Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1

Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

(2021) Runzhi Zhang et al.   Biology Direct

Infection trains the host for microbiota-enhanced resistance to pathogens

(2021) Apollo Stacy et al.   CELL

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

(2021) Francesco Asnicar et al.   NATURE MEDICINE

A uniform computational approach improved on existing pipelines to reveal microbiome biomarkers of non-response to immune checkpoint inhibitors

(2021) Fyza Y Shaikh et al.   CLINICAL CANCER RESEARCH

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients

(2021) Diwakar Davar et al.   SCIENCE

Pretreatment neutrophil-to-lymphocyte ratio and mutational burden as biomarkers of tumor response to immune checkpoint inhibitors

(2021) Cristina Valero et al.   Nature Communications

Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country

(2021) Jacky Dwiyanto et al.   Scientific Reports

Anti‐PD1‐Induced Immune‐Related Adverse Events and Survival Outcomes in Advanced Melanoma

(2020) Aleksi Suo et al.   ONCOLOGIST

Immune‐Related Adverse Events and Immune Checkpoint Inhibitor Efficacy in Patients with Gastrointestinal Cancer with Food and Drug Administration‐Approved Indications for Immunotherapy

(2020) Satya Das et al.   ONCOLOGIST

Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients

(2020) Lisa Derosa et al.   EUROPEAN UROLOGY

Dendritic cell–derived hepcidin sequesters iron from the microbiota to promote mucosal healing

(2020) Nicholas J. Bessman et al.   SCIENCE

Correlation between immune-related adverse events and prognosis in patients with various cancers treated with anti PD-1 antibody

(2020) Hiroshi Matsuoka et al.   BMC CANCER

The diagnostic and predictive role of NLR, d-NLR and PLR in COVID-19 patients

(2020) Ai-Ping Yang et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Gut microbiota composition is associated with newborn functional brain connectivity and behavioral temperament

(2020) Caroline M. Kelsey et al.   BRAIN BEHAVIOR AND IMMUNITY

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

(2020) Erez N. Baruch et al.   SCIENCE

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

(2020) Angelo Limeta et al.   JCI Insight

Long-term safety of pembrolizumab monotherapy and relationship with clinical outcome: A landmark analysis in patients with advanced melanoma

(2020) Caroline Robert et al.   EUROPEAN JOURNAL OF CANCER

Proteomic test for anti-PD-1 checkpoint blockade treatment of metastatic melanoma with and without BRAF mutations

(2019) Paolo A. Ascierto et al.   Journal for ImmunoTherapy of Cancer

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Evaluate Cutpoints: Adaptable continuous data distribution system for determining survival in Kaplan-Meier estimator

(2019) Magdalena Ogłuszka et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis

(2019) Angela Horvath et al.   Scientific Reports

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

Association of Immune-Related Adverse Events With Nivolumab Efficacy in Non–Small-Cell Lung Cancer

(2018) Koji Haratani et al.   JAMA Oncology

Baseline neutrophil-to-lymphocyte ratio (NLR) and derived NLR could predict overall survival in patients with advanced melanoma treated with nivolumab

(2018) Mariaelena Capone et al.   Journal for ImmunoTherapy of Cancer

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Microbiota and cancer immunotherapy: in search of microbial signals

(2018) Raad Z Gharaibeh et al.   GUT

Phase Ib/II Study of Pembrolizumab and Pegylated-Interferon Alfa-2b in Advanced Melanoma

(2018) Diwakar Davar et al.   JOURNAL OF CLINICAL ONCOLOGY

Gut microbiota diversity across ethnicities in the United States

(2018) Andrew W. Brooks et al.   PLOS BIOLOGY

Safety Profile of Nivolumab Monotherapy: A Pooled Analysis of Patients With Advanced Melanoma

(2017) Jeffrey S. Weber et al.   JOURNAL OF CLINICAL ONCOLOGY

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

The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy

(2017) Canaan M. Whitfield-Cargile et al.   Scientific Reports

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

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

(2017) Amnon Amir et al.   mSystems

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Unexpected links reflect the noise in networks

(2016) Anatoly Yambartsev et al.   Biology Direct

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

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

(2016) Krista Dubin et al.   Nature Communications

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

(2016) Anastassia Gorvitovskaia et al.   Microbiome

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Nivolumab in Resected and Unresectable Metastatic Melanoma: Characteristics of Immune-Related Adverse Events and Association with Outcomes

(2015) M. Freeman-Keller et al.   CLINICAL CANCER RESEARCH

Cloning, characterization, and production of three α-l-fucosidases fromClostridium perfringensATCC 13124

(2015) Shuquan Fan et al.   JOURNAL OF BASIC MICROBIOLOGY

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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

The role of the microbiota in inflammation, carcinogenesis, and cancer therapy

(2014) Amiran Dzutsev et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing

(2014) Jason M. Knight et al.   Scientific Reports

Distinct functions of polysaccharide deacetylases in cell shape, neutral polysaccharide synthesis and virulence ofBacillus anthracis

(2013) Stavroula Balomenou et al.   MOLECULAR MICROBIOLOGY

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

Management of Immune-Related Adverse Events and Kinetics of Response With Ipilimumab

(2012) Jeffrey S. Weber et al.   JOURNAL OF CLINICAL ONCOLOGY

A framework for human microbiome research

(2012)   NATURE

MR1 presents microbial vitamin B metabolites to MAIT cells

(2012) Lars Kjer-Nielsen et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

(2012) Dirk Gevers et al.   PLOS BIOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Identification and Characterization of a Glycosyltransferase Involved in Acinetobacter baumannii Lipopolysaccharide Core Biosynthesis

(2010) N. R. Luke et al.   INFECTION AND IMMUNITY

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

(2008) E.A. Eisenhauer et al.   EUROPEAN JOURNAL OF CANCER