‘TIME’: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data

Dissection of the module network implementation “LemonTree”: enhancements towards applications in metagenomics and translation in autoimmune maladies

(2017) Youtao Lu et al.   Molecular BioSystems

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer

(2017) Simon J. S. Cameron et al.   PLoS One

Reconstruction of Complex Directional Networks with Group Lasso Nonlinear Conditional Granger Causality

(2017) Guanxue Yang et al.   Scientific Reports

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Web-igloo: a web based platform for multivariate data visualization

(2016) Bhusan K. Kuntal et al.   BIOINFORMATICS

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

Metagenomics meets time series analysis: unraveling microbial community dynamics

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

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

(2015) Hiromi Kato et al.   DNA RESEARCH

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes

(2014) Annick V. Hartstra et al.   DIABETES CARE

Gut Microbiomes of Indian Children of Varying Nutritional Status

(2014) Tarini Shankar Ghosh et al.   PLoS One

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Visualizing time-related data in biology, a review

(2013) Maria Secrier et al.   BRIEFINGS IN BIOINFORMATICS

Community-Analyzer: A platform for visualizing and comparing microbial community structure across microbiomes

(2013) Bhusan K. Kuntal et al.   GENOMICS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Causality and Persistence in Ecological Systems: A Nonparametric Spectral Granger Causality Approach

(2012) Matteo Detto et al.   AMERICAN NATURALIST

Lake microbial communities are resilient after a whole-ecosystem disturbance

(2012) Ashley Shade et al.   ISME Journal

METAGENassist: a comprehensive web server for comparative metagenomics

(2012) D. Arndt et al.   NUCLEIC ACIDS RESEARCH

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

(2011) Rachel J Parsons et al.   ISME Journal

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GATE: software for the analysis and visualization of high-dimensional time series expression data

(2009) Ben D. MacArthur et al.   BIOINFORMATICS