Learning representations of microbe–metabolite interactions

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

(2019) Himel Mallick et al.   Nature Communications

Latent variable modeling for the microbiome

(2018) Kris Sankaran et al.   BIOSTATISTICS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

(2018) Tami L. Swenson et al.   Nature Communications

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

Niche partitioning of a pathogenic microbiome driven by chemical gradients

(2018) Robert A. Quinn et al.   Science Advances

Rhamnolipids from Pseudomonas aeruginosa disperse the biofilms of sulfate-reducing bacteria

(2018) Thammajun L. Wood et al.   npj Biofilms and Microbiomes

Commensal Propionibacterium strain UF1 mitigates intestinal inflammation via Th17 cell regulation

(2017) Natacha Colliou et al.   JOURNAL OF CLINICAL INVESTIGATION

Advances in Principal Balances for Compositional Data

(2017) J. A. Martín-Fernández et al.   Mathematical Geosciences

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

(2017) Shabnam Shalapour et al.   NATURE

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Dimension reduction techniques for the integrative analysis of multi-omics data

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

Immunomodulation properties of multi-species fermented milks

(2016) Benoît Foligné et al.   FOOD MICROBIOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Klebsiella pneumoniae: Going on the Offense with a Strong Defense

(2016) Michelle K. Paczosa et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

A multi-omic future for microbiome studies

(2016) Janet K. Jansson et al.   Nature Microbiology

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

(2016) Cecilia Noecker et al.   mSystems

Combining selected immunomodulatoryPropionibacterium freudenreichiiandLactobacillus delbrueckiistrains: Reverse engineering development of an anti-inflammatory cheese

(2015) Coline Plé et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Exometabolite niche partitioning among sympatric soil bacteria

(2015) Richard Baran et al.   Nature Communications

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

(2014) Robert A Quinn et al.   ISME Journal

PLS-DA for compositional data with application to metabolomics

(2014) Alžběta Kalivodová et al.   JOURNAL OF CHEMOMETRICS

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

(2012) W. J. Moree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Metabolomics of Fecal Extracts Detects Altered Metabolic Activity of Gut Microbiota in Ulcerative Colitis and Irritable Bowel Syndrome

(2011) Gwénaëlle Le Gall et al.   JOURNAL OF PROTEOME RESEARCH

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Matrix Factorization Techniques for Recommender Systems

(2009) Yehuda Koren et al.   COMPUTER