Research Topics
Genomes and Genes | S E BrennerSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
An unappreciated role for RNA surveillanceR Tyler Hillman
Department of Bioengineering, University of California, Berkeley, CA 94720-3102, USA
Genome Biol 5:R8. 2004..Several genes with mRNA isoforms that we identified as PTC+--calpain-10, the CDC-like kinases (CLKs) and LARD--show how previous experimental results may be understood in light of NMD...- Structural genomics and structural biology: compare and contrastJohn-Marc Chandonia
Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 5:343. 2004 - The ASTRAL compendium for protein structure and sequence analysisS 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/.. - Expectations from structural genomicsS 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... 
Target selection for structural genomicsS 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...- A tour of structural genomicsS 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... - Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrapGavin A Price
Department of Bioengineering, University of California, Berkeley, 94720, USA
Bioinformatics 21:3824-31. 2005..AVAILABILITY: The sequence sets and code for performing these analyses are available from http://compbio.berkeley.edu/. Contact: ... - A generalized affine gap model significantly improves protein sequence alignment accuracyMarcus 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... - The PRESAGE database for structural genomicsS 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/.. - Target selection and deselection at the Berkeley Structural Genomics CenterJohn-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... - The impact of structural genomics: expectations and outcomesJohn-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.... - Measurements of protein sequence-structure correlationsGavin 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... - An alternative model of amino acid replacementGavin 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..The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment... - Alignment-free local structural search by writhe decompositionDegui 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... - Automated multi-model reconstruction from single-particle electron microscopy dataMaxim 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... - A method for the alignment of heterogeneous macromolecules from electron microscopyMaxim 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... - Pairwise alignment incorporating dipeptide covariationGavin 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..Therefore, the standard assumption that individual residues within protein sequences evolve independently of neighboring positions appears to be an efficient and appropriate approximation... - Protein molecular function prediction by Bayesian phylogenomicsBarbara 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... - Biases in Illumina transcriptome sequencing caused by random hexamer primingKasper 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... - ASTRAL compendium enhancementsJohn-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/... - Structural genomics of minimal organisms and protein fold spaceSung 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... - Protein secondary structure: entropy, correlations and predictionGavin 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.... - The ASTRAL Compendium in 2004John-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/... - Computational prediction of membrane-tethered transcription factorsJ 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... - Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexesWasantha 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... - Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approachesJohn-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... - Sulfotransferases and sulfatases in mycobacteriaJoseph 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... - Survey of large protein complexes in D. vulgaris reveals great structural diversityBong 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... - RNA structural motifs: building blocks of a modular biomoleculeDonna K Hendrix
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
Q Rev Biophys 38:221-43. 2005.... - Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAsMarco 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... - WebLogo: a sequence logo generatorGavin 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... - SCOR: Structural Classification of RNA, version 2.0Makio 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... - ANDY: a general, fault-tolerant tool for database searching on computer clustersAndrew Smith
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
Bioinformatics 22:618-20. 2006..berkeley.edu/proj/andy. SUPPLEMENTARY INFORMATION: Supplemental data, figures, and a more detailed overview of the software are found at http://compbio.berkeley.edu/proj/andy... - The evolving roles of alternative splicingLiana 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... - Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elementsLiana 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... - Common sense for our genomesSteven E Brenner
Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720, USA
Nature 449:783-4. 2007 - SCOP database in 2002: refinements accommodate structural genomicsLoredana 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... - The Bioperl toolkit: Perl modules for the life sciencesJason 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... - SCOP database in 2004: refinements integrate structure and sequence family dataAntonina 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... - Data growth and its impact on the SCOP database: new developmentsAntonina 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... - Developing computational biologyPhilip E Bourne
PLoS Comput Biol 3:1669. 2007 - The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein familiesShibu 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... - The RNA Ontology Consortium: an open invitation to the RNA communityNeocles B Leontis
RNA 12:533-41. 2006.... - PLoS Computational Biology: a new community journalPhilip E Bourne
PLoS Comput Biol 1:e4. 2005
Research Grants
- Protein function prediction by statistical phylogenomicsSteven 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. ..
- Protein function prediction by statistical phylogenomicsSteven 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. ..
- Nonsense-mediated mRNA decay induced by alternative splicingSteven Brenner; Fiscal Year: 2007..These studies will also be used to offer insight into the varied mechanisms of PTC-recognition in different species. ..
- Protein function prediction by statistical phylogenomicsSteven 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. ..
- ASTRAL: Foundation for structure and evolution studiesSteven 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. ..
- COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICSSteven 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. ..
- THE PRESAGE DATABASE FOR STRUCTURAL GENOMICSSteven 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. ..
- Protein function prediction by statistical phylogenomicsSteven 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. ..