ArticleNature communications2024
Trajectory inference across multiple conditions with condiments.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- SupeRJump: Determining normal and leukemic differentiation fate through semi-supervised jump diffusion modeling.bioRxiv : the preprint server for biology · 2026Article
- Autoinhibitory feedback preserves intestinal stem cell maintenance and fate commitment.The EMBO journal · 2026Article
- Local and circulating cytotoxic CD4medRxiv : the preprint server for health sciences · 2026Article
- Flow-Induced Yap/Taz Signaling Balances Endothelial and Hematopoietic Stem Cell Fates.bioRxiv : the preprint server for biology · 2026Article
- Kinemomics: spatiotemporal morphodynamic mapping of ventricular kinematic subpopulations in organotypic fetal heart slices.bioRxiv : the preprint server for biology · 2026Article
- SARS-CoV-2 infection reduces the number of spermatogonial stem cells and dysregulates the transcriptional landscape of the human testis.Research square · 2026Article
- Chronic Alcohol Consumption Reprograms Osteoclast Lineage Communications to Promote Osteoclastogenesis.Biology · 2026Article
- Maternal Obesity Reprograms Differentiation Trajectories of Fetal Hematopoietic Stem and Progenitor Cells Through Altered Inflammatory Signaling.bioRxiv : the preprint server for biology · 2026Article
- Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions.bioRxiv : the preprint server for biology · 2025Article
- Imbalance of stem-like and effector T cell states in children with early type 1 diabetes across conventional and regulatory subsets.Nature communications · 2025Article
- Comprehensive tumor-immune profiling reveals mediators of paradoxical immune sensitivity in sarcomatoid renal cell carcinoma.Cancer cell · 2025Article
- Human fetal kidney organoids model early human nephrogenesis and Notch-driven cell fate.The EMBO journal · 2025Article
- Joint representation and visualization of derailed cell states with Decipher.Genome biology · 2025Article
- Sequential transcriptional programs underpin activation of hippocampal stem cells.Science advances · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Multi-omics-based mapping of decidualization resistance in patients with a history of severe preeclampsia.Nature medicine · 2025Article
- Short-term heavy drinking in a non-human primate model skews monocytes toward a hypo-inflammatory phenotype.Frontiers in immunology · 2025Article
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Authors and funding
4 authors.
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Abstract
In single-cell RNA sequencing (scRNA-Seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolution. In such dynamic biological systems, cellular states form a continuum, e.g., for the differentiation of stem cells into mature cell types. This process is often represented via a trajectory in a reduced-dimensional representation of the scRNA-Seq dataset. While many methods have been suggested for trajectory inference, it is often unclear how to handle multiple biological groups or conditions, e.g., inferring and comparing the differentiation trajectories of wild-type and knock-out stem cell populations. In this manuscript, we present condiments, a method for the inference and downstream interpretation of cell trajectories across multiple conditions. Our framework allows the interpretation of differences between conditions at the trajectory, cell population, and gene expression levels. We start by integrating datasets from multiple conditions into a single trajectory. By comparing the cell's conditions along the trajectory's path, we can detect large-scale changes, indicative of differential progression or fate selection. We also demonstrate how to detect subtler changes by finding genes that exhibit different behaviors between these conditions along a differentiation path.
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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.