ArticleGenome biology2024
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A distinct CAR-T cell phenotype mediates therapeutic response at limited doses.Nature communications · 2026Trial
- Distinct cell type-specific mechanisms underlie cognitive dysfunction during persistent integrated stress response activation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.Cell reports methods · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- The H3K36me3 methyltransferase SETD2 contributes to PAF1C interactions with RNA Pol II and is required for neuronal differentiation.The EMBO journal · 2026Article
- scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq.bioRxiv : the preprint server for biology · 2026Article
- The automated computational workflow QUICHE reveals structural definitions of antitumor responses in triple-negative breast cancer.Nature cancer · 2026Article
- DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors.bioRxiv : the preprint server for biology · 2026Article
- Differential expression analysis in single cell and spatial RNASeq without model assumptions.bioRxiv : the preprint server for biology · 2025Article
- Mapping CMV-related immune signatures in blood, aorta and perivascular mediastinal adipose tissue.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Deep generative modeling of sample-level heterogeneity in single-cell genomics.Nature methods · 2025Article
- Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.Nature communications · 2025Article
- Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Article
- Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE.Genome biology · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
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