M. Olm

发表

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

J. Banfield, C. Brown, M. Olm, 2017, The ISME Journal.

Measurement of bacterial replication rates in microbial communities

Brian C. Thomas, J. Banfield, C. Brown, 2016, Nature Biotechnology.

dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes

J. Banfield, C. Brown, M. Olm, 2017, bioRxiv.

InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains

J. Banfield, B. Firek, M. Morowitz, 2020, bioRxiv.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

John Vu, Eric Mayer, J. Paul Robinson, 2015, eLife.

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria

Yun S. Song, J. Banfield, Nicholas Bhattacharya, 2019, Science Advances.

Consistent metagenome-derived metrics verify and define bacterial species boundaries

J. Banfield, P. M. Matheus Carnevali, M. Olm, 2019, bioRxiv.

Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes

J. Banfield, B. Firek, Robyn Baker, 2018, bioRxiv.

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.

Brian C. Thomas, D. Burstein, J. Banfield, 2017, Genome Research.

Clades of huge phages from across Earth’s ecosystems

Christine L. Sun, Alex D. Thomas, Alexander J. Probst, 2020, Nature.

Clades of huge phages from across Earth’s ecosystems

Christine L. Sun, Alex D. Thomas, Alexander J. Probst, 2019, bioRxiv.

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Brian C. Thomas, J. Banfield, F. Aarestrup, 2018, bioRxiv.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

Brian C. Thomas, J. Banfield, B. Firek, 2018, Microbiome.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

Brian C. Thomas, J. Banfield, B. Firek, 2018, Microbiome.

Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity

Yun S. Song, J. Banfield, Nicholas Bhattacharya, 2020, bioRxiv.

Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition

J. Banfield, B. Firek, M. Morowitz, 2021, Cell reports. Medicine.

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

J. Banfield, P. M. Matheus Carnevali, M. Olm, 2020, mSystems.

Reporting guidelines for human microbiome research: the STORMS checklist

Chris I. Hunter, Jennifer M. Fettweis, F. Bushman, 2021, Nature Medicine.

Using strain-resolved analysis to identify contamination in metagenomics data

J. Banfield, B. Firek, M. Morowitz, 2022, bioRxiv.

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

J. Banfield, B. Firek, M. Morowitz, 2021, Nature Biotechnology.

Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems

Travis N. Mavrich, M. Olm, G. Hatfull, 2016, Molecular microbiology.

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

J. Banfield, M. Olm, Matthew R. Olm, 2017, mSystems.

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network

Alexander J. Probst, J. Banfield, Karthik Anantharaman, 2019, The ISME Journal.

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

N. Neff, A. Jha, J. Sonnenburg, 2023, Cell.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

N. Neff, A. Jha, J. Sonnenburg, 2022, bioRxiv.

MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics

J. Sonnenburg, M. Olm, C. I. Kothe, 2024, bioRxiv.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

J. Banfield, Alexander D. Johnson, R. Hettich, 2020, bioRxiv.

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

J. Banfield, G. Schroth, S. Kuersten, 2020, mBio.

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Itai Sharon, Cindy J. Castelle, D. Burstein, 2019, Nature Communications.

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut

J. Banfield, Tali Raveh-Sadka, C. Brown, 2020, PloS one.

Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut

J. Banfield, Tali Raveh-Sadka, C. Brown, 2018, bioRxiv.

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

J. Banfield, B. Firek, M. Morowitz, 2019, Microbiome.

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

Brian C. Thomas, J. Banfield, Cristina N Butterfield, 2017, mBio.

Microbial diversity and metabolic potential in cyanotoxin producing cyanobacterial mats throughout a river network

Alexander J. Probst, J. Banfield, Karthik Anantharaman, 2018, bioRxiv.

Hospitalization throws the preterm gut microbiome off-key.

M. Olm, Jing Qian, Emily N Yeo, 2024, Cell host & microbe.