ArticleGenome biology2023
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn's disease.Nature genetics · 2026Article
- A tonsil organoid model reveals Epstein-Barr virus-infected germinal center B cell states during primary infection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Systematic clustering alignment and feature characterization for single-cell omics using ACE-OF-Clust.bioRxiv : the preprint server for biology · 2026Article
- Single-Cell Gene Module Inference Reveals Alternative Polyadenylation Dynamics Associated with Autism.International journal of molecular sciences · 2026Article
- Regulatory network architecture constrains inflammatory responses in tissue-resident alveolar macrophages.bioRxiv : the preprint server for biology · 2026Article
- Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts.Cell genomics · 2026Article
- Non-negative matrix factorization algorithms generally improve topic model fits.Statistics and computing · 2026Article
- Transcriptomic insights into the healthspan-enhancing effects of C. chinensis seed and E. ulmoides bark extracts in Caenorhabditis elegans.Biogerontology · 2025Article
- Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids.Genome research · 2025Article
- Imlunestrant a next-generation oral SERD overcomes ESR1 mutant resistance in estrogen receptor-positive breast cancer.JCI insight · 2025Article
- Review
- Covariate-moderated Empirical Bayes Matrix Factorization.Advances in neural information processing systems · 2025Article
- Transcriptome analysis of calcium hydroxide tolerance inFrontiers in microbiology · 2025Article
- Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures.Cell genomics · 2024Article
- A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection.Life science alliance · 2024Article
- Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids.bioRxiv : the preprint server for biology · 2024Article
- Eomes expression identifies the early bone marrow precursor to classical NK cells.Nature immunology · 2024Article
- Dissection and integration of bursty transcriptional dynamics for complex systems.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems.bioRxiv : the preprint server for biology · 2023Article
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7 authors.
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Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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