A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

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

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

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

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks

(2019) Pajau Vangay et al.   GigaScience

Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

(2019) Marc A. Sze et al.   mBio

Do no harm: a roadmap for responsible machine learning for health care

(2019) Jenna Wiens et al.   NATURE MEDICINE

Massive datasets and machine learning for computational biomedicine: trends and challenges

(2018) Anton Kocheturov et al.   ANNALS OF OPERATIONS RESEARCH

Phylogenetic convolutional neural networks in metagenomics

(2018) Diego Fioravanti et al.   BMC BIOINFORMATICS

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

(2018) Zhenwei Dai et al.   Microbiome

Optimized Scoring Systems: Toward Trust in Machine Learning for Healthcare and Criminal Justice

(2018) Cynthia Rudin et al.   INTERFACES

Erratum for Sze and Schloss, “Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors”

(2018) Marc A. Sze et al.   mBio

An Improved Method for Prediction of Cancer Prognosis by Network Learning

(2018) Minseon Kim et al.   Genes

The oral microbiota in colorectal cancer is distinctive and predictive

(2017) Burkhardt Flemer et al.   GUT

Guiding longitudinal sampling in IBD cohorts

(2017) Yoshiki Vázquez-Baeza et al.   GUT

Systematic evaluation of supervised classifiers for fecal microbiota-based prediction of colorectal cancer

(2017) Luoyan Ai et al.   Oncotarget

Classification of Paediatric Inflammatory Bowel Disease using Machine Learning

(2017) E. Mossotto et al.   Scientific Reports

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

(2017) Sarah L. Westcott et al.   mSphere

Shifts in the Fecal Microbiota Associated with Adenomatous Polyps

(2016) Vanessa L. Hale et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Quantitation of faecal Fusobacterium improves faecal immunochemical test in detecting advanced colorectal neoplasia

(2016) Sunny H Wong et al.   GUT

Stool DNA Testing for Screening Detection of Colorectal Neoplasia in Alaska Native People

(2016) Diana G. Redwood et al.   MAYO CLINIC PROCEEDINGS

Persistent microbiome alterations modulate the rate of post-dieting weight regain

(2016) Christoph A. Thaiss et al.   NATURE

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection

(2016) Emmanuel Montassier et al.   Genome Medicine

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

(2016) Nielson T. Baxter et al.   Genome Medicine

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

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

(2016) Nielson T. Baxter et al.   Microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

(2014) J. P. Zackular et al.   Cancer Prevention Research

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

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

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

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

Human-Associated Microbial Signatures: Examining Their Predictive Value

(2011) Dan Knights et al.   Cell Host & Microbe

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Permutation importance: a corrected feature importance measure

(2010) André Altmann et al.   BIOINFORMATICS

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