Our Projects, informally speaking
Here are some of the Bejerano Lab projects from a computational point of view:
- Many human patients are like a piece of code inflicted with a nasty bug. Most of it is functioning, but somewhere in its bowels lies that mistake that causes disease. We examine the code and output (genome and disease) of real patients at Stanford and elsewhere, to find the root cause of their suffering. This knowledge often leads to more directed and better care for the patient, it brings some relief and an ability to better plan the future to their families, and it helps us to do good in this world, through our keyboards.
- Despite seeing the human genome code in its entirety there are many parts of it we still do not understand. When pieces of code break you get to see what they do. But you can also learn more by comparing the code and output of human to that of different healthy animals. For example, some primates are immune to some of the worst diseases afflicting humanity. How do they do it? What code "modules" allow them to close the trapdoors exploited in our own code?
- Imagine you could solve a patient genome by spending 20 hours with it. Technology now allows a hospital to sequence 100 patient genomes who will benefit from genomic wisdom every week. But how can you spend 2,000 hours a week solving their genomes? This problem is most acute, but not unique to medical genomics. The genome is a wonderful "hypothesis generation machine". The process of hypothesis ranking is in desperate need of automation. We have teamed up with Chris Re's group to build the largest finest repository of genomic knowledge from free text to help us tackle this challenge.
- Like with real code, we can observe genomic assignments and control flow in "run time". Our lab observes the genome of cells that produce a region of our brain called the neocortex. The neocortex is perhaps the coolest brain structure, critical to our deepest thinking. We have been funded as part of the presidential BRAIN initiative, together with experimental colleagues, to examine genome run time in multiple mammals and discover some of the basic design principles that underlie making the neocortex through genomic "programming".
Sounds exciting but you haven't taken much Biology of recent? Neither have we when we first got started. That's why we will know how to get you started