Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Structure estimation for discrete graphical models: Generalized covariance matrices and their inverses

(2014) Po-Ling Loh et al.   ANNALS OF STATISTICS

Variable selection in regression with compositional covariates

(2014) W. Lin et al.   BIOMETRIKA

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

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

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

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

(2014) Soo Ching Lee et al.   PLoS Neglected Tropical Diseases

High-Dimensional Statistics with a View Toward Applications in Biology

(2014) Peter Bühlmann et al.   Annual Review of Statistics and Its Application

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

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

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Estimating the Number of Species in Microbial Diversity Studies

(2013) John Bunge et al.   Annual Review of Statistics and Its Application

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Role of the intestinal microbiome in health and disease: from correlation to causation

(2012) Willem M de Vos et al.   NUTRITION REVIEWS

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

High-dimensional covariance estimation by minimizing ℓ1-penalized log-determinant divergence

(2011) Pradeep Ravikumar et al.   Electronic Journal of Statistics

High-dimensional Ising model selection using ℓ 1 -regularized logistic regression

(2010) Pradeep Ravikumar et al.   ANNALS OF STATISTICS

Sparsistency and rates of convergence in large covariance matrix estimation

(2009) Clifford Lam et al.   ANNALS OF STATISTICS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community structure of marine bacterioplankton: patterns, networks, and relationships to function

(2008) JA Fuhrman et al.   AQUATIC MICROBIAL ECOLOGY

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology