메뉴 건너뛰기




Volumn 20, Issue 3, 2013, Pages 167-187

A robust method for transcript quantification with rna-seq data

Author keywords

RNA seq.; transcript quantification; transcriptome

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

EID: 84874734032     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0230     Document Type: Article
Times cited : (14)

References (35)
  • 1
    • 1842455195 scopus 로고    scopus 로고
    • Algorithms for variable length Markov chain modeling
    • Bejerano, G. 2004. Algorithms for variable length Markov chain modeling. Bioinformatics. 20, 788-789.
    • (2004) Bioinformatics , vol.20 , pp. 788-789
    • Bejerano, G.1
  • 2
    • 77954302477 scopus 로고    scopus 로고
    • RQuant.web: A tool for RNA-Seq-based transcript quantitation
    • Bohnert, R., and Ra?tsch, G. 2010. rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res. 38(Suppl 2), W348-W351.
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 2
    • Bohnert, R.1    Ratsch, G.2
  • 3
    • 75149179617 scopus 로고    scopus 로고
    • High-throughput quantification of splicing isoforms
    • Brosseau, J.P., Lucier, J.F., Lapointe, E., et al. 2010. High-throughput quantification of splicing isoforms. RNA. 16, 442-449.
    • (2010) RNA , vol.16 , pp. 442-449
    • Brosseau, J.P.1    Lucier, J.F.2    Lapointe, E.3
  • 4
    • 79952389472 scopus 로고    scopus 로고
    • Inference of isoforms from short sequence reads
    • Feng, J., Li, W., and Jiang, T. 2010. Inference of isoforms from short sequence reads. J. Comput. Biol. 18, 305-21.
    • (2010) J. Comput. Biol. , vol.18 , pp. 305-321
    • Feng, J.1    Li, W.2    Jiang, T.3
  • 6
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman, M., Garber, M., Levin, J.Z., et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3
  • 7
    • 0004151494 scopus 로고
    • Cambridge University Press Cambridge, United Kingdom
    • Horn, R.A., and Johnson, C.R. 1990. Matrix analysis. Cambridge University Press. Cambridge, United Kingdom.
    • (1990) Matrix Analysis
    • Horn, R.A.1    Johnson, C.R.2
  • 8
    • 77955457181 scopus 로고    scopus 로고
    • A probabilistic framework for aligning paired-end RNA-seq data
    • Hu, Y., Wang, K., He, X., et al. 2010. A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics. 26, 1950-1957.
    • (2010) Bioinformatics , vol.26 , pp. 1950-1957
    • Hu, Y.1    Wang, K.2    He, X.3
  • 9
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inferences for isoform expression in RNA-Seq
    • Jiang, H., and Wong, W.H. 2009. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics. 25, 1026- 1032.
    • (2009) Bioinformatics , vol.25 , pp. 1026-1032
    • Jiang, H.1    Wong, W.H.2
  • 10
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes
    • Kozarewa, I., Ning, Z., Quail, M.A., et al. 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat. Methods. 6, 291-5.
    • (2009) Nat. Methods. , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3
  • 11
    • 28044455878 scopus 로고    scopus 로고
    • The architecture of pre-mRNAs affects mechanisms of splice-site pairing
    • Kristi, L.F., Dou, Y., Bianca, J.L., et al. 2005. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc. Natl. Acad. Sci. U.S.A. 102, 16176-16181.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 16176-16181
    • Kristi, L.F.1    Dou, Y.2    Bianca, J.L.3
  • 13
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., et al. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R15.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3
  • 14
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B., and Dewey, C.N. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 12, 323.
    • (2011) BMC Bioinf. , Issue.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 15
    • 77949507153 scopus 로고    scopus 로고
    • RNA-Seq gene expression estimation with read mapping uncertainty
    • Li, B., Ruotti, V., Stewart, R.M., et al. 2010. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 26, 493-500.
    • (2010) Bioinformatics , vol.26 , pp. 493-500
    • Li, B.1    Ruotti, V.2    Stewart, R.M.3
  • 16
    • 77951940273 scopus 로고    scopus 로고
    • Modeling non-uniformity in short-read rates in RNA-Seq data
    • Li, J., Jiang, H., and Wong, W.H. 2010. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol. 11, R50.
    • (2010) Genome Biol , vol.11
    • Li, J.1    Jiang, H.2    Wong, W.H.3
  • 17
    • 79953186446 scopus 로고    scopus 로고
    • IsoLasso: A LASSO regression approach to rna-seq based transcriptome assembly
    • Li, W., Feng, J., and Jiang, T. 2011. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. RECOMB 2011. LNBI 6577, 168-188.
    • (2011) RECOMB 2011. LNBI , vol.6577 , pp. 168-188
    • Li, W.1    Feng, J.2    Jiang, T.3
  • 18
    • 84055216924 scopus 로고    scopus 로고
    • Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation
    • Lia, J., Jiang, C., Browna, J.B., et al. 2011. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. U.S.A.
    • (2011) Proc. Natl. Acad. Sci. U.S.A
    • Lia, J.1    Jiang, C.2    Browna, J.B.3
  • 19
    • 79955082292 scopus 로고    scopus 로고
    • Estimation of alternative splicing isoform frequencies from RNASeq data
    • Nicolae, M., Mangul, S., Mandoiu, I.I., et al. 2011. Estimation of alternative splicing isoform frequencies from RNASeq data. Algorithms for Molecular Biology 6, 9.
    • (2011) Algorithms for Molecular Biology , vol.6 , pp. 9
    • Nicolae, M.1    Mangul, S.2    Mandoiu, I.I.3
  • 20
    • 75649089283 scopus 로고    scopus 로고
    • Sequence-non-specific effects of RNA interference triggers and microRNA regulators
    • Olejniczak, M., Galka, P., and Krzyzosiak, W.J. 2010. Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Res. 38, 1-16.
    • (2010) Nucleic Acids Res , vol.38 , pp. 1-16
    • Olejniczak, M.1    Galka, P.2    Krzyzosiak, W.J.3
  • 21
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan, Q., Shai, O., Lee, L.J., et al. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415.
    • (2008) Nat. Genet. , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3
  • 22
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K.D., Tatusova, T., and Maglott, D.R. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 23
    • 77954127002 scopus 로고    scopus 로고
    • Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
    • Richard, H., Schulz, M.H., Sultan, M., et al. 2010. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 38, e112.
    • (2010) Nucleic Acids Res , vol.38
    • Richard, H.1    Schulz, M.H.2    Sultan, M.3
  • 24
    • 79952709611 scopus 로고    scopus 로고
    • Improving RNA-Seq expression estimates by correcting for fragment bias
    • Roberts, A., Trapnell, C., Donaghey, J., et al. 2011. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 12, R22.
    • (2011) Genome Biol , vol.12
    • Roberts, A.1    Trapnell, C.2    Donaghey, J.3
  • 26
    • 80053435328 scopus 로고    scopus 로고
    • FDM: A graph-based statistical method to detect differential transcription using RNA-seq data
    • Singh, D., Orellana, C.F., Hu, Y., et al. 2011. FDM: A graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics. 27, 2633-40.
    • (2011) Bioinformatics , vol.27 , pp. 2633-2640
    • Singh, D.1    Orellana, C.F.2    Hu, Y.3
  • 27
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani, R. 1996. Regression shrinkage and selection via the lasso. J. R. Stat. Soc. 58, 267-288.
    • (1996) J. R. Stat. Soc. , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 28
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C., Williams, B.A., Pertea, P., et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515.
    • (2010) Nat. Biotechnol. , Issue.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, P.3
  • 29
    • 79751531332 scopus 로고    scopus 로고
    • Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
    • Turro, E.S.S, and Concalves, A. 2011. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 12, R13.
    • (2011) Genome Biol. , vol.12
    • Turro, E.S.S.1    Concalves, A.2
  • 30
    • 85052549687 scopus 로고    scopus 로고
    • A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
    • Srivastava, S., and Chen, L. 2010. A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res. 38, e170.
    • (2010) Nucleic Acids Res. , Issue.38
    • Srivastava, S.1    Chen, L.2
  • 31
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang, E.T., Sandberg, R., Luo, S., et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature. 456, 470-476.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3
  • 32
    • 78649345104 scopus 로고    scopus 로고
    • MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
    • Wang, K., Singh, D., Zeng, Z., et al. 2010. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 38, 178.
    • (2010) Nucleic Acids Res , vol.38 , pp. 178
    • Wang, K.1    Singh, D.2    Zeng, Z.3
  • 33
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M., Snyder, M., et al. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 34
    • 80054931745 scopus 로고    scopus 로고
    • SpliceTrap: A method to quantify alternative splicing under single cellular conditions
    • Wu, J., Akerman, M., Sun, S., et al. 2011. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics. 27, 3010-3016.
    • (2011) Bioinformatics , vol.27 , pp. 3010-3016
    • Wu, J.1    Akerman, M.2    Sun, S.3
  • 35
    • 79951522882 scopus 로고    scopus 로고
    • Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
    • Wu, Z., Wang, X., and Zhang, X. 2011. Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics. 27, 502-508.
    • (2011) Bioinformatics , vol.27 , pp. 502-508
    • Wu, Z.1    Wang, X.2    Zhang, X.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.