Steven E. Brenner - Publications

Affiliations: 
Molecular and Cell Biology University of California, Berkeley, Berkeley, CA 
Area:
Computational Genomics
Website:
http://compbio.berkeley.edu/

120 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Chandonia JM, Fox NK, Brenner SE. SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. Nucleic Acids Research. PMID 30500919 DOI: 10.1093/nar/gky1134  0.32
2018 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, ... ... Brenner SE, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/nbt.4163  0.32
2016 Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The Evolution of Function within the Nudix homology Clan. Proteins. PMID 27936487 DOI: 10.1002/prot.25223  0.4
2016 Chandonia JM, Fox NK, Brenner SE. SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. Journal of Molecular Biology. PMID 27914894 DOI: 10.1016/j.jmb.2016.11.023  0.32
2016 Nguyen VN, Park A, Xu A, Srouji JR, Brenner SE, Kirsch JF. Substrate specificity characterization for eight putative Nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. Proteins. PMID 27618147 DOI: 10.1002/prot.25163  0.4
2016 Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, et al. Quantitative tagless co-purification: a method to validate and identify protein-protein interactions. Molecular & Cellular Proteomics : McP. PMID 27099342 DOI: 10.1074/mcp.M115.057117  0.32
2016 Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, ... ... Brenner SE, et al. Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Molecular & Cellular Proteomics : McP. PMID 26873250 DOI: 10.1074/mcp.M115.054692  0.32
2015 Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner SE, Zaitlen N, Goga A, Ziv E. Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. Human Molecular Genetics. PMID 26472073 DOI: 10.1093/hmg/ddv432  1
2015 Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins. 83: 2025-38. PMID 26313554 DOI: 10.1002/prot.24915  1
2015 Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. PMID 26294686 DOI: 10.1101/gr.192518.115  1
2015 Bourne PE, Brenner SE, Eisen MB. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. Plos Computational Biology. 11: e1004317. PMID 26107720 DOI: 10.1371/journal.pcbi.1004317  1
2015 Patel JP, Puck JM, Srinivasan R, Brown C, Sunderam U, Kundu K, Brenner SE, Gatti RA, Church JA. Nijmegen breakage syndrome detected by newborn screening for T cell receptor excision circles (TRECs). Journal of Clinical Immunology. 35: 227-33. PMID 25677497 DOI: 10.1007/s10875-015-0136-6  1
2015 Punwani D, Wang H, Chan AY, Cowan MJ, Mallott J, Sunderam U, Mollenauer M, Srinivasan R, Brenner SE, Mulder A, Claas FH, Weiss A, Puck JM. Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation. Journal of Clinical Immunology. 35: 135-46. PMID 25627829 DOI: 10.1007/s10875-014-0125-1  1
2015 Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 342-6. PMID 25592594  1
2015 Lareau LF, Brenner SE. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution. 32: 1072-9. PMID 25576366 DOI: 10.1093/molbev/msv002  1
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, ... ... Brenner SE, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/nature13668  1
2014 Li JJ, Huang H, Bickel PJ, Brenner SE. Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research. 24: 1086-101. PMID 24985912 DOI: 10.1101/gr.170100.113  1
2014 Shatsky M, Arbelaez P, Han BG, Typke D, Brenner SE, Malik J, Glaeser RM. Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs. Journal of Structural Biology. 187: 66-75. PMID 24694675 DOI: 10.1016/j.jsb.2014.03.017  1
2014 Fox NK, Brenner SE, Chandonia JM. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research. 42: D304-9. PMID 24304899 DOI: 10.1093/nar/gkt1240  1
2014 Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L. Personalized medicine: From genotypes and molecular phenotypes towards therapy 19th Pacific Symposium On Biocomputing, Psb 2014. 247-249.  1
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... Brenner SE, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/journal.pbio.1001638  1
2013 Shatsky M, Arbelaez P, Glaeser RM, Brenner SE. Optimal and fast rotational alignment of volumes with missing data in Fourier space. Journal of Structural Biology. 184: 345-7. PMID 23994045 DOI: 10.1016/j.jsb.2013.08.006  1
2013 Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with post-operative clinical course in Crohn's disease. Bmc Gastroenterology. 13: 131. PMID 23964800 DOI: 10.1186/1471-230X-13-131  1
2013 Brenner SE. Be prepared for the big genome leak. Nature. 498: 139. PMID 23765454 DOI: 10.1038/498139a  1
2013 Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF. Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. Proteins. 81: 1593-609. PMID 23671031 DOI: 10.1002/prot.24318  1
2013 Xu A, Desai AM, Brenner SE, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Analytical Biochemistry. 437: 178-84. PMID 23481913 DOI: 10.1016/j.ab.2013.02.023  1
2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, ... ... Brenner SE, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/nmeth.2340  0.36
2013 Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner SE, Puck J. Newborn screening for SCID identifies patients with ataxia telangiectasia. Journal of Clinical Immunology. 33: 540-9. PMID 23264026 DOI: 10.1007/s10875-012-9846-1  1
2012 Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, et al. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. Journal of Proteome Research. 11: 5720-35. PMID 23098413 DOI: 10.1021/pr300548d  1
2012 Soergel DA, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The Isme Journal. 6: 1440-4. PMID 22237546 DOI: 10.1038/ismej.2011.208  1
2011 Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. Rna (New York, N.Y.). 17: 1884-94. PMID 21865603 DOI: 10.1261/rna.2696311  1
2011 Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Research. 21: 1969-80. PMID 21784873 DOI: 10.1101/gr.104687.109  1
2011 Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, ... ... Brenner SE, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/nature09715  1
2011 Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research. 39: 2344-56. PMID 21071404 DOI: 10.1093/nar/gkq1046  1
2011 Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21: 193-202. PMID 20921232 DOI: 10.1101/gr.108662.110  1
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Brenner SE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/science.1198374  1
2010 Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research. 38: e131. PMID 20395217 DOI: 10.1093/nar/gkq224  1
2010 Zhi D, Shatsky M, Brenner SE. Alignment-free local structural search by writhe decomposition. Bioinformatics (Oxford, England). 26: 1176-84. PMID 20371498 DOI: 10.1093/bioinformatics/btq127  1
2010 Shatsky M, Hall RJ, Nogales E, Malik J, Brenner SE. Automated multi-model reconstruction from single-particle electron microscopy data. Journal of Structural Biology. 170: 98-108. PMID 20085819 DOI: 10.1016/j.jsb.2010.01.007  1
2009 Engelhardt BE, Jordan MI, Repo ST, Brenner SE. Phylogenetic molecular function annotation. Journal of Physics. Conference Series. 180: 12024. PMID 20664722 DOI: 10.1088/1742-6596/180/1/012024  1
2009 Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, et al. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proceedings of the National Academy of Sciences of the United States of America. 106: 16580-5. PMID 19805340 DOI: 10.1073/pnas.0813068106  1
2009 Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Plos Genetics. 5: e1000525. PMID 19543372 DOI: 10.1371/journal.pgen.1000525  1
2009 Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, ... Brenner SE, et al. Planning the human variome project: the Spain report. Human Mutation. 30: 496-510. PMID 19306394 DOI: 10.1002/humu.20972  1
2009 Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell. 33: 438-49. PMID 19250905 DOI: 10.1016/j.molcel.2009.01.022  1
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/j.str.2008.12.014  1
2009 Blencowe B, Brenner S, Hughes T, Morris Q. Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 545-8. PMID 19209730  1
2009 Shatsky M, Hall RJ, Brenner SE, Glaeser RM. A method for the alignment of heterogeneous macromolecules from electron microscopy. Journal of Structural Biology. 166: 67-78. PMID 19166941 DOI: 10.1016/j.jsb.2008.12.008  1
2008 Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research. 36: D419-25. PMID 18000004 DOI: 10.1093/nar/gkm993  1
2007 Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE. The coupling of alternative splicing and nonsense-mediated mRNA decay. Advances in Experimental Medicine and Biology. 623: 190-211. PMID 18380348  1
2007 Brenner SE. Common sense for our genomes. Nature. 449: 783-4. PMID 17943102 DOI: 10.1038/449783a  1
2007 Bourne PE, Brenner SE. Developing computational biology. Plos Computational Biology. 3: 1669. PMID 17907793 DOI: 10.1371/journal.pcbi.0030157  1
2007 Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 446: 926-9. PMID 17361132 DOI: 10.1038/nature05676  1
2007 Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, ... ... Brenner SE, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/journal.pbio.0050016  1
2006 Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/rna.2343206  1
2006 Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science (New York, N.Y.). 311: 347-51. PMID 16424331 DOI: 10.1126/science.1121018  1
2006 Smith A, Chandonia JM, Brenner SE. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics (Oxford, England). 22: 618-20. PMID 16397008 DOI: 10.1093/bioinformatics/btk020  1
2006 Stefan LR, Zhang R, Levitan AG, Hendrix DK, Brenner SE, Holbrook SR. MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Research.. 34: D131-134. PMID 16381830  1
2006 Chandonia JM, Kim SH, Brenner SE. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins. 62: 356-70. PMID 16276528 DOI: 10.1002/prot.20674  1
2006 Engelhardt BE, Jordan MI, Brenner SE. A graphical model for predicting protein molecular function Acm International Conference Proceeding Series. 148: 297-304. DOI: 10.1145/1143844.1143882  1
2005 Hendrix DK, Brenner SE, Holbrook SR. RNA structural motifs: building blocks of a modular biomolecule. Quarterly Reviews of Biophysics. 38: 221-43. PMID 16817983 DOI: 10.1017/S0033583506004215  1
2005 Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, ... ... Brenner SE, et al. Structural genomics of minimal organisms and protein fold space. Journal of Structural and Functional Genomics. 6: 63-70. PMID 16211501 DOI: 10.1007/s10969-005-2651-9  1
2005 Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/science.1112014  1
2005 Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation Bioinformatics. 21: 3704-3710. PMID 16123116 DOI: 10.1093/bioinformatics/bti616  1
2005 Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics. 21: 3824-3831. PMID 16105900 DOI: 10.1093/bioinformatics/bti627  1
2005 Bourne PE, Brenner SE, Eisen MB. PLoS Computational Biology: a new community journal. Plos Computational Biology. 1: e4. PMID 16103905 DOI: 10.1371/journal.pcbi.0010004  1
2005 Yassin AF, Brenner S. Nocardia elegans sp. nov., a member of the Nocardia vaccinii clade isolated from sputum International Journal of Systematic and Evolutionary Microbiology. 55: 1505-1509. PMID 16014473 DOI: 10.1099/ijs.0.63570-0  1
2005 Blanchette M, Green RE, Brenner SE, Rio DC. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes & Development. 19: 1306-14. PMID 15937219 DOI: 10.1101/gad.1314205  1
2005 Zachariah MA, Crooks GE, Holbrook SR, Brenner SE. A generalized affine gap model significantly improves protein sequence alignment accuracy Proteins: Structure, Function and Genetics. 58: 329-338. PMID 15562515 DOI: 10.1002/prot.20299  1
2005 Crooks GE, Brenner SE. An alternative model of amino acid replacement Bioinformatics. 21: 975-980. PMID 15531614 DOI: 10.1093/bioinformatics/bti109  1
2005 Chandonia JM, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 58: 166-79. PMID 15521074 DOI: 10.1002/prot.20298  1
2005 Brenner SE, Tramontano A. Sequences and topology: A decade of genomes Current Opinion in Structural Biology. 15: 245-247. DOI: 10.1016/j.sbi.2005.05.009  1
2005 Chandonia JM, Brenner SE. Update on the Pfam5000 strategy for selection of structural genomics targets Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 7: 751-755.  1
2004 Crooks GE, Wolfe J, Brenner SE. Measurements of protein sequence-structure correlations Proteins: Structure, Function and Genetics. 57: 804-810. PMID 15476257 DOI: 10.1002/prot.20262  1
2004 Chandonia JM, Earnest TN, Brenner SE. Structural genomics and structural biology: compare and contrast. Genome Biology. 5: 343. PMID 15345043 DOI: 10.1186/gb-2004-5-9-343  1
2004 Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Molecular Cell. 14: 775-86. PMID 15200955 DOI: 10.1016/j.molcel.2004.06.012  1
2004 Lareau LF, Green RE, Bhatnagar RS, Brenner SE. The evolving roles of alternative splicing. Current Opinion in Structural Biology. 14: 273-82. PMID 15193306 DOI: 10.1016/j.sbi.2004.05.002  1
2004 Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator Genome Research. 14: 1188-1190. PMID 15173120 DOI: 10.1101/gr.849004  1
2004 Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR. Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. Journal of Molecular Biology. 339: 103-16. PMID 15123424 DOI: 10.1016/j.jmb.2004.01.065  1
2004 Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Research. 32: 2342-52. PMID 15121895 DOI: 10.1093/nar/gkh537  1
2004 Crooks GE, Brenner SE. Protein secondary structure: Entropy, correlations and prediction Bioinformatics. 20: 1603-1611. PMID 14988117 DOI: 10.1093/bioinformatics/bth132  1
2004 Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biology. 5: R8. PMID 14759258 DOI: 10.1186/gb-2004-5-2-r8  1
2004 Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research. 32: D226-9. PMID 14681400 DOI: 10.1093/nar/gkh039  1
2004 Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Research. 32: D189-92. PMID 14681391 DOI: 10.1093/nar/gkh034  1
2004 Tamura M, Hendrix DK, Klosterman PS, Schimmelman NR, Brenner SE, Holbrook SR. SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Research. 32: D182-4. PMID 14681389 DOI: 10.1093/nar/gkh080  1
2003 Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics (Oxford, England). 19: i118-21. PMID 12855447 DOI: 10.1093/bioinformatics/btg1015  1
2003 Lewis BP, Green RE, Brenner SE. 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: 189-92. PMID 12502788 DOI: 10.1073/pnas.0136770100  1
2002 Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Research. 12: 1611-8. PMID 12368254 DOI: 10.1101/gr.361602  1
2002 Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. Sulfotransferases and sulfatases in mycobacteria. Chemistry & Biology. 9: 767-76. PMID 12144918 DOI: 10.1016/S1074-5521(02)00175-8  1
2002 Klosterman PS, Tamura M, Holbrook SR, Brenner SE. SCOR: a Structural Classification of RNA database. Nucleic Acids Research. 30: 392-4. PMID 11752346  1
2002 Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research. 30: 264-7. PMID 11752311  1
2002 Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Research. 30: 260-3. PMID 11752310  1
2002 Green RE, Brenner SE. Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison Proceedings of the Ieee. 90: 1834-1847. DOI: 10.1109/JPROC.2002.805303  1
2002 Brenner SE. Genome annotation and protein structure Proceedings - Ieee Computer Society Bioinformatics Conference, Csb 2002. 4. DOI: 10.1109/CSB.2002.1039322  1
2001 Zupicich J, Brenner SE, Skarnes WC. Computational prediction of membrane-tethered transcription factors. Genome Biology. 2: RESEARCH0050. PMID 11790253  1
2001 Brenner SE. A tour of structural genomics. Nature Reviews. Genetics. 2: 801-9. PMID 11584296 DOI: 10.1038/35093574  1
2000 Brenner SE. Target selection for structural genomics. Nature Structural Biology. 7: 967-9. PMID 11104002 DOI: 10.1038/80747  1
2000 Brenner SE, Levitt M. Expectations from structural genomics. Protein Science : a Publication of the Protein Society. 9: 197-200. PMID 10739263 DOI: 10.1110/ps.9.1.197  1
2000 Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Research. 28: 257-9. PMID 10592240 DOI: 10.1093/nar/25.1.236  1
2000 Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research. 28: 254-6. PMID 10592239  1
1999 Brenner SE. Errors in genome annotation. Trends in Genetics : Tig. 15: 132-3. PMID 10203816 DOI: 10.1016/S0168-9525(99)01706-0  1
1999 Wolf YI, Brenner SE, Bash PA, Koonin EV. Distribution of protein folds in the three superkingdoms of life. Genome Research. 9: 17-26. PMID 9927481  1
1999 Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP: a Structural Classification of Proteins database. Nucleic Acids Research. 27: 254-6. PMID 9847194 DOI: 10.1093/nar/27.1.254  1
1999 Brenner SE, Barken D, Levitt M. The PRESAGE database for structural genomics. Nucleic Acids Research. 27: 251-3. PMID 9847193 DOI: 10.1093/nar/27.1.251  1
1998 Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallographica. Section D, Biological Crystallography. 54: 1147-54. PMID 10089491 DOI: 10.1107/S0907444998009172  1
1998 Galperin MY, Brenner SE. Using metabolic pathway databases for functional annotation. Trends in Genetics : Tig. 14: 332-3. PMID 9724967 DOI: 10.1016/S0168-9525(98)01523-6  1
1998 Brenner SE, Chothia C, Hubbard TJ. 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: 6073-8. PMID 9600919 DOI: 10.1073/pnas.95.11.6073  1
1998 Brenner SE. Practical database searching Trends in Biotechnology. 16: XVII-XVIII.  1
1997 Brenner SE, Chothia C, Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology. 7: 369-76. PMID 9204279 DOI: 10.1016/S0959-440X(97)80054-1  1
1996 Brenner SE, Chothia C, Hubbard TJP, Murzin AG. [37] Understanding protein structure: Using scop for fold interpretation Methods in Enzymology. 266: 635-642. PMID 8743710  1
1995 Brenner SE. Blast, blitz, blocks and beauty; sequence comparison on the net Trends in Genetics. 11: 330-331. PMID 8585135  1
1995 Brenner SE. World Wide Web and molecular biology [3] Science. 268: 622-623. PMID 7732361  1
1995 Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: A structural classification of proteins database for the investigation of sequences and structures Journal of Molecular Biology. 247: 536-540. PMID 7723011 DOI: 10.1016/S0022-2836(05)80134-2  1
1995 Brenner SE, Hubbard TJ. A specification for defining and annotating regions of macromolecular structures Proceedings / . International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 3: 66-74. PMID 7584468  1
1995 Suzuki M, Brenner SE, Gerstein M, Yagi N. DNA recognition code of transcription factors Protein Engineering. 8: 319-328. PMID 7567917  1
1995 Suzuki M, Brenner SE. Classification of multi-helical DNA-binding domains and application to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC Febs Letters. 372: 215-221. PMID 7556672 DOI: 10.1016/0014-5793(95)00988-L  1
1995 Brenner SE, Hubbard T, Murzin A, Chothia C. Gene duplications in H. influenzae [7] Nature. 378: 140. PMID 7477316  1
1995 Brenner SE. Network sequence retrieval Trends in Genetics. 11: 247-248. DOI: 10.1016/S0168-9525(00)89059-9  1
1994 Brenner SE, Berry A. A quantitative methodology for the de novo design of proteins Protein Science. 3: 1871-1882. PMID 7849602  1
1994 Berry A, Brenner SE. A prototype computer system for de novo protein design Biochemical Society Transactions. 22: 1033-1036. PMID 7698402  1
1994 Brenner SE, Berry A. Protein design by optimization of a sequence-structure quality function Proceedings / . International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 44-52. PMID 7584417  1
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