ArticleCell systems2018
Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
128 citing papers in PubMed, 1 synthesis or guideline pooled it, 209 citations in OpenAlex.
- What are the applications of single-cell RNA sequencing in cancer research: a systematic review.Journal of experimental & clinical cancer research : CR · 2021Pooled it
- Dietary vitamin A restricts intestinal tuft cell differentiation.Cell reports · 2026Article
- Developmental factors drive the compartmentalized and discontinuous maturation of the small intestinal epithelium during the early postnatal period.PLoS biology · 2026Article
- Single-nucleus RNA-seq and ATAC-seq analyses provide molecular insights into cadmium-stress response in alfalfa roots.Horticulture research · 2026Article
- Gastrointestinal tuft cells: Recent insights and next questions.Science immunology · 2026Review
- Pathobiont-triggered induction of goblet cell response drives regional susceptibility to inflammatory bowel disease.The Journal of clinical investigation · 2026Article
- The differentiation and function of heterogeneous thymic dendritic cell subsets require signals provided by distinct thymocyte cell types.Nature immunology · 2026Article
- Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.Health science reports · 2026Article
- PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.Nature methods · 2025Article
- SmartImpute is a targeted imputation framework for single-cell transcriptome data.Cell reports methods · 2025Article
- Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients.Nature communications · 2025Article
- Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell.Cell stem cell · 2025Article
- Application of metal stable isotopes labeling and elemental mass spectrometry for biomacromolecule profiling.Biophysics reports · 2025Article
- Loss of mucin 2 and MHC II molecules causes rare resistance to murine RV infection.Journal of virology · 2025Article
- The role of the tuft cell-interleukin-25 axis in the pathogenesis of inflammatory bowel disease.Frontiers in immunology · 2025Review
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Deep crypt secretory cells shape region-specific mucin glycosylation patterns in the mouse colon.PloS one · 2025Article
- InTraSeq: A Multimodal Assay that Uncovers New Single-Cell Biology and Regulatory Mechanisms.Research square · 2024Article
- Tuft cells in the intestine, immunity and beyond.Nature reviews. Gastroenterology & hepatology · 2024Review
- Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM).Communications biology · 2024Article
68 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Modern single-cell technologies allow multiplexed sampling of cellular states within a tissue. However, computational tools that can infer developmental cell-state transitions reproducibly from such single-cell data are lacking. Here, we introduce p-Creode, an unsupervised algorithm that produces multi-branching graphs from single-cell data, compares graphs with differing topologies, and infers a statistically robust hierarchy of cell-state transitions that define developmental trajectories. We have applied p-Creode to mass cytometry, multiplex immunofluorescence, and single-cell RNA-seq data. As a test case, we validate cell-state-transition trajectories predicted by p-Creode for intestinal tuft cells, a rare, chemosensory cell type. We clarify that tuft cells are specified outside of the Atoh1-dependent secretory lineage in the small intestine. However, p-Creode also predicts, and we confirm, that tuft cells arise from an alternative, Atoh1-driven developmental program in the colon. These studies introduce p-Creode as a reliable method for analyzing large datasets that depict branching transition trajectories.
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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.