S E Brenner

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila
    Kasper Daniel Hansen
    Division of Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA, USA
    PLoS Genet 5:e1000525. 2009
  2. pmc A continuous fluorescence assay for the characterization of Nudix hydrolases
    Anting Xu
    Department of Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
    Anal Biochem 437:178-84. 2013
  3. pmc An unappreciated role for RNA surveillance
    R Tyler Hillman
    Department of Bioengineering, University of California, Berkeley, CA 94720 3102, USA
    Genome Biol 5:R8. 2004
  4. pmc Structural genomics and structural biology: compare and contrast
    John Marc Chandonia
    Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 5:343. 2004
  5. pmc Expectations from structural genomics
    S E Brenner
    Department of Structural Biology, Stanford University, California 94305 5126, USA
    Protein Sci 9:197-200. 2000
  6. ncbi Target selection for structural genomics
    S E Brenner
    Department of Plant and Microbial Biology, University of California, Berkeley 94720 3102, USA
    Nat Struct Biol 7:967-9. 2000
  7. ncbi A tour of structural genomics
    S E Brenner
    Department of Plant and Microbial Biology, University of California, 461A Koshland Hall, Berkeley, California 94720 3102, USA
    Nat Rev Genet 2:801-9. 2001
  8. pmc The ASTRAL compendium for protein structure and sequence analysis
    S E Brenner
    Department of Structural Biology, Stanford University, Fairchild Building D 109, Stanford, CA 94305 5126, USA
    Nucleic Acids Res 28:254-6. 2000
  9. ncbi Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
    Gavin A Price
    Department of Bioengineering, University of California, Berkeley, 94720, USA
    Bioinformatics 21:3824-31. 2005
  10. ncbi A generalized affine gap model significantly improves protein sequence alignment accuracy
    Marcus A Zachariah
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Proteins 58:329-38. 2005

Detail Information

Publications46

  1. pmc Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila
    Kasper Daniel Hansen
    Division of Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA, USA
    PLoS Genet 5:e1000525. 2009
    ..Most notably, we found that the NMD-target mRNAs had significantly longer 3' untranslated regions (UTRs) than the nontarget isoforms of the same genes, supporting a role for 3' UTR length in the recognition of NMD targets in fly...
  2. pmc A continuous fluorescence assay for the characterization of Nudix hydrolases
    Anting Xu
    Department of Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
    Anal Biochem 437:178-84. 2013
    ..Second, MutT also catalyzes the hydrolysis of 5-methyl-dCTP. Third, 8-oxo-dGTP was observed to be the best substrate for DR_1025 of the 41 compounds screened...
  3. pmc An unappreciated role for RNA surveillance
    R Tyler Hillman
    Department of Bioengineering, University of California, Berkeley, CA 94720 3102, USA
    Genome Biol 5:R8. 2004
    ....
  4. pmc Structural genomics and structural biology: compare and contrast
    John Marc Chandonia
    Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 5:343. 2004
  5. pmc Expectations from structural genomics
    S E Brenner
    Department of Structural Biology, Stanford University, California 94305 5126, USA
    Protein Sci 9:197-200. 2000
    ..Among the remaining ones, about half are likely to be evolutionarily related to proteins of known structure, even though the homology could not be readily detected by sequence analysis...
  6. ncbi Target selection for structural genomics
    S E Brenner
    Department of Plant and Microbial Biology, University of California, Berkeley 94720 3102, USA
    Nat Struct Biol 7:967-9. 2000
    ..Selection of the targets is principally a computational process of restricting candidate proteins to those that are tractable and of unknown structure, and prioritizing according to expected interest and accessibility...
  7. ncbi A tour of structural genomics
    S E Brenner
    Department of Plant and Microbial Biology, University of California, 461A Koshland Hall, Berkeley, California 94720 3102, USA
    Nat Rev Genet 2:801-9. 2001
    ..The pervasiveness of this information is likely to change the use of structure in molecular biology and biochemistry...
  8. pmc The ASTRAL compendium for protein structure and sequence analysis
    S E Brenner
    Department of Structural Biology, Stanford University, Fairchild Building D 109, Stanford, CA 94305 5126, USA
    Nucleic Acids Res 28:254-6. 2000
    ..Selected subsets of the domain database, with varying degrees of similarity measured in several different ways, are also available. ASTRALmay be accessed at http://astral.stanford.edu/..
  9. ncbi Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
    Gavin A Price
    Department of Bioengineering, University of California, Berkeley, 94720, USA
    Bioinformatics 21:3824-31. 2005
    ..We have developed, as an alternative, an unbiased statistical evaluation based on the Bayesian bootstrap, a resampling method operationally similar to the standard bootstrap...
  10. ncbi A generalized affine gap model significantly improves protein sequence alignment accuracy
    Marcus A Zachariah
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Proteins 58:329-38. 2005
    ..We conclude that generalized affine gap costs should be used when alignment accuracy carries more importance than aligned sequence length...
  11. pmc The PRESAGE database for structural genomics
    S E Brenner
    Department of Structural Biology, Stanford University, Fairchild Building D 109, Stanford, CA 94305 5126, USA
    Nucleic Acids Res 27:251-3. 1999
    ..The database is intended to enhance communication among structural genomics researchers and aid dissemination of their results. The PRESAGE database may be accessed at http://presage.stanford.edu/..
  12. ncbi Target selection and deselection at the Berkeley Structural Genomics Center
    John Marc Chandonia
    Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Proteins 62:356-70. 2006
    ..Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb...
  13. ncbi The impact of structural genomics: expectations and outcomes
    John Marc Chandonia
    Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 311:347-51. 2006
    ....
  14. pmc A method for the alignment of heterogeneous macromolecules from electron microscopy
    Maxim Shatsky
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    J Struct Biol 166:67-78. 2009
    ..Our method is tested on data from three model structures and one real dataset...
  15. pmc Protein molecular function prediction by Bayesian phylogenomics
    Barbara E Engelhardt
    Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 1:e45. 2005
    ..The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors...
  16. pmc Biases in Illumina transcriptome sequencing caused by random hexamer priming
    Kasper D Hansen
    Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720 7358, USA
    Nucleic Acids Res 38:e131. 2010
    ..We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias...
  17. pmc Alignment-free local structural search by writhe decomposition
    Degui Zhi
    Department of Plant and Microbial Biology, UC Berkeley and Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
    Bioinformatics 26:1176-84. 2010
    ..These methods offer a tremendous increase in speed over residue-level structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities...
  18. pmc Automated multi-model reconstruction from single-particle electron microscopy data
    Maxim Shatsky
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    J Struct Biol 170:98-108. 2010
    ..We propose the use of our approach as an efficient way to reconstruct distinct multiple models from heterogeneous data...
  19. ncbi Pairwise alignment incorporating dipeptide covariation
    Gavin E Crooks
    Department of Plant and Microbial Biology 111 Koshland Hall 3102 University of California, Berkeley, CA 94720 3102, USA
    Bioinformatics 21:3704-10. 2005
    ....
  20. ncbi Structural genomics of minimal organisms and protein fold space
    Sung Hou Kim
    Department of Chemistry, University of California, Berkeley, 94720 5230, USA
    J Struct Funct Genomics 6:63-70. 2005
    ..genitalium. Furthermore, about 1/2 of the structures of 'unique' protein sequences revealed new and novel folds, and over 2/3 of the structures of previously annotated 'hypothetical proteins' inferred their molecular functions...
  21. pmc ASTRAL compendium enhancements
    John Marc Chandonia
    Berkeley Structural Genomics Center, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 30:260-3. 2002
    ..Selected representative subsets of each of these libraries, based on multiple criteria and degrees of similarity, are also included. ASTRAL may be accessed at http://astral.stanford.edu/...
  22. ncbi An alternative model of amino acid replacement
    Gavin E Crooks
    Department of Plant and Microbial Biology 111 Koshland Hall 3102 University of California Berkeley, CA 94720 3102, USA
    Bioinformatics 21:975-80. 2005
    ....
  23. ncbi Measurements of protein sequence-structure correlations
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Proteins 57:804-10. 2004
    ..This suggests that knowledge-based contact potentials may be less important for structure predication than is generally believed...
  24. ncbi Protein secondary structure: entropy, correlations and prediction
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No 3102, Berkeley, CA 94720 3102, USA
    Bioinformatics 20:1603-11. 2004
    ....
  25. pmc The ASTRAL Compendium in 2004
    John Marc Chandonia
    Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 32:D189-92. 2004
    ..Several search tools have been added to ASTRAL to facilitate retrieval of data by individual users and automated methods. ASTRAL may be accessed at http://astral.stanford. edu/...
  26. pmc Computational prediction of membrane-tethered transcription factors
    J Zupicich
    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Genome Biol 2:RESEARCH0050. 2001
    ..To investigate the existence of other transmembrane transcription factors, we analyzed computationally all proteins in SWISS-PROT/TrEMBL for the combined presence of a DNA-binding domain and a transmembrane segment...
  27. pmc Survey of large protein complexes in D. vulgaris reveals great structural diversity
    Bong Gyoon Han
    Life Sciences, Genomics, Earth Sciences, and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:16580-5. 2009
    ..As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest...
  28. ncbi Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches
    John Marc Chandonia
    Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Proteins 58:166-79. 2005
    ..Random selection of targets from one or more genomes is similar to the Pfam5000 strategy in that proteins from larger families are more likely to be chosen, but substantial effort would be spent on small families...
  29. ncbi Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes
    Wasantha Ranatunga
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    J Mol Biol 339:103-16. 2004
    ..The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved...
  30. ncbi Sulfotransferases and sulfatases in mycobacteria
    Joseph D Mougous
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Chem Biol 9:767-76. 2002
    ..As sulfated molecules are common mediators of cell-cell interactions, the sulfotransferases and sulfatases may be involved in regulating host-pathogen interactions...
  31. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
    ..A command line interface and the complete, open WebLogo source code are available for local installation and customization...
  32. ncbi RNA structural motifs: building blocks of a modular biomolecule
    Donna K Hendrix
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    Q Rev Biophys 38:221-43. 2005
    ....
  33. ncbi Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs
    Marco Blanchette
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 14:775-86. 2004
    ..Immunopurification of nuclear RNP complexes showed that dU2AF50 associates with intronless mRNAs. These results reveal an unexpected role for the splicing factor dU2AF50 in the nuclear export of intronless mRNAs...
  34. pmc SCOR: Structural Classification of RNA, version 2.0
    Makio Tamura
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 32:D182-4. 2004
    ..RNA motifs reported in the literature, such as 'Kink turn' and 'GNRA loops', are now incorporated into the structural classification along with definitions and descriptions...
  35. ncbi Common sense for our genomes
    Steven E Brenner
    Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720, USA
    Nature 449:783-4. 2007
  36. ncbi Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
    Liana F Lareau
    Department of Molecular and Cell Biology and, University of California, Berkeley, California 94720, USA
    Nature 446:926-9. 2007
    ..We find that unproductive splicing associated with conserved regions has arisen independently in different SR genes, suggesting that splicing factors may readily acquire this form of regulation...
  37. ncbi The evolving roles of alternative splicing
    Liana F Lareau
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Curr Opin Struct Biol 14:273-82. 2004
    ..Evolutionary conservation of splicing patterns suggests functional importance and provides insight into the evolutionary history of alternative splicing...
  38. ncbi ANDY: a general, fault-tolerant tool for database searching on computer clusters
    Andrew Smith
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Bioinformatics 22:618-20. 2006
    ..Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms...
  39. pmc SCOP database in 2002: refinements accommodate structural genomics
    Loredana Lo Conte
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 30:264-7. 2002
    ..The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  40. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  41. pmc SCOP database in 2004: refinements integrate structure and sequence family data
    Antonina Andreeva
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 32:D226-9. 2004
    ..SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  42. pmc Data growth and its impact on the SCOP database: new developments
    Antonina Andreeva
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
    Nucleic Acids Res 36:D419-25. 2008
    ..SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  43. pmc The RNA Ontology Consortium: an open invitation to the RNA community
    Neocles B Leontis
    RNA 12:533-41. 2006
    ....
  44. pmc PLoS Computational Biology: a new community journal
    Philip E Bourne
    PLoS Comput Biol 1:e4. 2005
  45. pmc Developing computational biology
    Philip E Bourne
    PLoS Comput Biol 3:1669. 2007
  46. pmc The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e16. 2007
    ..Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature...

Research Grants14

  1. THE PRESAGE DATABASE FOR STRUCTURAL GENOMICS
    Steven Brenner; Fiscal Year: 2001
    ..We hope that PRESAGE will thus grow as an international resource for both producers of structural genomics data and for all those biologists who can use these data on genomics and protein structure to aid their research. ..
  2. Protein function prediction by statistical phylogenomics
    Steven E Brenner; Fiscal Year: 2010
    ..Application of SIFTER will also permit detailed understanding of pathogens'and commensal microbiota's proteins. These methods will be a foundation for the further study of any protein identified through genome projects. ..
  3. Protein function prediction by statistical phylogenomics
    Steven Brenner; Fiscal Year: 2009
    ..Application of SIFTER will also permit detailed understanding of pathogens' and commensal microbiota's proteins. These methods will be a foundation for the further study of any protein identified through genome projects. ..
  4. Nonsense-mediated mRNA decay induced by alternative splicing
    Steven Brenner; Fiscal Year: 2007
    ..These studies will also be used to offer insight into the varied mechanisms of PTC-recognition in different species. ..
  5. Protein function prediction by statistical phylogenomics
    Steven Brenner; Fiscal Year: 2007
    ..Application of SIFTER will also permit detailed understanding of pathogens' and commensal microbiota's proteins. These methods will be a foundation for the further study of any protein identified through genome projects. ..
  6. Nonsense-mediated mRNA decay induced by alternative splicing
    Steven Brenner; Fiscal Year: 2007
    ..These studies will also be used to offer insight into the varied mechanisms of PTC-recognition in different species. ..
  7. Nonsense-mediated mRNA decay by alternative splicing
    Steven Brenner; Fiscal Year: 2006
    ..These studies will also be used to offer insight into the varied mechanisms of PTC-recognition in different species. ..
  8. ASTRAL: Foundation for structure and evolution studies
    Steven Brenner; Fiscal Year: 2005
    ..c) Continue to produce new releases of ASTRAL. 2. Extend ASTRAL'S utility to more of the biomedical research community. 3. Develop resources to facilitate extension of ASTRAL by the bioinformatics community. ..
  9. Nonsense-mediated mRNA decay by alternative splicing
    Steven Brenner; Fiscal Year: 2005
    ..These studies will also be used to offer insight into the varied mechanisms of PTC-recognition in different species. ..
  10. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
    Steven Brenner; Fiscal Year: 2003
    ..I also plan to quantitatively combine sequence comparison with expression and other experimental functional data to improve computational molecular and cellular functional characterization. ..
  11. THE PRESAGE DATABASE FOR STRUCTURAL GENOMICS
    Steven Brenner; Fiscal Year: 2002
    ..We hope that PRESAGE will thus grow as an international resource for both producers of structural genomics data and for all those biologists who can use these data on genomics and protein structure to aid their research. ..
  12. Protein function prediction by statistical phylogenomics
    Steven Brenner; Fiscal Year: 2009
    ..Application of SIFTER will also permit detailed understanding of pathogens' and commensal microbiota's proteins. These methods will be a foundation for the further study of any protein identified through genome projects. ..