ArticleGenome biology2024
deMULTIplex2: robust sample demultiplexing for scRNA-seq.
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 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Comparing bulk and single-cell methodologies and models to profile gene expression, chromatin accessibility and regulatory links in endothelial cells treated with TNFα.Biochemistry and biophysics reports · 2026Article
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- Single-cell transcriptomics of human brain disorders.Molecular psychiatry · 2026Review
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.Cell genomics · 2026Article
- Post-vaccination expansion of extrafollicular Th10 and regulatory Tfr cells distinguishes strong from weak influenza vaccine responses in older adults.medRxiv : the preprint server for health sciences · 2026Article
- Comparing bulk and single-cell methodologies and models to profile gene expression, chromatin accessibility and regulatory links in endothelial cells treated with TNFα.bioRxiv : the preprint server for biology · 2026Article
- Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.Nature communications · 2026Article
- CMDdemux: an efficient single cell demultiplexing method.Nucleic acids research · 2026Article
- Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis.bioRxiv : the preprint server for biology · 2026Article
- Single cell RNA-sequencing reveals that testosterone reduces estrogen signaling in the healthy human mammary gland.Journal of mammary gland biology and neoplasia · 2026Article
- Early clonal dominance at priming sets the trajectory for broad HIV serum neutralization.bioRxiv : the preprint server for biology · 2026Article
- Article
- T cell engagers control solid tumors through clonal replacement and IL2-driven effector differentiation of CD8 T cells.bioRxiv : the preprint server for biology · 2026Article
- Single cell RNA-sequencing reveals an association between testosterone treatment and reduced hormone signaling in the human mammary gland.bioRxiv : the preprint server for biology · 2026Article
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Electroconvulsive Therapy Induces Dopaminergic Axon Regeneration, Corticostriatal Remodeling, and Restoration of Motor Function in Parkinsonian Mice.bioRxiv : the preprint server for biology · 2025Article
- A unified genetic perturbation language for human cellular programming.bioRxiv : the preprint server for biology · 2025Article
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.bioRxiv : the preprint server for biology · 2025Article
- Probability of stealth multiplets in sample-multiplexing for droplet-based single-cell analysis.BMC genomics · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-specific barcodes with cell-specific barcodes, then demultiplex sample identity post-sequencing. However, existing demultiplexing tools fail under many real-world conditions where barcode cross-contamination is an issue. We therefore developed deMULTIplex2, an algorithm inspired by a mechanistic model of barcode cross-contamination. deMULTIplex2 employs generalized linear models and expectation-maximization to probabilistically determine the sample identity of each cell. Benchmarking reveals superior performance across various experimental conditions, particularly on large or noisy datasets with unbalanced sample compositions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.