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Volumn 7, Issue 1, 2012, Pages

IQSeq: Integrated isoform quantification analysis based on next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

RNA ISOFORM; TRANSCRIPTOME; TCF7 PROTEIN, HUMAN; TRANSCRIPTION FACTOR 7;

EID: 84855443354     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029175     Document Type: Article
Times cited : (6)

References (22)
  • 1
    • 34250330777 scopus 로고    scopus 로고
    • What is a gene, post-encode? history and updated definition
    • Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, et al. (2007) What is a gene, post-encode? history and updated definition. Genome Res 17: 669-681.
    • (2007) Genome Res , vol.17 , pp. 669-681
    • Gerstein, M.B.1    Bruce, C.2    Rozowsky, J.S.3    Zheng, D.4    Du, J.5
  • 2
    • 0344622123 scopus 로고
    • Spliced segments at the 5′ terminus of adenovirus 2 late mrna
    • Berget SM, Moore C, Sharp PA, (1977) Spliced segments at the 5′ terminus of adenovirus 2 late mrna. Proc Natl Acad Sci U S A 74: 3171-3175.
    • (1977) Proc Natl Acad Sci U S A , vol.74 , pp. 3171-3175
    • Berget, S.M.1    Moore, C.2    Sharp, P.A.3
  • 3
    • 0017688583 scopus 로고
    • An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger rna
    • Chow LT, Gelinas RE, Broker TR, Roberts RJ, (1977) An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger rna. Cell 12: 1-8.
    • (1977) Cell , vol.12 , pp. 1-8
    • Chow, L.T.1    Gelinas, R.E.2    Broker, T.R.3    Roberts, R.J.4
  • 4
    • 0017405794 scopus 로고
    • One predominant 5′-undecanucleotide in adenovirus 2 late messen- ger rnas
    • Gelinas RE, Roberts RJ, (1977) One predominant 5′-undecanucleotide in adenovirus 2 late messen- ger rnas. Cell 11: 533-544.
    • (1977) Cell , vol.11 , pp. 533-544
    • Gelinas, R.E.1    Roberts, R.J.2
  • 5
    • 33748645500 scopus 로고    scopus 로고
    • Gencode: producing a reference annotation for encode
    • Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, et al. (2006) Gencode: producing a reference annotation for encode. Genome Biol 7 (Suppl 1): S4.1-S4.9.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1 , pp. 1-9
    • Harrow, J.1    Denoeud, F.2    Frankish, A.3    Reymond, A.4    Chen, C.K.5
  • 6
    • 33745156134 scopus 로고    scopus 로고
    • An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
    • Xing Y, Yu T, Wu YN, Roy M, Kim J, et al. (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 34: 3150-3160.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3150-3160
    • Xing, Y.1    Yu, T.2    Wu, Y.N.3    Roy, M.4    Kim, J.5
  • 7
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inferences for isoform expression in rna-seq
    • Jiang H, Wong WH, (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
  • 8
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol.
    • (2010) Nat Biotechnol
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 9
    • 77954127002 scopus 로고    scopus 로고
    • Prediction of alternative isoforms from exon expression levels in rna-seq experiments
    • Richard H, Schulz MH, Sultan M, Nrnberger A, Schrinner S, 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    Nrnberger, A.4    Schrinner, S.5
  • 14
    • 68249117657 scopus 로고    scopus 로고
    • Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants
    • Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, et al. (2009) Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol 5: e1000432.
    • (2009) PLoS Comput Biol , vol.5
    • Du, J.1    Bjornson, R.D.2    Zhang, Z.D.3    Kong, Y.4    Snyder, M.5
  • 16
    • 63849342015 scopus 로고    scopus 로고
    • Massively parallel sequencing of the polyadenylated transcriptome of c. elegans
    • Hillier LW, Reinke V, Green P, Hirst M, Marra MA, et al. (2009) Massively parallel sequencing of the polyadenylated transcriptome of c. elegans. Genome Res 19: 657-666.
    • (2009) Genome Res , vol.19 , pp. 657-666
    • Hillier, L.W.1    Reinke, V.2    Green, P.3    Hirst, M.4    Marra, M.A.5
  • 18
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the caenorhabditis elegans genome by the modencode project
    • Gerstein MB, Lu ZJ, Nostrand ELV, Cheng C, Arshinoff BI, et al. (2010) Integrative analysis of the caenorhabditis elegans genome by the modencode project. Science 330: 1775-1787.
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1    Lu, Z.J.2    Nostrand, E.L.V.3    Cheng, C.4    Arshinoff, B.I.5
  • 19
    • 77951940273 scopus 로고    scopus 로고
    • Modeling non-uniformity in short-read rates in rna-seq data
    • Li J, Jiang H, Wong WH, (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
  • 20
    • 77955883388 scopus 로고    scopus 로고
    • Biases in illumina transcriptome sequencing caused by random hexamer priming
    • Hansen KD, Brenner SE, Dudoit S, (2010) Biases in illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res.
    • (2010) Nucleic Acids Res
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 21
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normal- ization and differential expression in mrna-seq experiments
    • Bullard JH, Purdom E, Hansen KD, Dudoit S, (2010) Evaluation of statistical methods for normal- ization and differential expression in mrna-seq experiments. BMC Bioinformatics 11: 94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 22
    • 33748491517 scopus 로고    scopus 로고
    • The microarray quality control (maqc) project shows inter- and intraplatform reproducibility of gene expression measure- ments
    • Consortium MAQC
    • Shi L, Reid LH, Jones WD, Shippy R, et al. Consortium MAQC (2006) The microarray quality control (maqc) project shows inter- and intraplatform reproducibility of gene expression measure- ments. Nat Biotechnol 24: 1151-1161.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3    Shippy, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.