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Volumn , Issue , 2003, Pages 28-37

Modeling dependencies in protein-DNA binding sites

Author keywords

Bayesian networks; DNA sequence motifs; Transcription factors binding sites

Indexed keywords

BIOASSAY; DNA; GENES; MATHEMATICAL MODELS;

EID: 0038716277     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/640075.640079     Document Type: Conference Paper
Times cited : (172)

References (41)
  • 1
    • 0031652639 scopus 로고    scopus 로고
    • Detecling non-adjacent correlations within signals in DNA
    • P Agarwal and V Bafna. Detecling non-adjacent correlations within signals in DNA. In RECOMB'98. 1998.
    • (1998) RECOMB'98
    • Agarwal, P.1    Bafna, V.2
  • 2
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • TL Bailey and M Gribskov. Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14:48-54, 1998.
    • (1998) Bioinformatics , vol.14 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 3
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • TL Bailey and C Elkan. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In ISMB'94. 1994.
    • (1994) ISMB'94
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0001360583 scopus 로고    scopus 로고
    • A simple hyper-geometric approach for discovering putative transcription factor binding sites
    • Y Barash, G Bejerano, and N Friedman. A simple hyper-geometric approach for discovering putative transcription factor binding sites. In WABI'01. 2001.
    • (2001) WABI'01
    • Barash, Y.1    Bejerano, G.2    Friedman, N.3
  • 6
    • 0036100113 scopus 로고    scopus 로고
    • Context-specific Bayesian clustering for gene expression data
    • Y Barash and N Friedman. Context-specific Bayesian clustering for gene expression data. J. Camp. Bio., 9:169-191, 2002.
    • (2002) J. Camp. Bio. , vol.9 , pp. 169-191
    • Barash, Y.1    Friedman, N.2
  • 8
    • 0034823882 scopus 로고    scopus 로고
    • Finding motifs using random projections
    • J Buhler and M Tompa. Finding motifs using random projections. In RECOMB'01. 2001.
    • (2001) RECOMB'01
    • Buhler, J.1    Tompa, M.2
  • 9
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • ML Bulyk, PL Johnson, and GM Church. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nuc. Acids Res., 30:1255-61, 2002.
    • (2002) Nuc. Acids Res. , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.2    Church, G.M.3
  • 10
    • 0034136782 scopus 로고    scopus 로고
    • Modeling splice sites with Bayes networks
    • D Cai. A Deicher, B Kao, and S Kasif. Modeling splice sites with Bayes networks. Bioinformatics, 16:152-158, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 152-158
    • Cai, D.1    Deicher, A.2    Kao, B.3    Kasif, S.4
  • 11
    • 0031272327 scopus 로고    scopus 로고
    • Efficient approximations for the marginal likelihood of Bayesian networks with hidden variables
    • DM Chickering and D Heckerman. Efficient approximations for the marginal likelihood of Bayesian networks with hidden variables. Mach. Learn., 29:181-212, 1997.
    • (1997) Mach. Learn. , vol.29 , pp. 181-212
    • Chickering, D.M.1    Heckerman, D.2
  • 12
    • 84933530882 scopus 로고
    • Approximating discrete probability distributions with dependence trees
    • CK Chow and CN Liu. Approximating discrete probability distributions with dependence trees. IEEE Trans. on Info. Theory, 14:462-467, 1968.
    • (1968) IEEE Trans. on Info. Theory , vol.14 , pp. 462-467
    • Chow, C.K.1    Liu, C.N.2
  • 13
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • AP Dempster, NM Laird, and DB Rubin. Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Stat. Soc, B 39:1-39, 1977.
    • (1977) J. Roy. Stat. Soc B , vol.39 , pp. 1-39
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 15
    • 0001586968 scopus 로고    scopus 로고
    • Learning belief networks in the presence of missing values and hidden variables
    • N Friedman, Learning belief networks in the presence of missing values and hidden variables. In ICML'97, 1997.
    • (1997) ICML'97
    • Friedman, N.1
  • 16
    • 0000854197 scopus 로고    scopus 로고
    • The Bayesian structural EM algorithm
    • N Friedman. The Bayesian structural EM algorithm. In UAI'98. 1998.
    • (1998) UAI'98
    • Friedman, N.1
  • 19
    • 0002219642 scopus 로고    scopus 로고
    • Data analysis with Bayesian networks: A bootstrap approach
    • N Friedman, M Goldszmidt, and A Wyner. Data analysis with Bayesian networks: A bootstrap approach. In UAI'99. 1999.
    • (1999) UAI'99
    • Friedman, N.1    Goldszmidt, M.2    Wyner, A.3
  • 20
    • 0037262841 scopus 로고    scopus 로고
    • Being Bayesian about Bayesian network structure: A Bayesian approach to structure discovery in Bayesian networks
    • N Friedman and D Koller. Being Bayesian about Bayesian network structure: A Bayesian approach to structure discovery in Bayesian networks. Mach. Learn., 50:95-126, 2003.
    • (2003) Mach. Learn. , vol.50 , pp. 95-126
    • Friedman, N.1    Koller, D.2
  • 23
    • 34249761849 scopus 로고
    • Learning Bayesian networks: The combination of knowledge and statistical data
    • D Heckerman, D Geiger, and DM Chickering. Learning Bayesian networks: The combination of knowledge and statistical data. Mach. Learn., 20:197-243, 1995.
    • (1995) Mach. Learn. , vol.20 , pp. 197-243
    • Heckerman, D.1    Geiger, D.2    Chickering, D.M.3
  • 24
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • GZ Hertz and GD Stormo. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 15:563-77, 1999.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 25
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatury elements associated with groups of functional related genes in saccharomyces cerevisiae
    • JD Hughes. PE Estep. S Tavazoie. and GM Church. Computational identification of cis-regulatury elements associated with groups of functional related genes in saccharomyces cerevisiae. J. Mol. Bio., 296:1205-1214, 2000.
    • (2000) J. Mol. Bio. , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.E.2    Tavazoie, S.3    Church, G.M.4
  • 26
    • 0027960477 scopus 로고
    • Discovering structural correlations in α-Helices
    • TM Klingler and DL Brutlag. Discovering structural correlations in α-Helices. Prot. Sci., 3:1847-1857, 1994.
    • (1994) Prot. Sci. , vol.3 , pp. 1847-1857
    • Klingler, T.M.1    Brutlag, D.L.2
  • 28
    • 58149210716 scopus 로고
    • The EM algorithm for graphical association models with missing data
    • SL Lauritzen. The EM algorithm for graphical association models with missing data. Camp. Stat. and Data Analysis. 19:191-201, 1995.
    • (1995) Camp. Stat. and Data Analysis , vol.19 , pp. 191-201
    • Lauritzen, S.L.1
  • 29
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in saccharomyces cerevisiae
    • TI Lee et al. Transcriptional regulatory networks in saccharomyces cerevisiae. Science, 298:799 -804, 2002.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1
  • 30
    • 0035949674 scopus 로고    scopus 로고
    • A computational analysis of sequence features involved in recognition of short introns
    • LP Lim and CB Burge. A computational analysis of sequence features involved in recognition of short introns. PNAS. 98:11193-11198, 2001.
    • (2001) PNAS , vol.98 , pp. 11193-11198
    • Lim, L.P.1    Burge, C.B.2
  • 31
    • 0035228215 scopus 로고    scopus 로고
    • Bioprospector: Discovering conserved dna motifs in upstream regulatory regions of co-expressed genes
    • X Liu, DL Brutlag, and JS Liu. Bioprospector: discovering conserved dna motifs in upstream regulatory regions of co-expressed genes. In PSB'01. 2001.
    • (2001) PSB'01
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 32
    • 84898959728 scopus 로고    scopus 로고
    • Estimating dependency structure as a hidden variable
    • M Meila and MI Jordan. Estimating dependency structure as a hidden variable. In NIPS 10, 1998.
    • (1998) NIPS , vol.10
    • Meila, M.1    Jordan, M.I.2
  • 34
    • 0028971143 scopus 로고
    • MatInd and MatInspector - New fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • K Quandt. K Frech, H Karas, E Wingender, and T Werner. MatInd and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nuc. Acids Res., 23:4878-4884, 1995.
    • (1995) Nuc. Acids Res. , vol.23 , pp. 4878-4884
    • Quandt, K.1    Frech, K.2    Karas, H.3    Wingender, E.4    Werner, T.5
  • 35
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of dna binding proteins
    • B Ren et al. Genome-wide location and function of dna binding proteins. Science, 290:2306-9, 2000.
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1
  • 36
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • FP Roth, PW Hughes, JD Estep, and GM Church. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotech., 16:939-945, 1998.
    • (1998) Nat. Biotech. , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, P.W.2    Estep, J.D.3    Church, G.M.4
  • 38
    • 17944372930 scopus 로고    scopus 로고
    • Serial regulation of transcriptional regulators in the yeast cell cycle
    • I Simon et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106:697-708, 2001.
    • (2001) Cell , vol.106 , pp. 697-708
    • Simon, I.1
  • 40
    • 0034566082 scopus 로고    scopus 로고
    • Mining for putative regulatory elements in the yeast genome using gene expression data
    • J Vilo. A Brazma, I Jonassen, A Robinson, and E Ukkonen. Mining for putative regulatory elements in the yeast genome using gene expression data. In ISMB'00. 2000.
    • (2000) ISMB'00
    • Vilo, J.1    Brazma, A.2    Jonassen, I.3    Robinson, A.4    Ukkonen, E.5
  • 41
    • 0035172256 scopus 로고    scopus 로고
    • The TRANSFAC system on gene expression regulation
    • E Wingender it et al. The TRANSFAC system on gene expression regulation. Nuc. Acids Res., 29:281-283, 2001.
    • (2001) Nuc. Acids Res. , vol.29 , pp. 281-283
    • Wingender, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.