Trajectory Algorithms to Infer Stem Cell Fate Decisions

  • Edroaldo Lummertz da Rocha
  • Mohan Malleshaiah
Part of the Methods in Molecular Biology book series (MIMB, volume 1975)


Single-cell trajectory analysis is an active research area in single-cell genomics aiming at developing sophisticated algorithms to reconstruct complex cell-state transition trajectories. Here, we present a step-by-step protocol to use CellRouter, a multifaceted single-cell analysis platform that integrates subpopulation identification, gene regulatory networks, and trajectory inference to precisely and flexibly reconstruct complex single-cell trajectories. Subpopulations are either user-defined or identified by a graph-clustering approach in which a k-nearest neighbor graph (kNN) is created from cell-to-cell distances in a low-dimensional embedding. Edges in this graph are weighted by network similarity metrics (e.g., Jaccard index) to robustly encode phenotypic relatedness, creating a representation of single-cell transcriptomes suitable for community detection algorithms to identify clusters of densely connected cells. This subpopulation structure represents a map of putative cell-state transitions. CellRouter implements a flow network algorithm to explore this map and reconstruct cell-state transitions in complex single-cell, multidimensional omics datasets. We describe a step-by-step application of CellRouter to hematopoietic stem and progenitor cell differentiation toward four major lineages—erythrocytes, megakaryocytes, monocytes, and granulocytes—to demonstrate key components of CellRouter for single-cell trajectory analysis.

Key words

Single-cell genomics Stem cell differentiation Trajectory reconstruction Cell fate transitions Hematopoietic stem cells Single-cell analysis Computational biology Systems biology 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Edroaldo Lummertz da Rocha
    • 1
    • 2
    • 3
    • 4
  • Mohan Malleshaiah
    • 5
  1. 1.Stem Cell Transplantation Program, Division of Pediatric Hematology and OncologyBoston Children’s Hospital and Dana-Farber Cancer InstituteBostonUSA
  2. 2.Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUSA
  3. 3.Harvard Stem Cell InstituteCambridgeUSA
  4. 4.Manton Center for Orphan Disease ResearchBostonUSA
  5. 5.Division of Systems BiologyMontreal Clinical Research InstituteMontrealCanada

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