A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

(2014) Ali May et al.   BIOINFORMATICS

Variable selection in regression with compositional covariates

(2014) W. Lin et al.   BIOMETRIKA

Machine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics

(2014) Daniel Beck et al.   PLoS One

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

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

Stability

(2013) Bin Yu   BERNOULLI

Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data

(2013) Tanya P. Garcia et al.   BIOINFORMATICS

A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis

(2013) Fan Xia et al.   BIOMETRICS

Genetic susceptibility toCandidainfections

(2013) Sanne P. Smeekens et al.   EMBO Molecular Medicine

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping

(2013) Daniela M. Witten et al.   TECHNOMETRICS

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

A review of Candida species causing blood stream infection

(2012) AJ Kindo et al.   Indian Journal of Medical Microbiology

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tackling the Microbiome

(2012) L. Hood   SCIENCE

Optimized application of penalized regression methods to diverse genomic data

(2011) Levi Waldron et al.   BIOINFORMATICS

Epidemiology, clinical characteristics, and outcome of candidemia: experience in a tertiary referral center in the UK

(2011) I. Das et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Diagnosis of invasive candidiasis in the ICU

(2011) Philippe Eggimann et al.   Annals of Intensive Care

Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem

(2010) James G. Scott et al.   ANNALS OF STATISTICS

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Statistical challenges of high-dimensional data

(2009) I. M. Johnstone et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Mixtures ofgPriors for Bayesian Variable Selection

(2008) Feng Liang et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION