Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2008. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research 36:D419-D425. doi:10.1093/nar/gkm993 [PDF .33M]

^*Brenner SE. 2007. Common sense for our genomes. Nature 449:783-784. doi:10.1038/449783a [PDF .2M]

Bourne PE, Brenner SE. 2007. Developing computational biology. PLoS Computational Biology 3:e157. doi:10.1371/journal.pcbi.0030157 [PDF .05M]

^*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]

^*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]

^*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]

Engelhardt BE, Jordan MI, Brenner SE. 2006. A statistical graphical model for predicting protein molecular function. Proceedings of the 23rd International Conference on Machine Learning 038.1-038.8. doi:10.1145/1143844.1143882 [PDF .29M]

Leontis NB, Altman R, Berman HM, Brenner SE, Brown J, Engelke D, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson J, Williamson JR, Westhof E. 2006. The RNA Ontology Consortium: an open invitation to the RNA community. RNA 12:533-541. doi:10.1261/rna.2343206 [PDF .62M]

Smith A, Chandonia JM, Brenner SE. 2006. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics 22:618-620. doi:10.1093/bioinformatics/btk020 [PDF .1M] [supporting material .3M]

^*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]

Soergel DAW, Lareau LF, Brenner SE. 2006. Regulation of gene expression by the coupling of alternative splicing and nonsense-mediated mRNA decay. in Maquat L, ed., Nonsense-mediated mRNA decay. Landes Bioscience. 175-196. [PDF .27M]

Stefan LR, Zhang R, Levitan AG, Hendrix DK, Brenner SE, Holbrook SR. 2006. MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Research 34:D131-D134. doi:10.1093/nar/gkj058 [PDF .2M]

Hendrix DK, Brenner SE, Holbrook SR. 2005. RNA structural motifs: building blocks of a modular biomolecule. Quarterly Reviews of Biophysics 38:221-243. doi:10.1017/S0033583506004215 [PDF .56M]

Chandonia JM, Kim SH, Brenner SE. 2005. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins: Structure, Function, and Bioinformatics 62:356-370. doi:10.1002/prot.20674 [PDF .2M]

Price GA, Crooks GE, Green RE, Brenner SE. 2005. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics 21:3824-3831. doi:10.1093/bioinformatics/bti627 [PDF .59M] [supplementary figures 18.7 M]

Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim SJ, Das D, Shulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R. 2005. Structural genomics of minimal organisms and protein fold space. Journal of Structural and Functional Genomics 6:63-70. doi:10.1007/s10969-005-2651-9 [PDF .46M]

^*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, Green RE, Brenner SE. 2005. Pairwise alignment incorporating dipeptide covariation. Bioinformatics 21:3704-3710. doi:10.1093/bioinformatics/bti616 [PDF .4M]

Chandonia JM, Brenner SE. 2005. Update on the Pfam5000 strategy for selection of structural genomics targets. Proceedings of the 27^th IEEE EMBS Conference 751-755. [PDF .2M]

Carninci P, ... (12 authors) ..., Brenner SE, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563. doi:10.1126/science.1112014 [PDF .42M]

Bourne PE, Brenner SE, Eisen MB. 2005. PLoS Computational Biology: a new community journal. PLoS Computational Biology 1:e4. doi:10.1371/journal.pcbi.0010004 [PDF .45M]

Brenner SE, Tramontano A. 2005. Sequences and topology: a decade of genomes. Current Opinion in Structural Biology 15:245-247. doi:10.1016/j.sbi.2005.05.00 [PDF .06M]

Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. 2005. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes & Development 19:1306-1314. doi:10.1101/gad.1314205 [PDF .43M]

Crooks GE, Brenner SE. 2005. An alternative model of amino acid replacement. Bioinformatics 21:975-980. doi:10.1093/bioinformatics/bti109 [PDF .4M]

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE. 2005. A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins: Structure, Function, and Bioinformatics 58:329-338. doi:10.1002/prot.20299 [PDF .8M]

^*Chandonia JM, Brenner SE. 2005. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins: Structure, Function, and Bioinformatics 58:166-179. doi:10.1002/prot.20298 [PDF .64M]

^*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]

Chandonia JM, Earnest TN, Brenner SE. 2004. Structural genomics and structural biology: compare and contrast. Genome Biology 5:343. doi:10.1186/gb-2004-5-9-343 [PDF .06M]

Scott, EC, ...(40 authors) ..., Brenner SE, et al. 2004. The morphology of Steve. Annals of Improbable Research 10:24-29. [PDF .48M]

Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. 2004. Genome-wide analysis reveals a novel function for the Drosophila splicing factor U2AF⁵⁰ in the nuclear export of intronless mRNAs.Molecular Cell 14:775-776. doi:10.1016/j.molcel.2004.06.012 [PDF .66M]

Crooks GE, Brenner SE. 2004. Protein secondary structure: entropy, correlations, and prediction. Bioinformatics 20:1603-1611. doi:10.1093/bioinformatics/bth132 [PDF .16M]

^*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]

Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Research 14:1188-1190. doi:10.1101/gr.849004 [PDF .12M]

Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu WL, Bessman MJ, Brenner SE, Holbrook SR. 2004. Structural studies of the nudix hydrolase DR1025 from Deinococcus radiodurans and ligand complexes. Journal of Molecular Biology 339:103-116. doi:10.1016/j.jmb.2004.01.065 [PDF 2.3M]

Klosterman PS, Hendrix D, Tamura M, Holbrook SR, Brenner SE. 2004. Three-dimensional motifs from the SCOR, structuralclassification of RNA database: extruded strands, base triples, tetraloops, and U-turns. Nucleic Acids Research 8:2342-2352. doi:10.1093/nar/gkh537 [PDF .36M]

^*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]

Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2004. The ASTRAL compendium in 2004. Nucleic Acids Research 32:D182-D184. doi:10.1093/nar/gkh034 [PDF .12M]

Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2004. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 32:D226-D229. doi:10.1093/nar/gkh039 [PDF .05M]

Tamura M, Hendrix DK, Klosterman PS, Schimmelman NRB, Brenner SE, Holbrook SR. 2004. SCOR: structural classification of RNA, version 2.0. Nucleic Acids Research 32:D182-D184. doi:10.1093/nar/gkh080 [PDF .07M]

Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE. 2003. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19:i118-i121. doi:10.1093/bioinformatics/btg1015 [PDF .3M] [ISMB2003 Conference Abstract]

^*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]

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al.2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Research 12:1611-8. doi:10.1101/gr.361602 [PDF .28M]

Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. 2002. Sulfotransferases and sulfatases in mycobacteria. Chemistry & Biology 9:767-76. doi:10.1016/S1074-5521(02)00175-8 [PDF .6M]

^*Klosterman PS, Tamura M, Holbrook SR, Brenner SE. 2002. SCOR: a structural classification of RNA database. Nucleic Acids Research 30:392-394. [PDF .1M]

Chandonia J-M, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2002. ASTRAL compendium enhancements. Nucleic Acids Research 30:260-263. [PDF .38M]

Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2002. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research 30:264-267. [PDF .08M]

^*Zupicich J, Brenner SE, Skarnes WC. 2001. Computational prediction of membrane-tethered transcriptions factors. Genome Biology 2:research0050.1-0050.6. [PDF 2.2M]

^*Brenner SE. 2001. A tour of structural genomics. Nature Reviews Genetics 2:801-9. [PDF 2.3M]

Brenner SE. 2000. Target selection for structural genomics. Nature Structural Biology, Structural Genomics supplement. 7:967-969. [PDF .17M]

Yona G, Brenner SE. 2000. Sequence database searching. in Taylor WR, Higgins D, eds. Bioinformatics: A Practical Approach. Oxford University Press. 167-190.

Brenner SE, Levitt M. 2000. Expectations from structural genomics. Protein Science. 9:197-200. [PDF .26M]

Brenner SE, Koehl P, Levitt M. 2000. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research 28:254-256. [PDF .1M]

Lo Conte L, Ailey B, Hubbard TJP, Brenner SE, Murzin AG, Chothia C. 2000. SCOP: a structural classification of proteins database. Nucleic Acids Research 28:257-259. [PDF .07M]

^*Brenner SE. 1999. Errors in genome annotation. Trends in Genetics 15:132-133. [PDF .16M]

Brenner SE, Barken D, Levitt M. 1999. The PRESAGE database for structural genomics. Nucleic Acids Research. 27:251-253. [PDF .03M]

Hubbard TJP, Ailey B, Brenner SE, Murzin AG, Chothia C. 1999. SCOP, a structural classification of proteins database. Nucleic Acids Research 27:254-256. [PDF .04M]

Wolf YI, Brenner SE, Bash PA, Koonin EV. 1999. Distribution of protein folds in the three superkingdoms of life. Genome Research 9:17-26. [PDF 3.2M]

Brenner SE. 1998. Practical database searching. The Trends Guide to Bioinformatics. 9-12. (I am a guest editor of this supplement to the Elsevier Trends journals.) [PDF .09M]

Hubbard TJP, Ailey B, Brenner SE, Murzin AG, Chothia C. 1998. SCOP, structural classification of proteins database: applications to the evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallographica D54:1147-1154. [PDF .47M]

Galperin MY, Brenner SE. 1998. Using metabolic pathway databases for functional annotation. Trends in Genetics 14:332-333. [PDF .13M]

^*Brenner SE, Chothia C, Hubbard TJP. 1998. Assessing sequence comparison methods with reliable structurally-identified distant evolutionary relationships. Proceedings of the National Academy of Sciences of the United States of America 95:6073-6078. [PDF .3M]

^*Brenner SE, Chothia C, Hubbard TJP. 1997. Population statistics of protein structures. Current Opinion in Structural Biology 7:369-376. [PDF .2M]

Chothia C, Hubbard TJP, Brenner SE, Barns H, Murzin A. 1997. Protein folds in the all-a and all-b classes. Annual Reviews of Biophysics and Biomolecular Structure 26:597-627. [PDF 1.3M]

Hubbard TJP, Murzin AG, Brenner SE, Chothia C. 1997. SCOP: a structural classification of proteins database. Nucleic Acids Research 25:236-239. [PDF .16M]

^*Brenner SE, Aoki E. 1996. Introduction to CGI/Perl. New York: M&T Books, Henry Holt & Co. ISBN 1-55851-478-3. (Ranked in top 0.1% at Amazon.com as of 9/98; ~25,000 copies printed.)

Brenner SE, Chothia C, Hubbard TJP, Murzin AG. 1996. Understanding protein structure: Using SCOP for fold interpretation. Chap. 37 in: Doolittle RF, ed. Computer Methods for Macromolecular Sequence Analysis. Methods in Enzymology. Vol. 266. Orlando, FL: Academic Press. 635-643. [Scanned PDF 3.4M] [OCR PDF .19M]

^*Brenner SE, Hubbard T, Murzin A, Chothia C. 1995. Gene duplications in the H. influenzae genome. Nature 378:140. [Scanned PDF 9.7M] [OCR PDF 1.43M]

Suzuki M, Brenner SE. 1995. Classification of multi-helical DNA-binding domains and application to predict the DBD structures of s factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC. FEBS Letters 372:215-221. [PDF 4.14M]

Brenner SE. 1995. BLAST, Blitz, BLOCKS and BEAUTY: Sequence comparison on the Net. Trends in Genetics 11:330-331. [PDF 1.51M]

Brenner SE. 1995. World wide web and molecular biology. Science 268:622-623. [PDF .18M]

Brenner SE, Hubbard TJP. 1995. A specification for defining and annotating regions of macromolecular structure. In Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S, eds. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. Menlo Park, California: AAAI Press. pp. 66-74. [PDF 5.9M] [OCR PDF .76M]

Suzuki M, Brenner SE, Gerstein M, Yagi N. 1995. DNA recognition code of transcription factors. Protein Engineering 8:319-328. [Scanned PDF 6.7M] [OCR PDF 5M]

Brenner SE. 1995. Network sequence retrieval. Trends in Genetics 11:247-248. [PDF 1.42M]

^*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]

Berry A, Brenner SE. 1994. A prototype computer system for de novo protein design. Biochemical Society Transactions 22:1033-1036. [Scanned PDF 2.3M]

Brenner SE. 1994. Methods and algorithms for the design of proteins. In: Schulze-Kremer S, ed. Advances in Molecular Bioinformatics. Amsterdam, Holland: IOS Press. pp. 31-52. [PDF 9.75] [OCR PDF 6.28]

Brenner SE, Berry A. 1994. Protein design by optimization of a sequence-structure quality function. In: Altman R, Brutlag D, Karp P, Lathrop R, Searls D, eds. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. Menlo Park, California: AAAI Press. pp. 44-52. [PDF 6.54]

Brenner SE, Berry A. 1994. A quantitative methodology for the de novo design of proteins. Protein Science 3:1871-1882. [PDF 1.7M]

Brenner SE, Baack A, Pike G, eds. 1991. Computers at Harvard. 4th Ed. Cambridge, MA: Harvard Computer Society. 158 pages.

Aoki E, Brenner SE, eds. 1990. Computers at Harvard. 3rd Ed. Cambridge, MA: Harvard Computer Society. 128 pages.