Microbiome analyses of blood and tissues suggest cancer diagnostic approach

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

(2020) Shi Huang et al.   mSystems

Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

(2019) Timothy A. Blauwkamp et al.   Nature Microbiology

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells

(2019) Chengcheng Jin et al.   CELL

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions

(2019) Kuo-Ping Chiu et al.   PeerJ

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease

(2018) David K. Hong et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Association Between Bacteremia From Specific Microbes and Subsequent Diagnosis of Colorectal Cancer

(2018) Thomas N.Y. Kwong et al.   GASTROENTEROLOGY

Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA

(2018) Travis A. Clark et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host

(2018) Marlies Meisel et al.   NATURE

Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria

(2018) Christine M. Dejea et al.   SCIENCE

Gut microbiome–mediated bile acid metabolism regulates liver cancer via NKT cells

(2018) Chi Ma et al.   SCIENCE

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

(2018) Vyara Matson et al.   SCIENCE

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

(2018) Philip Burnham et al.   Nature Communications

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells

(2018) Haobin Ye et al.   CANCER CELL

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Integrated genomic and molecular characterization of cervical cancer

(2017)   NATURE

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

(2017) Leore T. Geller et al.   SCIENCE

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

(2017) V. Gopalakrishnan et al.   SCIENCE

Analysis ofFusobacteriumpersistence and antibiotic response in colorectal cancer

(2017) Susan Bullman et al.   SCIENCE

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

(2017) Bertrand Routy et al.   SCIENCE

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

(2017) Kelly M. Robinson et al.   Microbiome

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis

(2016) Kensuke Yamamura et al.   CLINICAL CANCER RESEARCH

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

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

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

(2014) C. Bettegowda et al.   Science Translational Medicine

Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

(2013) Iwijn De Vlaminck et al.   CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Viral and bacterial aetiologies of epithelial ovarian cancer

(2012) S. Shanmughapriya et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

Molecular Aspects of Microcystin-induced Hepatotoxicity and Hepatocarcinogenesis

(2010) Z. Svirčev et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART C-ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

(2008) Michael J Boedigheimer et al.   BMC GENOMICS