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Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics

PloS one, 2014-04, Vol.9 (4), p.e93827-e93827

2014

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Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

Environmental microbiology, 2020-08, Vol.22 (8), p.3394-3412

2020

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SAR11 bacteria linked to ocean anoxia and nitrogen loss

Nature (London), 2016-08, Vol.536 (7615), p.179-183

2016

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Nature communications, 2018-11, Vol.9 (1), p.5114-8, Article 5114

2018

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Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes

Environmental microbiology, 2020-06, Vol.22 (6), p.2094-2106

2020

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MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

Nucleic acids research, 2014-04, Vol.42 (8), p.e73

2014

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An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains

PloS one, 2013-07, Vol.8 (7), p.e68464-e68464

2013

Volltextzugriff (PDF)

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

Nucleic acids research, 2018-07, Vol.46 (W1), p.W282

2018

Volltextzugriff (PDF)

Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (7), p.2575-2580

2013

Volltextzugriff (PDF)

Why and how to use the SeqCode

mLife, 2024-03, Vol.3 (1), p.1-13

2024

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Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"

Nature communications, 2021-07, Vol.12 (1), p.4060-4060, Article 4060

2021

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ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

Nucleic acids research, 2016-10, Vol.45 (3), p.e14

2016

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How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Applied and environmental microbiology, 2018-03, Vol.84 (6)

2018

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Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

The ISME Journal, 2012-03, Vol.6 (3), p.502-512

2012

Volltextzugriff (PDF)

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Applied and environmental microbiology, 2016-05, Vol.82 (9), p.2872-2883

2016

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Towards estimating the number of strains that make up a natural bacterial population

Nature communications, 2024-01, Vol.15 (1), p.544-544, Article 544

2024

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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

mSystems, 2018-05, Vol.3 (3)

2018

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Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

Applied and environmental microbiology, 2020-03, Vol.86 (6)

2020

Volltextzugriff (PDF)

An ANI gap within bacterial species that advances the definitions of intra-species units

mBio, 2024-01, Vol.15 (1), p.e0269623-e0269623

2024

Volltextzugriff (PDF)

Comparative genomics identifies conserved and variable TAL effectors in African strains of the cotton pathogen Xanthomonas citri pv. malvacearum

Phytopathology, 2023-08, Vol.113 (8), p.1387-1393

2023

Volltextzugriff (PDF)

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Applied and Environmental Microbiology, 2014-03, Vol.80 (5), p.1777-1786

2014

Volltextzugriff (PDF)

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

The ISME Journal, 2019-03, Vol.13 (3), p.767-779

2019

Volltextzugriff (PDF)

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

Frontiers in microbiology, 2016-04, Vol.7 (APR), p.579-579

2016

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Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

Bioinformatics, 2014-03, Vol.30 (5), p.629-635

2014

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Estimating coverage in metagenomic data sets and why it matters

The ISME Journal, 2014-11, Vol.8 (11), p.2349-2351

2014

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Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

SAR11 bacteria linked to ocean anoxia and nitrogen loss

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

Why and how to use the SeqCode

Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Towards estimating the number of strains that make up a natural bacterial population

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

An ANI gap within bacterial species that advances the definitions of intra-species units

Comparative genomics identifies conserved and variable TAL effectors in African strains of the cotton pathogen Xanthomonas citri pv. malvacearum

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

Estimating coverage in metagenomic data sets and why it matters

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