메뉴 건너뛰기




Volumn 1, Issue 2, 2013, Pages 115-130

Modeling the specificity of protein-DNA interactions

Author keywords

Binding Energy; Binding Probability; Consensus Sequence; Ribosome Binding Site; Transcription Factor Binding Site

Indexed keywords


EID: 84885841612     PISSN: 20954689     EISSN: 20954697     Source Type: Journal    
DOI: 10.1007/s40484-013-0012-4     Document Type: Review
Times cited : (156)

References (95)
  • 1
    • 0020480251 scopus 로고
    • Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites in E. coli
    • PID: 7048259, COI: 1:CAS:528:DyaL38XktFygsLk%3D
    • Stormo, G. D., Schneider, T. D., Gold, L. and Ehrenfeucht, A. (1982) Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res., 10, 2997–3011.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 2997-3011
    • Stormo, G.D.1    Schneider, T.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 2
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • PID: 12419259, COI: 1:CAS:528:DC%2BD38Xot12ltLo%3D
    • Benos, P. V., Lapedes, A. S. and Stormo, G. D. (2002) Probabilistic code for DNA recognition by proteins of the EGR family. J. Mol. Biol., 323, 701–727.
    • (2002) J. Mol. Biol. , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 3
    • 29444434700 scopus 로고    scopus 로고
    • Ab initio prediction of transcription factor targets using structural knowledge
    • PID: 16103898
    • Kaplan, T., Friedman, N. and Margalit, H. (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput. Biol., 1, e1.
    • (2005) PLoS Comput. Biol. , vol.1
    • Kaplan, T.1    Friedman, N.2    Margalit, H.3
  • 4
    • 0033624684 scopus 로고    scopus 로고
    • DNA recognition by Cys2His2 zinc finger proteins
    • PID: 10940247, COI: 1:CAS:528:DC%2BD3cXlsFOntbc%3D
    • Wolfe, S. A., Nekludova, L. and Pabo, C. O. (2000) DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct., 29, 183–212.
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 183-212
    • Wolfe, S.A.1    Nekludova, L.2    Pabo, C.O.3
  • 5
    • 77952280117 scopus 로고    scopus 로고
    • The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation
    • PID: 20478078, COI: 1:CAS:528:DC%2BC3cXptlyrsbo%3D
    • Klug, A. (2010) The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q. Rev. Biophys., 43, 1–21.
    • (2010) Q. Rev. Biophys. , vol.43 , pp. 1-21
    • Klug, A.1
  • 6
    • 66249108559 scopus 로고    scopus 로고
    • Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
    • PID: 19401680
    • Foat, B. C. and Stormo, G. D. (2009) Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol. Syst. Biol., 5, 268.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 268
    • Foat, B.C.1    Stormo, G.D.2
  • 7
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most significant common sequence and structure motifs in a set of RNA sequences
    • PID: 9278497, COI: 1:CAS:528:DyaK2sXmsVansbo%3D
    • Gorodkin, J., Heyer, L. J. and Stormo, G. D. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res., 25, 3724–3732.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3724-3732
    • Gorodkin, J.1    Heyer, L.J.2    Stormo, G.D.3
  • 8
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • PID: 9918945, COI: 1:CAS:528:DyaK1MXktlCmtQ%3D%3D
    • Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755–763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 10
    • 0020480282 scopus 로고
    • Characterization of translational initiation sites in E. coli
    • PID: 7048258, COI: 1:CAS:528:DyaL38XktVamtrY%3D
    • Stormo, G. D., Schneider, T. D. and Gold, L. M. (1982) Characterization of translational initiation sites in E. coli. Nucleic Acids Res., 10, 2971–2996.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 2971-2996
    • Stormo, G.D.1    Schneider, T.D.2    Gold, L.M.3
  • 11
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • PID: 14597652, COI: 1:CAS:528:DC%2BD3sXovFWrsLk%3D
    • 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
  • 12
    • 0008261096 scopus 로고
    • A new method for sequencing DNA
    • PID: 265521, COI: 1:CAS:528:DyaE2sXhtFOhsbw%3D
    • Maxam, A. M. and Gilbert, W. (1977) A new method for sequencing DNA. Proc. Natl. Acad. Sci. U S A, 74, 560–564.
    • (1977) Proc. Natl. Acad. Sci. U S A , vol.74 , pp. 560-564
    • Maxam, A.M.1    Gilbert, W.2
  • 13
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • PID: 271968, COI: 1:CAS:528:DyaE1cXhtlaru7Y%3D
    • Sanger, F., Nicklen, S. and Coulson, A. R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U S A, 74, 5463–5467.
    • (1977) Proc. Natl. Acad. Sci. U S A , vol.74 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 14
    • 0018588890 scopus 로고
    • Regulatory sequences involved in the promotion and termination of RNA transcription
    • PID: 94251, COI: 1:CAS:528:DyaL3cXnt1eitg%3D%3D
    • Rosenberg, M. and Court, D. (1979) Regulatory sequences involved in the promotion and termination of RNA transcription. Annu. Rev. Genet. 13, 319–353.
    • (1979) Annu. Rev. Genet. , vol.13 , pp. 319-353
    • Rosenberg, M.1    Court, D.2
  • 15
    • 0021111879 scopus 로고
    • Compilation and analysis of Escherichia coli promoter DNA sequences
    • PID: 6344016, COI: 1:CAS:528:DyaL3sXktVWitrw%3D
    • Hawley, D. K. and McClure, W. R. (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res., 11, 2237–2255.
    • (1983) Nucleic Acids Res. , vol.11 , pp. 2237-2255
    • Hawley, D.K.1    McClure, W.R.2
  • 16
    • 0018867360 scopus 로고
    • E. coli RNA polymerase interacts homologously with two different promoters
    • PID: 6248238, COI: 1:CAS:528:DyaL3cXkvFSlurg%3D
    • Siebenlist, U., Simpson, R. B. and Gilbert, W. (1980) E. coli RNA polymerase interacts homologously with two different promoters. Cell, 20, 269–281.
    • (1980) Cell , vol.20 , pp. 269-281
    • Siebenlist, U.1    Simpson, R.B.2    Gilbert, W.3
  • 18
    • 0019178875 scopus 로고
    • The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments
    • PID: 7003539, COI: 1:CAS:528:DyaL3cXlvF2nt7s%3D
    • Scherer, G. F., Walkinshaw, M. D., Arnott, S. and Morré, D. J. (1980) The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments. Nucleic Acids Res., 8, 3895–3907.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 3895-3907
    • Scherer, G.F.1    Walkinshaw, M.D.2    Arnott, S.3    Morré, D.J.4
  • 19
    • 0020050314 scopus 로고
    • A catalogue of splice junction sequences
    • PID: 7063411, COI: 1:CAS:528:DyaL38XhtFKrurw%3D
    • Mount, S. M. (1982) A catalogue of splice junction sequences. Nucleic Acids Res., 10, 459–472.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 459-472
    • Mount, S.M.1
  • 20
    • 0021100793 scopus 로고
    • Search algorithm for pattern match analysis of nucleic acid sequences
    • PID: 6344023, COI: 1:CAS:528:DyaL3sXktlerur0%3D
    • Harr, R., Häggström, M. and Gustafsson, P. (1983) Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res., 11, 2943–2957.
    • (1983) Nucleic Acids Res. , vol.11 , pp. 2943-2957
    • Harr, R.1    Häggström, M.2    Gustafsson, P.3
  • 21
    • 0021760026 scopus 로고
    • Computer methods to locate signals in nucleic acid sequences
    • PID: 6364039, COI: 1:CAS:528:DyaL2cXpvFCjug%3D%3D
    • Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505–519.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 505-519
    • Staden, R.1
  • 22
    • 0041853625 scopus 로고    scopus 로고
    • MATCH: A tool for searching transcription factor binding sites in DNA sequences
    • PID: 12824369, COI: 1:CAS:528:DC%2BD3sXltVWju78%3D
    • Kel, A. E., Gössling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V. and Wingender, E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576–3579.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3576-3579
    • Kel, A.E.1    Gössling, E.2    Reuter, I.3    Cheremushkin, E.4    Kel-Margoulis, O.V.5    Wingender, E.6
  • 23
    • 0028971143 scopus 로고
    • MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • PID: 8532532, COI: 1:CAS:528:DyaK28XjsF2ksQ%3D%3D
    • 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
  • 24
    • 0021760063 scopus 로고
    • Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity
    • PID: 6364042, COI: 1:CAS:528:DyaL2cXhtlensb8%3D
    • Mulligan, M. E., Hawley, D. K., Entriken, R. and McClure, W. R. (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res., 12, 789–800.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 789-800
    • Mulligan, M.E.1    Hawley, D.K.2    Entriken, R.3    McClure, W.R.4
  • 25
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • PID: 3525846, COI: 1:CAS:528:DyaL28XktF2rsbk%3D
    • Schneider, T. D., Stormo, G. D., Gold, L. and Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415–431.
    • (1986) J. Mol. Biol. , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 26
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • PID: 2172928, COI: 1:CAS:528:DyaK3MXitVGmuw%3D%3D
    • 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
  • 28
    • 0141630791 scopus 로고
    • On the specificity of DNA-protein interactions
    • von Hippel, P. H. and Berg, O. G. (1986) On the specificity of DNA-protein interactions. Proc. Natl. Acad. Sci. U S A, 83, 1608–1612.
    • (1986) Proc. Natl. Acad. Sci. U S A , vol.83 , pp. 1608-1612
    • von Hippel, P.H.1    Berg, O.G.2
  • 29
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • PID: 3612791, COI: 1:CAS:528:DyaL2sXktVeksrc%3D
    • Berg, O. G. and von Hippel, P. H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723–750.
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 31
    • 0032032780 scopus 로고    scopus 로고
    • Specificity, free energy and information content in protein-DNA interactions
    • PID: 9581503, COI: 1:CAS:528:DyaK1cXisVOmsLY%3D
    • Stormo, G. D. and Fields, D. S. (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci., 23, 109–113.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 109-113
    • Stormo, G.D.1    Fields, D.S.2
  • 32
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • PID: 16873464, COI: 1:CAS:528:DC%2BD28Xotl2rtLk%3D
    • Foat, B. C., Morozov, A. V. and Bussemaker, H. J. (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics, 22, e141–e149.
    • (2006) Bioinformatics , vol.22 , pp. e141-e149
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 33
    • 79955372696 scopus 로고    scopus 로고
    • Maximally efficient modeling of DNA sequence motifs at all levels of complexity
    • PID: 21300846, COI: 1:CAS:528:DC%2BC3MXmsVSgtr4%3D
    • Stormo, G. D. (2011) Maximally efficient modeling of DNA sequence motifs at all levels of complexity. Genetics, 187, 1219–1224.
    • (2011) Genetics , vol.187 , pp. 1219-1224
    • Stormo, G.D.1
  • 34
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • PID: 3908689, COI: 1:CAS:528:DyaL28XivFGqsA%3D%3D
    • Galas, D. J., Eggert, M. and Waterman, M. S. (1985) Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117–128.
    • (1985) J. Mol. Biol. , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 35
    • 0021665479 scopus 로고
    • Pattern recognition in several sequences: consensus and alignment
    • PID: 6509229, COI: 1:CAS:528:DyaL2MXlslWmtQ%3D%3D
    • Waterman, M. S., Arratia, R. and Galas, D. J. (1984) Pattern recognition in several sequences: consensus and alignment. Bull. Math. Biol., 46, 515–527.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 515-527
    • Waterman, M.S.1    Arratia, R.2    Galas, D.J.3
  • 36
    • 0000133199 scopus 로고
    • Identifying proteinbinding sites from unaligned DNA fragments
    • PID: 2919167, COI: 1:CAS:528:DyaL1MXhvVyrtro%3D
    • Stormo, G. D. and Hartzell, G. W. 3rd. (1989) Identifying proteinbinding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. U S A, 86, 1183–1187.
    • (1989) Proc. Natl. Acad. Sci. U S A , vol.86 , pp. 1183-1187
    • Stormo, G.D.1    Hartzell, G.W.2
  • 37
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • PID: 10487864, COI: 1:CAS:528:DyaK1MXntVWitb8%3D
    • Hertz, G. Z. and Stormo, G. D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563–577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 39
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • PID: 2184437, COI: 1:CAS:528:DyaK3cXitFWquro%3D
    • 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
  • 40
    • 0026602181 scopus 로고
    • Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments
    • PID: 1731067, COI: 1:CAS:528:DyaK38Xht1ajtLk%3D
    • Cardon, L. R. and Stormo, G. D. (1992) Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J. Mol. Biol., 223, 159–170.
    • (1992) J. Mol. Biol. , vol.223 , pp. 159-170
    • Cardon, L.R.1    Stormo, G.D.2
  • 41
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
    • PID: 8211139, COI: 1:CAS:528:DyaK3sXms1Gjsrk%3D
    • Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. and Wootton, J. C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208–214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 42
    • 84866937220 scopus 로고    scopus 로고
    • Inferring direct DNA binding from ChIP-seq
    • PID: 22610855, COI: 1:CAS:528:DC%2BC38XhsVeht7jK
    • Bailey, T. L. and Machanick, P. (2012) Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res., 40, e128.
    • (2012) Nucleic Acids Res. , vol.40
    • Bailey, T.L.1    Machanick, P.2
  • 43
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • PID: 12101404, COI: 1:CAS:528:DC%2BD38Xls1Clsrs%3D
    • Liu, X. S., Brutlag, D. L. and Liu, J. S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835–839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 44
    • 79958117256 scopus 로고    scopus 로고
    • MEME-ChIP: motif analysis of large DNA datasets
    • PID: 21486936, COI: 1:CAS:528:DC%2BC3MXntFGkurw%3D
    • Machanick, P. and Bailey, T. L. (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics, 27, 1696–1697.
    • (2011) Bioinformatics , vol.27 , pp. 1696-1697
    • Machanick, P.1    Bailey, T.L.2
  • 45
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • PID: 9788350, COI: 1:CAS:528:DyaK1cXms1Kgsrc%3D
    • Roth, F. P., Hughes, J. D., Estep, P. W. and Church, G. M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939–945.
    • (1998) Nat. Biotechnol. , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 46
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • PID: 18978777, COI: 1:CAS:528:DC%2BD1cXhtlCktrjM
    • 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.
    • (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
  • 47
    • 0023057575 scopus 로고
    • Quantitative analysis of the relationship between nucleotide sequence and functional activity
    • PID: 3092188, COI: 1:CAS:528:DyaL28Xls1Khtb0%3D
    • Stormo, G. D., Schneider, T. D. and Gold, L. (1986) Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14, 6661–6679.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 6661-6679
    • Stormo, G.D.1    Schneider, T.D.2    Gold, L.3
  • 48
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: how good an approximation is it?
    • PID: 12384591, COI: 1:CAS:528:DC%2BD38Xot1Cisro%3D
    • Benos, P. V., Bulyk, M. L. and Stormo, G. D. (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442–4451.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 49
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • PID: 11861919, COI: 1:CAS:528:DC%2BD38XitVOhsLc%3D
    • Bulyk, M. L., Johnson, P. L. and Church, G. M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255–1261.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.2    Church, G.M.3
  • 50
    • 0036966431 scopus 로고    scopus 로고
    • A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays
    • PID: 12495153
    • Lee, M. L., Bulyk, M. L., Whitmore, G. A. and Church, G. M. (2002) A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics, 58, 981–988.
    • (2002) Biometrics , vol.58 , pp. 981-988
    • Lee, M.L.1    Bulyk, M.L.2    Whitmore, G.A.3    Church, G.M.4
  • 51
    • 0035875327 scopus 로고    scopus 로고
    • Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
    • PID: 11410653, COI: 1:CAS:528:DC%2BD3MXltlOqsrY%3D
    • Man, T. K. and Stormo, G. D. (2001) Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res., 29, 2471–2478.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2471-2478
    • Man, T.K.1    Stormo, G.D.2
  • 52
    • 84863866025 scopus 로고    scopus 로고
    • Improved models for transcription factor binding site identification using nonindependent interactions
    • PID: 22505627, COI: 1:CAS:528:DC%2BC3sXjs1Oltr4%3D
    • Zhao, Y., Ruan, S., Pandey, M. and Stormo, G. D. (2012). Improved models for transcription factor binding site identification using nonindependent interactions. Genetics, 191, 781–790.
    • (2012) Genetics , vol.191 , pp. 781-790
    • Zhao, Y.1    Ruan, S.2    Pandey, M.3    Stormo, G.D.4
  • 53
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • PID: 17218526, COI: 1:CAS:528:DC%2BD2sXivFOjsQ%3D%3D
    • Maerkl, S. J. and Quake, S. R. (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science, 315, 233–237.
    • (2007) Science , vol.315 , pp. 233-237
    • Maerkl, S.J.1    Quake, S.R.2
  • 55
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • PID: 19997485
    • Zhao, Y., Granas, D. and Stormo, G. D. (2009) Inferring binding energies from selected binding sites. PLoS Comput. Biol., 5, e1000590.
    • (2009) PLoS Comput. Biol. , vol.5
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 56
    • 79958115193 scopus 로고    scopus 로고
    • Quantitative analysis demonstrates most transcription factors require only simple models of specificity
    • PID: 21654662, COI: 1:CAS:528:DC%2BC3MXntV2qtrg%3D
    • Zhao, Y. and Stormo, G. D. (2011) Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol., 29, 480–483.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 480-483
    • Zhao, Y.1    Stormo, G.D.2
  • 57
    • 0000058799 scopus 로고
    • Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically
    • PID: 2771938, COI: 1:CAS:528:DyaL1MXmtFSksrs%3D
    • Sarai, A. and Takeda, Y. (1989) Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl. Acad. Sci. U S A, 86, 6513–6517.
    • (1989) Proc. Natl. Acad. Sci. U S A , vol.86 , pp. 6513-6517
    • Sarai, A.1    Takeda, Y.2
  • 58
    • 0005830941 scopus 로고
    • Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments
    • PID: 2911590, COI: 1:CAS:528:DyaL1MXhtV2iurk%3D
    • Takeda, Y., Sarai, A. and Rivera, V. M. (1989) Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc. Natl. Acad. Sci. U S A, 86, 439–443.
    • (1989) Proc. Natl. Acad. Sci. U S A , vol.86 , pp. 439-443
    • Takeda, Y.1    Sarai, A.2    Rivera, V.M.3
  • 59
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • PID: 11175784, COI: 1:CAS:528:DC%2BD3MXhtFGktLk%3D
    • 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
  • 60
    • 34347237542 scopus 로고    scopus 로고
    • Predictive modeling of genome-wide mRNA expression: from modules to molecules
    • PID: 17311525, COI: 1:CAS:528:DC%2BD2sXnsVahu7o%3D
    • Bussemaker, H. J., Foat, B. C. and Ward, L. D. (2007) Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annu. Rev. Biophys. Biomol. Struct., 36, 329–347.
    • (2007) Annu. Rev. Biophys. Biomol. Struct. , vol.36 , pp. 329-347
    • Bussemaker, H.J.1    Foat, B.C.2    Ward, L.D.3
  • 61
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • PID: 16809671, COI: 1:CAS:528:DC%2BD28Xot1Kktbw%3D
    • Tanay, A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962–972.
    • (2006) Genome Res. , vol.16 , pp. 962-972
    • Tanay, A.1
  • 62
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • PID: 20877328, COI: 1:CAS:528:DC%2BC3cXhtlShsLvK
    • Stormo, G. D. and Zhao, Y. (2010) Determining the specificity of protein-DNA interactions. Nature reviews. Genetics, 11, 751–760.
    • (2010) Nature reviews. Genetics , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 63
    • 77956654773 scopus 로고    scopus 로고
    • De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    • PID: 20802496, COI: 1:CAS:528:DC%2BC3cXhtVyiu7zI
    • Fordyce, P. M., Gerber, D., Tran, D., Zheng, J., Li, H., DeRisi, J. L. and Quake, S. R. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970–975.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 970-975
    • Fordyce, P.M.1    Gerber, D.2    Tran, D.3    Zheng, J.4    Li, H.5    DeRisi, J.L.6    Quake, S.R.7
  • 64
    • 37748998907 scopus 로고    scopus 로고
    • fREDUCE: detection of degenerate regulatory elements using correlation with expression
    • PID: 17941998
    • Wu, R. Z., Chaivorapol, C., Zheng, J., Li, H. and Liang, S. (2007) fREDUCE: detection of degenerate regulatory elements using correlation with expression. BMC Bioinformatics, 8, 399.
    • (2007) BMC Bioinformatics , vol.8 , pp. 399
    • Wu, R.Z.1    Chaivorapol, C.2    Zheng, J.3    Li, H.4    Liang, S.5
  • 65
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • PID: 2200121, COI: 1:CAS:528:DyaK3cXlt1OltLY%3D
    • Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505–510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 66
    • 0031571660 scopus 로고    scopus 로고
    • Quantitative specificity of the Mnt repressor
    • PID: 9268651, COI: 1:CAS:528:DyaK2sXls12lsbw%3D
    • Fields, D. S., He, Y., Al-Uzri, A. Y. and Stormo, G. D. (1997) Quantitative specificity of the Mnt repressor. J. Mol. Biol., 271, 178–194.
    • (1997) J. Mol. Biol. , vol.271 , pp. 178-194
    • Fields, D.S.1    He, Y.2    Al-Uzri, A.Y.3    Stormo, G.D.4
  • 67
    • 77953006022 scopus 로고    scopus 로고
    • Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
    • PID: 20378718, COI: 1:CAS:528:DC%2BC3cXnsFyjs7g%3D
    • Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J. M., Yan, J., Sillanpää, M. J., et al. (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res., 20, 861–873.
    • (2010) Genome Res. , vol.20 , pp. 861-873
    • Jolma, A.1    Kivioja, T.2    Toivonen, J.3    Cheng, L.4    Wei, G.5    Enge, M.6    Taipale, M.7    Vaquerizas, J.M.8    Yan, J.9    Sillanpää, M.J.10
  • 68
    • 75649122221 scopus 로고    scopus 로고
    • Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing
    • PID: 19843614
    • Zykovich, A., Korf, I. and Segal, D. J. (2009) Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res., 37, e151.
    • (2009) Nucleic Acids Res. , vol.37
    • Zykovich, A.1    Korf, I.2    Segal, D.J.3
  • 70
    • 83255188878 scopus 로고    scopus 로고
    • Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
    • PID: 22153072, COI: 1:CAS:528:DC%2BC3MXhs1SgtrzK
    • Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J., et al. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell, 147, 1270–1282.
    • (2011) Cell , vol.147 , pp. 1270-1282
    • Slattery, M.1    Riley, T.2    Liu, P.3    Abe, N.4    Gomez-Alcala, P.5    Dror, I.6    Zhou, T.7    Rohs, R.8    Honig, B.9    Bussemaker, H.J.10
  • 71
    • 45449088853 scopus 로고    scopus 로고
    • Design of compact, universal DNA microarrays for protein binding microarray experiments
    • PID: 18651798, COI: 1:CAS:528:DC%2BD1cXhtVOmurnF
    • Philippakis, A. A., Qureshi, A. M., Berger, M. F. and Bulyk, M. L. (2008) Design of compact, universal DNA microarrays for protein binding microarray experiments. Journal of Computational Biology, 15, 655–665.
    • (2008) Journal of Computational Biology , vol.15 , pp. 655-665
    • Philippakis, A.A.1    Qureshi, A.M.2    Berger, M.F.3    Bulyk, M.L.4
  • 72
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • PID: 16998473, COI: 1:CAS:528:DC%2BD28XhtFyqtL%2FL
    • Berger, M. F., Philippakis, A. A., Qureshi, A. M., He, F. S., Estep, P.W. 3rd, and Bulyk, M. L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429–1435.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep, P.W.5    Bulyk, M.L.6
  • 73
    • 78651303899 scopus 로고    scopus 로고
    • UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
    • PID: 21037262, COI: 1:CAS:528:DC%2BC3sXivF2ltbg%3D
    • Robasky, K. and Bulyk, M. L. (2011) UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res., 39, D124–D128.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D124-D128
    • Robasky, K.1    Bulyk, M.L.2
  • 76
    • 23444446753 scopus 로고    scopus 로고
    • A bacterial onehybrid system for determining the DNA-binding specificity of transcription factors
    • PID: 16041365, COI: 1:CAS:528:DC%2BD2MXntVSrtrk%3D
    • Meng, X., Brodsky, M. H. and Wolfe, S. A. (2005) A bacterial onehybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol., 23, 988–994.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 988-994
    • Meng, X.1    Brodsky, M.H.2    Wolfe, S.A.3
  • 77
    • 34547093905 scopus 로고    scopus 로고
    • Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method
    • PID: 17537811
    • Meng, X., Thibodeau-Beganny, S., Jiang, T., Joung, J. K. and Wolfe, S. A. (2007) Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res., 35, e81.
    • (2007) Nucleic Acids Res. , vol.35
    • Meng, X.1    Thibodeau-Beganny, S.2    Jiang, T.3    Joung, J.K.4    Wolfe, S.A.5
  • 78
    • 43349107222 scopus 로고    scopus 로고
    • A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    • PID: 18332042, COI: 1:CAS:528:DC%2BD1cXlslymu78%3D
    • Noyes, M. B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M. H. and Wolfe, S. A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res., 36, 2547–2560.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2547-2560
    • Noyes, M.B.1    Meng, X.2    Wakabayashi, A.3    Sinha, S.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 79
    • 79960225382 scopus 로고    scopus 로고
    • A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
    • PID: 21507886, COI: 1:CAS:528:DC%2BC3MXoslOgtLw%3D
    • Christensen, R. G., Gupta, A., Zuo, Z., Schriefer, L. A., Wolfe, S. A. and Stormo, G. D. (2011) A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res., 39, e83.
    • (2011) Nucleic Acids Res. , vol.39
    • Christensen, R.G.1    Gupta, A.2    Zuo, Z.3    Schriefer, L.A.4    Wolfe, S.A.5    Stormo, G.D.6
  • 81
    • 84861982214 scopus 로고    scopus 로고
    • An optimized two-finger archive for ZFN-mediated gene targeting
    • PID: 22543349, COI: 1:CAS:528:DC%2BC38Xmt1GrsL4%3D
    • Gupta, A., Christensen, R. G., Rayla, A. L., Lakshmanan, A., Stormo, G. D. and Wolfe, S. A. (2012) An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods, 9, 588–590.
    • (2012) Nat. Methods , vol.9 , pp. 588-590
    • Gupta, A.1    Christensen, R.G.2    Rayla, A.L.3    Lakshmanan, A.4    Stormo, G.D.5    Wolfe, S.A.6
  • 82
    • 78651341148 scopus 로고    scopus 로고
    • Zinc finger protein-dependent and-independent contributions to the in vivo off-target activity of zinc finger nucleases
    • PID: 20843781, COI: 1:CAS:528:DC%2BC3MXhtlCmur0%3D
    • Gupta, A., Meng, X., Zhu, L. J., Lawson, N. D. and Wolfe, S. A. (2011) Zinc finger protein-dependent and-independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res., 39, 381–392.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 381-392
    • Gupta, A.1    Meng, X.2    Zhu, L.J.3    Lawson, N.D.4    Wolfe, S.A.5
  • 84
    • 83455164709 scopus 로고    scopus 로고
    • Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
    • PID: 22146299
    • Siggers, T., Duyzend, M. H., Reddy, J., Khan, S. and Bulyk, M. L. (2011) Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol. Syst. Biol., 7, 555.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 555
    • Siggers, T.1    Duyzend, M.H.2    Reddy, J.3    Khan, S.4    Bulyk, M.L.5
  • 85
    • 79960277492 scopus 로고    scopus 로고
    • Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
    • PID: 21706015, COI: 1:CAS:528:DC%2BC3MXotV2gs78%3D
    • Nutiu, R., Friedman, R. C., Luo, S., Khrebtukova, I., Silva, D., Li, R., Zhang, L., Schroth, G. P. and Burge, C. B. (2011) Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol., 29, 659–664.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 659-664
    • Nutiu, R.1    Friedman, R.C.2    Luo, S.3    Khrebtukova, I.4    Silva, D.5    Li, R.6    Zhang, L.7    Schroth, G.P.8    Burge, C.B.9
  • 86
    • 78049440479 scopus 로고    scopus 로고
    • High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions
    • Agius, P., Arvey, A., Chang, W., Noble, W. S. and Leslie, C. (2010) High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput. Biol., 6, 6.
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 6
    • Agius, P.1    Arvey, A.2    Chang, W.3    Noble, W.S.4    Leslie, C.5
  • 87
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • PID: 21106904, COI: 1:CAS:528:DC%2BC3MXjt1aisbo%3D
    • Pique-Regi, R., Degner, J. F., Pai, A. A., Gaffney, D. J., Gilad, Y. and Pritchard, J. K. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res., 21, 447–455.
    • (2011) Genome Res. , vol.21 , pp. 447-455
    • Pique-Regi, R.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.J.4    Gilad, Y.5    Pritchard, J.K.6
  • 88
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • PID: 17997593
    • Narlikar, L., Gordân, R. and Hartemink, A.J. (2007) A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput. Biol., 3, e215.
    • (2007) PLoS Comput. Biol. , vol.3
    • Narlikar, L.1    Gordân, R.2    Hartemink, A.J.3
  • 93
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
    • PID: 21850043, COI: 1:CAS:528:DC%2BC3MXhtVeiurrP
    • Cooper, G. M. and Shendure, J. (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 628–640.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 95
    • 84866361701 scopus 로고    scopus 로고
    • Circuitry and dynamics of human transcription factor regulatory networks
    • PID: 22959076, COI: 1:CAS:528:DC%2BC38XhtlSgt7fE
    • Neph, S., Stergachis, A. B., Reynolds, A., Sandstrom, R., Borenstein, E. and Stamatoyannopoulos, J. A. (2012) Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150, 1274–1286.
    • (2012) Cell , vol.150 , pp. 1274-1286
    • Neph, S.1    Stergachis, A.B.2    Reynolds, A.3    Sandstrom, R.4    Borenstein, E.5    Stamatoyannopoulos, J.A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.