journal article

• Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.  Nature Microbiology. 2025
• Hospitalization throws the preterm gut microbiome off-key..  Cell Host and Microbe. 1651-1653. 2024
• Milk to mucus: How B. fragilis colonizes the gut.  Cell Host and Microbe. 149-150. 2024
• Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.  Science. 1220-+. 2022
• Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity.  Genome Research. 2021
• Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow.  The ISME Journal: multidisciplinary journal of microbial ecology. 1834-1846. 2020
• Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut.  PLoS One. 2020
• Clades of huge phages from across Earth's ecosystems.  Nature. 425-+. 2020
• Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.  mSystems. 2020
• Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.  Science Advances. 2019
• Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.  The ISME Journal: multidisciplinary journal of microbial ecology. 1618-1634. 2019
• Megaphages infect Prevotella and variants are widespread in gut microbiomes.  Nature Microbiology. 693-700. 2019
• Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms.  Microbiome. 2019
• Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.  Nature Communications. 2019
• The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.  Microbiome. 2018
• Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.  mBio. 2018
• Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome..  mSystems. 2018
• dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.  The ISME Journal: multidisciplinary journal of microbial ecology. 2864-2868. 2017
• Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.  Nature Communications. 2017
• Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.  Genome Research. 601-612. 2017
• The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.  mBio. 2017
• Measurement of bacterial replication rates in microbial communities.  Nature Biotechnology. 1256-1263. 2016
• Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems.  Molecular Microbiology. 625-644. 2016
• Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotypes.  Journal of Virology. 2461-2480. 2014