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RESCRIPt: Reproducible sequence taxonomy reference database management

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009581

2021

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Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

Applied and Environmental Microbiology, 2013-04, Vol.79 (8), p.2519-2526

2013

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The Microbiology of Malting and Brewing

Microbiology and Molecular Biology Reviews, 2013-06, Vol.77 (2), p.157-172

2013

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Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

Applied and Environmental Microbiology, 2013-09, Vol.79 (17), p.5214-5223

2013

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Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Proceedings of the National Academy of Sciences - PNAS, 2014-01, Vol.111 (1), p.E139-E148

2014

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Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Microbiome, 2018-05, Vol.6 (1), p.90-90, Article 90

2018

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Antibiotics, birth mode, and diet shape microbiome maturation during early life

Science translational medicine, 2016-06, Vol.8 (343), p.343ra82

2016

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Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

Nature medicine, 2016-03, Vol.22 (3), p.250-253

2016

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Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009876-e1009876

2022

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The soil microbiome influences grapevine-associated microbiota

mBio, 2015-03, Vol.6 (2)

2015

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Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

mBio, 2016-06, Vol.7 (3)

2016

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Monitoring Seasonal Changes in Winery-Resident Microbiota

PloS one, 2013-06, Vol.8 (6), p.e66437

2013

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Learning representations of microbe-metabolite interactions

Nature methods, 2019-12, Vol.16 (12), p.1306

2019

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Species abundance information improves sequence taxonomy classification accuracy

Nature communications, 2019-10, Vol.10 (1), p.4643-10, Article 4643

2019

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Indigenous bacteria and fungi drive traditional kimoto sake fermentations

Applied and Environmental Microbiology, 2014-09, Vol.80 (17), p.5522-5529

2014

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Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale

PloS one, 2012-04, Vol.7 (4), p.e35507

2012

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Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Frontiers in microbiology, 2021-04, Vol.12, p.673810-673810

2021

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Next-generation sequencing reveals significant bacterial diversity of botrytized wine

PloS one, 2012-05, Vol.7 (5), p.e36357

2012

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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

mSystems, 2018-11, Vol.3 (6)

2018

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Human Milk Glycomics and Gut Microbial Genomics in Infant Feces Show a Correlation between Human Milk Oligosaccharides and Gut Microbiota: A Proof-of-Concept Study

Journal of proteome research, 2015-01, Vol.14 (1), p.491-502

2015

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Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

Journal of Clinical Microbiology, 2013-08, Vol.51 (8), p.2617-2624

2013

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Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

eLife, 2015-03, Vol.4

2015

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Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women

Journal of translational medicine, 2018-09, Vol.16 (1), p.244-244, Article 244

2018

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Next-generation approaches to the microbial ecology of food fermentations

BMB Reports, 2012, 45(7), , pp.377-389

2012

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Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

Frontiers in microbiology, 2021-06, Vol.12, p.644487-644487

2021

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RESCRIPt: Reproducible sequence taxonomy reference database management

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

The Microbiology of Malting and Brewing

Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Antibiotics, birth mode, and diet shape microbiome maturation during early life

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment

The soil microbiome influences grapevine-associated microbiota

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

Monitoring Seasonal Changes in Winery-Resident Microbiota

Learning representations of microbe-metabolite interactions

Species abundance information improves sequence taxonomy classification accuracy

Indigenous bacteria and fungi drive traditional kimoto sake fermentations

Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Next-generation sequencing reveals significant bacterial diversity of botrytized wine

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

Human Milk Glycomics and Gut Microbial Genomics in Infant Feces Show a Correlation between Human Milk Oligosaccharides and Gut Microbiota: A Proof-of-Concept Study

Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women

Next-generation approaches to the microbial ecology of food fermentations

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

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