Differentiation dynamics from high-dimensional single cell snapshots

1 December 2017

Allon Klein
Department of Systems Biology
Harvard Medical School


I will discuss our efforts to link cell states to cell fates using single cell gene expression measurements and lineage tracing, with bone marrow hematopoiesis and the early embryo as examples. There are several challenges in reconstructing dynamic processes of cell differentiation in these systems, which can be generalized to other contexts. The structure of gene expression space shows non-trivial features in both cases, which do not always correspond to the cartoon-like views differentiation as a branching process. In general, it is not possible to infer the dynamics of single cells from static observations, and thinking about why this should be the case can help to avoid pitfalls in interpreting high-dimensional data. If time permits I will introduce practical tools from spectral graph theory that predict cell fate from cell state under certain assumptions, with some success. I will also challenge the popular notion of "potential landscapes" in cell regulation.

current theory lunch schedule