A two-part mixed-effects model for analyzing longitudinal microbiome compositional data

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohnʼs Disease

(2015) Dale Lee et al.   INFLAMMATORY BOWEL DISEASES

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

Long Term Development of Gut Microbiota Composition in Atopic Children: Impact of Probiotics

(2015) N. B. M. M. Rutten et al.   PLoS One

Analyzing the Human Microbiome: A “How To” guide for Physicians

(2014) Andrea D Tyler et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

The dynamic microbiome

(2014) Georg K. Gerber   FEBS LETTERS

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

(2014) Manon D. Schulz et al.   NATURE

Patterned progression of bacterial populations in the premature infant gut

(2014) P. S. La Rosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women

(2014) Roberto Romero et al.   Microbiome

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

(2012) Omry Koren et al.   CELL

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

(2012) Junjie Qin et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

A general class of zero-or-one inflated beta regression models

(2011) Raydonal Ospina et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Characterizing microbial communities through space and time

(2011) Antonio Gonzalez et al.   CURRENT OPINION IN BIOTECHNOLOGY

Application of Two-Part Statistics for Comparison of Sequence Variant Counts

(2011) Brandie D. Wagner et al.   PLoS One

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY