The initial state of the human gut microbiome determines its reshaping by antibiotics

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beanplot: A Boxplot Alternative for Visual Comparison of Distributions

(2015) Peter Kampstra   Journal of Statistical Software

Metagenomic insights into the human gut resistome and the forces that shape it

(2014) Kristoffer Forslund et al.   BIOESSAYS

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Estimating coverage in metagenomic data sets and why it matters

(2014) Luis M Rodriguez-R et al.   ISME Journal

Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans

(2014) Juan Wang et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

MLST reveals potentially high-risk international clones of Enterobacter cloacae*

(2014) R. Izdebski et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

(2014) Tarini Shankar Ghosh et al.   PLoS One

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats

(2014) Zhigang Ren et al.   TRANSPLANTATION

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Beta diversity as the variance of community data: dissimilarity coefficients and partitioning

(2013) Pierre Legendre et al.   ECOLOGY LETTERS

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Genetic characterization of tigecycline resistance in clinical isolates of Enterobacter cloacae and Enterobacter aerogenes

(2013) M. Veleba et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

(2012) Kjersti Aagaard et al.   FASEB JOURNAL

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis

(2011) Charlie G. Buffie et al.   INFECTION AND IMMUNITY

Iron Depletion and Repletion with Ferrous Sulfate or Electrolytic Iron Modifies the Composition and Metabolic Activity of the Gut Microbiota in Rats

(2011) Alexandra Dostal et al.   JOURNAL OF NUTRITION

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comparative Metagenomic Study of Alterations to the Intestinal Microbiota and Risk of NosocomialClostridum difficile–Associated Disease

(2010) Amee R. Manges et al.   JOURNAL OF INFECTIOUS DISEASES

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr

(2008) J. Baysarowich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY