[Home]     Brenner Computational Genomics Research Group
Steven E. Brenner

Professor, Department of Plant and Microbial Biology, University of California, Berkeley
Adjunct Professor, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
Faculty Scientist, Physical Biosciences, Lawrence Berkeley National Laboratory
Affiliated Professor, Department of Molecular & Cell Biology
Affiliated Professor, Department of Bioengineering
Member, Center for Computational Biology
Member, Institute for Human Genetics

Member, Computational Biology graduate program
Member, Designated Emphasis in Computational and Genomic Biology
Member, Biophysics Graduate Group
Member, UCSF/UCB Bioengineering Graduate Group
Member, Comparative Biochemistry Graduate Group
Member, Infectious Diseases & Immunity
Member, Biological and Medical Informatics Graduate Program of the Integrated Program in Quantitative Biology

A.B. 1992. Harvard University
M.Phil. 1994. University of Cambridge
Ph.D. 1997. University of Cambridge and MRC Laboratory of Molecular Biology
Visitor. 1997. Japan National Institute of Bioscience
Sloan/DOE Postdoctoral Fellow. 1999. Stanford University

2001 Searle Scholar
1998-2001 & 2002-2006 Director, International Society for Computational Biology
2001-2006 Founding Director, Open Bioinformatics Foundation, and Founding Coordinator, The Bioperl Project
2003 Sloan Research Fellow
2007-2008 Miller Professor
2008 AAAS Fellow
2010 ISCB Overton Prize awardee
2015 ISCB Senior Member
2016 ISCB Fellow

Selected Publications  (full list)

The Critical Assessment of Genome Interpretation Consortium. 2024. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology 25:53. PMID:38389099. PMC10882881 https://doi.org/10.1186/s13059-023-03113-6
Rastogi R, Chung R, Li S, Li C, Lee K, Woo J, Kim D, Keum C, Babbi G, Martelli PL, Savojardo C, Casadio R, Chennen K, Weber T, Poch O, Ancien F, Cia G, Pucci F, Raimondi D, Vranken W, Rooman M, Marquet C, Olenyi T, Rost B, Andreoletti G, Kamandula A, Peng Y, Bakolitsa C, Mort M, Cooper DN, Bergquist T, Pejaver V, Liu X, Radivojac P, Brenner SE, Ioannidis NM. 2024. Critical assessment of missense variant effect predictors on disease-relevant variant data. bioRxiv. https://doi.org/10.1101/2024.06.06.597828
Pejaver V, Byrne AB, Feng B-J, Pagel KA, Mooney SD, Karchin R, O’Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE, ClinGen Sequence Variant Interpretation Working Group. 2022. Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria. American Journal of Human Genetics 109:2163-2177. PMID:36413997 PMC9748256 https://doi.org/10.1016/j.ajhg.2022.10.013
Sharo AG, Hu Z, Sunyaev SR, Brenner SE. 2022. StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants. American Journal of Human Genetics 109:195-209. PMID:35032432 PMC8874149 https://doi.org/10.1016/j.ajhg.2021.12.007 [PDF] [supplemental information]
Adhikari AN, Gallagher RC, Wang Y, Currier RJ, Amatuni G, Bassaganyas L, Chen F, Kundu K, Kvale M, Mooney SD, Nussbaum RL, Randi SS, Sanford J, Shieh JT, Srinivasan R, Sunderam U, Tang H, Vaka D, Zou YY, Koenig BA, Kwok PY, Risch N, Puck JM, Brenner SE. 2020. The role of exome sequencing in newborn screening for inborn errors of metabolism. Nature Medicine 26:1392-1397. PMID:32778825 https://doi.org/10.1038/s41591-020-0966-5 [PDF] [SuppFig1] [SuppTables]
French CE, Wei G, Lloyd JPB, Hu Z, Brooks AN, Brenner SE. 2020. Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential. bioRxiv. doi:10.1101/2020.07.01.183327 [PDF]
Desai A, Hu Z, French CE, Lloyd JPB, Brenner SE. 2020. Networks of splice factor regulation by unproductive splicing coupled with nonsense mediated mRNA decay. bioRxiv. doi:10.1101/2020.05.20.107375 [PDF]
Lloyd JPB, French CE, Brenner SE. 2020. Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay. bioRxiv. doi:10.1101/2020.03.08.981811 [PDF]
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 PMC27936487 https://doi.org/10.1002/prot.25223 [PDF 0.9M] [Supp 2.4M]
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 PMC4980276 https://doi.org/10.1038/tpj.2015.93 [PDF 2.3M] [Methods 162k] [Figures 3.3M]
Punwani D, Zhang Y, Yu J, Cowan MJ, Rana S, Kwan A, Adhikari A, Lizama CO, Mendelsohn BA, Fahl SP, Chellappan A, Srinivasan R, Brenner SE, Wiest DL, Puck JM. 2016. Multisystem anomalies in severe combined immunodeficiency with mutant Bcl11b. New England Journal of Medicine 375:2165-2176. PMID:27959755 PMC5215776 https://doi.org/10.1056/NEJMoa1509164 [PDF 0.6M] [Appendix 5.9M]
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 25:1771-80. PMID:26294686 PMC4617972 https://doi.org/10.1101/gr.192518.115 [Advance access PDF 5M] Supp materials[Figures 5.3M] [Table 1 3k] [Table 2 6k] [Table 3 15M] [Table 4 1.3M] [Table 5 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 PMC4379411 https://doi.org/10.1093/molbev/msv002 [PDF 0.8M] [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 PMC4352190 https://doi.org/10.1007/s10875-015-0136-6 [PDF .3M]
Gerstein M, ... , Li JJ, ... , Bickel PB, ... , Huang H, ... , Brenner SE, ... , et al. 2014. Comparative analysis of the transcriptome across distant species. Nature 512:445-448. PMID:25164755 PMC4155737 https://doi.org/10.1038/nature13424 [PDF 4M]
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 PMC4079965 https://doi.org/10.1101/gr.170100.113 [PDF 3.6M] [supplementary material 18M]
Fox NK, Brenner SE, Chandonia JM. 2014. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research 42:D304-9. PMID:24304899 PMC3965108 https://doi.org/10.1093/nar/gkt1240 [PDF 2.4M]
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 PMC3848607 https://doi.org/10.1186/1471-230X-13-131 [PDF .7M] [supplementary content: tables and figures]
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 PMC3591536 https://doi.org/10.1007/s10875-012-9846-1 [PDF 445K]
Radivojac P, (9 authors) , Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, (82 authors) , Brenner SE, et al. 2013. A large-scale evaluation of computational protein function prediction. Nature Methods 10:221-227. PMID:23353650 PMC3584181 https://doi.org/10.1038/nmeth.2340 [PDF 720K] [supplementary information (3.0M)]
Soergel DAW, 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 PMC3379642 https://doi.org/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 PMC3205580 https://doi.org/10.1101/gr.104687.109 [PDF 1.2M]
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 PMC3075879 https://doi.org/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)]
Brooks AN, Yang L, Duff MO, Hansen KD, Dudoit S, Brenner SE, Graveley BR. 2010. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research 21:193-202. PMID:20921232 PMC3032923 https://doi.org/10.1101/gr.108662.110 [PDF .8M] [supplementary information (2.1MB) datasets 1 (4K) 2 (2K) 3 (471K) 4 (6K) 5 (4K) spa5.pl]
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 PMC2689934 https://doi.org/10.1371/journal.pgen.1000525 [PDF .5M]
Brenner SE. 2007. Common sense for our genomes. Nature 449:783-784. PMID:17943102 https://doi.org/10.1038/449783a [PDF .2M]
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. 190-211. PMID:18380348 https://doi.org/10.1007/978-0-387-77374-2_12 https://link.springer.com/chapter/10.1007/978-0-387-77374-2_12 [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 https://doi.org/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 PMC1821046 https://doi.org/10.1371/journal.pbio.0050016 [PDF 3M] [Cover PDF 19M]
Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-351. PMID:16424331 https://doi.org/10.1126/science.1121018 [PDF .2M] [supporting material 1.2M]
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Computational Biology 1:e45. PMID:16217548 PMC1246806 https://doi.org/10.1371/journal.pcbi.0010045 [PDF 1.4M] [Cover PDF 5M] [Cover image 4M]
Crooks GE, Wolfe J, Brenner SE. 2004. Measurements of protein sequence-structure correlations. Proteins: Structure, Function, and Bioinformatics 57:804-810. PMID:15476257 https://doi.org/10.1002/prot.20262 [PDF .18M]
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 https://doi.org/10.1016/j.sbi.2004.05.002 [PDF .18M]
Hillman RT, Green RE, Brenner SE. 2004. An unappreciated role for RNA surveillance. Genome Biology 5:R8.1-R8.16. PMID:14759258 PMC395752 https://doi.org/10.1186/gb-2004-5-2-r8 [PDF .36M]
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 PMC140922 https://doi.org/10.1073/pnas.0136770100 [PDF .25M]
Brenner SE. 1999. Errors in genome annotation. Trends in Genetics 15:132-133. PMID:10203816 https://doi.org/10.1016/S0168-9525(99)01706-0 [PDF .16M]
Brenner SE, Hubbard T, Murzin A, Chothia C. 1995. Gene duplications in H. influenzae. Nature 378:140. PMID:7477316 https://doi.org/10.1038/378140a0 [OCR PDF 1.43M]
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 https://doi.org/10.1016/S0022-2836(05)80134-2 [PDF 3.4M]


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