the bioinformatics chat

An αβ T-cell receptor is composed of two highly variable protein chains, the α chain and the β chain. However, based only on bulk DNA or RNA sequencing it is impossible to determine which of the α chain and β chain sequences were paired in the same receptor.

In this episode, Kristina Grigaityte talks about her analysis of 200,000 paired αβ sequences, which have been obtained by targeted single-cell RNA sequencing. Kristina used the power law distribution to model the T-cell clone sizes, which led her to reject the commonly held assumptions about the independence of the α and β chains. We also talk about Bayesian inference of power law distributions and about mixtures of power laws.

Links:

• Single-cell sequencing reveals αβ chain pairing shapes the T cell repertoire. Kristina Grigaityte, Jason A. Carter, Stephen J. Goldfless, Eric W. Jeffery, Ronald J. Hause, Yue Jiang, David Koppstein, Adrian W. Briggs, George M. Church, Francois Vigneault, Gurinder S. Atwal
• Bayesian inference of power law distributions. Kristina Grigaityte, Gurinder Atwal
• Mathematics in modern immunology. Castro M, Lythe G, Molina-París C, Ribeiro RM.
• Power laws, Pareto distributions and Zipf’s law. M. E. J. Newman
• So You Think You Have a Power Law — Well Isn’t That Special?

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