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

Intestinal Microbiota and Relapse After Hematopoietic-Cell Transplantation

(2017) Jonathan U. Peled et al.   JOURNAL OF CLINICAL ONCOLOGY

Microbiome-Modulated Metabolites at the Interface of Host Immunity

(2017) Eran Blacher et al.   JOURNAL OF IMMUNOLOGY

Nivolumab in metastatic urothelial carcinoma after platinum therapy (CheckMate 275): a multicentre, single-arm, phase 2 trial

(2017) Padmanee Sharma et al.   LANCET ONCOLOGY

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

(2017) Whijae Roh et al.   Science Translational Medicine

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

(2017) Takahiro Tsujikawa et al.   Cell Reports

Sporadic colorectal cancer: microbial contributors to disease prevention, development and therapy

(2016) Julia L Drewes et al.   BRITISH JOURNAL OF CANCER

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

RECIST 1.1—Update and clarification: From the RECIST committee

(2016) Lawrence H. Schwartz et al.   EUROPEAN JOURNAL OF CANCER

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

(2016) Monkol Lek et al.   NATURE

The genomic landscape of cutaneous melanoma

(2016) Tongwu Zhang et al.   Pigment Cell & Melanoma Research

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

(2016) P.-L. Chen et al.   Cancer Discovery

Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade

(2016) D. B. Johnson et al.   Cancer Immunology Research

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Distinct clinical patterns and immune infiltrates are observed at time of progression on targeted therapy versus immune checkpoint blockade for melanoma

(2016) Zachary A. Cooper et al.   OncoImmunology

Immune Checkpoint Blockade: A Common Denominator Approach to Cancer Therapy

(2015) Suzanne L. Topalian et al.   CANCER CELL

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

Nivolumab in Previously Untreated Melanoma without BRAF Mutation

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

Pembrolizumab versus Ipilimumab in Advanced Melanoma

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

Microbial growth dynamics and human disease

(2015) J. A. Segre   SCIENCE

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

(2015) A. Sivan et al.   SCIENCE

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Cancer and the microbiota

(2015) W. S. Garrett   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation

(2014) Y. Taur et al.   BLOOD

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

Response to BRAF Inhibition in Melanoma Is Enhanced When Combined with Immune Checkpoint Blockade

(2014) Z. A. Cooper et al.   Cancer Immunology Research

Cancer immunoediting: antigens, mechanisms, and implications to cancer immunotherapy

(2013) Matthew D. Vesely et al.   Annals of the New York Academy of Sciences

RCytoscape: tools for exploratory network analysis

(2013) Paul T Shannon et al.   BMC BIOINFORMATICS

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

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

(2013) N. Iida et al.   SCIENCE

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks

(2013) Paul Blanche et al.   STATISTICS IN MEDICINE

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE