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Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis.
- Published in:
- Environmental Microbiome, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s40793-022-00425-1
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- Article
COVID-19 pandemic reveals the peril of ignoring metadata standards.
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- Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-0524-5
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- Article
Immunogenicity of the Monovalent Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine in People Living with HIV (PLWH).
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- Vaccines, 2024, v. 12, n. 7, p. 785, doi. 10.3390/vaccines12070785
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The MG-RAST metagenomics database and portal in 2015.
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- Nucleic Acids Research, 2016, v. 44, p. D590, doi. 10.1093/nar/gkv1322
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FIGfams: yet another set of protein families.
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- Nucleic Acids Research, 2009, v. 37, n. 20, p. 6643, doi. 10.1093/nar/gkp698
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GISMO—gene identification using a support vector machine for ORF classification.
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- Nucleic Acids Research, 2007, v. 35, n. 2, p. 540
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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
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- Nucleic Acids Research, 2007, v. 35, p. d347, doi. 10.1093/nar/gkl947
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An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud.
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- Concurrency & Computation: Practice & Experience, 2011, v. 23, n. 17, p. 2250, doi. 10.1002/cpe.1799
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Unlocking the potential of metagenomics through replicated experimental design.
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- Nature Biotechnology, 2012, v. 30, n. 6, p. 513, doi. 10.1038/nbt.2235
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Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
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- Nature Biotechnology, 2006, v. 24, n. 8, p. 997, doi. 10.1038/nbt1232
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- Article
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2014, v. 8, n. 1, p. 1, doi. 10.1038/ismej.2013.176
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- Article
Structure, fluctuation and magnitude of a natural grassland soil metagenome.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 9, p. 1677, doi. 10.1038/ismej.2011.197
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- Article
The Future of microbial metagenomics (or is ignorance bliss?).
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2011, v. 5, n. 5, p. 777, doi. 10.1038/ismej.2010.178
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- Article
Identification of herbal teas and their compounds eliciting antiviral activity against SARS-CoV-2 in vitro.
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- BMC Biology, 2022, v. 20, n. 1, p. 1, doi. 10.1186/s12915-022-01468-z
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- Article
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.
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- Applied Microbiology & Biotechnology, 2010, v. 88, n. 6, p. 1333, doi. 10.1007/s00253-010-2921-8
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- Article
Genomic Standards Consortium Projects.
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- Standards in Genomic Sciences, 2014, v. 9, n. 3, p. 599, doi. 10.4056/sigs.5559680
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The 15th Genomic Standards Consortium meeting.
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- Standards in Genomic Sciences, 2013, v. 8, n. 1, p. 124, doi. 10.4056/sigs.3457
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- Article
The metagenomic data life-cycle: standards and best practices.
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- GigaScience, 2017, v. 6, n. 8, p. 1, doi. 10.1093/gigascience/gix047
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Intestinal Tissues Induce an SNP Mutation in Pseudomonas aeruginosa That Enhances Its Virulence: Possible Role in Anastomotic Leak.
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- PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0044326
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- Article
The United States of America and Scientific Research.
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- PLoS ONE, 2010, v. 5, n. 8, p. 1, doi. 10.1371/journal.pone.0012203
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- Article
Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling.
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- PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010518
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- Article
Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics.
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- Proteomics, 2004, v. 4, n. 1, p. 46, doi. 10.1002/pmic.200300501
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- Article
Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.
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- MicrobiologyOpen, 2023, v. 12, n. 2, p. 1, doi. 10.1002/mbo3.1347
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Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition.
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- Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1267270
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- Article
UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example.
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- BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10539-0
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- Article
The RAST Server: Rapid Annotations using Subsystems Technology.
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- BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-75
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- Article
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.
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- BMC Bioinformatics, 2012, v. 13, n. 1, p. 183, doi. 10.1186/1471-2105-13-183
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- Article
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools.
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- BMC Bioinformatics, 2012, v. 13, n. 1, p. 141, doi. 10.1186/1471-2105-13-141
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- Article
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.
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- BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S21
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- Article
Immune responses in COVID-19 patients during breakthrough infection with SARS-CoV-2 variants Delta, Omicron-BA.1 and Omicron-BA.5.
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- Frontiers in Immunology, 2023, p. 1, doi. 10.3389/fimmu.2023.1150667
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- Article
GenDB—an open source genome annotation system for prokaryote genomes.
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- Nucleic Acids Research, 2003, v. 31, n. 8, p. 2187, doi. 10.1093/nar/gkg312
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- Article
The MG-RAST API explorer: an on-ramp for RESTful query composition.
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- BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-2993-0
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- Article
A RESTful API for Accessing Microbial Community Data for MG-RAST.
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- PLoS Computational Biology, 2015, v. 11, n. 1, p. 1, doi. 10.1371/journal.pcbi.1004008
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- Article
A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE.
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- PLoS Computational Biology, 2012, v. 8, n. 6, p. 1, doi. 10.1371/journal.pcbi.1002541
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- Article
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes.
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- PLoS Computational Biology, 2009, v. 5, n. 12, p. 1, doi. 10.1371/journal.pcbi.1000593
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MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis.
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- Briefings in Bioinformatics, 2019, p. 1151, doi. 10.1093/bib/bbx105
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Federation in genomics pipelines: techniques and challenges.
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- Briefings in Bioinformatics, 2019, v. 20, n. 1, p. 235, doi. 10.1093/bib/bbx102
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- Article
Spatial scale drives patterns in soil bacterial diversity.
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- Environmental Microbiology, 2016, v. 18, n. 6, p. 2039, doi. 10.1111/1462-2920.13231
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- Article
The complete genome sequence for putative H<sub>2</sub>- and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.
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- Environmental Microbiology, 2014, v. 16, n. 11, p. 3443, doi. 10.1111/1462-2920.12453
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- Article
Whole genome analysis of the marine Bacteroidetes‘ Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter.
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- Environmental Microbiology, 2006, v. 8, n. 12, p. 2201, doi. 10.1111/j.1462-2920.2006.01152.x
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- Article
Functional predictions from inference and observation in sequence-based inflammatory bowel disease research.
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- Genome Biology, 2012, v. 13, n. 9, p. 169, doi. 10.1186/gb4042
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Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil.
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- PLoS ONE, 2016, v. 11, n. 11, p. 1, doi. 10.1371/journal.pone.0166578
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The Genomic Standards Consortium.
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- PLoS Biology, 2011, v. 9, n. 6, p. 1, doi. 10.1371/journal.pbio.1001088
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BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
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- Bioinformatics, 2005, v. 21, n. 7, p. 853, doi. 10.1093/bioinformatics/bti091
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Development of joint application strategies for two microbial gene finders.
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- Bioinformatics, 2004, v. 20, n. 10, p. 1622, doi. 10.1093/bioinformatics/bth137
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PathFinder: reconstruction and dynamic visualization of metabolic pathways.
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- Bioinformatics, 2002, v. 18, n. 1, p. 124, doi. 10.1093/bioinformatics/18.1.124
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- Article
Diagnosis of Inflammatory Bowel Disease and Colorectal Cancer through Multi-View Stacked Generalization Applied on Gut Microbiome Data.
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- Diagnostics (2075-4418), 2022, v. 12, n. 10, p. 2514, doi. 10.3390/diagnostics12102514
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- Article
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
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- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-537
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- Article
BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).
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- BMC Genomics, 2011, v. 12, n. 1, p. 278, doi. 10.1186/1471-2164-12-278
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- Article