Reconstruction of complex single-cell trajectories using CellRouter
Author(s)Lummertz da Rocha, Edroaldo; Rowe, R. Grant; Lundin, Vanessa; Malleshaiah, Mohan; Jha, Deepak Kumar; Rambo, Carlos R.; Li, Hu; North, Trista E.; Collins, James J.; Daley, George Q.; ... Show more Show less
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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.
DepartmentMassachusetts Institute of Technology. Institute for Medical Engineering & Science; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Synthetic Biology Center
Nature Publishing Group
Lummertz da Rocha, Edroaldo, et al. “Reconstruction of Complex Single-Cell Trajectories Using CellRouter.” Nature Communications 9, 1 (March 2018): 892 © 2018 The Author(s)
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