ArticleBioinformatics (Oxford, England)2024
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 3 citations in OpenAlex.
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- Non-negative matrix factorization and deconvolution as a dual simplex problem.Genome biology · 2026Article
- iDDN: determining trans-omics network structure and rewiring with integrative differential dependency networks.Bioinformatics advances · 2025Article
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12 authors at 8 institutions in 3 countries.
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Abstract
motivationComplex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments.
resultsWe previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable. AVAILABILITY AND IMPLEMENTATION: The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.
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