Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Stable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian Gut

(2020) Bryan B. Hsu et al.   mSystems

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria

(2020) Jordan E. Bisanz et al.   Cell Host & Microbe

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans

(2020) Alessio Basolo et al.   NATURE MEDICINE

In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials

(2020) Kurt Selle et al.   mBio

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

(2020) Nathan T. Porter et al.   Nature Microbiology

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

In situ reprogramming of gut bacteria by oral delivery

(2020) Bryan B. Hsu et al.   Nature Communications

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

(2019) Paola Soto-Perez et al.   Cell Host & Microbe

Depletion of microbiome-derived molecules in the host using Clostridium genetics

(2019) Chun-Jun Guo et al.   SCIENCE

ggCyto: Next Generation Open-Source Visualization Software for Cytometry

(2018) Phu Van et al.   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

(2018) Antoine Vigouroux et al.   Molecular Systems Biology

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria

(2018) Vincent M Isabella et al.   NATURE BIOTECHNOLOGY

Biotechnological mass production of DNA origami

(2017) Florian Praetorius et al.   NATURE

Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus

(2017) Joo Youn Park et al.   Scientific Reports

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

Measuring the biodiversity of microbial communities by flow cytometry

(2016) Ruben Props et al.   Methods in Ecology and Evolution

Filamentous Bacteriophage Promote Biofilm Assembly and Function

(2015) Patrick R. Secor et al.   Cell Host & Microbe

Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress

(2015) Sheila I. Jensen et al.   Scientific Reports

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

(2014) Robert J Citorik et al.   NATURE BIOTECHNOLOGY

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

One-Step Cloning and Chromosomal Integration of DNA

(2013) François St-Pierre et al.   ACS Synthetic Biology

Phage survival: The biodegradability of M13 phage display libraryin vitro

(2012) L'ubomíra Tóthová et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

(2009) T. K. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

(2008) M. S. Dillingham et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS