Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

Advances in Principal Balances for Compositional Data

(2017) J. A. Martín-Fernández et al.   Mathematical Geosciences

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice

(2017) Jaques Belik et al.   Scientific Reports

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

(2017) Julia Fukuyama et al.   PLoS Computational Biology

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

(2017) Alex D. Washburne et al.   PeerJ

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro

(2017) Hasinika K. A. H. Gamage et al.   Scientific Reports

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

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

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

(2016) Gregory B. Gloor et al.   CANADIAN JOURNAL OF MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Oscillatory dynamics in a bacterial cross-protection mutualism

(2016) Eugene Anatoly Yurtsev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model

(2016) Marisol Aguirre et al.   RESEARCH IN MICROBIOLOGY

Metagenomics meets time series analysis: unraveling microbial community dynamics

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

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities

(2015) Sandi Yen et al.   JOURNAL OF PROTEOME RESEARCH

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal and spatial variation of the human microbiota during pregnancy

(2015) Daniel B. DiGiulio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment

(2015) Hannah R. Meredith et al.   PLoS Computational Biology

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

(2015) Jennifer M. Auchtung et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

The dynamic microbiome

(2014) Georg K. Gerber   FEBS LETTERS

Impact of Technical Sources of Variation on the Hand Microbiome Dynamics of Healthcare Workers

(2014) Mariana Rosenthal et al.   PLoS One

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Antivirulence Activity of the Human Gut Metabolome

(2014) L. C. M. Antunes et al.   mBio

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

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

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis

(2013) Fan Xia et al.   BIOMETRICS

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Temporal and spatial oscillations in bacteria

(2011) Peter Lenz et al.   NATURE REVIEWS MICROBIOLOGY

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Advances and perspectives in in vitro human gut fermentation modeling

(2011) Amanda N. Payne et al.   TRENDS IN BIOTECHNOLOGY

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

The prebiotic, oligofructose-enriched inulin modulates the faecal metabolite profile: An in vitro analysis

(2010) Vicky De Preter et al.   MOLECULAR NUTRITION & FOOD RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changes through time: integrating microorganisms into the study of succession

(2010) Noah Fierer et al.   RESEARCH IN MICROBIOLOGY

Non-Euclidean statistics for covariance matrices, with applications to diffusion tensor imaging

(2009) Ian L. Dryden et al.   Annals of Applied Statistics

Generating random correlation matrices based on vines and extended onion method

(2009) Daniel Lewandowski et al.   JOURNAL OF MULTIVARIATE ANALYSIS

Microbial awakenings

(2009) Slava S. Epstein   NATURE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Characterizing mixed microbial population dynamics using time-series analysis

(2008) Pål Trosvik et al.   ISME Journal

Chaos in a long-term experiment with a plankton community

(2008) Elisa Benincà et al.   NATURE