic gene prediction. PMID:33635857
Streamlining data-intensive biology with workflow systems. PMID:33438730
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. PMID:33304336
Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential. PMID:33202171
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
A catalogue of biochemically diverse CRISPR-Cas9 orthologs. PMID:33139742
Pfam: The protein families database in 2021. PMID:33125078
Diversity and evolution of B-family DNA polymerases. PMID:32976577
A novel universal primer pair for prokaryotes with improved performances for anammox containing communities. PMID:32973284
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. PMID:32804439
The human gut archaeome: identification of diverse haloarchaea in Korean subjects. PMID:32753050
A unified catalog of 204,938 reference genomes from the human gut microbiome. PMID:32690973
COVID-19 pandemic reveals the peril of ignoring metadata standards. PMID:32561801
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. PMID:32556166
NetConfer: a web application for comparative analysis of multiple biological networks. PMID:32430035
A practical guide to amplicon and metagenomic analysis of microbiome data. PMID:32394199
A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion. PMID:32380653
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604 -
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
PubMed citations: 86.
86 articles citing: EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus. PMID:35896693
Fast-HBR: Fast hash based duplicate read remover. PMID:35815196
A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses. PMID:35739325
Lactobacillus acidophilus and HKL Suspension Alleviates Ulcerative Colitis in Rats by Regulating Gut Microbiota, Suppressing TLR9, and Promoting Metabolism. PMID:35600873
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. PMID:35484115
Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. PMID:35258340
Identification of antimicrobial peptides from the human gut microbiome using deep learning. PMID:35241840
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. PMID:34873061
Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. PMID:34859349
MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. PMID:34592929
Persistence of functional microbiota composition across generations. PMID:34561474
Significant Gene Biomarker Tyrosine Kinase Non-receptor 2 Mediated Cell Proliferation and Invasion in Colon Cancer. PMID:34421982
Bioprospecting marine actinomycetes for antileishmanial drugs: current perspectives and future prospects. PMID:34409179
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Forming Consensus To Advance Urobiome Research. PMID:34282932
Refget: standardised access to reference sequences. PMID:34260694
KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data. PMID:34075103
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. PMID:34046429
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. PMID:34012005
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. PMID:33864455
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. PMID:33737920
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. PMID:33649565
geneRFinder: gene finding in distinct metagenomic data complexities. PMID:33632132
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. PMID:33563787
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level. PMID:33468706
Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. PMID:33430705
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. PMID:33221926
Macroecological laws describe variation and diversity in microbial communities. PMID:32958773
The Association between Insertion Sequences and Antibiotic Resistance Genes. PMID:32878926
Metagenomic Studies in Inflammatory Skin Diseases. PMID:32813091
Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire. PMID:32747713
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. PMID:32690954
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. PMID:32482164
CSN: unsupervised approach for inferring biological networks based on the genome alone. PMID:32414319
Every fifth published metagenome is not available to science. PMID:32243442
Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. PMID:32108314
Data mining of metagenomes to find novel enzymes: a non-computationally intensive method. PMID:32099729
Integrating Computational Methods to Investigate the Macroecology of Microbiomes. PMID:32010196
MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research. PMID:32008578
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. PMID:31957879
Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context. PMID:31947979
Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. PMID:31911822
omicplotR: visualizing omic datasets as compositions. PMID:31729955
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. PMID:31728526
Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species. PMID:31723319
The European Nucleotide Archive in 2019. PMID:31722421
MGnify: the microbiome analysis resource in 2020. PMID:31696235
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. PMID:31675414
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. PMID:31647547
Recruitment of Reverse Transcriptase-Cas1 Fusion Proteins by Type VI-A CRISPR-Cas Systems. PMID:31572350
Functional metagenomic analysis of dust-associated microbiomes above the Red Sea. PMID:31551441
Beyond cells - The virome in the human holobiont. PMID:31528630
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
CCMP: software-as-a-service approach for fully-automated microbiome profiling. PMID:31482150
Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. PMID:31402174
Prediction of interresidue contacts with DeepMetaPSICOV in CASP13. PMID:31298436
Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. PMID:31289280
Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity. PMID:31217298
Probiotics: current landscape and future horizons. PMID:31114711
Antibiotic resistomes of healthy pig faecal metagenomes. PMID:31091181
Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. PMID:31069462
Genomic Characterization of Arcobacter butzleri Isolated From Shellfish: Novel Insight Into Antibiotic Resistance and Virulence Determinants. PMID:31057492
The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant. PMID:30973601
New approaches for metagenome assembly with short reads. PMID:30815668
A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining. PMID:30747914
A new genomic blueprint of the human gut microbiota. PMID:30745586
Kelpie: generating full-length 'amplicons' from whole-metagenome datasets. PMID:30723610
Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome. PMID:30700057
Eleven quick tips to build a usable REST API for life sciences. PMID:30543619
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. PMID:30462168
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
UniProt: a worldwide hub of protein knowledge. PMID:30395287
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. PMID:30365027
Simulated reactive zone with emulsified vegetable oil for the long-term remediation of Cr(VI)-contaminated aquifer: dynamic evolution of geological parameters and groundwater microbial community. PMID:30306441
The microgenderome revealed: sex differences in bidirectional interactions between the microbiota, hormones, immunity and disease susceptibility. PMID:30298433
'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets. PMID:30287886
A novel insight in favor of structure-function relationship for 16S rRNA. PMID:30047038
YAMP: a containerized workflow enabling reproducibility in metagenomics research. PMID:29917068
HMMER web server: 2018 update. PMID:29905871
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments. PMID:29762668
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. PMID:29755441
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510 -
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data
PubMed citations: 47.
47 articles citing: EBI metagenomics--a new resource for the analysis and archiving of metagenomic data
Bacterial Adaptation to Venom in Snakes and Arachnida. PMID:35604233
MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. PMID:34592929
Gut microbiome and its meta-omics perspectives: profound implications for cardiovascular diseases. PMID:34170211
A Review on Viral Metagenomics in Extreme Environments. PMID:31749771
Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data. PMID:31308384
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. PMID:31174603
Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks. PMID:31042284
Enhanced Microbial Bile Acid Deconjugation and Impaired Ileal Uptake in Pregnancy Repress Intestinal Regulation of Bile Acid Synthesis. PMID:30983011
The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant. PMID:30973601
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
ASaiM: a Galaxy-based framework to analyze microbiota data. PMID:29790941
Flexible metagenome analysis using the MGX framework. PMID:29690922
Identification of fungi in shotgun metagenomics datasets. PMID:29444186
Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. PMID:29268781
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation. PMID:28821731
A clinician's guide to microbiome analysis. PMID:28790452
An isolated cellulolytic Escherichia coli from bovine rumen produces ethanol and hydrogen from corn straw. PMID:28652866
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool. PMID:28350876
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation. PMID:27822531
Computational workflow for the fine-grained analysis of metagenomic samples. PMID:27801291
MetaStorm: A Public Resource for Customizable Metagenomics Annotation. PMID:27632579
COMAN: a web server for comprehensive metatranscriptomics analysis. PMID:27515514
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. PMID:27383682
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PMID:27332861
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PMID:27327495
Value, but high costs in post-deposition data curation. PMID:26861660
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
Web Resources for Metagenomics Studies. PMID:26602607
EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data. PMID:26582919
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. PMID:26578596
Metagenome Sequencing of the Greater Kudu (Tragelaphus strepsiceros) Rumen Microbiome. PMID:26272573
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Metabolic network modeling of microbial communities. PMID:26109480
Databases for Microbiologists. PMID:26013493
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. PMID:25886935
Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. PMID:25859244
Open source libraries and frameworks for biological data visualisation: a guide for developers. PMID:25475079
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Content discovery and retrieval services at the European Nucleotide Archive. PMID:25404130
Rfam 12.0: updates to the RNA families database. PMID:25392425
A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PMID:25122209
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579 - http://dx.doi.org/10.1093/nar/gkx967
- http://dx.doi.org/10.1093/nar/gkv1195
Tags:
Tags
More detailed information about this field from each metasource.
16s rrna
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene prediction
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metagenome
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
microbiome
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
non-coding rna
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
fungal genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
bioinformatics
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
functional analysis
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.735983
Tags
More detailed information about this field from each metasource.
16s rrna
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metagenome
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
microbiome
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
non-coding rna
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: MGnify; MGnify; DOI: https://doi.org/10.25504/FAIRsharing.dxj07r; Last edited: July 6, 2021, 2:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
fungal genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
bioinformatics
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
functional analysis
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: MGnify; editing status 2020-01-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34W68 last accessed: 2022-11-04
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:06.735983
16s rrna dna sequences gene gene prediction genome metagenome microbiome non-coding rna sequence annotation genomics fungal genome bioinformatics functional analysis genomics metagenomics
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