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Volumn 39, Issue 18, 2011, Pages

STEME: Efficient em to find motifs in large data sets

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; QUALITY CONTROL; SUFFIX TREE EM FOR MOTIF ELICITATION ALGORITHM; THEORETICAL STUDY;

EID: 80054070341     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr574     Document Type: Article
Times cited : (44)

References (42)
  • 1
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 669-680
    • Park, P.J.1
  • 2
    • 70349576551 scopus 로고    scopus 로고
    • ChIP-Chip: Algorithms for calling binding sites
    • Liu, X.S. and Meyer, C.A. (2009) ChIP-Chip: algorithms for calling binding sites. Methods Mol. Biol., 556, 165-175.
    • (2009) Methods Mol. Biol. , vol.556 , pp. 165-175
    • Liu, X.S.1    Meyer, C.A.2
  • 4
    • 67849122301 scopus 로고    scopus 로고
    • Using ChIP-chip and ChIP-seq to study the regulation of gene expression: Genome-wide localization studies reveal widespread regulation of transcription elongation
    • Gilchrist, D.A., Fargo, D.C. and Adelman, K. (2009) Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods, 48, 398-408.
    • (2009) Methods , vol.48 , pp. 398-408
    • Gilchrist, D.A.1    Fargo, D.C.2    Adelman, K.3
  • 5
    • 68949162986 scopus 로고    scopus 로고
    • Transcriptional programs: Modelling higher order structure in transcriptional control
    • Reid, J.E., Ott, S. and Wernisch, L. (2009) Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics, 10, 218.
    • (2009) BMC Bioinformatics , vol.10 , pp. 218
    • Reid, J.E.1    Ott, S.2    Wernisch, L.3
  • 6
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • DOI 10.1093/nar/gki791
    • Hu, J., Li, B. and Kihara, D. (2005) Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res., 33, 4899-4913. (Pubitemid 41418889)
    • (2005) Nucleic Acids Research , vol.33 , Issue.15 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 7
    • 33646229522 scopus 로고    scopus 로고
    • Practical strategies for discovering regulatory DNA sequence motifs
    • MacIsaac, K.D. and Fraenkel, E. (2006) Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput. Biol., 2, e36.
    • (2006) PLoS Comput. Biol. , vol.2
    • MacIsaac, K.D.1    Fraenkel, E.2
  • 8
    • 33747064917 scopus 로고    scopus 로고
    • How does DNA sequence motif discovery work?
    • D'haeseleer, P. (2006) How does DNA sequence motif discovery work? Nat. Biotechnol., 24, 959-961.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 959-961
    • D'Haeseleer, P.1
  • 9
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das, M.K. and Dai, H.-K. (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics, 8(Suppl. 7), S21.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 7
    • Das, M.K.1    Dai, H.-K.2
  • 10
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the em Algorithm
    • Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM Algorithm. J. Roy. Stat. Soc. Ser. B, 39, 1-38.
    • (1977) J. Roy. Stat. Soc. Ser. B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 11
    • 0001956238 scopus 로고
    • Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images
    • Geman, S. and Geman, D. (1993) Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. J. Appl. Stat., 20, 25-62.
    • (1993) J. Appl. Stat. , vol.20 , pp. 25-62
    • Geman, S.1    Geman, D.2
  • 12
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • Lawrence, C.E. and Reilly, A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51. (Pubitemid 20102601)
    • (1990) Proteins: Structure, Function and Genetics , vol.7 , Issue.1 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 13
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 14
    • 0037461026 scopus 로고    scopus 로고
    • Greedy mixture learning for multiple motif discovery in biological sequences
    • DOI 10.1093/bioinformatics/btg037
    • Blekas, K., Fotiadis, D.I. and Likas, A. (2003) Greedy mixture learning for multiple motif discovery in biological sequences. Bioinformatics, 19, 607-617. (Pubitemid 36417055)
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 607-617
    • Blekas, K.1    Fotiadis, D.I.2    Likas, A.3
  • 16
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • Sinha, S., Blanchette, M. and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5, 170.
    • (2004) BMC Bioinformatics , vol.5 , pp. 170
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 17
    • 2442693190 scopus 로고    scopus 로고
    • Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures
    • Moses, A.M., Chiang, D.Y. and Eisen, M.B. (2004) Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures. Pac. Symp. Biocomput., 324-335.
    • (2004) Pac. Symp. Biocomput. , pp. 324-335
    • Moses, A.M.1    Chiang, D.Y.2    Eisen, M.B.3
  • 18
    • 29244482771 scopus 로고    scopus 로고
    • Genetic interaction motif finding by expectation maximization-a novel statistical model for inferring gene modules from synthetic lethality
    • Qi, Y., Ye, P. and Bader, J.S. (2005) Genetic interaction motif finding by expectation maximization-a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics, 6, 288.
    • (2005) BMC Bioinformatics , vol.6 , pp. 288
    • Qi, Y.1    Ye, P.2    Bader, J.S.3
  • 19
    • 32544434809 scopus 로고    scopus 로고
    • A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
    • DOI 10.1093/bioinformatics/bti815
    • MacIsaac, K.D., Gordon, D.B., Nekludova, L., Odom, D.T., Schreiber, J., Gifford, D.K., Young, R.A. and Fraenkel, E. (2006) A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics, 22, 423-429. (Pubitemid 43231416)
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 423-429
    • MacIsaac, K.D.1    Gordon, D.B.2    Nekludova, L.3    Odom, D.T.4    Schreiber, J.5    Gifford, D.K.6    Young, R.A.7    Fraenkel, E.8
  • 20
    • 59649113226 scopus 로고    scopus 로고
    • GADEM: A genetic algorithm guided formation of spaced dyads coupled with an em algorithm for motif discovery
    • Li, L. (2009) GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J. Comput. Biol., 16, 317-329.
    • (2009) J. Comput. Biol. , vol.16 , pp. 317-329
    • Li, L.1
  • 22
    • 0029962489 scopus 로고    scopus 로고
    • ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool
    • Grundy, W.N., Bailey, T.L. and Elkan, C.P. (1996) ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput. Appl. Biosci., 12, 303-310.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 303-310
    • Grundy, W.N.1    Bailey, T.L.2    Elkan, C.P.3
  • 24
    • 57049178944 scopus 로고    scopus 로고
    • GPU-MEME: Using graphics hardware to accelerate motif finding in DNA sequences
    • Chetty, M., Ngom, A., and Ahmad, S., (eds) Pattern Recognition in Bioinformatics Springer, Berlin/Heidelberg
    • Chen, C., Schmidt, B., Weiguo, L., and Müller-Wittig, W. (2008) GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. In Chetty, M., Ngom, A., and Ahmad, S., (eds), Pattern Recognition in Bioinformatics, Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 448-459.
    • (2008) Lecture Notes in Computer Science , pp. 448-459
    • Chen, C.1    Schmidt, B.2    Weiguo, L.3    Müller-Wittig, W.4
  • 26
    • 38849131252 scopus 로고    scopus 로고
    • High-throughput sequence alignment using Graphics Processing Units
    • Schatz, M., Trapnell, C., Delcher, A. and Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics, 8, 474.
    • (2007) BMC Bioinformatics , vol.8 , pp. 474
    • Schatz, M.1    Trapnell, C.2    Delcher, A.3    Varshney, A.4
  • 28
    • 78650487811 scopus 로고    scopus 로고
    • Unified view of backward backtracking in short read mapping
    • Elomaa, T., Mannila, H., and Orponen, P. (eds) Algorithms and Applications Springer, Berlin/Heidelberg
    • Mäkinen, V., Välimäki, N., Laaksonen, A., and Katainen, R. (2010) Unified view of backward backtracking in short read mapping. In Elomaa, T., Mannila, H., and Orponen, P. (eds), Algorithms and Applications, Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 182-195.
    • (2010) Lecture Notes in Computer Science , pp. 182-195
    • Mäkinen, V.1    Välimäki, N.2    Laaksonen, A.3    Katainen, R.4
  • 29
    • 69849083725 scopus 로고    scopus 로고
    • Suffix tree characterization of maximal motifs in biological sequences
    • Federico, M. and Pisanti, N. (2009) Suffix tree characterization of maximal motifs in biological sequences. Theor. Comput. Sci., 410, 4391-4401.
    • (2009) Theor. Comput. Sci. , vol.410 , pp. 4391-4401
    • Federico, M.1    Pisanti, N.2
  • 30
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification
    • Marsan, L. and Sagot, M.F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-362.
    • (2000) J. Comput. Biol. , vol.7 , pp. 345-362
    • Marsan, L.1    Sagot, M.F.2
  • 31
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • Pavesi, G., Mauri, G. and Pesole, G. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17(Suppl. 1), S207-S214. (Pubitemid 33793512)
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 32
    • 33750959240 scopus 로고    scopus 로고
    • Fast index based algorithms and software for matching position specific scoring matrices
    • Beckstette, M., Homann, R., Giegerich, R. and Kurtz, S. (2006) Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics, 7, 389.
    • (2006) BMC Bioinformatics , vol.7 , pp. 389
    • Beckstette, M.1    Homann, R.2    Giegerich, R.3    Kurtz, S.4
  • 33
    • 0001704377 scopus 로고
    • On-line construction of suffix trees
    • Ukkonen, E. (1995) On-line construction of suffix trees. Algorithmica, 14, 249-260.
    • (1995) Algorithmica , vol.14 , pp. 249-260
    • Ukkonen, E.1
  • 34
    • 39549090389 scopus 로고    scopus 로고
    • SeqAn an efficient, generic C++library for sequence analysis
    • Döring, A., Weese, D., Rausch, T. and Reinert, K. (2008) SeqAn an efficient, generic C++library for sequence analysis. BMC Bioinformatics, 9, 11.
    • (2008) BMC Bioinformatics , vol.9 , pp. 11
    • Döring, A.1    Weese, D.2    Rausch, T.3    Reinert, K.4
  • 35
    • 77349099959 scopus 로고    scopus 로고
    • Variable structure motifs for transcription factor binding sites
    • Reid, J.E., Evans, K.J., Dyer, N., Wernisch, L. and Ott, S. (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics, 11, 30.
    • (2010) BMC Genomics , vol.11 , pp. 30
    • Reid, J.E.1    Evans, K.J.2    Dyer, N.3    Wernisch, L.4    Ott, S.5
  • 37
    • 54549103162 scopus 로고    scopus 로고
    • Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression
    • Liao, W., Schones, D.E., Oh, J., Cui, Y., Cui, K., Roh, T.-Y., Zhao, K. and Leonard, W.J. (2008) Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat. Immunol., 9, 1288-1296.
    • (2008) Nat. Immunol. , vol.9 , pp. 1288-1296
    • Liao, W.1    Schones, D.E.2    Oh, J.3    Cui, Y.4    Cui, K.5    Roh, T.-Y.6    Zhao, K.7    Leonard, W.J.8
  • 41
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Nov
    • Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300, Nov.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 42
    • 0002759539 scopus 로고
    • Unsupervised Learning of Multiple Motifs in Biopolymers Using em
    • Bailey, T.L. and Elkan, C. (1995) Unsupervised Learning of Multiple Motifs In Biopolymers Using EM. Mach. Learn., 51-80.
    • (1995) Mach. Learn. , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2


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