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For: Ryvkin P, Leung YY, Silverman IM, Childress M, Valladares O, Dragomir I, Gregory BD, Wang LS. HAMR: high-throughput annotation of modified ribonucleotides. RNA 2013;19:1684-92. [PMID: 24149843 PMCID: PMC3884653 DOI: 10.1261/rna.036806.112] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 08/23/2013] [Indexed: 05/17/2023]
Number Cited by Other Article(s)
101
Marbaniang CN, Vogel J. Emerging roles of RNA modifications in bacteria. Curr Opin Microbiol 2016;30:50-57. [PMID: 26803287 DOI: 10.1016/j.mib.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/24/2015] [Accepted: 01/06/2016] [Indexed: 01/28/2023]
102
Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD. Genome-Wide Approaches for RNA Structure Probing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;907:29-59. [PMID: 27256381 DOI: 10.1007/978-3-319-29073-7_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
103
RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification. PLoS Genet 2015;11:e1005671. [PMID: 26720005 PMCID: PMC4697793 DOI: 10.1371/journal.pgen.1005671] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022]  Open
104
O’Connell MA, Mannion NM, Keegan LP. The Epitranscriptome and Innate Immunity. PLoS Genet 2015;11:e1005687. [PMID: 26658668 PMCID: PMC4675516 DOI: 10.1371/journal.pgen.1005687] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
105
Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. DASHR: database of small human noncoding RNAs. Nucleic Acids Res 2015;44:D216-22. [PMID: 26553799 PMCID: PMC4702848 DOI: 10.1093/nar/gkv1188] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/25/2015] [Indexed: 11/20/2022]  Open
106
Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. BMC Bioinformatics 2015;16:354. [PMID: 26530785 PMCID: PMC4632369 DOI: 10.1186/s12859-015-0800-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022]  Open
107
The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 2015;16:727-41. [PMID: 26530390 DOI: 10.1038/nrm4085] [Citation(s) in RCA: 626] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
108
Lockhart J. Revealing the Elusive Plant Epitranscriptome. THE PLANT CELL 2015;27:3019-3020. [PMID: 26561560 PMCID: PMC4682309 DOI: 10.1105/tpc.15.00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
109
Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang LS, Gregory BD. Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis. THE PLANT CELL 2015;27:3024-37. [PMID: 26561561 PMCID: PMC4682304 DOI: 10.1105/tpc.15.00591] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/22/2015] [Indexed: 05/03/2023]
110
Fray RG, Simpson GG. The Arabidopsis epitranscriptome. CURRENT OPINION IN PLANT BIOLOGY 2015;27:17-21. [PMID: 26048078 DOI: 10.1016/j.pbi.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
111
Foley SW, Vandivier LE, Kuksa PP, Gregory BD. Transcriptome-wide measurement of plant RNA secondary structure. CURRENT OPINION IN PLANT BIOLOGY 2015;27:36-43. [PMID: 26119389 PMCID: PMC5096376 DOI: 10.1016/j.pbi.2015.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 05/19/2023]
112
Guo Y, Bosompem A, Mohan S, Erdogan B, Ye F, Vickers KC, Sheng Q, Zhao S, Li CI, Su PF, Jagasia M, Strickland SA, Griffiths EA, Kim AS. Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes. BMC Genomics 2015;16:727. [PMID: 26400237 PMCID: PMC4581457 DOI: 10.1186/s12864-015-1929-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/16/2015] [Indexed: 11/10/2022]  Open
113
Hauenschild R, Tserovski L, Schmid K, Thüring K, Winz ML, Sharma S, Entian KD, Wacheul L, Lafontaine DLJ, Anderson J, Alfonzo J, Hildebrandt A, Jäschke A, Motorin Y, Helm M. The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Res 2015;43:9950-64. [PMID: 26365242 PMCID: PMC4787781 DOI: 10.1093/nar/gkv895] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/27/2015] [Indexed: 12/26/2022]  Open
114
Cozen AE, Quartley E, Holmes AD, Hrabeta-Robinson E, Phizicky EM, Lowe TM. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat Methods 2015;12:879-84. [PMID: 26237225 PMCID: PMC4553111 DOI: 10.1038/nmeth.3508] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/09/2015] [Indexed: 01/02/2023]
115
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods 2015;12:767-72. [PMID: 26121403 PMCID: PMC4487409 DOI: 10.1038/nmeth.3453] [Citation(s) in RCA: 1135] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 05/28/2015] [Indexed: 12/27/2022]
116
Torres AG, Piñeyro D, Rodríguez-Escribà M, Camacho N, Reina O, Saint-Léger A, Filonava L, Batlle E, Ribas de Pouplana L. Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Nucleic Acids Res 2015;43:5145-57. [PMID: 25916855 PMCID: PMC4446420 DOI: 10.1093/nar/gkv277] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022]  Open
117
Pang YLJ, Abo R, Levine SS, Dedon PC. Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res 2014;42:e170. [PMID: 25348403 PMCID: PMC4267671 DOI: 10.1093/nar/gku945] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
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