Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses

Reprograming of gut microbiome energy metabolism by the FUT2 Crohn’s disease risk polymorphism

(2014) Maomeng Tong et al.   ISME Journal

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform

(2014) Erik Dassi et al.   JOURNAL OF BIOTECHNOLOGY

Composition of Archaea in Seawater, Sediment, and Sponges in the Kepulauan Seribu Reef System, Indonesia

(2014) Ana R. M. Polónia et al.   MICROBIAL ECOLOGY

Seasonal Variation in Human Gut Microbiome Composition

(2014) Emily R. Davenport et al.   PLoS One

The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients

(2014) Shoko Iwai et al.   PLoS One

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

(2013) Andrew H Loudon et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic prediction of the maximum per capita rate of population growth

(2013) W. F. Fagan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differences in gut microbiota composition between obese and lean children: a cross-sectional study

(2013) Liene Bervoets et al.   Gut Pathogens

Phylogenetic eigenvector maps: a framework to model and predict species traits

(2013) Guillaume Guénard et al.   Methods in Ecology and Evolution

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Virtual metagenome reconstruction from 16S rRNA gene sequences

(2012) Shujiro Okuda et al.   Nature Communications

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Using phylogenetic information to predict species tolerances to toxic chemicals

(2011) Guillaume Guénard et al.   ECOLOGICAL APPLICATIONS

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

(2011) Daniel McDonald et al.   ISME Journal

Why the Phylogenetic Regression Appears Robust to Tree Misspecification

(2011) Eric A. Stone   SYSTEMATIC BIOLOGY

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH