메뉴 건너뛰기




Volumn 16, Issue 4, 2014, Pages 629-639

Alternative applications for distinct RNA sequencing strategies

Author keywords

Data mining; Exogenous RNA; Mutation; RNAseq; SNP

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTOME;

EID: 84938562598     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbu032     Document Type: Article
Times cited : (32)

References (114)
  • 1
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 2
    • 84884418044 scopus 로고    scopus 로고
    • Finding the lost treasures in exome sequencing data
    • Samuels DC, Han L, Li J, et al. Finding the lost treasures in exome sequencing data. Trends Genet 2013;29:593-9.
    • (2013) Trends Genet , vol.29 , pp. 593-599
    • Samuels, D.C.1    Han, L.2    Li, J.3
  • 3
    • 84888871954 scopus 로고    scopus 로고
    • Assessment of transcript reconstruction methods for RNA-seq
    • Steijger T, Abril JF, Engstrom PG, et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 2013;10:1177-84.
    • (2013) Nat Methods , vol.10 , pp. 1177-1184
    • Steijger, T.1    Abril, J.F.2    Engstrom, P.G.3
  • 4
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010;11:345-55.
    • (2010) Nat Rev Genet , vol.11 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 5
    • 84904756759 scopus 로고    scopus 로고
    • The emerging era of genomic data integration for analyzing splice isoform function
    • Li HD, Menon R, Omenn GS, et al. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014;30:340-7.
    • (2014) Trends Genet , vol.30 , pp. 340-347
    • Li, H.D.1    Menon, R.2    Omenn, G.S.3
  • 6
    • 84887617966 scopus 로고    scopus 로고
    • Opportunities and methods for studying alternative splicing in cancer with RNA-Seq
    • Feng H, Qin Z, Zhang X. Opportunities and methods for studying alternative splicing in cancer with RNA-Seq. Cancer Lett 2013;340:179-91.
    • (2013) Cancer Lett , vol.340 , pp. 179-191
    • Feng, H.1    Qin, Z.2    Zhang, X.3
  • 7
    • 62049085786 scopus 로고    scopus 로고
    • Transcriptome sequencing to detect gene fusions in cancer
    • Maher CA, Kumar-Sinha C, Cao X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009; 458:97-101.
    • (2009) Nature , vol.458 , pp. 97-101
    • Maher, C.A.1    Kumar-Sinha, C.2    Cao, X.3
  • 8
    • 68149176840 scopus 로고    scopus 로고
    • Chimeric transcript discovery by paired-end transcriptome sequencing
    • Maher CA, Palanisamy N, Brenner JC, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. ProcNatl Acad SciUSA 2009;106:12353-8.
    • (2009) ProcNatl Acad SciUSA , vol.106 , pp. 12353-12358
    • Maher, C.A.1    Palanisamy, N.2    Brenner, J.C.3
  • 9
    • 84889000676 scopus 로고    scopus 로고
    • Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives
    • Wang Q, Xia J, Jia P, et al. Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform 2013;14: 506-19.
    • (2013) Brief Bioinform , vol.14 , pp. 506-519
    • Wang, Q.1    Xia, J.2    Jia, P.3
  • 10
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 11
    • 84885300845 scopus 로고    scopus 로고
    • Reliable identification of genomic variants from RNA-seq data
    • Piskol R, Ramaswami G, Li JB. Reliable identification of genomic variants from RNA-seq data. Am J Hum Genet 2013;93:641-51.
    • (2013) Am J Hum Genet , vol.93 , pp. 641-651
    • Piskol, R.1    Ramaswami, G.2    Li, J.B.3
  • 12
    • 84863229628 scopus 로고    scopus 로고
    • Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
    • Peng Z, Cheng Y, Tan BC, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 2012;30:253-60.
    • (2012) Nat Biotechnol , vol.30 , pp. 253-260
    • Peng, Z.1    Cheng, Y.2    Tan, B.C.3
  • 13
    • 84861970552 scopus 로고    scopus 로고
    • Accurate identification of human Alu and non-Alu RNA editing sites
    • Ramaswami G, Lin W, Piskol R, et al. Accurate identification of human Alu and non-Alu RNA editing sites. NatMethods 2012;9:579-81.
    • (2012) NatMethods , vol.9 , pp. 579-581
    • Ramaswami, G.1    Lin, W.2    Piskol, R.3
  • 14
    • 84873414540 scopus 로고    scopus 로고
    • Identifying RNA editing sites using RNA sequencing data alone
    • Ramaswami G, Zhang R, Piskol R, et al. Identifying RNA editing sites using RNA sequencing data alone. NatMethods 2013;10:128-32.
    • (2013) NatMethods , vol.10 , pp. 128-132
    • Ramaswami, G.1    Zhang, R.2    Piskol, R.3
  • 15
    • 77955299096 scopus 로고    scopus 로고
    • High-resolution analysis of parent-of-origin allelic expression in the mouse brain
    • Gregg C, Zhang J, Weissbourd B, et al. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010;329:643-8.
    • (2010) Science , vol.329 , pp. 643-648
    • Gregg, C.1    Zhang, J.2    Weissbourd, B.3
  • 16
    • 84894651954 scopus 로고    scopus 로고
    • Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing
    • Zhang R, Li X, Ramaswami G, et al. Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. NatMethods 2014;11:51-4.
    • (2014) NatMethods , vol.11 , pp. 51-54
    • Zhang, R.1    Li, X.2    Ramaswami, G.3
  • 17
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011;25: 1915-27.
    • (2011) Genes Dev , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 18
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature 2012;489:101-8.
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1    Davis, C.A.2    Merkel, A.3
  • 19
    • 84881229283 scopus 로고    scopus 로고
    • Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq
    • Khoury JD, Tannir NM, Williams MD, et al. Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq. J Virol 2013;87: 8916-26.
    • (2013) J Virol , vol.87 , pp. 8916-8926
    • Khoury, J.D.1    Tannir, N.M.2    Williams, M.D.3
  • 20
    • 84885109819 scopus 로고    scopus 로고
    • The landscape of viral expression and host gene fusion and adaptation in human cancer
    • Tang KW, Alaei-Mahabadi B, Samuelsson T, et al. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun 2013;4:2513.
    • (2013) Nat Commun , vol.4 , pp. 2513
    • Tang, K.W.1    Alaei-Mahabadi, B.2    Samuelsson, T.3
  • 21
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium EP, Bernstein BE, Birney E, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1    Bernstein, B.E.2    Birney, E.3
  • 22
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song L, Zhang Z, Grasfeder LL, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011;21: 1757-67.
    • (2011) Genome Res , vol.21 , pp. 1757-1767
    • Song, L.1    Zhang, Z.2    Grasfeder, L.L.3
  • 23
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007;128:707-19.
    • (2007) Cell , vol.128 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 24
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton MP, Cheng AW, Welstead GG, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010;107: 21931-6.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1    Cheng, A.W.2    Welstead, G.G.3
  • 25
    • 84887072795 scopus 로고    scopus 로고
    • Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
    • Parker SC, Stitzel ML, Taylor DL, et al. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci USA 2013;110:17921-6.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 17921-17926
    • Parker, S.C.1    Stitzel, M.L.2    Taylor, D.L.3
  • 26
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, Kheradpour P, Mikkelsen TS, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011;473:43-9.
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3
  • 27
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cisregulatory sequences in the mouse genome
    • Shen Y, Yue F, McCleary DF, et al. A map of the cisregulatory sequences in the mouse genome. Nature 2012; 488:116-20.
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1    Yue, F.2    McCleary, D.F.3
  • 28
    • 84876842759 scopus 로고    scopus 로고
    • Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    • Danko CG, Hah N, Luo X, et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell 2013;50:212-22.
    • (2013) Mol Cell , vol.50 , pp. 212-222
    • Danko, C.G.1    Hah, N.2    Luo, X.3
  • 29
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008;322:1845-8.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 30
    • 6344270167 scopus 로고    scopus 로고
    • Global position and recruitment of HATs and HDACs in the yeast genome
    • Robert F, Pokholok DK, Hannett NM, et al. Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell 2004;16:199-209.
    • (2004) Mol Cell , vol.16 , pp. 199-209
    • Robert, F.1    Pokholok, D.K.2    Hannett, N.M.3
  • 31
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, et al. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007;130:77-88.
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3
  • 32
    • 36549061004 scopus 로고    scopus 로고
    • RNA polymerase is poised for activation across the genome
    • Muse GW, Gilchrist DA, Nechaev S, et al. RNA polymerase is poised for activation across the genome. Nat Genet 2007; 39:1507-11.
    • (2007) Nat Genet , vol.39 , pp. 1507-1511
    • Muse, G.W.1    Gilchrist, D.A.2    Nechaev, S.3
  • 33
    • 36549013619 scopus 로고    scopus 로고
    • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    • Zeitlinger J, Stark A, Kellis M, et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 2007;39: 1512-16.
    • (2007) Nat Genet , vol.39 , pp. 1512-1516
    • Zeitlinger, J.1    Stark, A.2    Kellis, M.3
  • 34
    • 34247627984 scopus 로고    scopus 로고
    • Transcription elongation controls cell fate specification in the Drosophila embryo
    • Wang X, Lee C, Gilmour DS, et al. Transcription elongation controls cell fate specification in the Drosophila embryo. Genes Dev 2007;21:1031-6.
    • (2007) Genes Dev , vol.21 , pp. 1031-1036
    • Wang, X.1    Lee, C.2    Gilmour, D.S.3
  • 35
    • 84896859718 scopus 로고    scopus 로고
    • Argonaute-bound small RNAs from promoter-proximal RNA polymerase II
    • Zamudio JR, Kelly TJ, Sharp PA. Argonaute-bound small RNAs from promoter-proximal RNA polymerase II. Cell 2014;156:920-34.
    • (2014) Cell , vol.156 , pp. 920-934
    • Zamudio, J.R.1    Kelly, T.J.2    Sharp, P.A.3
  • 36
    • 70449953975 scopus 로고    scopus 로고
    • The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs
    • Jacquier A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 2009;10:833-44.
    • (2009) Nat Rev Genet , vol.10 , pp. 833-844
    • Jacquier, A.1
  • 37
    • 84874175008 scopus 로고    scopus 로고
    • Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    • Kwak H, Fuda NJ, Core LJ, et al. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013;339:950-3.
    • (2013) Science , vol.339 , pp. 950-953
    • Kwak, H.1    Fuda, N.J.2    Core, L.J.3
  • 38
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011;469:368-73.
    • (2011) Nature , vol.469 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 39
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011;25: 1915-27.
    • (2011) Genes Dev , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 40
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Bernstein BE, Birney E, Dunham I, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3
  • 41
    • 79960417564 scopus 로고    scopus 로고
    • Pathogen detection using short-RNA deep sequencing subtraction and assembly
    • Isakov O, Modai S, Shomron N. Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics 2011;27:2027-30.
    • (2011) Bioinformatics , vol.27 , pp. 2027-2030
    • Isakov, O.1    Modai, S.2    Shomron, N.3
  • 42
    • 79955778143 scopus 로고    scopus 로고
    • PathSeq: software to identify or discover microbes by deep sequencing of human tissue
    • Kostic AD, Ojesina AI, Pedamallu CS, et al. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol 2011;29:393-6.
    • (2011) Nat Biotechnol , vol.29 , pp. 393-396
    • Kostic, A.D.1    Ojesina, A.I.2    Pedamallu, C.S.3
  • 43
    • 84874720727 scopus 로고    scopus 로고
    • ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
    • Li JW, Wan R, Yu CS, et al. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics 2013;29: 649-51.
    • (2013) Bioinformatics , vol.29 , pp. 649-651
    • Li, J.W.1    Wan, R.2    Yu, C.S.3
  • 44
    • 84872583615 scopus 로고    scopus 로고
    • VirusSeq: software to identify viruses and their integration sites using nextgeneration sequencing of human cancer tissue
    • Chen Y, Yao H, Thompson EJ, et al. VirusSeq: software to identify viruses and their integration sites using nextgeneration sequencing of human cancer tissue. Bioinformatics 2013; 29:266-7.
    • (2013) Bioinformatics , vol.29 , pp. 266-267
    • Chen, Y.1    Yao, H.2    Thompson, E.J.3
  • 45
    • 84878151016 scopus 로고    scopus 로고
    • VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data
    • Wang Q, Jia P, Zhao Z. VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One 2013;8:e64465.
    • (2013) PLoS One , vol.8
    • Wang, Q.1    Jia, P.2    Zhao, Z.3
  • 46
    • 84880213242 scopus 로고    scopus 로고
    • REDItools: high-throughput RNA editing detection made easy
    • Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics 2013;29: 1813-14.
    • (2013) Bioinformatics , vol.29 , pp. 1813-1814
    • Picardi, E.1    Pesole, G.2
  • 47
    • 77954505224 scopus 로고    scopus 로고
    • DARNED: a DAtabase of RNa EDiting in humans
    • Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 2010;26:1772-6.
    • (2010) Bioinformatics , vol.26 , pp. 1772-1776
    • Kiran, A.1    Baranov, P.V.2
  • 49
    • 33846048733 scopus 로고    scopus 로고
    • dbRES: a web-oriented database for annotated RNA editing sites
    • He T, Du P, Li Y. dbRES: a web-oriented database for annotated RNA editing sites. Nucleic Acids Res 2007;35: D141-4.
    • (2007) Nucleic Acids Res , vol.35 , pp. D141-D144
    • He, T.1    Du, P.2    Li, Y.3
  • 50
    • 84856753476 scopus 로고    scopus 로고
    • A statistical framework for eQTL mapping using RNA-seq data
    • Sun W. A statistical framework for eQTL mapping using RNA-seq data. Biometrics 2012;68:1-11.
    • (2012) Biometrics , vol.68 , pp. 1-11
    • Sun, W.1
  • 51
    • 80051489977 scopus 로고    scopus 로고
    • AlleleSeq: analysis of allele-specific expression and binding in a network framework
    • Rozowsky J, Abyzov A, Wang J, et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol 2011;7:522.
    • (2011) Mol Syst Biol , vol.7 , pp. 522
    • Rozowsky, J.1    Abyzov, A.2    Wang, J.3
  • 52
    • 84875286904 scopus 로고    scopus 로고
    • RNA-seq-based mapping and candidate identification of mutations from forward genetic screens
    • Miller AC, Obholzer ND, Shah AN, et al. RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res 2013;23:679-86.
    • (2013) Genome Res , vol.23 , pp. 679-686
    • Miller, A.C.1    Obholzer, N.D.2    Shah, A.N.3
  • 53
    • 84860505950 scopus 로고    scopus 로고
    • Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data
    • Duitama J, Srivastava P, Mandoiu I. Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. BMCGenomics 2012;13:S6.
    • (2012) BMCGenomics , vol.13 , pp. S6
    • Duitama, J.1    Srivastava, P.2    Mandoiu, I.3
  • 55
    • 77249117360 scopus 로고    scopus 로고
    • Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
    • Chepelev I, Wei G, Tang Q, et al. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res 2009;37:e106.
    • (2009) Nucleic Acids Res , vol.37
    • Chepelev, I.1    Wei, G.2    Tang, Q.3
  • 57
    • 40449115382 scopus 로고    scopus 로고
    • A new arenavirus in a cluster of fatal transplant-associated diseases
    • Palacios G, Druce J, Du L, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. NEnglJMed 2008;358: 991-8.
    • (2008) NEnglJMed , vol.358 , pp. 991-998
    • Palacios, G.1    Druce, J.2    Du, L.3
  • 58
    • 64149083137 scopus 로고    scopus 로고
    • Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach
    • Nakamura S, Yang CS, Sakon N, et al. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 2009;4:e4219.
    • (2009) PLoS One , vol.4
    • Nakamura, S.1    Yang, C.S.2    Sakon, N.3
  • 59
    • 77952738982 scopus 로고    scopus 로고
    • Astrovirus encephalitis in boy with X-linked agammaglobulinemia
    • Quan PL, Wagner TA, Briese T, et al. Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Emerg Infect Dis 2010;16:918-25.
    • (2010) Emerg Infect Dis , vol.16 , pp. 918-925
    • Quan, P.L.1    Wagner, T.A.2    Briese, T.3
  • 60
    • 67249156188 scopus 로고    scopus 로고
    • Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa
    • Briese T, Paweska JT, McMullan LK, et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 2009;5:e1000455.
    • (2009) PLoS Pathog , vol.5
    • Briese, T.1    Paweska, J.T.2    McMullan, L.K.3
  • 61
    • 58449125226 scopus 로고    scopus 로고
    • Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration
    • Geuking MB, Weber J, Dewannieux M, et al. Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science 2009;323:393-6.
    • (2009) Science , vol.323 , pp. 393-396
    • Geuking, M.B.1    Weber, J.2    Dewannieux, M.3
  • 62
    • 33646413672 scopus 로고    scopus 로고
    • The global health burden of infectionassociated cancers in the year 2002
    • Parkin DM. The global health burden of infectionassociated cancers in the year 2002. Int J Cancer 2006;118: 3030-44.
    • (2006) Int J Cancer , vol.118 , pp. 3030-3044
    • Parkin, D.M.1
  • 63
    • 78049490308 scopus 로고    scopus 로고
    • Herpesviruses and chromosomal integration
    • Morissette G, Flamand L. Herpesviruses and chromosomal integration. JVirol 2010;84:12100-9.
    • (2010) JVirol , vol.84 , pp. 12100-12109
    • Morissette, G.1    Flamand, L.2
  • 64
    • 0029808295 scopus 로고    scopus 로고
    • Frequent provirus insertional mutagenesis of Notch1 in thymomas of MMTVD/myc transgenic mice suggests a collaboration of c-myc and Notch1 for oncogenesis
    • Girard L, Hanna Z, Beaulieu N, et al. Frequent provirus insertional mutagenesis of Notch1 in thymomas of MMTVD/myc transgenic mice suggests a collaboration of c-myc and Notch1 for oncogenesis. Genes Dev 1996;10: 1930-44.
    • (1996) Genes Dev , vol.10 , pp. 1930-1944
    • Girard, L.1    Hanna, Z.2    Beaulieu, N.3
  • 65
    • 0035165280 scopus 로고    scopus 로고
    • Murine Leukemia virus proviral insertions between the N-ras and unr genes in B-cell lymphoma DNA affect the expression of N-ras only
    • Martín-Hernández J, Sørensen AB, Pedersen FS. Murine Leukemia virus proviral insertions between the N-ras and unr genes in B-cell lymphoma DNA affect the expression of N-ras only. JVirol 2001;75:11907-12.
    • (2001) JVirol , vol.75 , pp. 11907-11912
    • Martín-Hernández, J.1    Sørensen, A.B.2    Pedersen, F.S.3
  • 66
    • 79955860099 scopus 로고    scopus 로고
    • Hepatitis B virus induces G1 phase arrest by regulating cell cycle genes in HepG2.2.15 cells
    • Wang T, Zhao R, Wu Y, et al. Hepatitis B virus induces G1 phase arrest by regulating cell cycle genes in HepG2.2.15 cells. VirolJ 2011;8:231.
    • (2011) VirolJ , vol.8 , pp. 231
    • Wang, T.1    Zhao, R.2    Wu, Y.3
  • 67
    • 82255181690 scopus 로고    scopus 로고
    • Applications of nextgeneration sequencing technologies to diagnostic virology
    • Barzon L, Lavezzo E, Militello V, et al. Applications of nextgeneration sequencing technologies to diagnostic virology. IntJMol Sci 2011;12:7861-84.
    • (2011) IntJMol Sci , vol.12 , pp. 7861-7884
    • Barzon, L.1    Lavezzo, E.2    Militello, V.3
  • 68
    • 84865130203 scopus 로고    scopus 로고
    • Application of next-generation sequencing technologies in virology
    • Radford AD, Chapman D, Dixon L, et al. Application of next-generation sequencing technologies in virology. J GenVirol 2012;93:1853-68.
    • (2012) J GenVirol , vol.93 , pp. 1853-1868
    • Radford, A.D.1    Chapman, D.2    Dixon, L.3
  • 69
    • 84860273551 scopus 로고    scopus 로고
    • New virologic tools for management of chronic hepatitis B and C
    • Chevaliez S, Rodriguez C, Pawlotsky JM. New virologic tools for management of chronic hepatitis B and C. Gastroenterology 2012;142:1303-1313e1.
    • (2012) Gastroenterology , vol.142 , pp. 1303-1313
    • Chevaliez, S.1    Rodriguez, C.2    Pawlotsky, J.M.3
  • 70
    • 80053357460 scopus 로고    scopus 로고
    • From orphan virus to pathogen: the path to the clinical lab
    • Li L, Delwart E. From orphan virus to pathogen: the path to the clinical lab. Curr OpinVirol 2011;1:282-8.
    • (2011) Curr OpinVirol , vol.1 , pp. 282-288
    • Li, L.1    Delwart, E.2
  • 74
    • 84857374518 scopus 로고    scopus 로고
    • RNA editing underlies temperature adaptation in K+ channels from polar octopuses
    • Garrett S, Rosenthal JJ. RNA editing underlies temperature adaptation in K+ channels from polar octopuses. Science 2012;335:848-51.
    • (2012) Science , vol.335 , pp. 848-851
    • Garrett, S.1    Rosenthal, J.J.2
  • 75
    • 84883176120 scopus 로고    scopus 로고
    • Comparative RNA editing in autistic and neurotypical cerebella
    • Eran A, Li JB, Vatalaro K, et al. Comparative RNA editing in autistic and neurotypical cerebella. MolPsychiatry 2012;18: 1041-8.
    • (2012) MolPsychiatry , vol.18 , pp. 1041-1048
    • Eran, A.1    Li, J.B.2    Vatalaro, K.3
  • 76
    • 84873531277 scopus 로고    scopus 로고
    • Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma
    • Chen L, Li Y, Lin CH, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med 2013;19:209-16.
    • (2013) Nat Med , vol.19 , pp. 209-216
    • Chen, L.1    Li, Y.2    Lin, C.H.3
  • 77
    • 84897997022 scopus 로고    scopus 로고
    • A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma
    • Chan TH, Lin CH, Qi L, et al. A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Gut 2013;63:832-43.
    • (2013) Gut , vol.63 , pp. 832-843
    • Chan, T.H.1    Lin, C.H.2    Qi, L.3
  • 78
    • 84870935782 scopus 로고    scopus 로고
    • The difficult calls in RNA editing. Interviewed by H Craig Mak
    • Bass B, Hundley H, Li JB, et al. The difficult calls in RNA editing. Interviewed by H Craig Mak. Nat Biotechnol 2012; 30:1207-9.
    • (2012) Nat Biotechnol , vol.30 , pp. 1207-1209
    • Bass, B.1    Hundley, H.2    Li, J.B.3
  • 79
    • 84858328300 scopus 로고    scopus 로고
    • Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''
    • author reply 1302
    • Kleinman CL, Majewski J. Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''. Science 2012;335:1302; author reply 1302.
    • (2012) Science , vol.335 , pp. 1302
    • Kleinman, C.L.1    Majewski, J.2
  • 80
    • 84858328300 scopus 로고    scopus 로고
    • Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''
    • author reply 1302
    • Lin W, Piskol R, Tan MH, et al. Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''. Science 2012;335:1302; author reply 1302.
    • (2012) Science , vol.335 , pp. 1302
    • Lin, W.1    Piskol, R.2    Tan, M.H.3
  • 81
    • 84858328300 scopus 로고    scopus 로고
    • Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''
    • author reply 1302
    • Pickrell JK, Gilad Y, Pritchard JK. Comment on ''Widespread RNA and DNA sequence differences in the human transcriptome''. Science 2012;335:1302; author reply 1302.
    • (2012) Science , vol.335 , pp. 1302
    • Pickrell, J.K.1    Gilad, Y.2    Pritchard, J.K.3
  • 82
    • 84855320189 scopus 로고    scopus 로고
    • Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
    • Bahn JH, Lee JH, Li G, et al. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 2012;22:142-50.
    • (2012) Genome Res , vol.22 , pp. 142-150
    • Bahn, J.H.1    Lee, J.H.2    Li, G.3
  • 83
    • 84863229628 scopus 로고    scopus 로고
    • Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
    • Peng Z, Cheng Y, Tan BC, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 2012;30:253-60.
    • (2012) Nat Biotechnol , vol.30 , pp. 253-260
    • Peng, Z.1    Cheng, Y.2    Tan, B.C.3
  • 84
    • 84861970552 scopus 로고    scopus 로고
    • Accurate identification of human Alu and non-Alu RNA editing sites
    • Ramaswami G, Lin W, Piskol R, et al. Accurate identification of human Alu and non-Alu RNA editing sites. NatMethods 2012;9:579-81.
    • (2012) NatMethods , vol.9 , pp. 579-581
    • Ramaswami, G.1    Lin, W.2    Piskol, R.3
  • 85
    • 84865858631 scopus 로고    scopus 로고
    • RNA editing in the human ENCODE RNA-seq data
    • Park E, Williams B, Wold BJ, et al. RNA editing in the human ENCODE RNA-seq data. Genome Rese 2012;22: 1626-33.
    • (2012) Genome Rese , vol.22 , pp. 1626-1633
    • Park, E.1    Williams, B.2    Wold, B.J.3
  • 86
    • 84878087827 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants
    • Lee JH, Ang JK, Xiao X. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. RNA 2013; 19:725-32.
    • (2013) RNA , vol.19 , pp. 725-732
    • Lee, J.H.1    Ang, J.K.2    Xiao, X.3
  • 87
    • 84873414540 scopus 로고    scopus 로고
    • Identifying RNA editing sites using RNA sequencing data alone
    • Ramaswami G, Zhang R, Piskol R, et al. Identifying RNA editing sites using RNA sequencing data alone. NatMethods 2013;10:128-32.
    • (2013) NatMethods , vol.10 , pp. 128-132
    • Ramaswami, G.1    Zhang, R.2    Piskol, R.3
  • 88
    • 84859935298 scopus 로고    scopus 로고
    • High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
    • Danecek P, Nellaker C, McIntyre RE, et al. High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol 2012;13:26.
    • (2012) Genome Biol , vol.13 , pp. 26
    • Danecek, P.1    Nellaker, C.2    McIntyre, R.E.3
  • 89
    • 84891797364 scopus 로고    scopus 로고
    • RADAR: a rigorously annotated database of A-to-I RNA editing
    • Ramaswami G, Li JB. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res 2013; 42:D109-13.
    • (2013) Nucleic Acids Res , vol.42 , pp. D109-D113
    • Ramaswami, G.1    Li, J.B.2
  • 90
    • 0037623912 scopus 로고    scopus 로고
    • Cis-acting variation in the expression of a high proportion of genes in human brain
    • Bray NJ, Buckland PR, Owen MJ, et al. Cis-acting variation in the expression of a high proportion of genes in human brain. Hum Genet 2003;113:149-53.
    • (2003) Hum Genet , vol.113 , pp. 149-153
    • Bray, N.J.1    Buckland, P.R.2    Owen, M.J.3
  • 91
    • 84882547010 scopus 로고    scopus 로고
    • Whole transcriptome RNA-Seq allelic expression in human brain
    • Smith RM, Webb A, Papp AC, et al. Whole transcriptome RNA-Seq allelic expression in human brain. BMC Genomics 2013;14:571.
    • (2013) BMC Genomics , vol.14 , pp. 571
    • Smith, R.M.1    Webb, A.2    Papp, A.C.3
  • 92
    • 76049102972 scopus 로고    scopus 로고
    • Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing
    • Heap GA, Yang JH, Downes K, et al. Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. HumMol Genet 2010;19:122-34.
    • (2010) HumMol Genet , vol.19 , pp. 122-134
    • Heap, G.A.1    Yang, J.H.2    Downes, K.3
  • 93
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    • Degner JF, Marioni JC, Pai AA, et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009;25:3207-12.
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3
  • 94
    • 84874524608 scopus 로고    scopus 로고
    • Evaluation of allele frequency estimation using pooled sequencing data simulation
    • Guo Y, Samuels DC, Li J, et al. Evaluation of allele frequency estimation using pooled sequencing data simulation. ScientificWorldJournal 2013;2013:895496.
    • (2013) ScientificWorldJournal , vol.2013
    • Guo, Y.1    Samuels, D.C.2    Li, J.3
  • 95
    • 84881042224 scopus 로고    scopus 로고
    • Sources of bias in measures of allele-specific expression derived from RNAseq data aligned to a single reference genome
    • Stevenson KR, Coolon JD, Wittkopp PJ. Sources of bias in measures of allele-specific expression derived from RNAseq data aligned to a single reference genome. BMC Genomics 2013;14:536.
    • (2013) BMC Genomics , vol.14 , pp. 536
    • Stevenson, K.R.1    Coolon, J.D.2    Wittkopp, P.J.3
  • 96
    • 84901013670 scopus 로고    scopus 로고
    • Three-stage quality control strategies for DNA re-sequencing data
    • Guo Y, Ye F, Sheng Q, et al. Three-stage quality control strategies for DNA re-sequencing data. Brief Bioinformatics 2014;15:879-89.
    • (2014) Brief Bioinformatics , vol.15 , pp. 879-889
    • Guo, Y.1    Ye, F.2    Sheng, Q.3
  • 97
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011;43:491-8.
    • (2011) Nat Genet , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3
  • 98
    • 84863229597 scopus 로고    scopus 로고
    • VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012;22: 568-76.
    • (2012) Genome Res , vol.22 , pp. 568-576
    • Koboldt, D.C.1    Zhang, Q.2    Larson, D.E.3
  • 99
    • 84874025843 scopus 로고    scopus 로고
    • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    • Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013;31: 213-19.
    • (2013) Nat Biotechnol , vol.31 , pp. 213-219
    • Cibulskis, K.1    Lawrence, M.S.2    Carter, S.L.3
  • 100
    • 78649714014 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying isoform regulation
    • Katz Y, Wang ET, Airoldi EM, et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation. NatMethods 2010;7:1009-15.
    • (2010) NatMethods , vol.7 , pp. 1009-1015
    • Katz, Y.1    Wang, E.T.2    Airoldi, E.M.3
  • 101
    • 84864390703 scopus 로고    scopus 로고
    • Pre-mRNA splicing in disease and therapeutics
    • Singh RK, Cooper TA. Pre-mRNA splicing in disease and therapeutics. TrendsMolMed 2012;18:472-82.
    • (2012) TrendsMolMed , vol.18 , pp. 472-482
    • Singh, R.K.1    Cooper, T.A.2
  • 102
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • Ramskold D, Wang ET, Burge CB, et al. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 2009;5: e1000598.
    • (2009) PLoS Comput Biol , vol.5
    • Ramskold, D.1    Wang, E.T.2    Burge, C.B.3
  • 103
    • 84875451981 scopus 로고    scopus 로고
    • Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data
    • Quinn EM, Cormican P, Kenny EM, et al. Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data. PloS One 2013;8:e58815.
    • (2013) PloS One , vol.8
    • Quinn, E.M.1    Cormican, P.2    Kenny, E.M.3
  • 104
    • 84875286904 scopus 로고    scopus 로고
    • RNA-seq-based mapping and candidate identification of mutations from forward genetic screens
    • Miller AC, Obholzer ND, Shah AN, et al. RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res 2013;23:679-86.
    • (2013) Genome Res , vol.23 , pp. 679-686
    • Miller, A.C.1    Obholzer, N.D.2    Shah, A.N.3
  • 105
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013;14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3
  • 106
    • 84863289036 scopus 로고    scopus 로고
    • FX: an RNA-Seq analysis tool on the cloud
    • Hong D, Rhie A, Park SS, et al. FX: an RNA-Seq analysis tool on the cloud. Bioinformatics 2012;28:721-3.
    • (2012) Bioinformatics , vol.28 , pp. 721-723
    • Hong, D.1    Rhie, A.2    Park, S.S.3
  • 107
    • 84864134986 scopus 로고    scopus 로고
    • OSA: a fast and accurate alignment tool for RNA-Seq
    • Hu J, Ge H, Newman M, et al. OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics 2012;28: 1933-4.
    • (2012) Bioinformatics , vol.28 , pp. 1933-1934
    • Hu, J.1    Ge, H.2    Newman, M.3
  • 108
    • 84904994551 scopus 로고    scopus 로고
    • PRADA: pipeline for RNA sequencing data analysis
    • Torres-Garcia W, Zheng S, Sivachenko A, et al. PRADA: pipeline for RNA sequencing data analysis. Bioinformatics 2014;30:2224-6.
    • (2014) Bioinformatics , vol.30 , pp. 2224-2226
    • Torres-Garcia, W.1    Zheng, S.2    Sivachenko, A.3
  • 109
    • 84880068437 scopus 로고    scopus 로고
    • Comprehensive genomeand transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers
    • Yoon K, Lee S, Han TS, et al. Comprehensive genomeand transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. GenomeRes 2013;23:1109-17.
    • (2013) GenomeRes , vol.23 , pp. 1109-1117
    • Yoon, K.1    Lee, S.2    Han, T.S.3
  • 110
    • 84875596464 scopus 로고    scopus 로고
    • Identification of somatic mutations in human prostate cancer by RNA-Seq
    • Xu X, Zhu K, Liu F, et al. Identification of somatic mutations in human prostate cancer by RNA-Seq. Gene 2013; 519:343-7.
    • (2013) Gene , vol.519 , pp. 343-347
    • Xu, X.1    Zhu, K.2    Liu, F.3
  • 111
    • 84880334767 scopus 로고    scopus 로고
    • Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)
    • Zheng X, Pan C, Diao Y, et al. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae). BMC Genomics 2013;14:490.
    • (2013) BMC Genomics , vol.14 , pp. 490
    • Zheng, X.1    Pan, C.2    Diao, Y.3
  • 112
    • 84877092705 scopus 로고    scopus 로고
    • A novel approach for characterizing microsatellite instability in cancer cells
    • Lu Y, Soong TD, Elemento O. A novel approach for characterizing microsatellite instability in cancer cells. PLoS One 2013;8:e63056.
    • (2013) PLoS One , vol.8
    • Lu, Y.1    Soong, T.D.2    Elemento, O.3
  • 113
    • 79957932376 scopus 로고    scopus 로고
    • Dindel: accurate indel calls from short-read data
    • Albers CA, Lunter G, MacArthur DG, et al. Dindel: accurate indel calls from short-read data. Genome Res 2011;21: 961-73.
    • (2011) Genome Res , vol.21 , pp. 961-973
    • Albers, C.A.1    Lunter, G.2    MacArthur, D.G.3
  • 114
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999;27: 573-80.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.