Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

(2021) Francesco Asnicar et al.   NATURE MEDICINE

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade

(2021) Miles C. Andrews et al.   NATURE MEDICINE

Multivariable association discovery in population-scale meta-omics studies

(2021) Himel Mallick et al.   PLoS Computational Biology

Systematic review: the effects of proton pump inhibitors on the microbiome of the digestive tract-evidence from next-generation sequencing studies

(2020) Lukas Macke et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma

(2020) Thijs T. Wind et al.   MELANOMA RESEARCH

Gut Microbiome Modulation Via Fecal Microbiota Transplant to Augment Immunotherapy in Patients with Melanoma or Other Cancers

(2020) Jennifer L. McQuade et al.   Current Oncology Reports

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma

(2020) Angelo Limeta et al.   JCI Insight

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

(2019) Edoardo Pasolli et al.   CELL

The neuroactive potential of the human gut microbiota in quality of life and depression

(2019) Mireia Valles-Colomer et al.   Nature Microbiology

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

(2019) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients

(2019) Brandilyn A. Peters et al.   Genome Medicine

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

(2018) Vyara Matson et al.   SCIENCE

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Neoadjuvant immune checkpoint blockade in high-risk resectable melanoma

(2018) Rodabe N. Amaria et al.   NATURE MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Survival Outcomes in Patients With Previously Untreated BRAF Wild-Type Advanced Melanoma Treated With Nivolumab Therapy

(2018) Paolo A. Ascierto et al.   JAMA Oncology

Gut Dysbiosis Featured by Abundant Ruminococcus Gnavus Heralds the Manifestation of Allergic Diseases in Infants

(2017) Yen H. Ni et al.   GASTROENTEROLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

(2017) Francesco Beghini et al.   ISME Journal

Healthful and Unhealthful Plant-Based Diets and the Risk of Coronary Heart Disease in U.S. Adults

(2017) Ambika Satija et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

(2017) Cristina Llorente et al.   Nature Communications

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients

(2017) Arthur E. Frankel et al.   NEOPLASIA

Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis

(2016) Krista Dubin et al.   Nature Communications

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

Evaluation of a screener to assess diet quality in the Netherlands

(2015) Linde van Lee et al.   BRITISH JOURNAL OF NUTRITION

Proton pump inhibitors affect the gut microbiome

(2015) Floris Imhann et al.   GUT

Identification of Poly-N-acetylglucosamine as a Major Polysaccharide Component of theBacillus subtilisBiofilm Matrix

(2015) Damien Roux et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma

(2015) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

More than a marine propeller – the flagellum of the probiotic Escherichia coli strain Nissle 1917 is the major adhesin mediating binding to human mucus

(2012) Anja Troge et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS