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

Microbial abundance, activity and population genomic profiling with mOTUs2

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

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The Human Gut Microbiome: From Association to Modulation

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Integrative analysis of exogenous, endogenous, tumour and immune factors for precision medicine

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Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria

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Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

(2018) Zhenwei Dai et al.   Microbiome

Reproducible protocols for metagenomic analysis of human faecal phageomes

(2018) Andrey N. Shkoporov et al.   Microbiome

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer

(2017) Manasi S Shah et al.   GUT

Discovery of novel plasma proteins as biomarkers for the development of incisional hernias after midline incision in patients with colorectal cancer: The ColoCare study

(2017) Jürgen Böhm et al.   SURGERY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome Medicine

MOCAT2: a metagenomic assembly, annotation and profiling framework

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The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study

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Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

(2015) Jun Yu et al.   GUT

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Fecal metabolomics: assay performance and association with colorectal cancer

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Microbes, Microbiota, and Colon Cancer

(2014) Cynthia L. Sears et al.   Cell Host & Microbe

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

The Bacteroides fragilis Toxin Gene Is Prevalent in the Colon Mucosa of Colorectal Cancer Patients

(2014) Annemarie Boleij et al.   CLINICAL INFECTIOUS DISEASES

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

A fair comparison

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Secondary bile acids: an underrecognized cause of colon cancer

(2014) Hana Ajouz et al.   World Journal of Surgical Oncology

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer

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Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment

(2013) Aleksandar D. Kostic et al.   Cell Host & Microbe

Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin

(2013) Mara Roxana Rubinstein et al.   Cell Host & Microbe

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome

(2013) Shin Yoshimoto et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

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Data, information, knowledge and principle: back to metabolism in KEGG

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Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults

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Metabotyping of human colorectal cancer using two-dimensional gas chromatography mass spectrometry

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Efficacy of a Nationwide Screening Colonoscopy Program for Colorectal Cancer

(2012) Christian P. Pox et al.   GASTROENTEROLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

(2012) Harold Tjalsma et al.   NATURE REVIEWS MICROBIOLOGY

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

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pROC: an open-source package for R and S+ to analyze and compare ROC curves

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Red meat consumption and cancer: Reasons to suspect involvement of bovine infectious factors in colorectal cancer

(2011) Harald zur Hausen   INTERNATIONAL JOURNAL OF CANCER

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field

(2010) S. Ogino et al.   GUT

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

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Isolation and characterization of a bile acid inducible 7α-dehydroxylating operon in Clostridium hylemonae TN271

(2009) Jason M. Ridlon et al.   ANAEROBE

Pitfalls of supervised feature selection

(2009) Pawel Smialowski et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry

(2009) A. Hirayama et al.   CANCER RESEARCH

Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR

(2009) Jean-Pierre Furet et al.   FEMS MICROBIOLOGY ECOLOGY

Colon cancer in inflammatory bowel disease: recent trends, questions and answers

(2009) S. Viennot et al.   GASTROENTEROLOGIE CLINIQUE ET BIOLOGIQUE

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

(2009) Shaoguang Wu et al.   NATURE MEDICINE

Metabolite profiling of human colon carcinoma – deregulation of TCA cycle and amino acid turnover

(2008) Carsten Denkert et al.   Molecular Cancer