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

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

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

Innate immune signaling and regulation in cancer immunotherapy

(2016) Leticia Corrales et al.   CELL RESEARCH

Enterococcus hirae and Barnesiella intestinihominis Facilitate Cyclophosphamide-Induced Therapeutic Immunomodulatory Effects

(2016) Romain Daillère et al.   IMMUNITY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity

(2015) Stefani Spranger et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Pembrolizumab versus Ipilimumab in Advanced Melanoma

(2015) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

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

(2015) M. Vetizou et al.   SCIENCE

Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy

(2015) W. Peng et al.   Cancer Discovery

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment

(2013) N. Iida et al.   SCIENCE

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting thegroELGene

(2012) Jana Junick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

Application of quantitative real-time PCR for rapid identification of Bacteroides fragilis group and related organisms in human wound samples

(2011) Jia Tong et al.   ANAEROBE

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

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Genotyping of Enterococcus faecalis and Enterococcus faecium Isolates by Use of a Set of Eight Single Nucleotide Polymorphisms

(2010) I. U. Rathnayake et al.   JOURNAL OF CLINICAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Establishment of an Analytical System for the Human Fecal Microbiota, Based on Reverse Transcription-Quantitative PCR Targeting of Multicopy rRNA Molecules

(2009) K. Matsuda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Use of aBacteroides thetaiotaomicron-specific α-1-6, mannanase quantitative PCR to detect human faecal pollution in water

(2008) H. Yampara-Iquise et al.   JOURNAL OF APPLIED MICROBIOLOGY

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Locked Nucleic Acid Pentamers as Universal PCR Primers for Genomic DNA Amplification

(2008) Zhen Sun et al.   PLoS One