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Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.
- Published in:
- Viruses (1999-4915), 2024, v. 16, n. 3, p. 430, doi. 10.3390/v16030430
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- Publication type:
- Article
Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California.
- Published in:
- Microorganisms, 2023, v. 11, n. 11, p. 2803, doi. 10.3390/microorganisms11112803
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- Publication type:
- Article
Metabolic versatility of Caldarchaeales from geothermal features of Hawai’i and Chile as revealed by five metagenome-assembled genomes.
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- Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1216591
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- Publication type:
- Article
Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.
- Published in:
- Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05299-8
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- Publication type:
- Article
The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.
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- Microbiome, 2023, v. 11, n. 1, p. 1, doi. 10.1186/s40168-023-01634-7
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- Publication type:
- Article
The Coronavirus Standards Working Group's roadmap for improved population testing.
- Published in:
- 2022
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- Publication type:
- Letter
Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns.
- Published in:
- Viruses (1999-4915), 2022, v. 14, n. 10, p. N.PAG, doi. 10.3390/v14102128
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- Publication type:
- Article
Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles.
- Published in:
- Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.934708
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- Publication type:
- Article
Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles.
- Published in:
- Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.934708
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- Publication type:
- Article
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.
- Published in:
- Bioinformatics, 2022, v. 38, n. 10, p. 2700, doi. 10.1093/bioinformatics/btac176
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- Publication type:
- Article
Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28.
- Published in:
- Microorganisms, 2022, v. 10, n. 5, p. 866, doi. 10.3390/microorganisms10050866
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- Publication type:
- Article
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes.
- Published in:
- Frontiers in Genetics, 2022, v. 12, p. 1, doi. 10.3389/fgene.2021.821715
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- Publication type:
- Article
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.
- Published in:
- Bioinformatics, 2021, v. 37, n. 7, p. 1024, doi. 10.1093/bioinformatics/btaa710
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- Publication type:
- Article
Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya.
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- PLoS Neglected Tropical Diseases, 2021, v. 15, n. 2, p. 1, doi. 10.1371/journal.pntd.0008991
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- Publication type:
- Article
The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.
- Published in:
- Life (2075-1729), 2021, v. 11, n. 1, p. 7, doi. 10.3390/life11010007
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- Publication type:
- Article
Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate.
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- G3: Genes | Genomes | Genetics, 2020, v. 10, n. 8, p. 2573, doi. 10.1534/g3.120.401489
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- Publication type:
- Article
Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing.
- Published in:
- 2020
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- Publication type:
- research
Novel Insights Into the Spread of Enteric Pathogens Using Genomics.
- Published in:
- 2020
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- Publication type:
- journal article
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.
- Published in:
- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-58356-1
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- Publication type:
- Article
Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus.
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- Clinical Infectious Diseases, 2020, v. 70, n. 3, p. 464, doi. 10.1093/cid/ciz234
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- Publication type:
- Article
Advances and Challenges in Metatranscriptomic Analysis.
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- Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00904
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- Publication type:
- Article
Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions.
- Published in:
- Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.00102
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- Publication type:
- Article
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 1, p. 67, doi. 10.1093/nar/gkw1027
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- Publication type:
- Article
Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones.
- Published in:
- Genome Biology & Evolution, 2016, v. 8, n. 6, p. 2036, doi. 10.1093/gbe/evw135
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- Publication type:
- Article
ADEPT, a dynamic next generation sequencing data error-detection program with trimming.
- Published in:
- 2016
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- Publication type:
- Product Review
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.
- Published in:
- Frontiers in Microbiology, 2015, v. 6, p. 1, doi. 10.3389/fmicb.2015.01205
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- Publication type:
- Article
CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA.
- Published in:
- PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0135481
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- Publication type:
- Article
Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.
- Published in:
- Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s40793-015-0041-x
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- Publication type:
- Article
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 10, p. 1
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- Publication type:
- Article
Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals Extensive Population Genetic Diversity.
- Published in:
- PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0120311
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- Publication type:
- Article
Rapid evaluation and quality control of next generation sequencing data with FaQCs.
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- BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/s12859-014-0366-2
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- Publication type:
- Article
Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs.
- Published in:
- Scientific Reports, 2014, p. 1, doi. 10.1038/srep06480
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- Publication type:
- Article
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains.
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- PLoS Biology, 2014, v. 12, n. 8, p. 1, doi. 10.1371/journal.pbio.1001920
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- Publication type:
- Article
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres.
- Published in:
- PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0095380
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- Publication type:
- Article
Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes.
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- PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0084963
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- Publication type:
- Article
Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics.
- Published in:
- Environmental Microbiology, 2013, v. 15, n. 10, p. 2850, doi. 10.1111/1462-2920.12154
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- Publication type:
- Article
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
- Published in:
- Nature Communications, 2013, v. 4, n. 5, p. 1854, doi. 10.1038/ncomms2884
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- Publication type:
- Article
Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants.
- Published in:
- Frontiers in Plant Science, 2013, v. 4, p. 1, doi. 10.3389/fpls.2013.00120
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- Publication type:
- Article
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.
- Published in:
- Nature Communications, 2013, v. 4, n. 3, p. 1601, doi. 10.1038/ncomms2615
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- Publication type:
- Article
Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2.
- Published in:
- PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0048228
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- Publication type:
- Article
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
- Published in:
- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 9, p. 1715, doi. 10.1038/ismej.2012.59
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- Publication type:
- Article
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia.
- Published in:
- PLoS ONE, 2012, v. 7, n. 4, p. 1, doi. 10.1371/journal.pone.0035314
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- Publication type:
- Article
Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics.
- Published in:
- Briefings in Functional Genomics, 2011, v. 10, n. 6, p. 322
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- Publication type:
- Article
The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes.
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- PLoS ONE, 2011, v. 6, n. 3, p. 1, doi. 10.1371/journal.pone.0016876
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- Publication type:
- Article
The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate.
- Published in:
- Genome Biology & Evolution, 2009, v. 1, p. 439, doi. 10.1093/gbe/evp047
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- Publication type:
- Article
Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation.
- Published in:
- Environmental Microbiology, 2007, v. 9, n. 12, p. 2993, doi. 10.1111/j.1462-2920.2007.01409.x
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- Publication type:
- Article
The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2.
- Published in:
- PLoS Biology, 2006, v. 4, n. 12, p. 2196, doi. 10.1371/journal.pbio.0040383
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- Publication type:
- Article