Contact Name: Samuel Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
We have a developed a predictive environment and gene regulatory influence network (EGRIN) for S. Cerevisiae. This network uses publicly available and in-house gene expression data from microarrays to predict genetic regulation and cellular responses. We intend to expand it to a stochastically robust EGRIN 2.0 that we will use to engineer yeast to produce economically relevant compounds in peroxisomes.
10-week Project #1: Write a framework for generating multiple EGRINs so that the EGRIN 2.0 can be generated with additional processor time. This project would involving using the gene biclustering program cMonkey in [R] or python and interacting with a Sun Grid Engine cluster. There would be plenty of opportunity to improve the cMonkey algorithm.
Familiarity with the [R] statistical programming language or Python.
Familiarity with Unix shell scripting and cluster computing using the Sun Grid Engine (SGE) or similar system.