Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model

Robust and automatic definition of microbiome states

(2019) Beatriz García-Jiménez et al.   PeerJ

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes

(2019) Angela C. Poole et al.   Cell Host & Microbe

Unsupervised learning of mixture regression models for longitudinal data

(2018) Peirong Xu et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Association of microbiome and plasma cytokine dynamics to nivolumab response in metastatic renal cell carcinoma (mRCC).

(2018) Manuel C. Maia et al.   JOURNAL OF CLINICAL ONCOLOGY

Analyzing differences between microbiome communities using mixture distributions

(2018) Konstantin Shestopaloff et al.   STATISTICS IN MEDICINE

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

(2017) Erin M. Hill-Burns et al.   MOVEMENT DISORDERS

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

(2016) Meital Gury-BenAri et al.   CELL

The salivary microbiome for differentiating individuals: proof of principle

(2016) Sarah L. Leake et al.   MICROBES AND INFECTION

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Colonic bacterial composition in Parkinson's disease

(2015) Ali Keshavarzian et al.   MOVEMENT DISORDERS

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics

(2015) Bo-Young Hong et al.   PLoS One

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data

(2015) Lizhen Xu et al.   PLoS One

WB-index: A sum-of-squares based index for cluster validity

(2014) Qinpei Zhao et al.   DATA & KNOWLEDGE ENGINEERING

Unsupervised clustering and feature weighting based on Generalized Dirichlet mixture modeling

(2014) Mohamed Maher Ben Ismail et al.   INFORMATION SCIENCES

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

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

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

Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis

(2013) Jun Chen et al.   Annals of Applied Statistics

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Comparison of Self-Collected and Physician-Collected Vaginal Swabs for Microbiome Analysis

(2010) L. J. Forney et al.   JOURNAL OF CLINICAL MICROBIOLOGY