[Home] Brenner Computational Genomics Research Group
Brenner Group Undergraduate Research Projects
About the group
We develop computational methods for the analysis and integration of molecular sequence and structure. Our aim is to understand organismal biology by interpreting the information encoded in complete genomes. This work is presently focused on the areas of structural and functional genomics. Here are further details about our research interests.
Notes about all projects
Projects are available in several of the group's areas of interest and will be tailored to the abilities and interests of the student apprentice and current membership of the group. Students should expect to spend at least 12 hours per week on the project. The ideal student will have a strong molecular biology background and considerable programming experience. Students with < 3.6 GPA will only be considered in exceptional circumstances.
The flood of data generated by modern sequencing technologies makes functional assignment of proteins a challenging yet essential task. Our SIFTER program (http://sifter.berkeley.edu/) combines evolutionary principles and statistical methods to predict protein functions from sequence more accurately than other programs. Assessment of the accuracy and improvements to the SIFTER algorithm require that critical function predictions be validated in case studies.
This project aims at improving SIFTER's performance by validating its functional assessment experimentally. Specifically, we have chosen as our test bed the Nudix protein family, a large and diverse protein family with critical biological roles in metabolite sanitation. The project involves computational prediction of Nudix protein functions, purification of selected target proteins and characterization of their enzymatic activities. Results will be provided to computation experts in our team to refine SIFTER's prediction.
Depending on his/her interests and skills, the apprentice will participate in one or more of the following: 1) Nudix protein expression, purification and characterization and 2) compiling Nudix experimental evidence and running SIFTER to predict functions of Nudix proteins.
Proteins often fold into compact structural units, called domains. Protein domains are basic units of protein function and evolution. Delineating domain boundaries is a prerequisite for further analyses of protein structures. However, this process is largely a manual process and the accuracy of these computer programs is still not satisfactory. This project will include two parts: critical assessment of current protein domain identification programs, and development of approaches to improve the accuracy by combining existing computer programs. Students interested in AJAX web development are also invited to help improve the web interface for displaying current data on protein domain architectures.
The ideal candidate is willing to learn and knows how to write programs (in any language); knowledge of protein structures is a plus.
Other projects may also be open to suitable students.
How to apply
Applicants should apply through URAP or other undergraduate research programs in order to get credit (and possibly money) for your work.