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Volumn 21, Issue 7, 2005, Pages 922-931

Vocabulon: A dictionary model approach for reconstruction and localization of transcription factor binding sites

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

EID: 16344377461     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti083     Document Type: Article
Times cited : (16)

References (23)
  • 1
    • 0035920119 scopus 로고    scopus 로고
    • Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media
    • Avison,M.B., Horton,R.E., Walsh,T.R. and Bennett,P.M. (2001) Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media. J. Biol. Chem., 29, 26955-26961.
    • (2001) J. Biol. Chem. , vol.29 , pp. 26955-26961
    • Avison, M.B.1    Horton, R.E.2    Walsh, T.R.3    Bennett, P.M.4
  • 2
    • 0001862769 scopus 로고
    • 'An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes'
    • Baum,L.E. (1972) 'An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes.' Inequalities, 3, 1-8.
    • (1972) Inequalities , vol.3 , pp. 1-8
    • Baum, L.E.1
  • 4
    • 0034730161 scopus 로고    scopus 로고
    • Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
    • Bussemaker,H.J., Li,H. and Siggia,E.D. (2000) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl Acad. Sci., 97, 10096-10100.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 10096-10100
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 5
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker,H.J., Li,H. and Siggia,E.D. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
    • (2001) Nat. Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 6
    • 0037453009 scopus 로고    scopus 로고
    • Integrating regulatory motif discovery and genome-wide expression analysis
    • Colon,E., Liu,X., Lieb,J. and Liu,J.S. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci., 100, 3339-3344.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 3339-3344
    • Colon, E.1    Liu, X.2    Lieb, J.3    Liu, J.S.4
  • 7
    • 0035023305 scopus 로고    scopus 로고
    • Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli
    • Courcelle,J., Khodursky,A., Peter,B., Brown,P.O. and Hanawalt,PC. (2001) Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics, 158, 41-64.
    • (2001) Genetics , vol.158 , pp. 41-64
    • Courcelle, J.1    Khodursky, A.2    Peter, B.3    Brown, P.O.4    Hanawalt, P.C.5
  • 8
    • 0022205224 scopus 로고
    • Baum's forward-backward algorithm revisited
    • Devijver,P.A. (1985) Baum's forward-backward algorithm revisited. Pattern Recogn. Lett., 3, 369-373.
    • (1985) Pattern Recogn. Lett. , vol.3 , pp. 369-373
    • Devijver, P.A.1
  • 9
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • Djordjevic,M., Sengupta,A.M. and Shraiman,B.I. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res., 13, 2381-2390.
    • (2003) Genome Res. , vol.13 , pp. 2381-2390
    • Djordjevic, M.1    Sengupta, A.M.2    Shraiman, B.I.3
  • 10
    • 0037361669 scopus 로고    scopus 로고
    • Discovery of conserved sequence patterns using a stochastic dictionary model
    • Gupta,M. and Liu,J.S. (2003) Discovery of conserved sequence patterns using a stochastic dictionary model. J. Am. Statist. Assoc. 98, 55-66.
    • (2003) J. Am. Statist. Assoc. , vol.98 , pp. 55-66
    • Gupta, M.1    Liu, J.S.2
  • 11
    • 0027183315 scopus 로고
    • Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: A molecular analysis
    • Jennings,M. and Beacham,I.R. (1993) Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis. Mol. Microbiol., 9, 155-164.
    • (1993) Mol. Microbiol. , vol.9 , pp. 155-164
    • Jennings, M.1    Beacham, I.R.2
  • 12
    • 0036740483 scopus 로고    scopus 로고
    • Identification of regulatory elements using a feature selection method
    • Keles,M., van der Laan,M. and Eisen,M. (2002) Identification of regulatory elements using a feature selection method. Bioinformatics, 18, 1167-1175.
    • (2002) Bioinformatics , vol.18 , pp. 1167-1175
    • Keles, M.1    van der Laan, M.2    Eisen, M.3
  • 13
    • 77950023906 scopus 로고    scopus 로고
    • Optimization transfer using surrogate objective functions
    • (with discussion)
    • Lange,K., HunterD.R. and Yang,I. (2000) Optimization transfer using surrogate objective functions (with discussion). J. Comput. Graph. Statist., 9, 1-59.
    • (2000) J. Comput. Graph. Statist. , vol.9 , pp. 1-59
    • Lange, K.1    Hunter, D.R.2    Yang, I.3
  • 14
    • 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.
    • (1990) Proteins , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 15
  • 16
    • 0345824737 scopus 로고    scopus 로고
    • Network component analysis: Reconstruction of regulatory signals in biological systems
    • Liao,J., Boscolo,R., Yang,Y., Tran,L., Sabatti,C. and Roychowdhury,V (2003) Network component analysis: reconstruction of regulatory signals in biological systems. Proc. Natl Acad. Sci., 100, 15522-15527.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 15522-15527
    • Liao, J.1    Boscolo, R.2    Yang, Y.3    Tran, L.4    Sabatti, C.5    Roychowdhury, V.6
  • 18
    • 0035928603 scopus 로고    scopus 로고
    • Novel F-dependent genes of Escherichia chia coli found using a specified promoter consensus
    • Park,K., Choi,S., Ko,M. and Park,C. (2001) Novel F-dependent genes of Escherichia chia coli found using a specified promoter consensus. FEMS Microbiol. Lett., 202, 243-250.
    • (2001) FEMS Microbiol. Lett. , vol.202 , pp. 243-250
    • Park, K.1    Choi, S.2    Ko, M.3    Park, C.4
  • 19
    • 0028971143 scopus 로고
    • MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 4878-4884
    • Quandt, K.1    Frech, K.2    Karas, H.3    Wingender, E.4    Werner, T.5
  • 20
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome
    • Robison,K., McGuire,A.M. and Church,G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome. J. Mol. Biol., 284, 241-254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 21
    • 1342280632 scopus 로고    scopus 로고
    • Genomewide motif identification using a dictionary model
    • Sabatti,C. and Lange,K. (2002) Genomewide motif identification using a dictionary model. IEEE Proc., 90, 1803-1810.
    • (2002) IEEE Proc. , vol.90 , pp. 1803-1810
    • Sabatti, C.1    Lange, K.2
  • 22
    • 0036640105 scopus 로고    scopus 로고
    • Co-expression pattern from DNA microarray experiments as a tool for operon prediction
    • Sabatti,C., Rohlin,L., Oh,M. and Liao,J. (2002) Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res., 30, 2886-2893.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2886-2893
    • Sabatti, C.1    Rohlin, L.2    Oh, M.3    Liao, J.4
  • 23
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.