Computational challenges of single cell profiling

Readings due before class on Tuesday, September 8, 2020

Required

• [Macosko et al (2015) Cell] (https://www.cell.com/fulltext/S0092-8674%2915%2900549-8)(Please watch video and try to undestand up to Figures 1, 2, and S2. You don’t need to read the whole paper.)

• Candida albicans single cell project (my lab)

Recommended Reading

• Laehnemann et al. (2020) Elevn grand challenges in single-cell data science. Genome Biology (Try to understand the intuition of each of the 11 challenges.)

• Trapnell (2018) Defining cell types and states with single-cell genomes. Genome Research

Action items

• Assignment #4

• Project

• Start to prepare for final

Points of Reflection

• How can Simpson’s paradoxes be resolved with single cell sequencing?

• What are the reasons that isogenic cells vary from individual to individual? in mammalian tissue? in bacteria or fungal populations?

• In your area of interest, how could single cell technologies and analytics assist in our understanding of important biologies?