| Year |
Citation |
Score |
| 2021 |
Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE. SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. Nucleic Acids Research. PMID 34850923 DOI: 10.1093/nar/gkab1054 |
0.318 |
|
| 2019 |
Milko LV, Chen F, Chan K, Brower AM, Agrawal PB, Beggs AH, Berg JS, Brenner SE, Holm IA, Koenig BA, Parad RB, Powell CM, Kingsmore SF. FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation. Npj Genomic Medicine. 4: 32. PMID 31839987 DOI: 10.1038/S41525-019-0105-8 |
0.322 |
|
| 2019 |
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Brenner SE, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8 |
0.633 |
|
| 2019 |
Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, ... ... Brenner SE, et al. Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Human Mutation. PMID 31342580 DOI: 10.1002/Humu.23875 |
0.315 |
|
| 2019 |
Andreoletti G, Pal LR, Moult J, Brenner SE. Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation. Human Mutation. PMID 31334884 DOI: 10.1002/Humu.23876 |
0.328 |
|
| 2019 |
Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, Jiang Y, Joseph T, Katsonis P, Kotte S, Kundu K, ... ... Brenner SE, et al. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Human Mutation. PMID 31322791 DOI: 10.1002/Humu.23874 |
0.621 |
|
| 2019 |
Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, ... ... Brenner SE, et al. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants. Human Mutation. PMID 31301157 DOI: 10.1002/Humu.23868 |
0.313 |
|
| 2019 |
Hu Z, Yu C, Furutsuki M, Andreoletti G, Ly M, Hoskins R, Adhikari AN, Brenner SE. VIPdb, a genetic Variant Impact Predictor Database. Human Mutation. PMID 31283070 DOI: 10.1002/Humu.23858 |
0.303 |
|
| 2019 |
Monzon AM, Carraro M, Chiricosta L, Reggiani F, Han J, Ozturk K, Wang Y, Miller M, Bromberg Y, Capriotti E, Savojardo C, Babbi G, Martelli PL, Casadio R, Katsonis P, ... ... Brenner SE, et al. Performance of computational methods for the evaluation of Pericentriolar Material 1 missense variants in CAGI-5. Human Mutation. PMID 31260570 DOI: 10.1002/Humu.23856 |
0.32 |
|
| 2019 |
Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, ... ... Brenner S, et al. Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Human Mutation. PMID 31241222 DOI: 10.1002/Humu.23849 |
0.318 |
|
| 2019 |
Savojardo C, Petrosino M, Babbi G, Bovo S, Corbi-Verge C, Casadio R, Fariselli P, Folkman L, Garg A, Karimi M, Katsonis P, Kim PM, Lichtarge O, Martelli PL, Pasquo A, ... ... Brenner S, et al. Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Human Mutation. PMID 31209948 DOI: 10.1002/Humu.23843 |
0.363 |
|
| 2019 |
Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, ... ... Brenner SE, et al. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Human Mutation. PMID 31144778 DOI: 10.1002/Humu.23823 |
0.332 |
|
| 2019 |
McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan RG, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, ... ... Brenner S, et al. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation. PMID 31140652 DOI: 10.1002/Humu.23825 |
0.324 |
|
| 2018 |
Chandonia JM, Fox NK, Brenner SE. SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. Nucleic Acids Research. PMID 30500919 DOI: 10.1093/Nar/Gky1134 |
0.432 |
|
| 2018 |
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, ... ... Brenner SE, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/Nbt.4163 |
0.378 |
|
| 2017 |
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 R, Li X, Pal LR, ... ... Brenner SE, et al. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation. PMID 28634997 DOI: 10.1002/Humu.23280 |
0.323 |
|
| 2017 |
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, Grace Yeo HT, Fan J, Sengupta S, ... ... Brenner SE, et al. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. PMID 28544481 DOI: 10.1002/Humu.23265 |
0.617 |
|
| 2017 |
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, ... ... Brenner SE, et al. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation. PMID 28440912 DOI: 10.1002/Humu.23235 |
0.63 |
|
| 2017 |
Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, et al. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics. PMID 28096516 DOI: 10.1542/Peds.2016-2252 |
0.336 |
|
| 2016 |
Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The Evolution of Function within the Nudix homology Clan. Proteins. PMID 27936487 DOI: 10.1002/Prot.25223 |
0.615 |
|
| 2016 |
Chandonia JM, Fox NK, Brenner SE. SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. Journal of Molecular Biology. PMID 27914894 DOI: 10.1016/J.Jmb.2016.11.023 |
0.419 |
|
| 2016 |
Nguyen VN, Park A, Xu A, Srouji JR, Brenner SE, Kirsch JF. Substrate specificity characterization for eight putative Nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. Proteins. PMID 27618147 DOI: 10.1002/Prot.25163 |
0.513 |
|
| 2016 |
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, ... ... Brenner SE, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6 |
0.637 |
|
| 2016 |
Karačić Z, Vukelić B, Ho GH, Jozić I, Sučec I, Salopek-Sondi B, Kozlović M, Brenner SE, Ludwig-Müller J, Abramić M. A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III. Biological Chemistry. PMID 27467751 DOI: 10.1515/Hsz-2016-0141 |
0.334 |
|
| 2016 |
Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, et al. Quantitative tagless co-purification: a method to validate and identify protein-protein interactions. Molecular & Cellular Proteomics : McP. PMID 27099342 DOI: 10.1074/Mcp.M115.057117 |
0.34 |
|
| 2016 |
Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, ... ... Brenner SE, et al. Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Molecular & Cellular Proteomics : McP. PMID 26873250 DOI: 10.1074/Mcp.M115.054692 |
0.343 |
|
| 2016 |
Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, ... ... Brenner SE, et al. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. The Pharmacogenomics Journal. PMID 26856248 DOI: 10.1038/Tpj.2015.93 |
0.311 |
|
| 2016 |
Oetting WS, Brenner SE, 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. Human Mutation. PMID 26791113 DOI: 10.1002/Humu.22958 |
0.318 |
|
| 2015 |
Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins. 83: 2025-38. PMID 26313554 DOI: 10.1002/Prot.24915 |
0.382 |
|
| 2015 |
Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. PMID 26294686 DOI: 10.1101/Gr.192518.115 |
0.412 |
|
| 2015 |
Bourne PE, Brenner SE, Eisen MB. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. Plos Computational Biology. 11: e1004317. PMID 26107720 DOI: 10.1371/Journal.Pcbi.1004317 |
0.541 |
|
| 2015 |
Sahraeian SM, Luo KR, Brenner SE. SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Research. 43: W141-7. PMID 25979264 DOI: 10.1093/Nar/Gkv461 |
0.377 |
|
| 2015 |
Lareau LF, Brenner SE. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution. 32: 1072-9. PMID 25576366 DOI: 10.1093/Molbev/Msv002 |
0.752 |
|
| 2014 |
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, ... ... Brenner SE, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668 |
0.516 |
|
| 2014 |
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, ... Brenner SE, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424 |
0.522 |
|
| 2014 |
Fox NK, Brenner SE, Chandonia JM. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research. 42: D304-9. PMID 24304899 DOI: 10.1093/Nar/Gkt1240 |
0.416 |
|
| 2013 |
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... Brenner SE, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/Journal.Pbio.1001638 |
0.521 |
|
| 2013 |
Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with post-operative clinical course in Crohn's disease. Bmc Gastroenterology. 13: 131. PMID 23964800 DOI: 10.1186/1471-230X-13-131 |
0.745 |
|
| 2013 |
Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF. Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. Proteins. 81: 1593-609. PMID 23671031 DOI: 10.1002/Prot.24318 |
0.374 |
|
| 2013 |
Xu A, Desai AM, Brenner SE, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Analytical Biochemistry. 437: 178-84. PMID 23481913 DOI: 10.1016/J.Ab.2013.02.023 |
0.5 |
|
| 2013 |
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, ... ... Brenner SE, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340 |
0.659 |
|
| 2012 |
Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, et al. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. Journal of Proteome Research. 11: 5720-35. PMID 23098413 DOI: 10.1021/Pr300548D |
0.305 |
|
| 2012 |
Soergel DA, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The Isme Journal. 6: 1440-4. PMID 22237546 DOI: 10.1038/Ismej.2011.208 |
0.78 |
|
| 2011 |
Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. Rna (New York, N.Y.). 17: 1884-94. PMID 21865603 DOI: 10.1261/Rna.2696311 |
0.434 |
|
| 2011 |
Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Research. 21: 1969-80. PMID 21784873 DOI: 10.1101/Gr.104687.109 |
0.414 |
|
| 2011 |
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, ... Brenner SE, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715 |
0.576 |
|
| 2011 |
Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research. 39: 2344-56. PMID 21071404 DOI: 10.1093/Nar/Gkq1046 |
0.336 |
|
| 2011 |
Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21: 193-202. PMID 20921232 DOI: 10.1101/Gr.108662.110 |
0.433 |
|
| 2010 |
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Brenner SE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.414 |
|
| 2010 |
Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research. 38: e131. PMID 20395217 DOI: 10.1093/Nar/Gkq224 |
0.346 |
|
| 2010 |
Zhi D, Shatsky M, Brenner SE. Alignment-free local structural search by writhe decomposition. Bioinformatics (Oxford, England). 26: 1176-84. PMID 20371498 DOI: 10.1093/Bioinformatics/Btq127 |
0.331 |
|
| 2009 |
Engelhardt BE, Jordan MI, Repo ST, Brenner SE. Phylogenetic molecular function annotation. Journal of Physics. Conference Series. 180: 12024. PMID 20664722 DOI: 10.1088/1742-6596/180/1/012024 |
0.305 |
|
| 2009 |
Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, et al. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proceedings of the National Academy of Sciences of the United States of America. 106: 16580-5. PMID 19805340 DOI: 10.1073/Pnas.0813068106 |
0.348 |
|
| 2009 |
Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Plos Genetics. 5: e1000525. PMID 19543372 DOI: 10.1371/Journal.Pgen.1000525 |
0.787 |
|
| 2009 |
Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, ... Brenner SE, et al. Planning the human variome project: the Spain report. Human Mutation. 30: 496-510. PMID 19306394 DOI: 10.1002/Humu.20972 |
0.316 |
|
| 2009 |
Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell. 33: 438-49. PMID 19250905 DOI: 10.1016/J.Molcel.2009.01.022 |
0.684 |
|
| 2009 |
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014 |
0.552 |
|
| 2008 |
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research. 36: D419-25. PMID 18000004 DOI: 10.1093/Nar/Gkm993 |
0.721 |
|
| 2007 |
Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE. The coupling of alternative splicing and nonsense-mediated mRNA decay. Advances in Experimental Medicine and Biology. 623: 190-211. PMID 18380348 DOI: 10.1007/978-0-387-77374-2_12 |
0.768 |
|
| 2007 |
Brenner SE. Common sense for our genomes. Nature. 449: 783-4. PMID 17943102 DOI: 10.1038/449783A |
0.338 |
|
| 2007 |
Bourne PE, Brenner SE. Developing computational biology. Plos Computational Biology. 3: 1669. PMID 17907793 DOI: 10.1371/Journal.Pcbi.0030157 |
0.303 |
|
| 2007 |
Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 446: 926-9. PMID 17361132 DOI: 10.1038/Nature05676 |
0.794 |
|
| 2007 |
Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, ... ... Brenner SE, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/Journal.Pbio.0050016 |
0.799 |
|
| 2006 |
Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/Rna.2343206 |
0.338 |
|
| 2006 |
Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science (New York, N.Y.). 311: 347-51. PMID 16424331 DOI: 10.1126/Science.1121018 |
0.335 |
|
| 2006 |
Chandonia JM, Kim SH, Brenner SE. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins. 62: 356-70. PMID 16276528 DOI: 10.1002/Prot.20674 |
0.36 |
|
| 2005 |
Chandonia JM, Brenner S. Update on the pfam5000 strategy for selection of structural genomics targets. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 751-5. PMID 17282292 DOI: 10.1109/IEMBS.2005.1616523 |
0.319 |
|
| 2005 |
Hendrix DK, Brenner SE, Holbrook SR. RNA structural motifs: building blocks of a modular biomolecule. Quarterly Reviews of Biophysics. 38: 221-43. PMID 16817983 DOI: 10.1017/S0033583506004215 |
0.361 |
|
| 2005 |
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. Protein molecular function prediction by Bayesian phylogenomics. Plos Computational Biology. 1: e45. PMID 16217548 DOI: 10.1371/Journal.Pcbi.0010045 |
0.373 |
|
| 2005 |
Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, ... ... Brenner SE, et al. Structural genomics of minimal organisms and protein fold space. Journal of Structural and Functional Genomics. 6: 63-70. PMID 16211501 DOI: 10.1007/S10969-005-2651-9 |
0.434 |
|
| 2005 |
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014 |
0.78 |
|
| 2005 |
Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation Bioinformatics. 21: 3704-3710. PMID 16123116 DOI: 10.1093/Bioinformatics/Bti616 |
0.538 |
|
| 2005 |
Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics. 21: 3824-3831. PMID 16105900 DOI: 10.1093/Bioinformatics/Bti627 |
0.596 |
|
| 2005 |
Bourne PE, Brenner SE, Eisen MB. PLoS Computational Biology: a new community journal. Plos Computational Biology. 1: e4. PMID 16103905 DOI: 10.1371/Journal.Pcbi.0010004 |
0.513 |
|
| 2005 |
Blanchette M, Green RE, Brenner SE, Rio DC. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes & Development. 19: 1306-14. PMID 15937219 DOI: 10.1101/Gad.1314205 |
0.524 |
|
| 2005 |
Zachariah MA, Crooks GE, Holbrook SR, Brenner SE. A generalized affine gap model significantly improves protein sequence alignment accuracy Proteins: Structure, Function and Genetics. 58: 329-338. PMID 15562515 DOI: 10.1002/Prot.20299 |
0.361 |
|
| 2005 |
Crooks GE, Brenner SE. An alternative model of amino acid replacement Bioinformatics. 21: 975-980. PMID 15531614 DOI: 10.1093/Bioinformatics/Bti109 |
0.348 |
|
| 2005 |
Chandonia JM, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 58: 166-79. PMID 15521074 DOI: 10.1002/Prot.20298 |
0.43 |
|
| 2005 |
Brenner SE, Tramontano A. Sequences and topology: A decade of genomes Current Opinion in Structural Biology. 15: 245-247. DOI: 10.1016/J.Sbi.2005.05.009 |
0.343 |
|
| 2004 |
Crooks GE, Wolfe J, Brenner SE. Measurements of protein sequence-structure correlations Proteins: Structure, Function and Genetics. 57: 804-810. PMID 15476257 DOI: 10.1002/Prot.20262 |
0.376 |
|
| 2004 |
Chandonia JM, Earnest TN, Brenner SE. Structural genomics and structural biology: compare and contrast. Genome Biology. 5: 343. PMID 15345043 DOI: 10.1186/Gb-2004-5-9-343 |
0.328 |
|
| 2004 |
Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Molecular Cell. 14: 775-86. PMID 15200955 DOI: 10.1016/J.Molcel.2004.06.012 |
0.553 |
|
| 2004 |
Lareau LF, Green RE, Bhatnagar RS, Brenner SE. The evolving roles of alternative splicing. Current Opinion in Structural Biology. 14: 273-82. PMID 15193306 DOI: 10.1016/J.Sbi.2004.05.002 |
0.793 |
|
| 2004 |
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator Genome Research. 14: 1188-1190. PMID 15173120 DOI: 10.1101/Gr.849004 |
0.359 |
|
| 2004 |
Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Research. 32: 2342-52. PMID 15121895 DOI: 10.1093/Nar/Gkh537 |
0.337 |
|
| 2004 |
Crooks GE, Brenner SE. Protein secondary structure: Entropy, correlations and prediction Bioinformatics. 20: 1603-1611. PMID 14988117 DOI: 10.1093/Bioinformatics/Bth132 |
0.408 |
|
| 2004 |
Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biology. 5: R8. PMID 14759258 DOI: 10.1186/Gb-2004-5-2-R8 |
0.561 |
|
| 2004 |
Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research. 32: D226-9. PMID 14681400 DOI: 10.1093/Nar/Gkh039 |
0.745 |
|
| 2004 |
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Research. 32: D189-92. PMID 14681391 DOI: 10.1093/Nar/Gkh034 |
0.621 |
|
| 2004 |
Tamura M, Hendrix DK, Klosterman PS, Schimmelman NR, Brenner SE, Holbrook SR. SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Research. 32: D182-4. PMID 14681389 DOI: 10.1093/Nar/Gkh080 |
0.342 |
|
| 2003 |
Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics (Oxford, England). 19: i118-21. PMID 12855447 DOI: 10.1093/Bioinformatics/Btg1015 |
0.769 |
|
| 2003 |
Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proceedings of the National Academy of Sciences of the United States of America. 100: 189-92. PMID 12502788 DOI: 10.1073/Pnas.0136770100 |
0.574 |
|
| 2002 |
Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. Sulfotransferases and sulfatases in mycobacteria. Chemistry & Biology. 9: 767-76. PMID 12144918 DOI: 10.1016/S1074-5521(02)00175-8 |
0.535 |
|
| 2002 |
Klosterman PS, Tamura M, Holbrook SR, Brenner SE. SCOR: a Structural Classification of RNA database. Nucleic Acids Research. 30: 392-4. PMID 11752346 DOI: 10.1093/Nar/30.1.392 |
0.323 |
|
| 2002 |
Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research. 30: 264-7. PMID 11752311 DOI: 10.1093/Nar/30.1.264 |
0.723 |
|
| 2002 |
Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Research. 30: 260-3. PMID 11752310 DOI: 10.1093/Nar/30.1.260 |
0.64 |
|
| 2002 |
Chandonia J, Konerding DE, Allen DG, Choi I, Yokota H, Brenner SE. Computational Structural Genomics of a Complete Minimal Organism Genome Informatics. 13: 390-391. DOI: 10.11234/Gi1990.13.390 |
0.449 |
|
| 2002 |
Green RE, Brenner SE. Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison Proceedings of the Ieee. 90: 1834-1847. DOI: 10.1109/JPROC.2002.805303 |
0.454 |
|
| 2002 |
Brenner SE. Genome annotation and protein structure Proceedings - Ieee Computer Society Bioinformatics Conference, Csb 2002. 4. DOI: 10.1109/CSB.2002.1039322 |
0.353 |
|
| 2001 |
Zupicich J, Brenner SE, Skarnes WC. Computational prediction of membrane-tethered transcription factors. Genome Biology. 2: RESEARCH0050. PMID 11790253 DOI: 10.1186/Gb-2001-2-12-Research0050 |
0.305 |
|
| 2001 |
Brenner SE. A tour of structural genomics. Nature Reviews. Genetics. 2: 801-9. PMID 11584296 DOI: 10.1038/35093574 |
0.369 |
|
| 2000 |
Brenner SE. Target selection for structural genomics. Nature Structural Biology. 7: 967-9. PMID 11104002 DOI: 10.1038/80747 |
0.388 |
|
| 2000 |
Brenner SE, Levitt M. Expectations from structural genomics. Protein Science : a Publication of the Protein Society. 9: 197-200. PMID 10739263 DOI: 10.1110/Ps.9.1.197 |
0.649 |
|
| 2000 |
Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Research. 28: 257-9. PMID 10592240 DOI: 10.1093/Nar/25.1.236 |
0.752 |
|
| 2000 |
Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research. 28: 254-6. PMID 10592239 DOI: 10.1093/Nar/28.1.254 |
0.651 |
|
| 1999 |
Wolf YI, Brenner SE, Bash PA, Koonin EV. Distribution of protein folds in the three superkingdoms of life. Genome Research. 9: 17-26. PMID 9927481 DOI: 10.1101/Gr.9.1.17 |
0.406 |
|
| 1999 |
Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP: a Structural Classification of Proteins database. Nucleic Acids Research. 27: 254-6. PMID 9847194 DOI: 10.1093/nar/27.1.254 |
0.719 |
|
| 1999 |
Brenner SE, Barken D, Levitt M. The PRESAGE database for structural genomics. Nucleic Acids Research. 27: 251-3. PMID 9847193 DOI: 10.1093/Nar/27.1.251 |
0.612 |
|
| 1998 |
Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallographica. Section D, Biological Crystallography. 54: 1147-54. PMID 10089491 DOI: 10.1107/S0907444998009172 |
0.742 |
|
| 1998 |
Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proceedings of the National Academy of Sciences of the United States of America. 95: 6073-8. PMID 9600919 DOI: 10.1073/Pnas.95.11.6073 |
0.706 |
|
| 1998 |
Brenner SE. Practical database searching Trends in Biotechnology. 16: XVII-XVIII. DOI: 10.1016/S0167-7799(98)00128-0 |
0.303 |
|
| 1997 |
Chothia C, Hubbard T, Brenner S, Barns H, Murzin A. Protein folds in the all-β and all-α classes Annual Review of Biophysics and Biomolecular Structure. 26: 597-627. PMID 9241431 DOI: 10.1146/Annurev.Biophys.26.1.597 |
0.674 |
|
| 1997 |
Brenner SE, Chothia C, Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology. 7: 369-76. PMID 9204279 DOI: 10.1016/S0959-440X(97)80054-1 |
0.715 |
|
| 1996 |
Brenner SE, Chothia C, Hubbard TJP, Murzin AG. [37] Understanding protein structure: Using scop for fold interpretation Methods in Enzymology. 266: 635-642. PMID 8743710 DOI: 10.1016/S0076-6879(96)66039-X |
0.732 |
|
| 1995 |
Brenner SE. Blast, blitz, blocks and beauty; sequence comparison on the net Trends in Genetics. 11: 330-331. PMID 8585135 DOI: 10.1016/S0168-9525(00)89094-0 |
0.337 |
|
| 1995 |
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: A structural classification of proteins database for the investigation of sequences and structures Journal of Molecular Biology. 247: 536-540. PMID 7723011 DOI: 10.1016/S0022-2836(05)80134-2 |
0.734 |
|
| 1995 |
Suzuki M, Brenner SE, Gerstein M, Yagi N. DNA recognition code of transcription factors Protein Engineering. 8: 319-328. PMID 7567917 DOI: 10.1093/Protein/8.4.319 |
0.521 |
|
| 1995 |
Suzuki M, Brenner SE. Classification of multi-helical DNA-binding domains and application to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC Febs Letters. 372: 215-221. PMID 7556672 DOI: 10.1016/0014-5793(95)00988-L |
0.325 |
|
| 1995 |
Brenner SE, Hubbard T, Murzin A, Chothia C. Gene duplications in H. influenzae [7] Nature. 378: 140. PMID 7477316 DOI: 10.1038/378140A0 |
0.65 |
|
| 1994 |
Brenner SE, Berry A. A quantitative methodology for the de novo design of proteins Protein Science. 3: 1871-1882. PMID 7849602 DOI: 10.1002/Pro.5560031026 |
0.428 |
|
| 1993 |
Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B, Aparicio S. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature. 366: 265-8. PMID 8232585 DOI: 10.1038/366265A0 |
0.362 |
|
| 1973 |
Celis JE, Smith JD, Brenner S. Correlation between genetic and translational maps of gene 23 in bacteriophage T4. Nature. 241: 130-132. PMID 4573386 DOI: 10.1038/Newbio241130A0 |
0.317 |
|
| 1971 |
Altman S, Brenner S, Smith JD. Identification of an ochre-suppressing anticodon. Journal of Molecular Biology. 56: 195-7. PMID 4929886 DOI: 10.1016/0022-2836(71)90094-5 |
0.336 |
|
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