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    Brenner, Steven

    TitleBiologist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/643-9131
    vCardDownload vCard

      Collapse Bibliographic 
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner S. Reports from CAGI: The Critical Assessment of Genome Interpretation. Hum Mutat. 2017 Sep; 38(9):1039-1041. PMID: 28817245.
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      2. Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner S, Morgan AA. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 2017 Sep; 38(9):1182-1192. PMID: 28634997.
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      3. Cai B, Li B, Kiga N, Thusberg J, Bergquist T, 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 RA, Repo S, Church G, Brenner S, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Hum Mutat. 2017 Sep; 38(9):1266-1276. PMID: 28544481.
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      4. 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 S, Moult J, Tosatto SCE. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat. 2017 Sep; 38(9):1042-1050. PMID: 28440912.
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      5. Srouji JR, Xu A, Park A, Kirsch JF, Brenner S. The evolution of function within the Nudix homology clan. Proteins. 2017 May; 85(5):775-811. PMID: 27936487.
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      6. Oetting WS, Béroud C, Brenner S, Greenblatt M, Karchin R, Mooney SD, Sunyaev S. Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat. 2017 Apr; 38(4):460-463. PMID: 28054414.
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      7. Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner S, Brower AM, Cakici JA, 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 BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, 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. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics. 2017 Feb; 139(2). PMID: 28096516.
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      8. Karacic Z, Vukelic B, Ho GH, Jozic I, Sucec I, Salopek-Sondi B, Kozlovic M, Brenner S, Ludwig-Müller J, Abramic M. A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III. Biol Chem. 2017 Jan 01; 398(1):101-112. PMID: 27467751.
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      9. Punwani D, Zhang Y, Yu J, Cowan MJ, Rana S, Kwan A, Adhikari AN, Lizama CO, Mendelsohn BA, Fahl SP, Chellappan A, Srinivasan R, Brenner S, Wiest DL, Puck JM. Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B. N Engl J Med. 2016 12 01; 375(22):2165-2176. PMID: 27959755.
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      10. Nguyen VN, Park A, Xu A, Srouji JR, Brenner S, Kirsch JF. Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. Proteins. 2016 Dec; 84(12):1810-1822. PMID: 27618147.
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      11. Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner S, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 Sep 07; 17(1):184. PMID: 27604469; PMCID: PMC5015320.
      12. Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner S, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics. 2016 Jun; 15(6):2186-202. PMID: 27099342.
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      13. 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, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner S, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics. 2016 May; 15(5):1539-55. PMID: 26873250; PMCID: PMC4858938 [Available on 05/01/17].
      14. Oetting WS, Brenner S, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE. Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat. 2016 Apr; 37(4):406-11. PMID: 26791113; PMCID: PMC4783187 [Available on 04/01/17].
      15. Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner S, Weiss A, Puck JM. A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70. J Exp Med. 2016 Feb 08; 213(2):155-65. PMID: 26783323; PMCID: PMC4749924.
      16. Brenner S, Kingsmore S, Mooney SD, Nussbaum R, Puck J. USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:568-75. PMID: 26776219.
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      17. Morgan AA, Mooney SD, Aronow BJ, Brenner S. PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY. Pac Symp Biocomput. 2016; 21:243-8. PMID: 26776190.
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      18. Morgan AA, Crawford DC, Denny JC, Mooney SD, Aronow BJ, Brenner S. PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY. Pac Symp Biocomput. 2016; 22:348-355. PMID: 27896988.
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      19. Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner S, Zaitlen N, Goga A, Ziv E. Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. Hum Mol Genet. 2015 Dec 20; 24(25):7421-31. PMID: 26472073; PMCID: PMC4664170.
      20. Fox NK, Brenner S, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins. 2015 Nov; 83(11):2025-38. PMID: 26313554; PMCID: PMC4609302.
      21. Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Booth BW, Celniker SE, Graveley BR, Brenner S. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res. 2015 Nov; 25(11):1771-80. PMID: 26294686; PMCID: PMC4617972.
      22. Bourne PE, Brenner S, Eisen MB. Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput Biol. 2015 Jun; 11(6):e1004317. PMID: 26107720; PMCID: PMC4479580.
      23. Sahraeian SM, Luo KR, Brenner S. SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Res. 2015 Jul 01; 43(W1):W141-7. PMID: 25979264; PMCID: PMC4489292.
      24. Patel JP, Puck JM, Srinivasan R, Brown C, Sunderam U, Kundu K, Brenner S, 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. PMID: 25677497; PMCID: PMC4352190.
      25. Punwani D, Wang H, Chan AY, Cowan MJ, Mallott J, Sunderam U, Mollenauer M, Srinivasan R, Brenner S, 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. PMID: 25627829; PMCID: PMC4352191.
      26. Lareau LF, Brenner S. 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. PMID: 25576366; PMCID: PMC4379411.
      27. Dudley JT, Listgarten J, Stegle O, Brenner S, Parts L. Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pac Symp Biocomput. 2015; 342-6. PMID: 25592594.
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      28. 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 S, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8. PMID: 25164755; PMCID: PMC4155737.
      29. 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 S, 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. PMID: 25164757; PMCID: PMC4336544.
      30. Li JJ, Huang H, Bickel PJ, Brenner S. 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. PMID: 24985912; PMCID: PMC4079965.
      31. Shatsky M, Arbelaez P, Han BG, Typke D, Brenner S, 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. PMID: 24694675.
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      32. Listgarten J, Stegle O, Morris Q, Brenner S, Parts L. Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp Biocomput. 2014; 19:224-8. PMID: 24297549.
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      33. Listgarten J, Stegle O, Morris Q, Brenner S, Parts L. PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS THERAPY. Pac Symp Biocomput. 2014; 19:224-228. PMID: 28828395.
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      34. Fox NK, Brenner S, Chandonia JM. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014 Jan; 42(Database issue):D304-9. PMID: 24304899; PMCID: PMC3965108.
      35. Shatsky M, Arbelaez P, Glaeser RM, Brenner S. Optimal and fast rotational alignment of volumes with missing data in Fourier space. J Struct Biol. 2013 Nov; 184(2):345-7. PMID: 23994045.
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      36. 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 S, 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. PMID: 24013487; PMCID: PMC3754883.
      37. Dey N, Soergel DA, Repo S, Brenner S. Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterol. 2013 Aug 22; 13:131. PMID: 23964800; PMCID: PMC3848607.
      38. Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner S, 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. PMID: 23671031; PMCID: PMC3823064.
      39. Brenner S. Be prepared for the big genome leak. Nature. 2013 Jun 13; 498(7453):139. PMID: 23765454.
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      40. Xu A, Desai AM, Brenner S, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem. 2013 Jun 15; 437(2):178-84. PMID: 23481913; PMCID: PMC3744803.
      41. 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 S, 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. PMID: 23353650; PMCID: PMC3584181.
      42. Morris Q, Brenner S, Listgarten J, Stegle O. The future of genome-based medicine. Pac Symp Biocomput. 2013; 456-8. PMID: 23424151.
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      43. Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner S, Puck J. Newborn screening for SCID identifies patients with ataxia telangiectasia. J Clin Immunol. 2013 Apr; 33(3):540-9. PMID: 23264026; PMCID: PMC3591536.
      44. Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner S, 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 07; 11(12):5720-35. PMID: 23098413; PMCID: PMC3516867.
      45. Soergel DA, Dey N, Knight R, Brenner S. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012 Jul; 6(7):1440-4. PMID: 22237546; PMCID: PMC3379642.
      46. Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner S. 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. PMID: 21865603; PMCID: PMC3185920.
      47. Engelhardt BE, Jordan MI, Srouji JR, Brenner S. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res. 2011 Nov; 21(11):1969-80. PMID: 21784873; PMCID: PMC3205580.
      48. 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, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner S, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974; PMCID: PMC3192495.
      49. 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 S, 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. PMID: 21179090; PMCID: PMC3075879.
      50. Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner S, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res. 2011 Mar; 39(6):2344-56. PMID: 21071404; PMCID: PMC3064769.
      51. Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner S, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. 2011 Feb; 21(2):193-202. PMID: 20921232; PMCID: PMC3032923.
      52. Hansen KD, Brenner S, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 2010 Jul; 38(12):e131. PMID: 20395217; PMCID: PMC2896536.
      53. Zhi D, Shatsky M, Brenner S. Alignment-free local structural search by writhe decomposition. Bioinformatics. 2010 May 01; 26(9):1176-84. PMID: 20371498; PMCID: PMC2859133.
      54. Shatsky M, Hall RJ, Nogales E, Malik J, Brenner S. Automated multi-model reconstruction from single-particle electron microscopy data. J Struct Biol. 2010 Apr; 170(1):98-108. PMID: 20085819; PMCID: PMC2841227.
      55. 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 S, 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. PMID: 19805340; PMCID: PMC2742403.
      56. Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner S. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet. 2009 Jun; 5(6):e1000525. PMID: 19543372; PMCID: PMC2689934.
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