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    22837 Publications
    3073 Total Profiles
    22 Edited Profiles

    Brenner, Steven

    TitleBiologist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/643-9131

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins. 2015 Nov; 83(11):2025-38.
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      2. Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Booth BW, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res. 2015 Nov; 25(11):1771-80.
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      3. Bourne PE, Brenner SE, Eisen MB. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput Biol. 2015 Jun; 11(6):e1004317.
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      4. Sahraeian SM, Luo KR, Brenner SE. SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Res. 2015 Jul 1; 43(W1):W141-7.
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      5. 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). J Clin Immunol. 2015 Feb; 35(2):227-33.
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      6. 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. J Clin Immunol. 2015 Feb; 35(2):135-46.
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      7. Lareau LF, Brenner SE. Regulation of Splicing Factors by Alternative Splicing and NMD Is Conserved between Kingdoms Yet Evolutionarily Flexible. Mol Biol Evol. 2015 Apr; 32(4):1072-9.
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      8. Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pac Symp Biocomput. 2015; 20:342-6.
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      9. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8.
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      10. 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, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6.
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      11. 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 Res. 2014 Jul; 24(7):1086-101.
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      12. 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. J Struct Biol. 2014 Jul; 187(1):66-75.
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      13. Fox NK, Brenner SE, Chandonia JM. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014 Jan 1; 42(1):D304-9.
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      14. Shatsky M, Arbelaez P, Glaeser RM, Brenner SE. Optimal and fast rotational alignment of volumes with missing data in Fourier space. J Struct Biol. 2013 Nov; 184(2):345-7.
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      15. 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, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. The COMBREX project: design, methodology, and initial results. PLoS Biol. 2013; 11(8):e1001638.
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      16. Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterol. 2013; 13:131.
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      17. 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 Ia subfamily. Proteins. 2013 Sep; 81(9):1593-609.
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      18. Brenner SE. Be prepared for the big genome leak. Nature. 2013 Jun 13; 498(7453):139.
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      19. Xu A, Desai AM, Brenner SE, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem. 2013 Jun 15; 437(2):178-84.
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      20. 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, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 Mar; 10(3):221-7.
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      21. Morris Q, Brenner SE, Listgarten J, Stegle O. The future of genome-based medicine. Pac Symp Biocomput. 2013; 456-8.
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      22. 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. J Clin Immunol. 2013 Apr; 33(3):540-9.
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      23. 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, Biggin MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 7; 11(12):5720-35.
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      24. Soergel DA, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012 Jul; 6(7):1440-4.
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      25. 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. 2011 Oct; 17(10):1884-94.
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      26. Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res. 2011 Nov; 21(11):1969-80.
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      27. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97.
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      28. 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, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):473-9.
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      29. 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 Res. 2011 Mar; 39(6):2344-56.
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      30. 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 Res. 2011 Feb; 21(2):193-202.
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      31. Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 2010 Jul; 38(12):e131.
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      32. Zhi D, Shatsky M, Brenner SE. Alignment-free local structural search by writhe decomposition. Bioinformatics. 2010 May 1; 26(9):1176-84.
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      33. Shatsky M, Hall RJ, Nogales E, Malik J, Brenner SE. Automated multi-model reconstruction from single-particle electron microscopy data. J Struct Biol. 2010 Apr; 170(1):98-108.
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      34. 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, Biggin MD, Glaeser RM. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39):16580-5.
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      35. 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 Genet. 2009 Jun; 5(6):e1000525.
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      36. 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, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS. Planning the human variome project: the Spain report. Hum Mutat. 2009 Apr; 30(4):496-510.
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      37. 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. Mol Cell. 2009 Feb 27; 33(4):438-49.
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      38. 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, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9.
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      39. Shatsky M, Hall RJ, Brenner SE, Glaeser RM. A method for the alignment of heterogeneous macromolecules from electron microscopy. J Struct Biol. 2009 Apr; 166(1):67-78.
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      40. 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 Res. 2008 Jan; 36(Database issue):D419-25.
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      41. Brenner SE. Common sense for our genomes. Nature. 2007 Oct 18; 449(7164):783-4.
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      42. Bourne PE, Brenner SE. Developing computational biology. PLoS Comput Biol. 2007 Sep; 3(9):1669.
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      43. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 2007 Apr 19; 446(7138):926-9.
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      44. 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, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16.
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      45. Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE. The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol. 2007; 623:190-211.
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      46. Hendrix DK, Brenner SE, Holbrook SR. RNA structural motifs: building blocks of a modular biomolecule. Q Rev Biophys. 2005 Aug; 38(3):221-43.
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      47. 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. 2006 Apr; 12(4):533-41.
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      48. Chandonia JM, Kim SH, Brenner SE. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins. 2006 Feb 1; 62(2):356-70.
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      49. Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science. 2006 Jan 20; 311(5759):347-51.
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      50. Smith A, Chandonia JM, Brenner SE. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics. 2006 Mar 1; 22(5):618-20.
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      51. 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 Res. 2006 Jan 1; 34(Database issue):D131-4.
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      52. Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol. 2005 Oct; 1(5):e45.
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      53. Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation. Bioinformatics. 2005 Oct 1; 21(19):3704-10.
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      54. Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics. 2005 Oct 15; 21(20):3824-31.
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      55. Blanchette M, Green RE, Brenner SE, Rio DC. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 2005 Jun 1; 19(11):1306-14.
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      56. Bourne PE, Brenner SE, Eisen MB. PLoS Computational Biology: a new community journal. PLoS Comput Biol. 2005 Jun; 1(1):e4.
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      57. Zachariah MA, Crooks GE, Holbrook SR, Brenner SE. A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins. 2005 Feb 1; 58(2):329-38.
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      58. Chandonia JM, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 2005 Jan 1; 58(1):166-79.
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      59. Chandonia JM, Brenner S. Update on the pfam5000 strategy for selection of structural genomics targets. Conf Proc IEEE Eng Med Biol Soc. 2005; 1:751-5.
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      60. 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, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R. Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics. 2005; 6(2-3):63-70.
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      61. Crooks GE, Wolfe J, Brenner SE. Measurements of protein sequence-structure correlations. Proteins. 2004 Dec 1; 57(4):804-10.
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      62. Crooks GE, Brenner SE. An alternative model of amino acid replacement. Bioinformatics. 2005 Apr 1; 21(7):975-80.
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      63. Chandonia JM, Earnest TN, Brenner SE. Structural genomics and structural biology: compare and contrast. Genome Biol. 2004; 5(9):343.
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      64. 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. Mol Cell. 2004 Jun 18; 14(6):775-86.
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      65. Lareau LF, Green RE, Bhatnagar RS, Brenner SE. The evolving roles of alternative splicing. Curr Opin Struct Biol. 2004 Jun; 14(3):273-82.
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      66. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun; 14(6):1188-90.
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      67. 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. J Mol Biol. 2004 May 21; 339(1):103-16.
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      68. 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 Res. 2004; 32(8):2342-52.
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      69. Crooks GE, Brenner SE. Protein secondary structure: entropy, correlations and prediction. Bioinformatics. 2004 Jul 10; 20(10):1603-11.
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      70. Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biol. 2004; 5(2):R8.
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      71. Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D189-92.
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      72. 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 Res. 2004 Jan 1; 32(Database issue):D226-9.
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      73. Tamura M, Hendrix DK, Klosterman PS, Schimmelman NR, Brenner SE, Holbrook SR. SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D182-4.
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      74. 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. 2003; 19 Suppl 1:i118-21.
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      75. Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A. 2003 Jan 7; 100(1):189-92.
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      76. 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, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct; 12(10):1611-8.
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      77. Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. Sulfotransferases and sulfatases in mycobacteria. Chem Biol. 2002 Jul; 9(7):767-76.
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      78. Klosterman PS, Tamura M, Holbrook SR, Brenner SE. SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 2002 Jan 1; 30(1):392-4.
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      79. Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Res. 2002 Jan 1; 30(1):260-3.
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      80. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res. 2002 Jan 1; 30(1):264-7.
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