ArticleGenome biology2025
A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Value of Machine Learning Models for Cell-Free DNA-Based Multi-Cancer Early Detection: A Systematic Review and Meta-Analysis.Technology in cancer research & treatmentPooled it
- Circulating Cell-free DNA as a biomarker for radiation-induced injury: From mechanistic insights to clinical translation.Cancer metastasis reviews · 2026Review
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Cell-free DNA size deconvolution resolves nucleosomal origins and reveals tumor-associated fragmentomic alterations.Nature communications · 2026Article
- fRagmentomics: an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation.Bioinformatics (Oxford, England) · 2026Article
- ctDNA monitoring using tumor-informed copy number analysis.EMBO molecular medicine · 2026Article
- DNAvi: integration, statistics, and visualization of cell-free DNA fragment traces.Bioinformatics (Oxford, England) · 2026Article
- From multi-omics to deep learning: advances in cfDNA-based liquid biopsy for multi-cancer screening.Biomarker research · 2025Review
- Early cancer detection via multi-omics cfDNA fragmentation using early-late fusion neural network with sample-modality evaluation.Briefings in bioinformatics · 2025Article
- Fragmentation signatures in cancer patients resemble those of patients with vascular or autoimmune diseases.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.Genome biology · 2025Article
- Article
- FinaleToolkit: accelerating cell-free DNA fragmentation analysis with a high-speed computational toolkit.Bioinformatics advances · 2025Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes and validated in 1182 plasma samples from published studies. Our results clarify the variations from library preparation and feature quantification methods. We design the Trim Align Pipeline and cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualization to standardize multi-modal feature engineering and integration for machine learning.
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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.