ArticleGenome biology2024
Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq.
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.
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- Condition-Associated Pattern Extraction and Recovery From Multi-Condition Single-Cell RNA-seq Data With CAPER.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dynamic uterine microenvironment drives endometrial adenocarcinoma carcinogenesis and progression.Communications biology · 2026Article
- STEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference.National science review · 2026Article
- Shape-constrained, changepoint additive models for time series omics data with cpam.Nucleic acids research · 2026Article
- FOXF2 regulates pericyte-endothelial signaling required for vascular homeostasis after neonatal hyperoxic lung injury.Nature communications · 2026Article
- Transcriptome analysis ofMicrobiology spectrum · 2026Article
- Deep Learning-Based Identification of Pathogenicity Genes inPlants (Basel, Switzerland) · 2026Article
- PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime.Bioinformatics (Oxford, England) · 2025Article
- AI-Driven Quality Monitoring and Control in Stem Cell Cultures: A Comprehensive Review.Biotechnology journal · 2025Review
- Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Computational modeling of single-cell dynamics data.Briefings in bioinformatics · 2025Review
- The tumor microenvironment across four dimensions: assessing space and time in cancer biology.Frontiers in immunology · 2025Review
- Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis.Discover oncology · 2024Article
- Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq.Genome biology · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses hierarchical structure linear additive mixed models to model the correlated cells within an individual. As a result, TDEseq demonstrates powerful performance in identifying four potential temporal expression patterns within a specific cell type. Extensive simulation studies and the analysis of four published scRNA-seq datasets show that TDEseq can produce well-calibrated p-values and up to 20% power gain over the existing methods for detecting temporal gene expression patterns.
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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 Socratic graph.