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UBC Statistics Seminar on Tue, Nov 21: Bayesian latent variable models for understanding (pseudo-) time-series single-cell gene expression data

Tuesday, November 21, 2017 - 11:00 to 12:00
Kieran Campbell, UBC Statistics Post-doctoral Student
Statistics Seminar
Room 4192, Earth Sciences Building (2207 Main Mall)

In the past five years biotechnological innovations have enabled the measurement of transcriptome-wide gene expression in single-cells. However, the destructive nature of the measurement process precludes genuine time-series analysis of e.g. differentiating cells. This has led to the pseudotime estimation (or cell ordering) problem: given static gene expression measurements alone, can we (approximately) infer the developmental progression (or "pseudotime") of each cell? In this talk I will introduce the problem from the typical perspective of manifold learning before re-casting it as a (Bayesian) latent variable problem. I will discuss approaches including nonlinear factor analysis and Gaussian Process Latent Variable Models, before introducing a new class of covariate-adjusted latent variable models that can infer such pseudotimes in the presence of heterogeneous environmental and genetic backgrounds.