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Open AccessJournal ArticleDOI

Differential abundance analysis for microbial marker-gene surveys

Joseph N. Paulson, +3 more
- 01 Dec 2013 - 
- Vol. 10, Iss: 12, pp 1200-1202
TLDR
It is shown that metagenomeSeq outperforms the tools currently used in this field and relies on a novel normalization technique and a statistical model that accounts for undersampling in large-scale marker-gene studies.
Abstract: 
We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.

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Citations
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Journal ArticleDOI

Kinetic Foundation of the Zero-Inflated Negative Binomial Model for Single-Cell RNA Sequencing Data

Chen Jia
- 28 May 2020 - 
TL;DR: Single-cell RNA sequencing data have complex features such as dropout events, overdispersion, and high-magnitude outliers, resulting in complicated probability distributions of mRNA abundances that...
Journal ArticleDOI

Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders.

Nikolas Dovrolis, +3 more
- 21 May 2019 - 
TL;DR: This review of current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications presents bioinformatics tools used in exploring these synergies.
Journal ArticleDOI

Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops

Sarah M. Allard, +8 more
- 20 May 2019 - 
TL;DR: Insight is provided into the impact of irrigation water on fresh produce microbiota, revealing that, although irrigation did influence crop-associated microbiota in the field, bacterial pathogens were not likely transferred to the crop.
Journal ArticleDOI

Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States

Erin A. Tripp, +6 more
- 01 Aug 2016 - 
TL;DR: The findings of a reverse latitudinal gradient and a relative lack of impact of urbanization on lichen propagules and/or lichen-forming fungal spores suggest that core concepts in biogeography are better informed via consideration of additional patterns from other, less well studied groups of organisms.
Journal ArticleDOI

Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in bipolar disorder with current major depressive episode patients

Wen-tao Lai, +18 more
- 01 Jan 2021 - 
TL;DR: The present findings enable a better understanding of changes in gastrointestinal microbiome and MiTBamp in BPD and Alterations of microbes may have potential as biomarkers for distinguishing the BPD patients form HCs.
References
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Journal ArticleDOI

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

Mark D. Robinson, +2 more
- 01 Jan 2010 - 
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI

QIIME allows analysis of high-throughput community sequencing data.

J. Gregory Caporaso, +27 more
- 11 Apr 2010 - 
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Qiong Wang, +3 more
- 15 Aug 2007 - 
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Journal ArticleDOI

Differential expression analysis for sequence count data.

Simon Anders, +1 more
- 27 Oct 2010 - 
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI

Metagenomic biomarker discovery and explanation

Nicola Segata, +7 more
- 24 Jun 2011 - 
TL;DR: A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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