Negative binomial factor regression with application to microbiome data analysis

Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation

(2021) Taylor A. Breuninger et al.   Microbiome

tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data

(2021) Johannes Ostner et al.   Frontiers in Genetics

Zero‐inflated Poisson factor model with application to microbiome read counts

(2020) Tianchen Xu et al.   BIOMETRICS

Modulation of the Gut Microbiota by Olive Oil Phenolic Compounds: Implications for Lipid Metabolism, Immune System, and Obesity

(2020) Marta Farràs et al.   Nutrients

Health and disease markers correlate with gut microbiome composition across thousands of people

(2020) Ohad Manor et al.   Nature Communications

Generalized co-sparse factor regression

(2020) Aditya Mishra et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

High Oleic Acid Peanut Oil and Extra Virgin Olive Oil Supplementation Attenuate Metabolic Syndrome in Rats by Modulating the Gut Microbiota

(2019) Zhihao Zhao et al.   Nutrients

Latent variable modeling for the microbiome

(2018) Kris Sankaran et al.   BIOSTATISTICS

Leveraging mixed and incomplete outcomes via reduced-rank modeling

(2018) Chongliang Luo et al.   JOURNAL OF MULTIVARIATE ANALYSIS

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Majorization-Minimization Algorithms in Signal Processing, Communications, and Machine Learning

(2017) Ying Sun et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

Sequential Co-Sparse Factor Regression

(2017) Aditya Mishra et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

(2017) Vinod K. Gupta et al.   Frontiers in Microbiology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Regularization Methods for High-Dimensional Instrumental Variables Regression With an Application to Genetical Genomics

(2015) Wei Lin et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

Regression Models for Count Data inR

(2015) Achim Zeileis et al.   Journal of Statistical Software

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Joint variable and rank selection for parsimonious estimation of high-dimensional matrices

(2013) Florentina Bunea et al.   ANNALS OF STATISTICS

Poisson factor models with applications to non-normalized microRNA profiling

(2013) Seonjoo Lee et al.   BIOINFORMATICS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine

(2012) Nicole de Wit et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Sparse Reduced-Rank Regression for Simultaneous Dimension Reduction and Variable Selection

(2012) Lisha Chen et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Probiotics, Prebiotics, and Synbiotics: Gut and Beyond

(2012) Usha Vyas et al.   Gastroenterology Research and Practice

Optimal selection of reduced rank estimators of high-dimensional matrices

(2011) Florentina Bunea et al.   ANNALS OF STATISTICS

Reduced rank stochastic regression with a sparse singular value decomposition

(2011) Kun Chen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Football fever: goal distributions and non-Gaussian statistics

(2008) E. Bittner et al.   EUROPEAN PHYSICAL JOURNAL B

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY