메뉴 건너뛰기




Volumn 93, Issue 4, 2013, Pages 641-651

Reliable identification of genomic variants from RNA-seq data

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84885300845     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2013.08.008     Document Type: Article
Times cited : (269)

References (54)
  • 11
    • 84855320189 scopus 로고    scopus 로고
    • Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
    • J.H. Bahn, J.H. Lee, G. Li, C. Greer, G. Peng, and X. Xiao Accurate identification of A-to-I RNA editing in human by transcriptome sequencing Genome Res. 22 2012 142 150
    • (2012) Genome Res. , vol.22 , pp. 142-150
    • Bahn, J.H.1    Lee, J.H.2    Li, G.3    Greer, C.4    Peng, G.5    Xiao, X.6
  • 13
    • 84861970552 scopus 로고    scopus 로고
    • Accurate identification of human Alu and non-Alu RNA editing sites
    • G. Ramaswami, W. Lin, R. Piskol, M.H. Tan, C. Davis, and J.B. Li Accurate identification of human Alu and non-Alu RNA editing sites Nat. Methods 9 2012 579 581
    • (2012) Nat. Methods , vol.9 , pp. 579-581
    • Ramaswami, G.1    Lin, W.2    Piskol, R.3    Tan, M.H.4    Davis, C.5    Li, J.B.6
  • 20
    • 84872186385 scopus 로고    scopus 로고
    • Lack of evidence for existence of noncanonical RNA editing
    • R. Piskol, Z. Peng, J. Wang, and J.B. Li Lack of evidence for existence of noncanonical RNA editing Nat. Biotechnol. 31 2013 19 20
    • (2013) Nat. Biotechnol. , vol.31 , pp. 19-20
    • Piskol, R.1    Peng, Z.2    Wang, J.3    Li, J.B.4
  • 21
    • 84858328300 scopus 로고    scopus 로고
    • Comment on "widespread RNA and DNA sequence differences in the human transcriptome"
    • author reply 1302
    • W. Lin, R. Piskol, M.H. Tan, and J.B. Li Comment on "Widespread RNA and DNA sequence differences in the human transcriptome" Science 335 2012 1302 author reply 1302
    • (2012) Science , vol.335 , pp. 1302
    • Lin, W.1    Piskol, R.2    Tan, M.H.3    Li, J.B.4
  • 23
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Q. Pan, O. Shai, L.J. Lee, B.J. Frey, and B.J. Blencowe Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing Nat. Genet. 40 2008 1413 1415
    • (2008) Nat. Genet. , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 25
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • K.F. Au, H. Jiang, L. Lin, Y. Xing, and W.H. Wong Detection of splice junctions from paired-end RNA-seq data by SpliceMap Nucleic Acids Res. 38 2010 4570 4578
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4570-4578
    • Au, K.F.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.H.5
  • 26
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: discovering splice junctions with RNA-Seq Bioinformatics 25 2009 1105 1111
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 27
    • 79960914208 scopus 로고    scopus 로고
    • Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
    • Y.S. Ju, J.I. Kim, S. Kim, D. Hong, H. Park, J.Y. Shin, S. Lee, W.C. Lee, S. Kim, and S.B. Yu Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals Nat. Genet. 43 2011 745 752
    • (2011) Nat. Genet. , vol.43 , pp. 745-752
    • Ju, Y.S.1    Kim, J.I.2    Kim, S.3    Hong, D.4    Park, H.5    Shin, J.Y.6    Lee, S.7    Lee, W.C.8    Kim, S.9    Yu, S.B.10
  • 28
  • 33
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 34
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • H. Li, and N. Homer A survey of sequence alignment algorithms for next-generation sequencing Brief. Bioinform. 11 2010 473 483
    • (2010) Brief. Bioinform. , vol.11 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 35
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • B. Langmead, and S.L. Salzberg Fast gapped-read alignment with Bowtie 2 Nat. Methods 9 2012 357 359
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 36
    • 84870837088 scopus 로고    scopus 로고
    • The GEM mapper: Fast, accurate and versatile alignment by filtration
    • S. Marco-Sola, M. Sammeth, R. Guigó, and P. Ribeca The GEM mapper: fast, accurate and versatile alignment by filtration Nat. Methods 9 2012 1185 1188
    • (2012) Nat. Methods , vol.9 , pp. 1185-1188
    • Marco-Sola, S.1    Sammeth, M.2    Guigó, R.3    Ribeca, P.4
  • 39
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • W.J. Kent BLAT - the BLAST-like alignment tool Genome Res. 12 2002 656 664
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 40
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
    • K. Wang, M. Li, and H. Hakonarson ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Res. 38 2010 e164
    • (2010) Nucleic Acids Res. , vol.38 , pp. 164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 42
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 14 2013 R36
    • (2013) Genome Biol. , vol.14 , pp. 36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 47
    • 77952293063 scopus 로고    scopus 로고
    • Functions and regulation of RNA editing by ADAR deaminases
    • K. Nishikura Functions and regulation of RNA editing by ADAR deaminases Annu. Rev. Biochem. 79 2010 321 349
    • (2010) Annu. Rev. Biochem. , vol.79 , pp. 321-349
    • Nishikura, K.1
  • 48
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
    • (2009) Genome Biol. , vol.10 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 49
    • 84858328300 scopus 로고    scopus 로고
    • Comment on "widespread RNA and DNA sequence differences in the human transcriptome"
    • author reply 1302
    • C.L. Kleinman, and J. Majewski Comment on "Widespread RNA and DNA sequence differences in the human transcriptome" Science 335 2012 1302 author reply 1302
    • (2012) Science , vol.335 , pp. 1302
    • Kleinman, C.L.1    Majewski, J.2
  • 50
    • 84863385039 scopus 로고    scopus 로고
    • Comment on "widespread RNA and DNA sequence differences in the human transcriptome"
    • author reply 1302
    • J.K. Pickrell, Y. Gilad, and J.K. Pritchard Comment on "Widespread RNA and DNA sequence differences in the human transcriptome" Science 335 2012 1302 author reply 1302
    • (2012) Science , vol.335 , pp. 1302
    • Pickrell, J.K.1    Gilad, Y.2    Pritchard, J.K.3
  • 51
    • 84863556835 scopus 로고    scopus 로고
    • Evolution and functional impact of rare coding variation from deep sequencing of human exomes
    • Broad GO Seattle GO NHLBI Exome Sequencing Project
    • J.A. Tennessen, A.W. Bigham, T.D. O'Connor, W. Fu, E.E. Kenny, S. Gravel, S. McGee, R. Do, X. Liu, G. Jun Broad GO Seattle GO NHLBI Exome Sequencing Project Evolution and functional impact of rare coding variation from deep sequencing of human exomes Science 337 2012 64 69
    • (2012) Science , vol.337 , pp. 64-69
    • Tennessen, J.A.1    Bigham, A.W.2    O'Connor, T.D.3    Fu, W.4    Kenny, E.E.5    Gravel, S.6    McGee, S.7    Do, R.8    Liu, X.9    Jun, G.10
  • 52
    • 77951702343 scopus 로고    scopus 로고
    • Genetic heterogeneity in human disease
    • J. McClellan, and M.C. King Genetic heterogeneity in human disease Cell 141 2010 210 217
    • (2010) Cell , vol.141 , pp. 210-217
    • McClellan, J.1    King, M.C.2
  • 53
    • 79951766233 scopus 로고    scopus 로고
    • Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms
    • J.E. Seeb, G. Carvalho, L. Hauser, K. Naish, S. Roberts, and L.W. Seeb Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms Mol Ecol Resour 11 Suppl 1 2011 1 8
    • (2011) Mol Ecol Resour , vol.11 , Issue.SUPPL. 1 , pp. 1-8
    • Seeb, J.E.1    Carvalho, G.2    Hauser, L.3    Naish, K.4    Roberts, S.5    Seeb, L.W.6
  • 54
    • 84861234288 scopus 로고    scopus 로고
    • Mechanisms and consequences of widespread random monoallelic expression
    • A. Chess Mechanisms and consequences of widespread random monoallelic expression Nat. Rev. Genet. 13 2012 421 428
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 421-428
    • Chess, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.