ArticleGigaScience2019
A field guide for the compositional analysis of any-omics data.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers.
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Who cites it
175 citing papers in PubMed.
- Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.The ISME journal · 2025Trial
- Skin exposure to soil microbiota elicits changes in cell-mediated immunity to pneumococcal vaccine.Scientific reports · 2024Trial
- Calcium-Binding Protein Expression Cannot Serve as a General Classifier for GABAergic Neurons in the Macaque Cortex.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- Article
- Phase I Evaluation of Patients with Newly Diagnosed Glioblastoma Treated with Radiation, Nivolumab, and IDO1 Enzyme Inhibitor BMS-986205.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Proteomic health archetypes identified in disease-free adults enable risk assessment for diverse chronic diseases.Genome medicine · 2026Article
- Egg microbiome of the yellow-spotted Amazon river turtle (Podocnemis unifilis) modulates fusariosis fungal infection and hatching success.Communications biology · 2026Article
- Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.NPJ biofilms and microbiomes · 2026Article
- Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.bioRxiv : the preprint server for biology · 2026Article
- Inferring absolute counts from proportions by constraining multivariate normal distributions.NPJ systems biology and applications · 2026Article
- Chronic exposure to Salton Sea aerosols elicits pulmonary inflammation and shifts in murine lung and fecal microbiome diversity.Research square · 2026Article
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- State-Level Organization of Spontaneous Behavior and Its Association with Plasma Fatty-Acid Profiles in Healthy Rats.Biology · 2026Article
- Integration of Bulk and Single-Cell RNA Sequencing Analyses in Biomedicine.International journal of molecular sciences · 2026Review
- Rise-and-fall dynamics reveal a molecular and cellular vulnerability axis in prion-likebioRxiv : the preprint server for biology · 2026Article
- Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.medRxiv : the preprint server for health sciences · 2026Article
- Tumour-intrinsic features shape T cell differentiation through precursor to symptomatic multiple myeloma.Nature communications · 2026Article
- Scikit-bio: a fundamental Python library for biological omic data analysis.Nature methods · 2026Article
115 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. A cornerstone of NGS is the quantification of RNA or DNA presence as counts. However, these counts are not counts per se: their magnitude is determined arbitrarily by the sequencing depth, not by the input material. Consequently, counts must undergo normalization prior to use. Conventional normalization methods require a set of assumptions: they assume that the majority of features are unchanged and that all environments under study have the same carrying capacity for nucleotide synthesis. These assumptions are often untestable and may not hold when heterogeneous samples are compared.
resultsMethods developed within the field of compositional data analysis offer a general solution that is assumption-free and valid for all data. Herein, we synthesize the extant literature to provide a concise guide on how to apply compositional data analysis to NGS count data.
conclusionsIn highlighting the limitations of total library size, effective library size, and spike-in normalizations, we propose the log-ratio transformation as a general solution to answer the question, "Relative to some important activity of the cell, what is changing?"
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.