Steven E. Brenner

Affiliated Faculty, Bioengineering and MCB Associate Professor, Plant & Microbial Biology Core Member, UCB/UCSF Graduate Group in Bioengineering 461A Koshland Hall mailcode: MC 3102 (510) 643-9131 fax: (510) 666-2505 This e-mail address is being protected from spambots. You need JavaScript enabled to view it http://compbio.berkeley.edu Membership effective July 2000

Research Interests

The Brenner research lab has four key research interests involving computational and experimental genomics: Gene regulation by alternative splicing and nonsense-mediated mRNA decay, Prediction of protein function using Bayesian phylogenomics, Medical and environmental metagenomics, and Structural genomics and proteins complexes.

Research Summary

The Brenner research lab has four key research interests involving computational and experimental genomics.

Gene regulation by alternative splicing and nonsense-mediated mRNA decay
Nonsense-mediated mRNA decay (NMD) is a cellular RNA surveillance system that recognizes transcripts with premature termination codons and degrades them.  Several years ago, we discovered large numbers of natural alternative splice forms that appear to be targets for NMD, and we speculated that this might be a mode of gene regulation which we termed rust (regulated unproductive splicing and translation).

Prediction of protein function using Bayesian phylogenomics
In collaboration with Michael Jordan’s group, we have developed a statistical approach to predicting protein function that uses a protein family’s phylogenetic tree, as the natural structure for representing protein relationships.

Medical and environmental metagenomics
For example, the Sorcerer II global ocean sampling project, acid mine drainage, and the role of gut microbiota in Crohn’s disease.

Structural genomics and proteins complexes
We are involved in maintaining the scop: Structural Classification of Proteins and astral databases which are key resources for accessing and understanding protein structure data.  We therefore analyze structural genomics efforts and guide their future directons.

Selected Publications

Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of human SR genes associated with ultraconserved DNA elements. Nature in press.

Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1:432-445.

Yooseph S et al. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biology in press.

Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-351.