Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

(2020) Samuel E. Barnett et al.   BMC BIOINFORMATICS

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

(2020) Steven J. Blazewicz et al.   ISME Journal

Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

(2019) François Thomas et al.   ISME Journal

Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

(2018) Ember M. Morrissey et al.   ENVIRONMENTAL MICROBIOLOGY

Estimating taxon-specific population dynamics in diverse microbial communities

(2018) Benjamin J. Koch et al.   Ecosphere

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

(2018) Evan P. Starr et al.   Microbiome

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA

(2018) Katerina Papp et al.   ISME Journal

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

(2018) Roland C. Wilhelm et al.   ISME Journal

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent

(2016) Caroline S Fortunato et al.   ISME Journal

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP)

(2016) Michael Morando et al.   Frontiers in Microbiology

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

(2016) Charles Pepe-Ranney et al.   Frontiers in Microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

(2016) Nina Dombrowski et al.   Nature Microbiology

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil

(2013) Steven J. Blazewicz et al.   ECOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Dynamics of 18O Incorporation from H 2 18O into Soil Microbial DNA

(2011) Steven J. Blazewicz et al.   MICROBIAL ECOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

When metagenomics meets stable-isotope probing: progress and perspectives

(2010) Yin Chen et al.   TRENDS IN MICROBIOLOGY

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY