Steven E. Brenner
461A Koshland Hall 3102, University of California, Berkeley, EU.
brenner@compbio.berkeley.edu
Steven E. Brenner
461A Koshland Hall 3102, University of California, Berkeley, EU.
brenner@compbio.berkeley.edu
Protein sequences and structures are molecular palimpsests, whose detailed study reveals evolutionary histories and modern functions. Our research group develops methods to understand the ancestry of proteins from their sequences, which we use to make predictions of their biological role. We focus on developing new computational methodologies, so as to explicate our mastery of the approaches, to make the tools available to others, and to allow their application on a multi-genomic scale. While we employ the most sophisticated sequence analysis methods, some proteins have diverged so far that their sequences carry no informative signal. For these molecules, we study their three-dimensional structure, which appears to be amongst the most strongly conserved features in all of biology.
The power of sequence and structure analysis is exemplified by the growth of biological information. Today, we have access to 945 times as much sequence data as when I entered college. Molecular structure data is growing at a similar pace: we have as much three-dimensional structure data today as we had protein sequence data in 1995. Thus, while computational protein sequence and structure analysis are relatively mature fields, the landscape of available information upon which they operate has radically altered. At times, the deluge of data is an embarrassment of riches. Our research rapidly filters the data torrent to provide reliable biological insights into protein function.
In addition to developing protein analysis in light of expanding data, our lab explored new fields. We have developed a comprehensive classification of RNA three-dimensional structures. More recently, our lab has recently found that surprisingly many natural human mRNAs have premature termination codons. These transcripts are apparent targets of nonsense-mediated mRNA decay, which would cause them to be degraded rather than translated.
