Microbiome-based disease prediction with multimodal variational information bottlenecks

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

(2021) Isabel Moreno-Indias et al.   Frontiers in Microbiology

PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data

(2020) Derek Reiman et al.   IEEE Journal of Biomedical and Health Informatics

A Comprehensive Survey on Transfer Learning

(2020) Fuzhen Zhuang et al.   PROCEEDINGS OF THE IEEE

Modulating the microbiome to improve therapeutic response in cancer

(2019) Jennifer L McQuade et al.   LANCET ONCOLOGY

The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract

(2019) Luisa De Sordi et al.   Cell Host & Microbe

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

Multitable Methods for Microbiome Data Integration

(2019) Kris Sankaran et al.   Frontiers in Genetics

Gut microbiome diversity is associated with sleep physiology in humans

(2019) Robert P. Smith et al.   PLoS One

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

(2018) Ehsaneddin Asgari et al.   BIOINFORMATICS

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

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

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

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

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

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

The Human Microbiome: From Symbiosis to Pathogenesis

(2013) Emiley A. Eloe-Fadrosh et al.   Annual Review of Medicine

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

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

(2013) Fredrik H. Karlsson et al.   NATURE

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING