ArticleScience (New York, N.Y.)2020
Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Article in Science (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 433 papers.
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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
433 citing papers in PubMed.
- Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion.Nature communications · 2024Trial
- Deciphering bone marrow engraftment after allogeneic stem cell transplantation in humans using single-cell analyses.The Journal of clinical investigation · 2024Trial
- Monocytes in pneumonia: Functional plasticity and innate memory (Review).International journal of molecular medicine · 2026Review
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Canonical Notch2 signaling regulates development and maintenance of iron-recycling macrophages and iron homeostasis.Nature communications · 2026Article
- Apoptosis inhibition reprograms alveolar myofibroblasts toward ductal myofibroblasts.Cell reports · 2026Article
- FlowMap: Geometry-Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories.bioRxiv : the preprint server for biology · 2026Article
- Article
- Cell-level random splits leak group-owned answers in single-cell benchmarks.bioRxiv : the preprint server for biology · 2026Article
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- Learning stochastic dynamics and cell-fate landscapes from single-cell snapshots via optimal transport.Science advances · 2026Article
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- The development of single-cell lineage tracing technology and its application in immunotherapy.Molecular therapy. Advances · 2026Review
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- Tumor-intrinsic IFNγ signaling and niche adaptation drive early colonization in ovarian cancer metastasis.Nature communications · 2026Article
- CFM-GP: unified conditional flow matching to learn gene perturbation across cell types.NAR genomics and bioinformatics · 2026Article
- Understanding development and cellular plasticity in the pancreas in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics.Advanced genetics (Hoboken, N.J.) · 2026Article
- Developmental and MAPK-responsive transcription factors regulate distinct malignant cell states and associated genetic dependencies in pancreatic cancer.Nature genetics · 2026Article
- PROFET predicts continuous gene expression dynamics from scRNA-seq data to elucidate heterogeneity of cancer treatment responses.Cell systems · 2026Article
373 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
A challenge in biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Here, we used expressed DNA barcodes to clonally trace transcriptomes over time and applied this to study fate determination in hematopoiesis. We identified states of primed fate potential and located them on a continuous transcriptional landscape. We identified two routes of monocyte differentiation that leave an imprint on mature cells. Analysis of sister cells also revealed cells to have intrinsic fate biases not detectable by single-cell RNA sequencing. Finally, we benchmarked computational methods of dynamic inference from single-cell snapshots, showing that fate choice occurs earlier than is detected by state-of the-art algorithms and that cells progress steadily through pseudotime with precise and consistent dynamics.
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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.