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Stem Cell Systems Biology

We use theoretical approaches to gain insight into cellular mechanisms in vivo. Our main interests focus on development and regeneration, driven by diverse types of stem cells. These systems nevertheless share essential characteristics, such as the ability to specify and maintain cell fates in uncertain environments. Models reveal insight into cell dynamics and the mechanisms underpinning them. Recent papers.


We design new algorithms to analyze single-cell and multi-omic datasets. We build models of cellular signaling dynamics and cell fate decision-making. We develop methods for Bayesian parameter inference of multiscale models with heterogeneous data. Read more.

There is a lot we don't know about how cells work. Especially important are the cells that have not yet decided what type of cells they will be. Cells decide what to do using whispers they get from the inside and from the outside. The problem is that, just like in the child's game, these whispers can change as they pass between cells. So cells must decide what to do without knowing everything about what's out there. Even worse: many different whispers are sent out by different cells at the same time. To make sense of all of this, we need to come up with simple ideas about what a cell does for a given set of whispers, and try out many many many different sets of whispers on the cells, to see what they do. We use thinking-boxes to do all these try-outs: many more than we could do on real living things. This gives us smaller sets of ideas -- good ideas -- that we can go and try out on living things, and eventually, find out more about how cells work.

What is this?   |   Inspiration   |   #upgoerfive