标题
Multivariable association discovery in population-scale meta-omics studies
作者
关键词
Metadata, Microbiome, Simulation and modeling, Metagenomics, Measurement, Antibiotics, Statistical models, Taxonomy
出版物
PLoS Computational Biology
Volume 17, Issue 11, Pages e1009442
出版商
Public Library of Science (PLoS)
发表日期
2021-11-17
DOI
10.1371/journal.pcbi.1009442
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Statistical approaches for differential expression analysis in metatranscriptomics
- (2021) Yancong Zhang et al. BIOINFORMATICS
- A statistical model for describing and simulating microbial community profiles
- (2021) Siyuan Ma et al. PLoS Computational Biology
- Sequence count data are poorly fit by the negative binomial distribution
- (2020) Stijn Hawinkel et al. PLoS One
- CAMISIM: simulating metagenomes and microbial communities
- (2019) Adrian Fritz et al. Microbiome
- The Integrative Human Microbiome Project
- (2019) NATURE
- Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
- (2019) Jason Lloyd-Price et al. NATURE
- A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
- (2019) Courtney R. Armour et al. mSystems
- Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
- (2018) Melanie Schirmer et al. Nature Microbiology
- Species-level functional profiling of metagenomes and metatranscriptomes
- (2018) Eric A. Franzosa et al. NATURE METHODS
- Methods for normalizing microbiome data: an ecological perspective
- (2018) Donald T. McKnight et al. Methods in Ecology and Evolution
- Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes
- (2017) Viktor Jonsson et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Strains, functions and dynamics in the expanded Human Microbiome Project
- (2017) Jason Lloyd-Price et al. NATURE
- The MetaCyc database of metabolic pathways and enzymes
- (2017) Ron Caspi et al. NUCLEIC ACIDS RESEARCH
- Analysis of Microbiome Data in the Presence of Excess Zeros
- (2017) Abhishek Kaul et al. Frontiers in Microbiology
- 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
- Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice
- (2017) Thomas Sharpton et al. mSystems
- Mediation Analysis: A Practitioner's Guide
- (2016) Tyler J. VanderWeele Annual Review of Public Health
- A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
- (2016) Eric Z. Chen et al. BIOINFORMATICS
- Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
- (2016) Viktor Jonsson et al. BMC GENOMICS
- The Human Intestinal Microbiome in Health and Disease
- (2016) Susan V. Lynch et al. NEW ENGLAND JOURNAL OF MEDICINE
- Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
- (2016) Jonathan Thorsen et al. Microbiome
- The gut microbiome in health and in disease
- (2015) Andrew B. Shreiner et al. CURRENT OPINION IN GASTROENTEROLOGY
- Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data
- (2015) Xiaoling Peng et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Fitting Linear Mixed-Effects Models Usinglme4
- (2015) Douglas Bates et al. Journal of Statistical Software
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- Sequencing and beyond: integrating molecular 'omics' for microbial community profiling
- (2015) Eric A. Franzosa et al. NATURE REVIEWS MICROBIOLOGY
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease
- (2015) Xochitl C Morgan et al. GENOME BIOLOGY
- Regression Models for Count Data inR
- (2015) Achim Zeileis et al. Journal of Statistical Software
- Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
- (2014) Paul J. McMurdie et al. PLoS Computational Biology
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
- (2014) Charity W Law et al. GENOME BIOLOGY
- Differential abundance analysis for microbial marker-gene surveys
- (2013) Joseph N Paulson et al. NATURE METHODS
- phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
- (2013) Paul J. McMurdie et al. PLoS One
- Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
- (2012) Xochitl C Morgan et al. GENOME BIOLOGY
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started