ArticleGenome biology2016
A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes.Cell reports methods · 2022Article
- LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis.BMC bioinformatics · 2022Article
- A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation.Genetics · 2017Article
- TET Methylcytosine Oxidases in T Cell and B Cell Development and Function.Frontiers in immunology · 2017Review
- LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
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Registered trials
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