Research Opportunity: Bioengineering with the Yeast Gene Regulatory Network 2.0

Con­tact Name: Samuel Danziger

Con­tact Email: sam.danziger[at]

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.

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