ArticleNature communications2020
FastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Toward next-generation therapeutic HPV vaccines: A review on expanding the antigen repertoire and an integrated bioinformatics selection framework.Human vaccines & immunotherapeutics · 2026Review
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.Cell reports methods · 2026Article
- MyClone: rapid and precise reconstruction of clonal population structures for tumors.BMC bioinformatics · 2025Article
- Personalizing DNA Cancer Vaccines.Journal of personalized medicine · 2025Review
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.Nature biotechnology · 2025Article
- From Images to Genes: Radiogenomics Based on Artificial Intelligence to Achieve Non-Invasive Precision Medicine in Cancer Patients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
- Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens.Journal of biomedical science · 2024Review
- Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing.Bioinformatics (Oxford, England) · 2024Article
- Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma.Acta neuropathologica communications · 2024Article
- NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population.Bioinformatics (Oxford, England) · 2024Article
- Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Computational immunogenomic approaches to predict response to cancer immunotherapies.Nature reviews. Clinical oncology · 2024Review
- Bioinformatic Analyses and Integrated Machine Learning to Predict prognosis and therapeutic response Based on E3 Ligase-Related Genes in colon cancer.Journal of Cancer · 2024Article
- Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction.Nucleic acids research · 2023Article
- Quantitative characterization of cell physiological state based on dynamical cell mechanics for drug efficacy indication.Journal of pharmaceutical analysis · 2023Article
- Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data.Frontiers in bioinformatics · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Dissecting tumor heterogeneity is a key to understanding the complex mechanisms underlying drug resistance in cancers. The rich literature of pioneering studies on tumor heterogeneity analysis spurred a recent community-wide benchmark study that compares diverse modeling algorithms. Here we present FastClone, a top-performing algorithm in accuracy in this benchmark. FastClone improves over existing methods by allowing the deconvolution of subclones that have independent copy number variation events within the same chromosome regions. We characterize the behavior of FastClone in identifying subclones using stage III colon cancer primary tumor samples as well as simulated data. It achieves approximately 100-fold acceleration in computation for both simulated and patient data. The efficacy of FastClone will allow its application to large-scale data and clinical data, and facilitate personalized medicine in cancers.
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