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Steven E. Brenner

Associate Professor, Department of Plant and Microbial Biology, University of California, Berkeley

 Faculty Scientist, Physical Biosciences, Lawrence Berkeley National Laboratory
Affiliated Associate Professor, Department of Molecular & Cell Biology
Affiliated Associate Professor, Department of Bioengineering
Member, Biophysics Graduate Group
Member, UCSF/UCB Bioengineering Graduate Group
Member, Comparative Biochemistry Graduate Group

A.B. 1992. Harvard University
M.Phil. 1994. University of Cambridge
Ph.D. 1997. University of Cambridge and MRC Laboratory of Molecular Biology
Visitor. 1997. Japan National Institute of Bioscience
Sloan/DOE Postdoctoral Fellow. 1999. Stanford University

2001 Searle Scholar
1998-2001 & 2002-2006 Director, International Society for Computational Biology
2001-2006 Founding Director, Open Bioinformatics Foundation, and Founding Coordinator, The Bioperl Project
2003 Sloan Research Fellow
2007-2008 Miller Professor
2008 AAAS Fellow
Research Interests

Selected Publications  (full list)

Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. 2009. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genetics. in press.
Brenner SE. 2007. Common sense for our genomes. Nature 449:783-784. doi:10.1038/449783a [PDF .2M]
Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446:926-929. doi:10.1038/nature05676 [PDF 1.3M] [supplementary information .9M]
Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE. 2007. The coupling of alternative splicing and nonsense mediated mRNA decay. in Blencowe B & Graveley B, eds. Alternative splicing in the postgenomic era. Landes Biosciences. 191-212. http://www.eurekah.com/chapter/3531 [PDF 2.4M]
Yooseph S, ... (13 authors) ..., Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, ... (6 authors) ..., Brenner SE, ... (6 authors) ..., Venter JC. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biology 5:e16. doi:10.1371/journal.pbio.0050016 [PDF 3M] [Cover PDF 19M]
Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-351. doi:10.1126/science.1121018 [PDF .2M] [supporting material 1.2M]
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Computational Biology 1:e45. doi:10.1371/journal.pcbi.0010045 [PDF 1.4M] [Cover PDF 5M] [Cover image 4M]
Crooks GE, Wolfe J, Brenner SE. 2004. Measurements of protein sequence-structure correlations. Proteins: Structure, Function, and Bioinformatics 57:804-810. doi:10.1002/prot.20262 [PDF .18M]
Lareau LF, Green RE, Bhatnagar RS, Brenner SE. 2004. The evolving roles of alternative splicing. Current Opinion in Structural Biology 14:273-282. doi:10.1016/j.sbi.2004.05.002 [PDF .18M]
Hillman RT, Green RE, Brenner SE. 2004. An unappreciated role for RNA surveillance. Genome Biology 5:R8.1-R8.16 doi:10.1186/gb-2004-5-2-r8 [PDF .36M]
Lewis BP, Green RE, Brenner SE. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proceedings of the National Academy of Sciences of the United States of America 100:189-192. doi:10.1073/pnas.0136770100 [PDF .25M]
Green RE, Brenner SE. 2002. Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proceedings of the IEEE 9:1834-47. doi:10.1109/JPROC.2002.805303 [PDF 1.6M]
Brenner SE. 1999. Errors in genome annotation. Trends in Genetics 15:132-133. [PDF .16M]
Brenner SE, Hubbard T, Murzin A, Chothia C. 1995. Gene duplications in the H. influenzae genome. Nature 378:140. [OCR PDF 1.43M]
Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247:536-540. [PDF 3.4M]


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