ArticleNAR genomics and bioinformatics2023
mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- IRDRM: Exploring Biological Traits and Clinical Significance in Breast Cancer Through Gene Pairs and Somatic Mutation Profiles.Interdisciplinary sciences, computational life sciences · 2026Article
- Consensus Copy-Number Alteration Signatures from Clinical Panels Enable Pan-Cancer Risk Stratification and Therapy Response Association.International journal of molecular sciences · 2026Article
- HRD-Informed Digital Histology Model for Predicting Platinum Chemo-Response and Prognosis in High-Grade Serous Ovarian Cancer.Interdisciplinary sciences, computational life sciences · 2026Article
- Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome.bioRxiv : the preprint server for biology · 2026Article
- Tissue-specific mutagenesis from endogenous guanine damage is suppressed by Polκ and DNA repair.Nature communications · 2025Article
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- The long-term effects of chemotherapy on normal blood cells.Nature genetics · 2025Article
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- The complexity of tobacco smoke-induced mutagenesis in head and neck cancer.Nature genetics · 2025Article
- Geographic and age-related variations in mutational processes in colorectal cancer.medRxiv : the preprint server for health sciences · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm.Briefings in bioinformatics · 2024Article
- Article
- Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival.International journal of molecular sciences · 2024Article
- scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data.Cancers · 2023Article
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Authors and funding
5 authors.
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Abstract
Mutational signatures are characteristic patterns of mutations caused by endogenous or exogenous mutational processes. These signatures can be discovered by analyzing mutations in large sets of samples-usually somatic mutations in tumor samples. Most programs for discovering mutational signatures are based on non-negative matrix factorization (NMF). Alternatively, signatures can be discovered using hierarchical Dirichlet process (HDP) mixture models, an approach that has been less explored. These models assign mutations to clusters and view each cluster as being generated from the signature of a particular mutational process. Here, we describe mSigHdp, an improved approach to using HDP mixture models to discover mutational signatures. We benchmarked mSigHdp and state-of-the-art NMF-based approaches on four realistic synthetic data sets. These data sets encompassed 18 cancer types. In total, they contained 3.5 × 10
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