Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Data Sharing

(2016) Dan L. Longo et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fizzy: feature subset selection for metagenomics

(2015) Gregory Ditzler et al.   BMC BIOINFORMATICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota

(2015) Fei Teng et al.   Cell Host & Microbe

Decompensated cirrhosis and microbiome interpretation

(2015) Jasmohan S. Bajaj et al.   NATURE

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

(2015) Kristoffer Forslund et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Cross-study validation for the assessment of prediction algorithms

(2014) Christoph Bernau et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer

(2014) Levi Waldron et al.   JNCI-Journal of the National Cancer Institute

Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples

(2014) Markus Riester et al.   JNCI-Journal of the National Cancer Institute

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

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

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

(2014) Mariel M. Finucane et al.   PLoS One

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

The Human Microbiome: From Symbiosis to Pathogenesis

(2013) Emiley A. Eloe-Fadrosh et al.   Annual Review of Medicine

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

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

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

(2012) Dirk Gevers et al.   PLOS BIOLOGY

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology