메뉴 건너뛰기




Volumn 4, Issue 7, 2009, Pages

Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC POLYMORPHISM; GENOME ANALYSIS; HUMAN; NONHUMAN; QUANTITATIVE ANALYSIS; RELIABILITY; ANIMAL; ARABIDOPSIS; DROSOPHILA MELANOGASTER; EXON; GENETICS; GENOME; INTRON;

EID: 68149157998     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006323     Document Type: Article
Times cited : (21)

References (21)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 0036208669 scopus 로고    scopus 로고
    • OligoArray: Genome-scale oligonucleotide design for microarrays
    • Rouillard JM, Herbert CJ, Zuker M (2002) OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics 18: 486-487.
    • (2002) Bioinformatics , vol.18 , pp. 486-487
    • Rouillard, J.M.1    Herbert, C.J.2    Zuker, M.3
  • 3
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • Draghici S, Khatri P, Eklund AC, Szallasi Z (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22: 101-109.
    • (2006) Trends Genet , vol.22 , pp. 101-109
    • Draghici, S.1    Khatri, P.2    Eklund, A.C.3    Szallasi, Z.4
  • 5
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15: 674-680.
    • (2005) Genome Res , vol.15 , pp. 674-680
    • Gilad, Y.1    Rifkin, S.A.2    Bertone, P.3    Gerstein, M.4    White, K.P.5
  • 6
    • 33644855479 scopus 로고    scopus 로고
    • Expression profiling in primates reveals a rapid evolution of human transcription factors
    • Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
    • (2006) Nature , vol.440 , pp. 242-245
    • Gilad, Y.1    Oshlack, A.2    Smyth, G.K.3    Speed, T.P.4    White, K.P.5
  • 8
    • 33748917959 scopus 로고    scopus 로고
    • No Accelerated Rate of Protein Evolution in Male-Biased Drosophila pseudoobscura Genes
    • Metta M, G R, G JM, Schlotterer C (2006) No Accelerated Rate of Protein Evolution in Male-Biased Drosophila pseudoobscura Genes. Genetics 174: 411-420.
    • (2006) Genetics , vol.174 , pp. 411-420
    • Metta, M.G.R.G.J.1    Schlotterer, C.2
  • 9
    • 9144270582 scopus 로고    scopus 로고
    • Gene expression analysis of plant host-pathogen interactions by SuperSAGE
    • Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, et al. (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci U S A 100: 15718-15723.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 15718-15723
    • Matsumura, H.1    Reich, S.2    Ito, A.3    Saitoh, H.4    Kamoun, S.5
  • 10
    • 0034130561 scopus 로고    scopus 로고
    • Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays
    • Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634.
    • (2000) Nat Biotechnol , vol.18 , pp. 630-634
    • Brenner, S.1    Johnson, M.2    Bridgham, J.3    Golda, G.4    Lloyd, D.H.5
  • 11
  • 12
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 13
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11: 1725-1729.
    • (2001) Genome Res , vol.11 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 15
    • 53749083993 scopus 로고    scopus 로고
    • SeqMap: Mapping massive amount of oligonucleotides to the genome
    • Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395-2396.
    • (2008) Bioinformatics , vol.24 , pp. 2395-2396
    • Jiang, H.1    Wong, W.H.2
  • 16
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 17
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
    • (2005) Nature , vol.437 , pp. 1149-1152
    • Andolfatto, P.1
  • 18
    • 0034681511 scopus 로고    scopus 로고
    • Evidence for a high frequency of simultaneous double-nucleotide substitutions
    • Averof M, Rokas A, Wolfe KH, Sharp PM (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287: 1283-1286.
    • (2000) Science , vol.287 , pp. 1283-1286
    • Averof, M.1    Rokas, A.2    Wolfe, K.H.3    Sharp, P.M.4
  • 19
    • 40149098690 scopus 로고    scopus 로고
    • SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    • Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5: 247-252.
    • (2008) Nat Methods , vol.5 , pp. 247-252
    • Van Tassell, C.P.1    Smith, T.P.2    Matukumalli, L.K.3    Taylor, J.F.4    Schnabel, R.D.5
  • 20
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.