ArticleNature communications2024
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Circulating Cell-free DNA as a biomarker for radiation-induced injury: From mechanistic insights to clinical translation.Cancer metastasis reviews · 2026Review
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.Genome biology · 2026Article
- Naturally-occurring DNA fragment termini correlate with methylation at CpG sites in hair and blood plasma cell-free DNA.BMC genomics · 2026Article
- Integrated inference of cancer gene expression from cell-free plasma chromatin.bioRxiv : the preprint server for biology · 2026Article
- Improved circulating tumor DNA profiling by simultaneous extraction of DNA methylation and copy number information from methylated DNA sequencing data.NPJ precision oncology · 2025Article
- Article
- Promises and pitfalls of multi-cancer early detection using liquid biopsy tests.Nature reviews. Clinical oncology · 2025Review
- Liquid biopsy in gynecological cancers: a translational framework from molecular insights to precision oncology and clinical practice.Journal of experimental & clinical cancer research : CR · 2025Review
- Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection.Nature reviews. Cancer · 2025Review
- Noninvasive Multicancer Detection Using DNA Hypomethylation of LINE-1 Retrotransposons.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.Genome research · 2025Review
- Cell-free nucleic acid fragmentomics: A non-invasive window into cellular epigenomes.Translational oncology · 2024Review
- Precise control of transmembrane current via regulating bionic lipid membrane composition.Science advances · 2024Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.Nature communications · 2024Article
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17 authors.
Funding
Abstract
Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.
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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.