ArticleNature communications2018
Reconstruction of complex single-cell trajectories using CellRouter.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- Maturation and persistence of CAR T cells derived from human pluripotent stem cells via chemical inhibition of G9a/GLP.Cell stem cell · 2025Article
- PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods.Computational and structural biotechnology journal · 2025Article
- Transiently increased coordination in gene regulation during cell phenotypic transitions.PRX life · 2024Article
- Single-cell RNA-sequencing analysis of immune and mesenchymal cell crosstalk in the developing enthesis.Scientific reports · 2024Article
- Molecular cascade reveals sequential milestones underlying hippocampal neural stem cell development into an adult state.Cell reports · 2024Article
- Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas.BMC cancer · 2024Article
- Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON.Nature communications · 2023Article
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- Deep learning models will shape the future of stem cell research.Stem cell reports · 2023Review
- Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils.Frontiers in genetics · 2023Article
- Alignment of single-cell trajectory trees with CAPITAL.Nature communications · 2022Article
- Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.Nucleic acids research · 2022Article
- Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care.Biomolecules · 2022Review
- EZH1 repression generates mature iPSC-derived CAR T cells with enhanced antitumor activity.Cell stem cell · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
A better understanding of the cell-fate transitions that occur in complex cellular ecosystems in normal development and disease could inform cell engineering efforts and lead to improved therapies. However, a major challenge is to simultaneously identify new cell states, and their transitions, to elucidate the gene expression dynamics governing cell-type diversification. Here, we present CellRouter, a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data. We demonstrate its versatility by applying CellRouter to single-cell RNA sequencing data sets to reconstruct cell-state transition trajectories during hematopoietic stem and progenitor cell (HSPC) differentiation to the erythroid, myeloid and lymphoid lineages, as well as during re-specification of cell identity by cellular reprogramming of monocytes and B-cells to HSPCs. CellRouter opens previously undescribed paths for in-depth characterization of complex cellular ecosystems and establishment of enhanced cell engineering approaches.
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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.