Differential abundance analysis for microbial marker-gene surveys

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Bacterial identification and analytic challenges in clinical microbiome studies

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A framework for human microbiome research

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

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Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

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ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

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DNACLUST: accurate and efficient clustering of phylogenetic marker genes

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Metagenomic biomarker discovery and explanation

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Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

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Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

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QIIME allows analysis of high-throughput community sequencing data

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Vaginal microbiome of reproductive-age women

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Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

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Comparisons of Subgingival Microbial Profiles of Refractory Periodontitis, Severe Periodontitis, and Periodontal Health Using the Human Oral Microbe Identification Microarray

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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

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Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

A core gut microbiome in obese and lean twins

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