Brenton R. Graveley, Ph.D. - Publications

Affiliations: 
UConn Health Center, Farmington, CT, United States 
Area:
Genomics, alternative splicing, RNA biology

127 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Woodside WT, Vantsev N, Catchpole RJ, Garrett SC, Olson S, Graveley BR, Terns MP. Type III-A CRISPR-Cas systems as a versatile gene knockdown technology. Rna (New York, N.Y.). PMID 35618430 DOI: 10.1261/rna.079206.122  0.314
2022 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, et al. Author Correction: Perspectives on ENCODE. Nature. PMID 35474002 DOI: 10.1038/s41586-021-04213-8  0.621
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Graveley BR, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.764
2021 Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, ... ... Graveley BR, et al. Author Correction: A large-scale binding and functional map of human RNA-binding proteins. Nature. PMID 33402748 DOI: 10.1038/s41586-020-03067-w  0.473
2020 Leclair NK, Brugiolo M, Urbanski L, Lawson SC, Thakar K, Yurieva M, George J, Hinson JT, Cheng A, Graveley BR, Anczuków O. Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis. Molecular Cell. PMID 33176162 DOI: 10.1016/j.molcel.2020.10.019  0.333
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Graveley BR, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.809
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.732
2020 Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, ... ... Graveley BR, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature. 583: 711-719. PMID 32728246 DOI: 10.1038/S41586-020-2077-3  0.628
2020 Garrett S, Shiimori M, Watts EA, Clark L, Graveley BR, Terns MP. Primed CRISPR DNA uptake in Pyrococcus furiosus. Nucleic Acids Research. PMID 32421777 DOI: 10.1093/Nar/Gkaa381  0.328
2020 Guo LT, Adams RL, Wan H, Huston NC, Potapova O, Olson S, Gallardo CM, Graveley BR, Torbett BE, Pyle AM. Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase. Journal of Molecular Biology. PMID 32259542 DOI: 10.1016/J.Jmb.2020.03.022  0.423
2020 Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu XD, ... Graveley BR, et al. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biology. 21: 90. PMID 32252787 DOI: 10.1186/S13059-020-01982-9  0.576
2019 Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Communications Biology. 2: 19. PMID 31924889 DOI: 10.1038/s42003-018-0271-8  0.369
2019 Kim JG, Garrett S, Wei Y, Graveley BR, Terns MP. CRISPR DNA elements controlling site-specific spacer integration and proper repeat length by a Type II CRISPR-Cas system. Nucleic Acids Research. PMID 31392984 DOI: 10.1093/Nar/Gkz677  0.35
2019 Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, ... Graveley BR, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 178: 107-121.e18. PMID 31251911 DOI: 10.1016/J.Cell.2019.06.001  0.625
2019 Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, et al. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nature Communications. 10: 1338. PMID 30902979 DOI: 10.1038/S41467-019-09292-W  0.448
2019 Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, ... ... Graveley B, et al. Correction to: DNA copy number evolution in Drosophila cell lines. Genome Biology. 20: 53. PMID 30857560 DOI: 10.1186/S13059-019-1668-5  0.726
2019 Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Communications Biology. 2: 19. PMID 30652130 DOI: 10.1038/s42003-018-0271-8  0.369
2018 Yee B, Pratt G, Graveley B, Van Nostrand E, Yeo G. RBP-Maps enables robust generation of splicing regulatory maps. Rna (New York, N.Y.). PMID 30413564 DOI: 10.1261/Rna.069237.118  0.453
2018 Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ. Corrigendum: Tempo and mode of regulatory evolution in . Genome Research. 28: 1766. PMID 30385616 DOI: 10.1101/Gr.244087.118  0.63
2018 Webster MW, Chen YH, Stowell JAW, Alhusaini N, Sweet T, Graveley BR, Coller J, Passmore LA. mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases. Molecular Cell. 70: 1089-1100.e8. PMID 29932902 DOI: 10.1016/J.Molcel.2018.05.033  0.348
2018 Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Molecular Cell. 70: 854-867.e9. PMID 29883606 DOI: 10.1016/J.Molcel.2018.05.001  0.461
2018 Shiimori M, Garrett SC, Graveley BR, Terns MP. Cas4 Nucleases Define the PAM, Length, and Orientation of DNA Fragments Integrated at CRISPR Loci. Molecular Cell. 70: 814-824.e6. PMID 29883605 DOI: 10.1016/J.Molcel.2018.05.002  0.356
2018 Adamson SI, Zhan L, Graveley BR. Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency. Genome Biology. 19: 71. PMID 29859120 DOI: 10.1186/S13059-018-1437-X  0.385
2017 Zavolan M, Graveley BR. RNAs: dynamic and mutable. Genome Biology. 18: 226. PMID 29187228 DOI: 10.1186/S13059-017-1361-5  0.363
2017 Shiimori M, Garrett SC, Chambers DP, Glover CVC, Graveley BR, Terns MP. Role of free DNA ends and protospacer adjacent motifs for CRISPR DNA uptake in Pyrococcus furiosus. Nucleic Acids Research. PMID 29036456 DOI: 10.1093/Nar/Gkx839  0.344
2016 Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biology. 17: 203. PMID 27716375 DOI: 10.1186/S13059-016-1060-7  0.397
2016 Chen CY, Plocik A, Anderson NC, Moakley D, Boyi T, Dundes C, Lassiter C, Graveley BR, Grabel L. Transcriptome and in Vitro Differentiation Profile of Human Embryonic Stem Cell Derived NKX2.1-Positive Neural Progenitors. Stem Cell Reviews. PMID 27539622 DOI: 10.1007/S12015-016-9676-2  0.316
2016 Graveley BR. RNA Matchmaking: Finding Cellular Pairing Partners. Molecular Cell. 63: 186-9. PMID 27447984 DOI: 10.1016/J.Molcel.2016.07.001  0.427
2016 Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biology. 17: 74. PMID 27107712 DOI: 10.1186/S13059-016-0940-1  0.347
2016 Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lécuyer E, ... Graveley BR, et al. Resources for the Comprehensive Discovery of Functional RNA Elements. Molecular Cell. 61: 903-913. PMID 26990993 DOI: 10.1016/J.Molcel.2016.02.012  0.416
2016 Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. Distal Alternative Last Exons Localize mRNAs to Neural Projections. Molecular Cell. PMID 26907613 DOI: 10.1016/J.Molcel.2016.01.020  0.392
2015 Bolisetty MT, Rajadinakaran G, Graveley BR. Determining exon connectivity in complex mRNAs by nanopore sequencing. Genome Biology. 16: 204. PMID 26420219 DOI: 10.1186/S13059-015-0777-Z  0.416
2015 Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha K, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE. Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Research. PMID 26294687 DOI: 10.1101/Gr.182675.114  0.691
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  0.724
2015 Coolon JD, Stevenson KR, McManus CJ, Yang B, Graveley BR, Wittkopp PJ. Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome. Molecular Biology and Evolution. PMID 26041937 DOI: 10.1093/Molbev/Msv135  0.692
2015 Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M, Plocik A, Celniker SE, Graveley BR. Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature. 521: 376-9. PMID 25970244 DOI: 10.1038/Nature14475  0.698
2015 Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CV, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. Rna (New York, N.Y.). 21: 1147-58. PMID 25904135 DOI: 10.1261/Rna.049130.114  0.342
2015 Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ. Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation. Elife. 4. PMID 25866926 DOI: 10.7554/Elife.03700  0.481
2015 Graveley BR. Musings on 20 years of RNA. Rna (New York, N.Y.). 21: 506-7. PMID 25780115 DOI: 10.1261/Rna.051235.115  0.375
2015 Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, Coller J. Codon optimality is a major determinant of mRNA stability. Cell. 160: 1111-24. PMID 25768907 DOI: 10.1016/J.Cell.2015.02.029  0.343
2015 Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJ, Eisenberg E. The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. Elife. 4. PMID 25569156 DOI: 10.7554/Elife.05198  0.498
2014 Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Reports. 9: 1966-80. PMID 25544350 DOI: 10.1016/J.Celrep.2014.10.062  0.694
2014 Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, ... ... Graveley B, et al. DNA copy number evolution in Drosophila cell lines. Genome Biology. 15: R70. PMID 25262759 DOI: 10.1186/Gb-2014-15-8-R70  0.756
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, ... ... Graveley BR, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424  0.698
2014 Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, ... ... Graveley BR, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/Gr.159384.113  0.643
2014 Carte J, Christopher RT, Smith JT, Olson S, Barrangou R, Moineau S, Glover CV, Graveley BR, Terns RM, Terns MP. The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. Molecular Microbiology. 93: 98-112. PMID 24811454 DOI: 10.1111/Mmi.12644  0.342
2014 Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, ... ... Graveley BR, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 512: 393-9. PMID 24670639 DOI: 10.1038/Nature12962  0.71
2014 Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ. Tempo and mode of regulatory evolution in Drosophila. Genome Research. 24: 797-808. PMID 24567308 DOI: 10.1101/Gr.163014.113  0.697
2014 McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR. Evolution of splicing regulatory networks in Drosophila. Genome Research. 24: 786-96. PMID 24515119 DOI: 10.1101/Gr.161521.113  0.718
2014 Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJC, Eisenberg E. Author response: The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing Elife. DOI: 10.7554/Elife.05198.018  0.424
2014 Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ. Author response: Assessing long-distance RNA sequence connectivity via RNA-templated DNA–DNA ligation Elife. DOI: 10.7554/Elife.03700.022  0.403
2014 McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. Regulatory divergence in Drosophila revealed by mRNA-seq (Genome Research (2010) 20, (816-825)) Genome Research. 24: 1051.  0.678
2013 Miura SK, Martins A, Zhang KX, Graveley BR, Zipursky SL. Probabilistic splicing of Dscam1 establishes identity at the level of single neurons. Cell. 155: 1166-77. PMID 24267895 DOI: 10.1016/J.Cell.2013.10.018  0.386
2013 Bolisetty MT, Graveley BR. Circuitous route to transcription regulation. Molecular Cell. 51: 705-6. PMID 24074951 DOI: 10.1016/J.Molcel.2013.09.012  0.456
2013 Sasidharan V, Lu YC, Bansal D, Dasari P, Poduval D, Seshasayee A, Resch AM, Graveley BR, Palakodeti D. Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea. Rna (New York, N.Y.). 19: 1394-404. PMID 23974438 DOI: 10.1261/Rna.038653.113  0.674
2013 Marinotti O, Cerqueira GC, de Almeida LG, Ferro MI, Loreto EL, Zaha A, Teixeira SM, Wespiser AR, Almeida E Silva A, Schlindwein AD, Pacheco AC, Silva AL, Graveley BR, Walenz BP, Lima Bde A, et al. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Research. 41: 7387-400. PMID 23761445 DOI: 10.1093/Nar/Gkt484  0.34
2013 Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biology. 14: 113. PMID 23651518 DOI: 10.1186/Gb-2013-14-4-113  0.306
2013 Graveley BR. Tips for preparing mRNA-Seq libraries from poly(A)+ mRNA for Illumina transcriptome high-throughput sequencing. Cold Spring Harbor Protocols. 2013: 482-4. PMID 23637362 DOI: 10.1101/Pdb.Ip073908  0.344
2013 Elmore JR, Yokooji Y, Sato T, Olson S, Glover CV, Graveley BR, Atomi H, Terns RM, Terns MP. Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. Rna Biology. 10: 828-40. PMID 23535213 DOI: 10.4161/Rna.24084  0.352
2013 Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 152: 1252-69. PMID 23498935 DOI: 10.1016/J.Cell.2013.02.034  0.452
2013 Plocik AM, Graveley BR. New insights from existing sequence data: generating breakthroughs without a pipette. Molecular Cell. 49: 605-17. PMID 23438857 DOI: 10.1016/J.Molcel.2013.01.031  0.352
2013 Eipper-Mains JE, Kiraly DD, Duff MO, Horowitz MJ, McManus CJ, Eipper BA, Graveley BR, Mains RE. Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome. Genes, Brain, and Behavior. 12: 21-33. PMID 23094851 DOI: 10.1111/J.1601-183X.2012.00873.X  0.671
2013 Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, ... Graveley BR, et al. Errata to Global patterns of tissue-specific alternative polyadenylation in drosophila [Cell Reports, 1 (2012) 277-289] Cell Reports. 3: 969. DOI: 10.1016/j.celrep.2013.03.022  0.535
2012 Coolon JD, Stevenson KR, McManus CJ, Graveley BR, Wittkopp PJ. Genomic imprinting absent in Drosophila melanogaster adult females. Cell Reports. 2: 69-75. PMID 22840398 DOI: 10.1016/J.Celrep.2012.06.013  0.718
2012 Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, ... Graveley BR, et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports. 1: 277-89. PMID 22685694 DOI: 10.1016/J.Celrep.2012.01.001  0.682
2012 Resch AM, Palakodeti D, Lu YC, Horowitz M, Graveley BR. Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. Plos One. 7: e34447. PMID 22496805 DOI: 10.1371/Journal.Pone.0034447  0.706
2012 Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CV, Graveley BR, Terns RM, Terns MP. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Molecular Cell. 45: 292-302. PMID 22227116 DOI: 10.1016/J.Molcel.2011.10.023  0.402
2011 Graveley BR. Splicing up pluripotency. Cell. 147: 22-4. PMID 21962502 DOI: 10.1016/J.Cell.2011.09.004  0.326
2011 Hollenbach JP, Resch AM, Palakodeti D, Graveley BR, Heinen CD. Loss of DNA mismatch repair imparts a selective advantage in planarian adult stem cells. Plos One. 6: e21808. PMID 21747960 DOI: 10.1371/Journal.Pone.0021808  0.667
2011 Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, Eipper BA, Graveley BR. microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. Rna (New York, N.Y.). 17: 1529-43. PMID 21708909 DOI: 10.1261/Rna.2775511  0.67
2011 McManus CJ, Graveley BR. RNA structure and the mechanisms of alternative splicing. Current Opinion in Genetics & Development. 21: 373-9. PMID 21530232 DOI: 10.1016/J.Gde.2011.04.001  0.747
2011 Graveley BR. Getting in the loop: new insights into the mechanism of poly(A) site recognition. Structure (London, England : 1993). 19: 279-81. PMID 21397179 DOI: 10.1016/J.Str.2011.02.005  0.392
2011 Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biology. 12: R16. PMID 21324177 DOI: 10.1186/Gb-2011-12-2-R16  0.566
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, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715  0.736
2011 Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, ... ... Graveley BR, et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Research. 21: 301-14. PMID 21177962 DOI: 10.1101/Gr.112961.110  0.659
2011 Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Research. 21: 182-92. PMID 21177961 DOI: 10.1101/Gr.112466.110  0.719
2011 May GE, Olson S, McManus CJ, Graveley BR. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. Rna (New York, N.Y.). 17: 222-9. PMID 21159795 DOI: 10.1261/Rna.2521311  0.752
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  0.603
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, ... ... Graveley BR, 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  0.806
2010 McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 107: 12975-9. PMID 20615941 DOI: 10.1073/Pnas.1007586107  0.76
2010 McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research. 20: 816-25. PMID 20354124 DOI: 10.1101/Gr.102491.109  0.721
2010 Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 463: 457-63. PMID 20110989 DOI: 10.1038/Nature08909  0.425
2010 Lee C, Kim N, Roy M, Graveley BR. Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. Rna (New York, N.Y.). 16: 91-105. PMID 19934230 DOI: 10.1261/Rna.1812710  0.333
2009 Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell. 139: 945-56. PMID 19945378 DOI: 10.1016/J.Cell.2009.07.040  0.432
2009 Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. Rna (New York, N.Y.). 15: 1483-91. PMID 19553344 DOI: 10.1261/Rna.1702009  0.666
2009 Graveley BR. Alternative splicing: regulation without regulators. Nature Structural & Molecular Biology. 16: 13-5. PMID 19125169 DOI: 10.1038/Nsmb0109-13  0.446
2008 McManus CJ, Graveley BR. Getting the message out. Molecular Cell. 31: 4-6. PMID 18614041 DOI: 10.1016/J.Molcel.2008.06.010  0.715
2008 Graveley BR. Molecular biology: power sequencing. Nature. 453: 1197-8. PMID 18580940 DOI: 10.1038/4531197B  0.485
2008 Palakodeti D, Smielewska M, Lu YC, Yeo GW, Graveley BR. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. Rna (New York, N.Y.). 14: 1174-86. PMID 18456843 DOI: 10.1261/Rna.1085008  0.748
2008 Graveley BR. The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. Trends in Genetics : Tig. 24: 5-7. PMID 18054116 DOI: 10.1016/J.Tig.2007.10.004  0.328
2007 Olson S, Blanchette M, Park J, Savva Y, Yeo GW, Yeakley JM, Rio DC, Graveley BR. A regulator of Dscam mutually exclusive splicing fidelity. Nature Structural & Molecular Biology. 14: 1134-40. PMID 21188797 DOI: 10.1038/Nsmb1339  0.404
2007 Park JW, Graveley BR. Complex alternative splicing. Advances in Experimental Medicine and Biology. 623: 50-63. PMID 18380340 DOI: 10.1007/978-0-387-77374-2_4  0.404
2007 Yang L, Park J, Graveley BR. Splicing from the outside in. Molecular Cell. 27: 861-2. PMID 17889658 DOI: 10.1016/J.Molcel.2007.09.003  0.43
2006 Palakodeti D, Smielewska M, Graveley BR. MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology. Rna (New York, N.Y.). 12: 1640-9. PMID 16849698 DOI: 10.1261/Rna.117206  0.674
2006 Black DL, Graveley BR. Splicing bioinformatics to biology. Genome Biology. 7: 317. PMID 16732900 DOI: 10.1186/Gb-2006-7-5-317  0.375
2005 Park JW, Graveley BR. Use of RNA interference to dissect the roles of trans-acting factors in alternative pre-mRNA splicing. Methods (San Diego, Calif.). 37: 341-4. PMID 16314263 DOI: 10.1016/J.Ymeth.2005.07.016  0.5
2005 Kreahling JM, Graveley BR. The iStem, a long-range RNA secondary structure element required for efficient exon inclusion in the Drosophila Dscam pre-mRNA. Molecular and Cellular Biology. 25: 10251-60. PMID 16287842 DOI: 10.1128/Mcb.25.23.10251-10260.2005  0.405
2005 Graveley BR. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell. 123: 65-73. PMID 16213213 DOI: 10.1016/J.Cell.2005.07.028  0.457
2005 Celotto AM, Lee JW, Graveley BR. Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs. Methods in Molecular Biology (Clifton, N.J.). 309: 273-82. PMID 15990407 DOI: 10.1385/1-59259-935-4:273  0.491
2005 Hertel KJ, Graveley BR. RS domains contact the pre-mRNA throughout spliceosome assembly. Trends in Biochemical Sciences. 30: 115-8. PMID 15752982 DOI: 10.1016/J.Tibs.2005.01.002  0.317
2005 Graveley BR. Small molecule control of pre-mRNA splicing. Rna (New York, N.Y.). 11: 355-8. PMID 15661847 DOI: 10.1261/Rna.7229705  0.409
2004 Philipps DL, Park JW, Graveley BR. A computational and experimental approach toward a priori identification of alternatively spliced exons. Rna (New York, N.Y.). 10: 1838-44. PMID 15525709 DOI: 10.1261/Rna.7136104  0.448
2004 Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR. Identification of alternative splicing regulators by RNA interference in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 101: 15974-9. PMID 15492211 DOI: 10.1073/Pnas.0407004101  0.482
2004 Graveley BR, Kaur A, Gunning D, Zipursky SL, Rowen L, Clemens JC. The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. Rna (New York, N.Y.). 10: 1499-506. PMID 15383675 DOI: 10.1261/Rna.7105504  0.369
2004 Graveley BR. A protein interaction domain contacts RNA in the prespliceosome. Molecular Cell. 13: 302-4. PMID 14967137 DOI: 10.1016/S1097-2765(04)00055-3  0.338
2004 Celotto AM, Graveley BR. RNA interference of mRNA processing factors in Drosophila S2 cells. Methods in Molecular Biology (Clifton, N.J.). 257: 245-54. PMID 14770010 DOI: 10.1385/1-59259-750-5:245  0.456
2004 Celotto AM, Graveley BR. Using single-strand conformational polymorphism gel electrophoresis to analyze mutually exclusive alternative splicing. Methods in Molecular Biology (Clifton, N.J.). 257: 65-74. PMID 14769996 DOI: 10.1385/1-59259-750-5:065  0.356
2004 Kreahling J, Graveley BR. The origins and implications of Aluternative splicing. Trends in Genetics : Tig. 20: 1-4. PMID 14698612 DOI: 10.1016/J.Tig.2003.11.001  0.367
2003 Philipps D, Celotto AM, Wang QQ, Tarng RS, Graveley BR. Arginine/serine repeats are sufficient to constitute a splicing activation domain. Nucleic Acids Research. 31: 6502-8. PMID 14602908 DOI: 10.1093/Nar/Gkg845  0.315
2003 Lam BJ, Bakshi A, Ekinci FY, Webb J, Graveley BR, Hertel KJ. Enhancer-dependent 5'-splice site control of fruitless pre-mRNA splicing. The Journal of Biological Chemistry. 278: 22740-7. PMID 12646561 DOI: 10.1074/Jbc.M301036200  0.421
2003 Szymczyna BR, Bowman J, McCracken S, Pineda-Lucena A, Lu Y, Cox B, Lambermon M, Graveley BR, Arrowsmith CH, Blencowe BJ. Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes & Development. 17: 461-75. PMID 12600940 DOI: 10.1101/Gad.1060403  0.402
2002 Celotto AM, Graveley BR. Exon-specific RNAi: a tool for dissecting the functional relevance of alternative splicing. Rna (New York, N.Y.). 8: 718-24. PMID 12088145 DOI: 10.1017/S1355838202021064  0.477
2002 Graveley BR. Sex, AGility, and the regulation of alternative splicing. Cell. 109: 409-12. PMID 12086596 DOI: 10.1016/S0092-8674(02)00750-X  0.444
2002 Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L, Graveley BR. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics. 79: 587-97. PMID 11944992 DOI: 10.1006/Geno.2002.6734  0.463
2002 Shepard J, Reick M, Olson S, Graveley BR. Characterization of U2AF(6), a splicing factor related to U2AF(35). Molecular and Cellular Biology. 22: 221-30. PMID 11739736 DOI: 10.1128/Mcb.22.1.221-230.2002  0.393
2001 Celotto AM, Graveley BR. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics. 159: 599-608. PMID 11606537  0.305
2001 Graveley BR, Hertel KJ, Maniatis T. The role of U2AF35 and U2AF65 in enhancer-dependent splicing. Rna (New York, N.Y.). 7: 806-18. PMID 11421359 DOI: 10.1017/S1355838201010317  0.595
2001 Graveley BR. Alternative splicing: increasing diversity in the proteomic world. Trends in Genetics : Tig. 17: 100-7. PMID 11173120 DOI: 10.1016/S0168-9525(00)02176-4  0.458
2000 Graveley BR. Sorting out the complexity of SR protein functions. Rna (New York, N.Y.). 6: 1197-211. PMID 10999598 DOI: 10.1017/S1355838200000960  0.323
1999 Graveley BR, Hertel KJ, Maniatis T. SR proteins are 'locators' of the RNA splicing machinery. Current Biology : Cb. 9: R6-7. PMID 9889128 DOI: 10.1016/S0960-9822(99)80032-3  0.499
1998 Graveley BR, Hertel KJ, Maniatis T. A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. The Embo Journal. 17: 6747-56. PMID 9822617 DOI: 10.1093/Emboj/17.22.6747  0.587
1998 Graveley BR, Maniatis T. Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing. Molecular Cell. 1: 765-71. PMID 9660960 DOI: 10.1016/S1097-2765(00)80076-3  0.552
1996 Graveley BR, Fleming ES, Gilmartin GM. Restoration of both structure and function to a defective poly(A) site by in vitro selection. The Journal of Biological Chemistry. 271: 33654-63. PMID 8969235 DOI: 10.1074/Jbc.271.52.33654  0.749
1996 Schnapp G, Graveley BR, Grummt I. TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA. Molecular & General Genetics : Mgg. 252: 412-9. PMID 8879242 DOI: 10.1007/Bf02173006  0.438
1996 Graveley BR, Fleming ES, Gilmartin GM. RNA structure is a critical determinant of poly(A) site recognition by cleavage and polyadenylation specificity factor. Molecular and Cellular Biology. 16: 4942-51. PMID 8756653 DOI: 10.1128/Mcb.16.9.4942  0.753
1996 Graveley BR, Gilmartin GM. A common mechanism for the enhancement of mRNA 3' processing by U3 sequences in two distantly related lentiviruses. Journal of Virology. 70: 1612-7. PMID 8627681 DOI: 10.1128/Jvi.70.3.1612-1617.1996  0.733
1995 Gilmartin GM, Fleming ES, Oetjen J, Graveley BR. CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition. Genes & Development. 9: 72-83. PMID 7828853 DOI: 10.1101/Gad.9.1.72  0.734
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