Steven E. Brenner

More important publications noted with asterisk

Chandonia JM, Fox NK, Brenner SE. 2019. SCOPe: Classification of large macromolecular structures in the Structural Classification of Proteins—extended database. Nucleic Acids Research 47:475-481. PMID:30500919. doi:10.1093/nar/gky1134 [PDF 1.9M]

Brenner SE, Bulyk M, Crawford DC, Mesirov JP, Morgan AA, Radivojac P. 2019. Precision medicine: improving health through high-resolution analysis of personal data. Pacific Symposium on Biocomputing 24:220-223. [PDF 560KB]

Gürsoy G, Harmanci AO, Tang H, Ayday E, Brenner SE. 2019. When biology gets personal: hidden challenges of privacy and ethics in biological big data. Pacific Symposium on Biocomputing 24:386-390. [PDF 568.4KB]

Abou Tayoun AN, ClinGen SVI et al. 2018. Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion. Human Mutation. doi:10.1002/humu.23626

Dyke SOM, et al. Registered access: authorizing data access. European Journal of Human Genetics. doi:10.1038/s41431-018-0219-y

Arkin AP, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology 36:566-569. PMID:29979655. doi:10.1038/nbt.4163

Biesecker LG, Harrison SM on behalf of ClinGen Sequence Variant Working Group. The ACMG/AMP reputable source criteria for the interpretation of sequence variants. Genetics in Medicine 20:1687-1688. PMID:29543229. doi:10.1038/gim.2018.42

Tavtigian SV, Greenblatt MS, Harrison SM, Nussbaum RL, Prabhu SA, Boucher KM, Biesecker LG, on behalf of the ClinGen Sequence Variant Interpretation Task Team (ClinGen SVI). Modeling the ACMG/AMP Variant Classification Guidelines as a Bayesian Classification Framework.Genetics in Medicine 20:1054-1060. doi:10.1038/gim.2017.210

Oetting, WS, Beroud CC, Brenner SE, Brookes AJ, Greenblatt MS, Karchin R, Mooney SD. 2018 Methods and Tools for Assessing the Impact of Genome Variations: The 2017 Annual Scientific Meeting of the Human Genome Variation Society. Human Mutation 39 :454-458.PMID:29282786. PMCID:5805595. doi:10.1002/humu.23393

Lu JG, Bishop J, Cheyette S, Zhulin IB, Guo S, Sobreira N, Brenner SE. A novel PRRT2 pathogenic variant in a family with Paroxysmal Kinesigenic Dyskinesia and Benign Familial Infantile Seizures. Cold Spring Harbor Molecular Case Studies. PMID:29167286. doi:10.1101/mcs.a002287

Crawford DC, Morgan AA, Denny JC, Aronow BJ, and Brenner SE. 2018. Precision medicine: from diplotypes to disparities towards improved health and therapies. Pacific Symposium on Biocomputing 2018 :389-399. PMID: 29218899. doi:10.1142/9789813235533_0036

Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE. 2017. Reports from CAGI: The Critical Assessment of Genome Interpretation. Human Mutation 38:1039-1041. PMID:28544272 doi:10.1002/humu.23290

Daneshjou R, et al. 2017. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation 38:1182-1192. PMID:28634997. doi:10.1002/humu.23280 [PDF 997k] [supp figure 1 1.6M] [supp figure 2 4.2M] [supp figure 3 14M] [supp figure 4 8.4M] [supp method 94M]

Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. 2017. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation 38:1042-1050. PMID:28440912. doi:10.1002/humu.23235 [PDF 997k] [Supp 5.2M]

Cai B, Li B, Kiga N, Thusberg J, Bergquist B, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins R, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. 2017. Matching phenotypes to whole genomes: lessons learned from four iterations of the personal genome project community challenges. Human Mutation 38:1266-1276. PMID:28544481. doi:10.1002/humu.23265 [PDF 775k] [Supp 331k]

*Srouji JR, Xu A, Park A, Kirsch JK, Brenner SE. 2017. The evolution of function within the nudix homology clan. Proteins: Structure, Function, and Bioinformatics 85:775-811. PMID:27936487. PMCID:5389931. doi:10.1002/prot.25223 [Advance access PDF 2.1M] [Supp 2.4M]

Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, and Sunyaev S. 2017. Non-coding variation: the 2016 annual scientific meeting of the Human Genome Variation Society. Human Mutation 38:460-463. PMID:28054414. doi:10.1002/humu.23169 [PDF 143k]

*Chhibber A, French CE, Gamazon ER, Yee SW, Qin X, Theusch E, Webb A, Weiss S, Medina MW, Krauss RM, Scherer SE, Cox NJ, Giacomini KM, Brenner SE. 2017. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. The Pharmacogenomics Journal 17:137-145. PMID:26856248. PMCID:4980276. doi:10.1038/tpj.2015.93 [PDF 2M] [supp methods 0.1M] [supp figures 3.3M]

Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner SE, Brower AM, Butler I, Cakici J, Ceyhan, Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig B, Kwok P Lantos J, Leeder JS, Lewis MA, McGuire AL, Milko LV, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. 2017. Newborn Sequencing In Genomic medicine and public HealTh. Pediatrics 139. pii:e20162252. PMID:28096516. PMCID:PMC5260149. doi:10.1542/peds.2016-2252

Chandonia JM, Fox NK, Brenner SE. 2017. SCOPe: Manual curation and artifact removal in the structural classification of proteins-extended database. Journal of Molecular Biology 429:348-55. PMID: 27914894. PMCID:PMC5272801. doi:10.1016/j.jmb.2016.11.023 [PDF 0.4M]

Morgan AA, Crawford DC, Denny JC, Mooney SD, Aronow BJ, and Brenner SE. 2017. Precision medicine: data and discover for improved health and therapy. Pacific Symposium on Biocomputing 22:348-355. PMID:27896988. doi:10.1142/9789813207813_0033 [PDF 0.9M]

Karačić Z, Vukelić B, Ho GH, Jozić I, Sučec I, Salopek-Sondi B, Kozlović M, Brenner SE, Ludwig-Müller J, Abramić M. 2017. A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III. Biological Chemistry 398:101-12 . PMID:27467751. doi:10.1515/hsz-2016-0141 [PDF 0.8M]

*Punwani D et al. 2016. Multisystem anomalies in severe combined immunodeficiency with mutant BCL11B. New England Journal of Medicine 375:2165-2176. PMID:27959755. PMCID:5215776. doi:10.1056/NEJMoa1509164. [PDF 0.6M] [Appendix 5.9M]

Nguyen V, Park A, Xu A, Srouji J, Brenner SE, Kirsch JF. 2016. Substrate specificity characterization for eight putative Nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. Proteins: Structure, Function, and Bioinformatics 84:1810-1822. PMID:27618147. doi:10.1002/prot.25163 [PDF 0.4M] [supp info 0.07M]

Jiang Y et al. 2016. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology 17:184. PMID:27604469. PMCID:5015320. doi:10.1186/s13059-016-1037-6 [PDF 12.9M]

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, Biggin MD. 2016. Quantitative tagless copurification: a method to validate and identify protein-protein interactions. Mol Cell Proteomics 15:2186-202. PMID:27099342. PMCID:5083090. doi:10.1074/mcp.M115.057117 [PDF 1.0M] [supp info 2.5M] [dataset 1 13.0M] [dataset 2 18.4M] [dataset 3 25.0M] [dataset 4 0.1M] [dataset 5 0.1M] [dataset 6 6.0M] [dataset 7 20.6M] [dataset 8 13.0M] [dataset 9 5.7M]

Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang WSzakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. 2016. Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Molecular and Cellular Proteomics 15:1539-55. PMID:26873250. PMCID:4858938. doi:10.1074/mcp.M115.054692 [PDF 1.6M] [supp info 1.6M] [supp dataset S1-S2 31.5M] [supp dataset S3-S8 9.0M] [supp dataset S9-S18 1.8M] [supp dataset S19 0.9M]

Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE. 2016. Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Human Mutation 37:406-411. PMID:26791113. PMCID:4783187. doi:10.1002/humu.22958. [PDF 0.1M]

Dobbs D, Brenner SE, Honavar VG, Jernigan RL, Laederach A, Morris Q. 2016. Regulatory RNA. Pacific Symposium on Biocomputing 21:429-432. PMID:26776206. doi:10.1142/9789814749411_0039 [PDF 1.0M]

Morgan AA, Mooney SD, Aronow BJ, Brenner SE. 2016. Precision Medicine: Data and Discovery for Improved Health and Therapy. Pacific Symposium on Biocomputing 21:243-248. PMID:26776190. doi:10.1142/9789814749411_0023 [PDF 0.5M]

Brenner SE, Kingsmore S, Mooney SD, Nussbaum R, Puck J. 2016. Use of genome and exome data in newborns as a starting point for life-long precision medicine. Pacific Symposium on Biocomputing 21:568-575. PMID:26776219. doi:10.1142/9789814749411_0052 [PDF 0.5M]

Chan AY, Punwani D, Kadlecek TA, Cowan M, Brenner SE, Olson JL, Mathes EF, Sunderam U, Srinivasan R, Kuriyan J, Fu SM, Weiss A, Puck JM. 2016. Novel Autoimmune Syndrome Due to the Combined Actions of a Hypomorphic and an Activating Mutation of Zeta-Chain Associated Protein Kinase ZAP-70. Journal of Experimental Medicine. PMID:26783323. PMCID:4749924. doi:10.1084/jem.20150888 [PDF 2.0M] [supplementary material 0.4M] [figures 0.7M]

Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner SE, Goga A, Ziv E. 2015. Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. Human Molecular Genetics. PMID:26472073. PMCID:4664170. doi:10.1093/hmg/ddv432 [PDF 1.1M] [supplementary data 646k]

*Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR, Brenner SE. 2015. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. PMID:26294686. PMCID:4617972. doi:10.1101/gr.192518.115 [PDF 5M] Supp material[Figures 5.3M] [table 1 3k] [table 2 6k] [table 3 15M] [table 4 1.3M] [table 5 1.8M]

Fox NK, Brenner SE, Chandonia JM. 2015. The value of protein structure classification information—surveying the scientific literature. Proteins: Structure, Function, and Bioinformatics 83:2025-38. PMID:26313554. PMCID:4609302. doi:10.1002/prot.24915 [Advance access PDF 1.3M] [supplementary data Excel .18M] [supplementary notes .9M]

Bourne PE, Brenner SE, Eisen MB. 2015. Ten years of PLoS Computational Biology: a decade of appreciation and innovation. PLOS Computational Biology 11:e1004317. PMID:26107720. PMCID:4479580. doi:10.1371/journal.pcbi.1004317 [PDF .1M]

Sahraeian SME, Luo KR, Brenner SE. 2015. SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Research 43:W141-W147. PMID:25979264. PMCID:4489292. doi:10.1093/nar/gkv461 [PDF 1.8M]

*Lareau LF, Brenner SE. 2015. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution 32:1072-1079. PMID:25576366. PMCID:4379411. doi:10.1093/molbev/msv002 [PDF .8M] [supplementary data 6.3M]

*Patel JP, Puck JM, Srinivasan R, Brown C, Sunderam U, Kundu K, Brenner SE, Gatti RA, Church JA. 2015. Nijmegen breakage syndrome detected by newborn screening for T cell receptor excision circles (TRECs). Journal of Clinical Immunology 35:227-233. PMID:25677497. PMCID:4352190. doi:10.1007/s10875-015-0136-6. [PDF .3M]

Punwani D, Wang H, Chan AY, Cowan MJ, Mallott J, Sunderam U, Mollenauer M, Srinivasan R, Brenner SE, Mulder A, Claas FHJ, Weiss A, Puck JM. 2015. Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation. Journal of Clinical Immunology 32135-146. PMID:25627829. PMCID:4352191. doi:10.1007/s10875-014-0125-1 [PDF 1M]

Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. 2015. Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pac Symp Biocomput 2015:342-6. PMID:25592594. doi:10.1142/9789814644730_0033 [PDF .6M]

*Gerstein M, et al. 2014. Comparative analysis of the transcriptome across distant species. Nature 512:445-448. doi:10.1038/nature13424 [PDF 4M]

*Boyle A, et al. 2014. Comparative analysis of regulatory information and circuits across distant species. Nature 512:453-456. PMID:25164757. PMCID:4336544. doi:10.1038/nature13668 [PDF 9.5M]

*Li JJ, Huang H, Bickel PJ, Brenner SE. 2014. Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research 24:1086-1101. PMID:24985912. PMCID:4079965. doi:10.1101/gr.170100.113 [PDF 3.6M] [supplementary material 18M]

Shatsky M, Arbelaez P, Han B-G, Typke D, Brenner SE, Malik J, Glaeser RM. 2014. 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 [PDF 1.6M]

*Fox NK, Brenner SE, Chandonia JM. 2013. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research 42:D304-9. PMID:24304899. PMCID:3965108. doi:10.1093/nar/gkt1240 [PDF 2.4M]

Shatsky M, Arbelaez P, Glaeser RM, Brenner SE. 2013. Optimal and fast rotational alignment of volumes with missing data in Fourier space. Journal of Structural Biology 184:345-347. PMID:23994045. doi:10.1016/j.jsb.2013.08.006 [PDF .5M]

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF. 2013. Molecular function prediction for a family exhibiting evolutionary tendencies towards substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. Proteins: Structure, Function, and Bioinformatics 81:1593-1609. PMID:23671031. PMCID:3823064. doi:10.1002/prot.24318 [PDF .9M]

Anton BP, et al. 2013. The COMBREX project: design, methodology, and initial results. PLOS Biology 11:e1001638. PMID:24013487. PMCID:3754883. doi:10.1371/journal.pbio.1001638. [PDF .5M]

*Dey N, Soergel DAW, Repo ST, Brenner SE. 2013. Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterology 13:131. PMID:23964800. PMCID:3848607. doi:10.1186/1471-230X-13-131 [PDF .7M] [supplementary content: tables and figures]

Brenner SE. 2013. Be prepared for the big genome leak. Nature 498:139. PMID:23765454. doi:10.1038/498139a [original PDF .2M] [annotated PDF 1M] [archival commentary page]

Xu A, Desai AM, Brenner SE, Kirsch JF. 2013. A continuous fluorescence assay for the characterization of Nudix hydrolases. Analytical Biochemistry 437:178-184. PMID:23481913. PMCID:3744803. doi:10.1016/j.ab.2013.02.023 [PDF .6M]

*Mallott J, Kwan A, Church J, Gonzalez D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner SE, Puck J. 2013. Newborn screening for SCID identifies patients with ataxia telangiectasia. Journal of Clinical Immunology 33:540-549. PMID:23264026. PMCID:3591536. doi:10.1007/s10875-012-9846-1 [PDF .4M]

*Radivojac P, et al. 2013. A large-scale evaluation of computational protein function prediction. 2013. Nature Methods 10:221-227. PMID:23353650. PMCID:3584181. doi:10.1038/nmeth.2340 [PDF 720K]

Morris Q, Brenner SE, Listgarten J, Stegle O. 2013. The future of genome-based medicine. Pac Symp Biocomput 16:456-458. PMID:23424151 doi:10.1142/9789814447973_0046 [PDF 125K]

Walian P, Allen S, Shatsky M, Zeng L, Szakal E, Liu H, Hall S, Fisher S, Lam B, Singer M, Geller J, Brenner SE, Chandonia J-M, Hazen T, Witkowska H, Biggin M, Jap B. 2012. High-throughput isolation and characterization of untagged membrane protein complexes - outer membrane complexes of Desulfovibrio vulgaris. Journal of Proteome Research 11:5720-5735. PMID:23098413. PMCID:3516867. doi:10.1021/pr300548d [PDF .5M]

*Soergel DA, Dey N, Knight R, Brenner SE. 2012. Selection of primers for optimal taxonomic classification of environmental 16S sequences. The ISME Journal 6:1440-1444. PMID:2237546. PMCID:3379642. doi:10.1038/ismej.2011.208 [PDF 1.9M] [supplementary information 1(395K) 2(895K) fig. 1(174K) supplementary tables (595K)]

*Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. 2011. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Research 21:1969-1980. PMID:21784873. PMCID:3205580. doi:10.1101/gr.104687.109 [PDF 1.2M] [supplementary information (295L) supplementary data deaminase.tar.gz (82K) hundredfamilies.tar.gz (3.8M) sifter2.0.tar.gz (1.0M) sulfotransferase.tar.gz (147K)

Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. 2011. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA 17:1884-1894. PMID:21865603. PMCID:3185920. doi:10.1261/rna.269311 [PDF 1.5M] [supplementary information supp fig (2.8M) dataset (25K)

*Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin J, Yang L, et al. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471:473-479. PMID:21179090. PMCID:3075879. doi:10.1038/nature09715 [PDF 1.9M] [supplementary information (3.8M) supplementary tables 1-12 (11.7M) 13-18 (23M) 19-26 (19M) 27-34 (18M)]

Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. 2010. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research 39:2344-2356. PMID:21071404. PMCID:3064769. doi:10.1093/nar/gkq1046 [preprint PDF .6M] [supplementary information .3M]

*Brooks AN, Yang L, Duff MO, Hansen KD, Dudoit S, Brenner SE, Graveley BR. 2011. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research 21:193-202. PMID:20921232. PMCID:3032923. doi:10.1101/gr.108662.110 [PDF .8M] [supplementary information (2.1MB) datasets1 (4K) 2 (2K) 3 (471K) 4 (6K)5 (4K)]

The Drosophila modENCODE Consortium, et al. 2010. Identification of functional elements and regulatory circuits in Drosophila by large-scale data integration. Science 33:1787-1797. PMID:21177974. PMCID:3192495. doi:10.1126/science.1198374 [PDF 1.5M] [supporting material 11M]

Zhi D, Shatsky M, Brenner SE. 2010. Alignment-free local structural search by writhe decomposition. Bioinformatics 26:1176-1184. PMID:20371498. PMCID:2859133. doi:10.1093/bioinformatics/btq127 [PDF .4M]

Hansen KD, Brenner SE, Dudoit S. 2010. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research 38:e131. PMID:20395217. PMCID:2896536. doi:10.1093/nar/gkq224 [PDF .5M]

Shatsky M, Hall RJ, Nogales E, Malik J, Brenner SE. 2010. Automated multi-model reconstruction from single-particle electron microscopy data. Journal of Structural Biology 170:98-108. PMID:20085819. PMCID:2841227. doi:10.1016/j.jsb.2010.01.007 [PDF .5M]

Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowsa HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM. 2009. Survey of large protein complexes in D. vulgaris reveals unexpected structural diversity. Proceedings of the National Academy of Sciences of the United States of America 106:16580-16585. PMID:19805340. PMCID:2742403. doi:10.1073/pnas.0813068106 [PDF 1.4M] [appendix 2.9M]

Engelhardt BE, Jordan MI, Repo ST, Brenner SE. 2009. Phylogenetic molecular function annotation. Journal of Physics: Conference Series (SciDAC 2009) 180:012024. PMID:20664722. PMCID:2909777. doi:10.1088/1742-6596/180/1/012024 [PDF .3M]

*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 5:e1000525. PMID:19543372. PMCID:2689934. doi:10.1371/journal.pgen.1000525 [PDF .5M]

Celniker SE et al. 2009. Unlocking the secrets of the genome. Nature 459:927-930. PMID:19536255. PMCID:2843545. doi:10.1038/459927a [PDF 1M] [supplementary information 71K]

Kaput J, Cotton RGH, Hardman L, ... (11 authors) ..., Brenner SE, et al. 2009. Planning the Human Variome Project: the Spain report. Human Mutation 3:496-510. PMID:19306394. doi:10.1002/humu.20972 [PDF .2M]

Shatsky M, Hall RJ, Brenner SE, Glaeser RM. 2009. A method for the alignment of heterogeneous macromolecules from electron microscopy. Journal of Structural Biology 166:67-78. PMID:19166941. PMCID:2740748. doi:10.1016/j.jsb.2008.12.008 [PDF 1.3MB]

Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. 2009. Genome-wide analysis of alternative pre-mRNA splicing and RNA binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell 33:438-449. PMID:19250905. PMCID:2674966. doi:10.1016/j.molcel.2009.01.022 [PDF 1.1M]

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, et al. 2009. Outcome of a workshop on applications of protein models in biomedical research. Structure 17:151-159. PMID:19217386. PMCID:2739730. doi:10.1016/j.str.2008.12.014 [PDF .25M]

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. PMID:18000004. PMCID:2238974. doi:10.1093/nar/gkm993 [PDF .33M]

*Brenner SE. 2007. Common sense for our genomes. Nature 449:783-784. PMID:17943102. doi:10.1038/449783a [PDF .2M]

Bourne PE, Brenner SE. 2007. Developing computational biology. PLoS Computational Biology 3:e157. PMID:17907793. PMCID:1994973. 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. PMID:18380348. [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. PMID:17361132. 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. PMID:17355171. PMCID:1821046. 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. PMID:16484377. PMCID:1421088. 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. PMID:16397008. 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. PMID:16424331. 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. PMID:16381830. PMCID:1347421. 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. PMID:16817983. 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. PMID:16276528. 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. PMID:16105900. 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. PMID:16211501. 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. PMID:16217548. PMCID:1246806. 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. PMID:16123116. doi:10.1093/bioinformatics/bti616 [PDF .4M] [code 105M]

Chandonia JM, Brenner SE. 2005. Update on the Pfam5000 strategy for selection of structural genomics targets. Proceedings of the 27th IEEE EMBS Conference 751-755. PMID:17282292. doi:10.1109/IEMBS.2005.1616523 [PDF .2M]

Carninci P, ... (12 authors) ..., Brenner SE, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559-1563. PMID:16141072. 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. PMID:16103905. PMCID:1183510. 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/ [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. PMID:15937219. PMCID:1142554. doi:10.1101/gad.1314205 [PDF .43M]

Crooks GE, Brenner SE. 2005. An alternative model of amino acid replacement. Bioinformatics 21:975-980. PMID:15531614. 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. PMID:15562515. 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. PMID:15521074. 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. PMID:15476257. 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. PMID:15345043. PMCID:522866. 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. PMID:15200955. 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. PMID:14988117. 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. PMID:15193306. doi:10.1016/ [PDF .18M]

Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Research 14:1188-1190. PMID:15173120. PMCID:419797. 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. PMID:15123424. 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. PMID:15121895. PMCID:419439. 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. PMID:14759258. PMCID:395752. 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. PMID:14681391. PMCID:308768. 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. PMID:14681400. PMCID:308773. 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. PMID:14681389. PMCID:308814. 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. PMID:12855447. 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. PMID:12502788. PMCID:140922. 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. PMID:12368254. PMCID:187536. 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. PMID:12144918. 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. PMID:14684389. PMCID:99131. [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. PMID:11752310. PMCID:99063. [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. PMID:11752311. PMCID:99154. [PDF .08M]

*Zupicich J, Brenner SE, Skarnes WC. 2001. Computational prediction of membrane-tethered transcriptions factors. Genome Biology 2:research0050.1-0050.6. PMID:11790253. PMCID:64835. [PDF 2.2M]

*Brenner SE. 2001. A tour of structural genomics. Nature Reviews Genetics 2:801-9. PMID:11584296. doi:10.1038/35093574 [PDF 2.3M]

Brenner SE. 2000. Target selection for structural genomics. Nature Structural Biology, Structural Genomics supplement 7:967-969. PMID:11104002. doi:10.1038/80747 [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. PMID:10739263. PMCID:2144435. doi:10.1110/ps.9.1.197 [PDF .26M]

Brenner SE, Koehl P, Levitt M. 2000. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research 28:254-256. PMID:10592239. PMCID:102434. [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. PMID:10592240. PMCID:102479. [PDF .07M]

*Brenner SE. 1999. Errors in genome annotation. Trends in Genetics 15:132-133. PMID:10203816. [PDF .16M]

Brenner SE, Barken D, Levitt M. 1999. The PRESAGE database for structural genomics. Nucleic Acids Research. 27:251-253. PMID:9847193. PMCID:148148. [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. PMID:9847194. PMCID:148149. [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. PMID:10089491. [PDF .47M]

Galperin MY, Brenner SE. 1998. Using metabolic pathway databases for functional annotation. Trends in Genetics 14:332-333. PMID:9724967. [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. PMID:9600919. PMCID:27587. [PDF .3M]

*Brenner SE, Chothia C, Hubbard TJP. 1997. Population statistics of protein structures. Current Opinion in Structural Biology 7:369-376. PMID:9204279. [PDF .2M]

Chothia C, Hubbard TJP, Brenner SE, Barns H, Murzin A. 1997. Protein folds in the all-α and all-β classes. Annual Reviews of Biophysics and Biomolecular Structure 26:597-627. PMID:9241431. [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. PMID:7723011. [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 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. PMID:8743710. [Scanned PDF 3.4M] [OCR PDF .19M]

*Brenner SE, Hubbard T, Murzin A, Chothia C. 1995. Gene duplications in H. influenzae. Nature 378:140. PMID:7477316. [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. PMID:7556672. [PDF 4.14M]

Brenner SE. 1995. BLAST, Blitz, BLOCKS and BEAUTY: Sequence comparison on the Net. Trends in Genetics 11:330-331. PMID:8585135. [PDF 1.51M]

Brenner SE. 1995. World wide web and molecular biology. Science 268:622-623. PMID:7732361. [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. PMID:7584468. [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. PMID:7567917. [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. PMID:7723011. [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.