Species- and site-specific genome editing in complex bacterial communities

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

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

(2021) Christine He et al.   Nature Microbiology

Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation

(2021) Monica Viladomiu et al.   Cell Host & Microbe

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

(2021) Hualan Liu et al.   Cell Reports

Efficient retroelement-mediated DNA writing in bacteria

(2021) Fahim Farzadfard et al.   Cell Systems

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Metabolically cohesive microbial consortia and ecosystem functioning

(2020) Alberto Pascual-García et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Guide RNA Categorization Enables Target Site Choice in Tn7-CRISPR-Cas Transposons

(2020) Michael T. Petassi et al.   CELL

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

A versatile platform strain for high-fidelity multiplex genome editing

(2019) Robert G Egbert et al.   NUCLEIC ACIDS RESEARCH

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

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

(2017) Matthew R Olm et al.   ISME Journal

Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification

(2017) Lucia R. Wu et al.   Nature Biomedical Engineering

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

(2016) Lars Barquist et al.   BIOINFORMATICS

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation

(2014) Belgin Dogan et al.   INFLAMMATORY BOWEL DISEASES

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

(2014) Uli Klümper et al.   ISME Journal

Long-term manure exposure increases soil bacterial community potential for plasmid uptake

(2013) Sanin Musovic et al.   Environmental Microbiology Reports

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS