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Volumn 41, Issue 16, 2013, Pages

DNA motif elucidation using belief propagation

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; DNA;

EID: 84887011782     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt574     Document Type: Article
Times cited : (59)

References (74)
  • 2
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • Galas,D.J. and Schmitz,A. (1987) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
    • (1987) Nucleic Acids Res. , vol.5 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 3
    • 0019877067 scopus 로고
    • A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system
    • Garner,M.M. and Revzin,A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res., 9, 3047-3060.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 3047-3060
    • Garner, M.M.1    Revzin, A.2
  • 5
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson,D.S., Mortazavi,A., Myers,R.M. and Wold,B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 6
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments
    • Aug
    • Liu,X.S., Brutlag,D.L. and Liu,J.S. (Aug, 2002) An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation 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
  • 7
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Nov
    • Berger,M.F., Philippakis,A.A., Qureshi,A.M., He,F.S., Estep,P.W. and Bulyk,M.L. (Nov, 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
  • 8
    • 77956654773 scopus 로고    scopus 로고
    • De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    • 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
  • 9
    • 70350340058 scopus 로고    scopus 로고
    • Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
    • Hu,S., Xie,Z., Onishi,A., Yu,X., Jiang,L., Lin,J., Rho,H.S., Woodard,C., Wang,H., Jeong,J.S. et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell, 139, 610-622.
    • (2009) Cell , vol.139 , pp. 610-622
    • Hu, S.1    Xie, Z.2    Onishi, A.3    Yu, X.4    Jiang, L.5    Lin, J.6    Rho, H.S.7    Woodard, C.8    Wang, H.9    Jeong, J.S.10
  • 10
    • 33745614618 scopus 로고    scopus 로고
    • Linking DNA-binding proteins to their recognition sequences by using protein microarrays
    • Ho,S.W., Jona,G., Chen,C.T., Johnston,M. and Snyder,M. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc. Natl Acad. Sci. USA, 103, 9940-9945.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 9940-9945
    • Ho, S.W.1    Jona, G.2    Chen, C.T.3    Johnston, M.4    Snyder, M.5
  • 14
    • 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
    • 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
    • Robasky, K.1    Bulyk, M.L.2
  • 15
    • 84862214168 scopus 로고    scopus 로고
    • ScerTF: A comprehensive database of benchmarked position weight matrices for Saccharomyces species
    • Spivak,A.T. and Stormo,G.D. (2012) ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res., 40, D162-D168.
    • (2012) Nucleic Acids Res. , vol.40
    • Spivak, A.T.1    Stormo, G.D.2
  • 16
    • 75549090998 scopus 로고    scopus 로고
    • FlyTF: Improved annotation and enhanced functionality of the Drosophila transcription factor database
    • Pfreundt,U., James,D.P., Tweedie,S., Wilson,D., Teichmann,S.A. and Adryan,B. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res., 38, D443-D447.
    • (2010) Nucleic Acids Res. , vol.38
    • Pfreundt, U.1    James, D.P.2    Tweedie, S.3    Wilson, D.4    Teichmann, S.A.5    Adryan, B.6
  • 17
    • 84862169505 scopus 로고    scopus 로고
    • YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities
    • deBoer,C.G. and Hughes,T.R. (2012) YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res., 40, D169-D179.
    • (2012) Nucleic Acids Res. , vol.40
    • Deboer, C.G.1    Hughes, T.R.2
  • 18
    • 77950472891 scopus 로고    scopus 로고
    • HPDI: A database of experimental human protein-DNA interactions
    • Xie,Z., Hu,S., Blackshaw,S., Zhu,H. and Qian,J. (2010) hPDI: a database of experimental human protein-DNA interactions. Bioinformatics, 26, 287-289.
    • (2010) Bioinformatics , vol.26 , pp. 287-289
    • Xie, Z.1    Hu, S.2    Blackshaw, S.3    Zhu, H.4    Qian, J.5
  • 21
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe,N.M., Laskowski,R.A. and Thornton,J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 22
    • 0037439997 scopus 로고    scopus 로고
    • Structural classification of zinc fingers: Survey and summary
    • Krishna,S.S., Majumdar,I. and Grishin,N.V. (2003) Structural classification of zinc fingers: survey and summary. Nucleic Acids Res., 31, 532-550.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 532-550
    • Krishna, S.S.1    Majumdar, I.2    Grishin, N.V.3
  • 23
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • Luscombe,N.M. and Thornton,J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009.
    • (2002) J. Mol. Biol. , vol.320 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 25
    • 0346258292 scopus 로고    scopus 로고
    • Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
    • Jones,S., Shanahan,H.P., Berman,H.M. and Thornton,J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7189-7198
    • Jones, S.1    Shanahan, H.P.2    Berman, H.M.3    Thornton, J.M.4
  • 26
    • 33745317385 scopus 로고    scopus 로고
    • Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations
    • Gunewardena,S., Jeavons,P. and Zhang,Z. (2006) Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations. J. Comput. Biol., 13, 929-945.
    • (2006) J. Comput. Biol. , vol.13 , pp. 929-945
    • Gunewardena, S.1    Jeavons, P.2    Zhang, Z.3
  • 27
    • 20544460658 scopus 로고    scopus 로고
    • Protein-DNA recognition patterns and predictions
    • Sarai,A. and Kono,H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
    • (2005) Annu. Rev. Biophys. Biomol. Struct. , vol.34 , pp. 379-398
    • Sarai, A.1    Kono, H.2
  • 28
    • 47249118465 scopus 로고    scopus 로고
    • Extracting sequence features to predict protein-DNA interactions: A comparative study
    • Zhou,Q. and Liu,J.S. (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res., 36, 4137-4148.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4137-4148
    • Zhou, Q.1    Liu, J.S.2
  • 29
    • 1542400269 scopus 로고    scopus 로고
    • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    • Ahmad,S., Gromiha,M.M. and Sarai,A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
    • (2004) Bioinformatics , vol.20 , pp. 477-486
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 30
    • 54549096025 scopus 로고    scopus 로고
    • Protein- DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
    • Ahmad,S., Keskin,O., Sarai,A. and Nussinov,R. (2008) Protein- DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res., 36, 5922-5932.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5922-5932
    • Ahmad, S.1    Keskin, O.2    Sarai, A.3    Nussinov, R.4
  • 31
    • 27544474147 scopus 로고    scopus 로고
    • Computational discovery of transcriptional regulatory rules
    • Pham,T.H., Clemente,J.C., Satou,K. and Ho,T.B. (2005) Computational discovery of transcriptional regulatory rules. Bioinformatics, 21, 101-107.
    • (2005) Bioinformatics , vol.21 , pp. 101-107
    • Pham, T.H.1    Clemente, J.C.2    Satou, K.3    Ho, T.B.4
  • 32
    • 34547852238 scopus 로고    scopus 로고
    • Prediction of DNAbinding residues from sequence
    • Ofran,Y., Mysore,V. and Rost,B. (2007) Prediction of DNAbinding residues from sequence. Bioinformatics, 23, i347-i353.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Mysore, V.2    Rost, B.3
  • 33
    • 79960092508 scopus 로고    scopus 로고
    • Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm
    • Wong,K.C., Peng,C., Wong,M.H. and Leung,K.S. (2011) Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm. Soft. Comput., 15, 1631-1642.
    • (2011) Soft. Comput. , vol.15 , pp. 1631-1642
    • Wong, K.C.1    Peng, C.2    Wong, M.H.3    Leung, K.S.4
  • 36
    • 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
  • 38
    • 0023678091 scopus 로고
    • Computer methods for analyzing sequence recognition of nucleic acids
    • Stormo,G.D. (1988) Computer methods for analyzing sequence recognition of nucleic acids. Annu. Rev. BioChem., 17, 241-263.
    • (1988) Annu. Rev. BioChem. , vol.17 , pp. 241-263
    • Stormo, G.D.1
  • 39
    • 0346490298 scopus 로고    scopus 로고
    • Computational discovery of gene regulatory binding motifs: A Bayesian perspective
    • Jensen,S.T., Liu,X.S., Zhou,Q. and Liu,J.S. (2004) Computational discovery of gene regulatory binding motifs: a Bayesian perspective. Stat. Sci., 19, 188-204.
    • (2004) Stat. Sci. , vol.19 , pp. 188-204
    • Jensen, S.T.1    Liu, X.S.2    Zhou, Q.3    Liu, J.S.4
  • 41
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 42
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • Thijs,G., Lescot,M., Marchal,K., Rombauts,S., DeMoor,B., Rouze,P. and Moreau,Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
    • (2001) Bioinformatics , vol.17 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    Demoor, B.5    Rouze, P.6    Moreau, Y.7
  • 43
    • 4544295425 scopus 로고    scopus 로고
    • Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
    • Ao,W., Gaudet,J., Kent,W.J., Muttumu,S. and Mango,S.E. (2004) Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science, 305, 1743-1746.
    • (2004) Science , vol.305 , pp. 1743-1746
    • Ao, W.1    Gaudet, J.2    Kent, W.J.3    Muttumu, S.4    Mango, S.E.5
  • 45
    • 0033655171 scopus 로고    scopus 로고
    • ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
    • Workman,C.T. and Stormo,G.D. (2000) ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput., 467-478.
    • (2000) Pac. Symp. Biocomput. , pp. 467-478
    • Workman, C.T.1    Stormo, G.D.2
  • 46
    • 19544379737 scopus 로고    scopus 로고
    • A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
    • Favorov,A.V., Gelfand,M.S., Gerasimova,A.V., Ravcheev,D.A., Mironov,A.A. and Makeev,V.J. (2005) A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics, 21, 2240-2245.
    • (2005) Bioinformatics , vol.21 , pp. 2240-2245
    • Favorov, A.V.1    Gelfand, M.S.2    Gerasimova, A.V.3    Ravcheev, D.A.4    Mironov, A.A.5    Makeev, V.J.6
  • 47
    • 38849109559 scopus 로고    scopus 로고
    • TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
    • Chan,T.M., Leung,K.S. and Lee,K.H. (2008) TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. Bioinformatics, 24, 341-349.
    • (2008) Bioinformatics , vol.24 , pp. 341-349
    • Chan, T.M.1    Leung, K.S.2    Lee, K.H.3
  • 48
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • 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
  • 49
    • 1242264319 scopus 로고    scopus 로고
    • Finding functional sequence elements by multiple local alignment
    • Frith,M.C., Hansen,U., Spouge,J.L. and Weng,Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res., 32, 189-200.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 50
    • 0344376570 scopus 로고    scopus 로고
    • Finding composite regulatory patterns in DNA sequences
    • Eskin,E. and Pevzner,P.A. (2002) Finding composite regulatory patterns in DNA sequences. Bioinformatics, 18(Suppl. 1), S354-S363.
    • (2002) Bioinformatics , vol.18 SUPPL. 1
    • Eskin, E.1    Pevzner, P.A.2
  • 51
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
    • (1998) J. Mol. Biol. , vol.281 , pp. 827-842
    • Van Helden, J.1    Andre, B.2    Collado-Vides, J.3
  • 52
    • 39149128313 scopus 로고    scopus 로고
    • A hybrid model for robust detection of transcription factor binding sites
    • Gunewardena,S. and Zhang,Z. (2008) A hybrid model for robust detection of transcription factor binding sites. Bioinformatics, 24, 484-491.
    • (2008) Bioinformatics , vol.24 , pp. 484-491
    • Gunewardena, S.1    Zhang, Z.2
  • 53
    • 28444456845 scopus 로고    scopus 로고
    • Rare events and conditional events on random strings
    • Régnier,M. and Denise,A. (2004) Rare events and conditional events on random strings. Discrete Math., 6, 191-214.
    • (2004) Discrete Math. , vol.6 , pp. 191-214
    • Régnier, M.1    Denise, A.2
  • 54
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Pavesi,G., Mereghetti,P., Mauri,G. and Pesole,G. (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, 199-203.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 199-203
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 55
    • 0042905768 scopus 로고    scopus 로고
    • YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha,S. and Tompa,M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3586-3588
    • Sinha, S.1    Tompa, M.2
  • 57
    • 34547844155 scopus 로고    scopus 로고
    • RankMotif++: A motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
    • Chen,X., Hughes,T.R. and Morris,Q. (2007) RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics, 23, i72-i79.
    • (2007) Bioinformatics , vol.23
    • Chen, X.1    Hughes, T.R.2    Morris, Q.3
  • 58
    • 29144500327 scopus 로고    scopus 로고
    • Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
    • Foat,B.C., Houshmandi,S.S., Olivas,W.M. and Bussemaker,H.J. (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl Acad. Sci. USA, 102, 17675-17680.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17675-17680
    • Foat, B.C.1    Houshmandi, S.S.2    Olivas, W.M.3    Bussemaker, H.J.4
  • 59
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • 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
  • 60
    • 79958115193 scopus 로고    scopus 로고
    • Quantitative analysis demonstrates most transcription factors require only simple models of specificity
    • 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
  • 62
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • 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
  • 63
    • 79955372696 scopus 로고    scopus 로고
    • Maximally efficient modeling of DNA sequence motifs at all levels of complexity
    • 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
  • 67
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • Frey,B.J. and Dueck,D. (2007) Clustering by passing messages between data points. Science, 315, 972-976.
    • (2007) Science , vol.315 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 69
    • 0035246323 scopus 로고    scopus 로고
    • On the optimality of solutions of the max-product belief-propagation algorithm in arbitrary graphs
    • Weiss,Y. and Freeman,W.T. (2001) On the optimality of solutions of the max-product belief-propagation algorithm in arbitrary graphs. IEEE Trans. Inf. Theory., 47, 736-744.
    • (2001) IEEE Trans. Inf. Theory. , vol.47 , pp. 736-744
    • Weiss, Y.1    Freeman, W.T.2
  • 71
    • 34547569191 scopus 로고    scopus 로고
    • STAMP: A web tool for exploring DNA-binding motif similarities
    • Mahony,S. and Benos,P.V. (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
    • (2007) Nucleic Acids Res. , vol.35
    • Mahony, S.1    Benos, P.V.2
  • 73
    • 83755196322 scopus 로고    scopus 로고
    • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
    • Gordan,R., Murphy,K.F., McCord,R.P., Zhu,C., Vedenko,A. and Bulyk,M.L. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol., 12, R125.
    • (2011) Genome Biol. , vol.12
    • Gordan, R.1    Murphy, K.F.2    McCord, R.P.3    Zhu, C.4    Vedenko, A.5    Bulyk, M.L.6
  • 74
    • 79958153978 scopus 로고    scopus 로고
    • Jury remains out on simple models of transcription factor specificity
    • Morris,Q., Bulyk,M.L. and Hughes,T.R. (2011) Jury remains out on simple models of transcription factor specificity. Nat. Biotechnol., 29, 483-484.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 483-484
    • Morris, Q.1    Bulyk, M.L.2    Hughes, T.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.