A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluating Causality of Gut Microbiota in Obesity and Diabetes in Humans

(2017) Abraham S Meijnikman et al.   ENDOCRINE REVIEWS

Critical review of reporting of the data analysis step in metabolomics

(2017) E. C. Considine et al.   Metabolomics

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

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

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

Leaky gut – concept or clinical entity?

(2016) Eamonn M.M. Quigley   CURRENT OPINION IN GASTROENTEROLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Metabolomics: beyond biomarkers and towards mechanisms

(2016) Caroline H. Johnson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

(2016) Cecilia Noecker et al.   mSystems

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection

(2016) Vijay C. Antharam et al.   PLoS One

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

(2015) Tomas Cajka et al.   ANALYTICAL CHEMISTRY

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders

(2015) John R. Kelly et al.   Frontiers in Cellular Neuroscience

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

(2015) Alejandra Escobar-Zepeda et al.   Frontiers in Genetics

Specialized Metabolites from the Microbiome in Health and Disease

(2014) Gil Sharon et al.   Cell Metabolism

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis

(2012) J. Chen et al.   BIOSTATISTICS

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Data Analysis Tool for Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry

(2011) Sandra Castillo et al.   ANALYTICAL CHEMISTRY

Interactions Between Gut Microbiota and Host Metabolism Predisposing to Obesity and Diabetes

(2010) Giovanni Musso et al.   Annual Review of Medicine

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Weighted Gene Coexpression Network Analysis: State of the Art

(2010) Wei Zhao et al.   Journal of Biopharmaceutical Statistics

Development and Performance of a Gas Chromatography−Time-of-Flight Mass Spectrometry Analysis for Large-Scale Nontargeted Metabolomic Studies of Human Serum

(2009) Paul Begley et al.   ANALYTICAL CHEMISTRY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology