Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells

Cell Syst. 2016 Nov 23;3(5):480-490.e13. doi: 10.1016/j.cels.2016.11.001.


Many cellular effectors of pluripotency are dynamically regulated. In principle, regulatory mechanisms can be inferred from single-cell observations of effector activity across time. However, rigorous inference techniques suitable for noisy, incomplete, and heterogeneous data are lacking. Here, we introduce stochastic inference on lineage trees (STILT), an algorithm capable of identifying stochastic models that accurately describe the quantitative behavior of cell fate markers observed using time-lapse microscopy data collected from proliferating cell populations. STILT performs exact Bayesian parameter inference and stochastic model selection using a particle-filter-based algorithm. We use STILT to investigate the autoregulation of Nanog, a heterogeneously expressed core pluripotency factor, in mouse embryonic stem cells. STILT rejects the possibility of positive Nanog autoregulation with high confidence; instead, model predictions indicate weak negative feedback. We use STILT for rational experimental design and validate model predictions using novel experimental data. STILT is available for download as an open source framework from

Keywords: Bayesian inference; autoregulation; lineage trees; model selection; mouse embryonic stem cells; nanog; parameter inference; particle filtering; state space inference; stochastic modeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bayes Theorem
  • Cell Differentiation
  • Cell Lineage*
  • Homeodomain Proteins
  • Homeostasis
  • Mice
  • Models, Biological
  • Mouse Embryonic Stem Cells
  • Nanog Homeobox Protein


  • Homeodomain Proteins
  • Nanog Homeobox Protein