Metagenomic assembled plasmids of the human microbiome vary across disease cohorts

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation

(2020) Simone Rampelli et al.   mSystems

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

(2020) Tanya M. Monaghan et al.   Gut Microbes

What are the treatment options for resistant Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria?

(2020) Martina Spaziante et al.   EXPERT OPINION ON PHARMACOTHERAPY

High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project

(2020) Yi-ran Chen et al.   Scientific Reports

Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease

(2020) Yiwei Qian et al.   BRAIN

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

(2020) Frederic D. Bushman et al.   Cell Host & Microbe

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Giant oversights in the human gut virome

(2019) Thomas D S Sutton et al.   GUT

Plasmid evolution in carbapenemase‐producing Enterobacteriaceae : a review

(2019) Katlego Kopotsa et al.   Annals of the New York Academy of Sciences

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Unravelling plasmidome distribution and interaction with its hosting microbiome

(2019) Aya Brown Kav et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body

(2019) Manuela R. Pausan et al.   Frontiers in Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level

(2017) Wiley Barton et al.   GUT

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection

(2017) Dina Kao et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota

(2016) Tom Konikoff et al.   TRENDS IN MICROBIOLOGY

Transfer of DNA from Bacteria to Eukaryotes

(2016) Benoît Lacroix et al.   mBio

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers

(2014) L. Mira-Pascual et al.   JOURNAL OF GASTROENTEROLOGY

Fecal Microbial Composition of Ulcerative Colitis and Crohn’s Disease Patients in Remission and Subsequent Exacerbation

(2014) Edgar S. Wills et al.   PLoS One

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

The Comprehensive Antibiotic Resistance Database

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

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

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

Clostridium difficileand inflammatory bowel disease: Role in pathogenesis and implications in treatment

(2013) Orna Nitzan   WORLD JOURNAL OF GASTROENTEROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Insights into the bovine rumen plasmidome

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

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

(2012) Serena Dollive et al.   GENOME BIOLOGY

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

(2012) Lesley A. Ogilvie et al.   Bioengineered

Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks

(2011) M. Tamminen et al.   MOLECULAR BIOLOGY AND EVOLUTION

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

The Vexed Relationship Between Clostridium Difficile and Inflammatory Bowel Disease: An Assessment of Carriage in an Outpatient Setting Among Patients in Remission

(2009) Evelyn M Clayton et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS