Towards predicting the environmental metabolome from metagenomics with a mechanistic model

Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry

(2016) Juntuo Zhou et al.   ANALYST

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

(2015) Genivaldo Gueiros Z. Silva et al.   BIOINFORMATICS

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

(2015) Daniel R. Garza et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis

(2015) B. Vitali et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype

(2015) Claire A Merrifield et al.   ISME Journal

The human saliva metabolome

(2015) Zerihun T. Dame et al.   Metabolomics

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

Metabolome of human gut microbiome is predictive of host dysbiosis

(2015) Peter E. Larsen et al.   GigaScience

Microbiota of the indoor environment: a meta-analysis

(2015) Rachel I. Adams et al.   Microbiome

Metabolic pathways for the whole community

(2014) Niels W Hanson et al.   BMC GENOMICS

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

(2013) A Marcobal et al.   ISME Journal

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

Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles

(2012) Masahiro Sugimoto et al.   Metabolomics

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

(2012) Harold Tjalsma et al.   NATURE REVIEWS MICROBIOLOGY

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

Advances in metabolite identification

(2011) David S Wishart   Bioanalysis

Development of a Quantitative Metabolomic Approach to Study Clinical Human Fecal Water Metabolome Based on Trimethylsilylation Derivatization and GC/MS Analysis

(2010) Xianfu Gao et al.   ANALYTICAL CHEMISTRY

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY