메뉴 건너뛰기




Volumn 162, Issue 5, 2016, Pages 1203-1243

Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments

Author keywords

Diffeomorphic modes; Likelihood; Mutual information; Sequence function relationships; Sort Seq

Indexed keywords


EID: 84959088276     PISSN: 00224715     EISSN: 15729613     Source Type: Journal    
DOI: 10.1007/s10955-015-1398-3     Document Type: Article
Times cited : (18)

References (47)
  • 2
    • 9644268153 scopus 로고    scopus 로고
    • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    • Mukherjee, S., Berger, M., Jona, G., Wang, X., Muzzey, D., Snyder, M., Young, R., Bulyk, M.: Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36(12), 1331–1339 (2004)
    • (2004) Nat. Genet. , vol.36 , Issue.12 , pp. 1331-1339
    • Mukherjee, S.1    Berger, M.2    Jona, G.3    Wang, X.4    Muzzey, D.5    Snyder, M.6    Young, R.7    Bulyk, M.8
  • 3
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger, M., Philippakis, A., Qureshi, A., He, F., Estep, P., Bulyk, M.: Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol. 24(11), 1429–1435 (2006)
    • (2006) Nat. Biotechnol. , vol.24 , Issue.11 , pp. 1429-1435
    • Berger, M.1    Philippakis, A.2    Qureshi, A.3    He, F.4    Estep, P.5    Bulyk, M.6
  • 4
    • 23444446753 scopus 로고    scopus 로고
    • A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
    • Meng, X., Brodsky, M.H., Wolfe, S.A.: A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol. 23(8), 988–994 (2005)
    • (2005) Nat. Biotechnol. , vol.23 , Issue.8 , pp. 988-994
    • Meng, X.1    Brodsky, M.H.2    Wolfe, S.A.3
  • 5
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • Maerkl, S., Quake, S.: A systems approach to measuring the binding energy landscapes of transcription factors. Science 315(5809), 233–237 (2007)
    • (2007) Science , vol.315 , Issue.5809 , pp. 233-237
    • Maerkl, S.1    Quake, S.2
  • 6
    • 75649122221 scopus 로고    scopus 로고
    • Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing
    • Zykovich, A., Korf, I., Segal, D.J.: Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res. 37(22), e151 (2009)
    • (2009) Nucleic Acids Res. , vol.37 , Issue.22 , pp. 151
    • Zykovich, A.1    Korf, I.2    Segal, D.J.3
  • 7
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • Zhao, Y., Granas, D., Stormo, G.D.: Inferring binding energies from selected binding sites. PLoS Comput. Biol. 5(12), e1000590 (2009)
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.12 , pp. 1000590
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 11
    • 71849118573 scopus 로고    scopus 로고
    • High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan, R.P., Lee, C., Litvin, O., Young, D.L., Pe’er, D., Shendure, J.: High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27(12), 1173–1175 (2009)
    • (2009) Nat. Biotechnol. , vol.27 , Issue.12 , pp. 1173-1175
    • Patwardhan, R.P.1    Lee, C.2    Litvin, O.3    Young, D.L.4    Pe’er, D.5    Shendure, J.6
  • 12
    • 77952706498 scopus 로고    scopus 로고
    • Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    • Kinney, J.B., Murugan, A., Callan, C.G., Cox, E.C.: Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl. Acad. Sci. USA 107(20), 9158–9163 (2010)
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , Issue.20 , pp. 9158-9163
    • Kinney, J.B.1    Murugan, A.2    Callan, C.G.3    Cox, E.C.4
  • 15
    • 84869853147 scopus 로고    scopus 로고
    • Complex effects of nucleotide variants in a mammalian cis-regulatory element
    • Kwasnieski, J.C., Mogno, I., Myers, C.A., Corbo, J.C., Cohen, B.A.: Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc. Natl. Acad. Sci. USA 109(47), 19498–19503 (2012)
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , Issue.47 , pp. 19498-19503
    • Kwasnieski, J.C.1    Mogno, I.2    Myers, C.A.3    Corbo, J.C.4    Cohen, B.A.5
  • 17
  • 20
    • 84862546176 scopus 로고    scopus 로고
    • Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations
    • Schlinkmann, K.M., Honegger, A., Türeci, E., Robison, K.E., Lipovšek, D., Plückthun, A.: Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations. Proc. Natl. Acad. Sci. USA 109(25), 9810–9815 (2012)
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , Issue.25 , pp. 9810-9815
    • Schlinkmann, K.M.1    Honegger, A.2    Türeci, E.3    Robison, K.E.4    Lipovšek, D.5    Plückthun, A.6
  • 21
    • 84877983042 scopus 로고    scopus 로고
    • Massive functional mapping of a 5’-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
    • Holmqvist, E., Reimegård, J., Wagner, E.G.H.: Massive functional mapping of a 5’-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing. Nucleic Acids Res. 41(12), e122 (2013)
    • (2013) Nucleic Acids Res. , vol.41 , Issue.12 , pp. 122
    • Holmqvist, E.1    Reimegård, J.2    Wagner, E.G.H.3
  • 22
    • 84925283037 scopus 로고    scopus 로고
    • Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity
    • Peterman, N., Lavi-Itzkovitz, A., Levine, E.: Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity. Nucleic Acids Res. 42(19), 12177–12188 (2014)
    • (2014) Nucleic Acids Res. , vol.42 , Issue.19 , pp. 12177-12188
    • Peterman, N.1    Lavi-Itzkovitz, A.2    Levine, E.3
  • 23
    • 84898048208 scopus 로고    scopus 로고
    • Systematic identification of regulatory elements in conserved 3’ UTRs of human transcripts
    • Oikonomou, P., Goodarzi, H., Tavazoie, S.: Systematic identification of regulatory elements in conserved 3’ UTRs of human transcripts. Cell Rep. 7(1), 281–292 (2014)
    • (2014) Cell Rep. , vol.7 , Issue.1 , pp. 281-292
    • Oikonomou, P.1    Goodarzi, H.2    Tavazoie, S.3
  • 25
    • 84875967675 scopus 로고    scopus 로고
    • High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast
    • Liachko, I., Youngblood, R.A., Keich, U., Dunham, M.J.: High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res. 23(4), 698–704 (2013)
    • (2013) Genome Res. , vol.23 , Issue.4 , pp. 698-704
    • Liachko, I.1    Youngblood, R.A.2    Keich, U.3    Dunham, M.J.4
  • 26
    • 84927662735 scopus 로고    scopus 로고
    • Massively parallel determination and modeling of endonuclease substrate specificity
    • Thyme, S.B., Song, Y., Brunette, T.J., Szeto, M.D., Kusak, L., Bradley, P., Baker, D.: Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res. 42(22), 13839–13852 (2014)
    • (2014) Nucleic Acids Res. , vol.42 , Issue.22 , pp. 13839-13852
    • Thyme, S.B.1    Song, Y.2    Brunette, T.J.3    Szeto, M.D.4    Kusak, L.5    Bradley, P.6    Baker, D.7
  • 27
    • 33846351302 scopus 로고    scopus 로고
    • Precise physical models of protein-DNA interaction from high-throughput data
    • Kinney, J.B., Tkacik, G., Callan, C.G.: Precise physical models of protein-DNA interaction from high-throughput data. Proc. Natl. Acad. Sci. USA 104(2), 501–506 (2007)
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , Issue.2 , pp. 501-506
    • Kinney, J.B.1    Tkacik, G.2    Callan, C.G.3
  • 28
    • 84896855185 scopus 로고    scopus 로고
    • Parametric inference in the large data limit using maximally informative models
    • Kinney, J.B., Atwal, G.S.: Parametric inference in the large data limit using maximally informative models. Neural Comput. 26(4), 637–653 (2014)
    • (2014) Neural Comput. , vol.26 , Issue.4 , pp. 637-653
    • Kinney, J.B.1    Atwal, G.S.2
  • 30
    • 0347423195 scopus 로고    scopus 로고
    • Convergence properties of three spike-triggered analysis techniques
    • Paninski, L.: Convergence properties of three spike-triggered analysis techniques. Network-Comput. Neural 14(3), 437–464 (2003)
    • (2003) Network-Comput. Neural , vol.14 , Issue.3 , pp. 437-464
    • Paninski, L.1
  • 31
    • 0345768782 scopus 로고    scopus 로고
    • Analyzing neural responses to natural signals: maximally informative dimensions
    • Sharpee, T., Rust, N., Bialek, W.: Analyzing neural responses to natural signals: maximally informative dimensions. Neural Comput. 16(2), 223–250 (2004)
    • (2004) Neural Comput. , vol.16 , Issue.2 , pp. 223-250
    • Sharpee, T.1    Rust, N.2    Bialek, W.3
  • 32
    • 33644556164 scopus 로고    scopus 로고
    • Adaptive filtering enhances information transmission in visual cortex
    • Sharpee, T., Sugihara, H., Kurgansky, A., Rebrik, S., Stryker, M., Miller, K.: Adaptive filtering enhances information transmission in visual cortex. Nature 439(7079), 936–942 (2006)
    • (2006) Nature , vol.439 , Issue.7079 , pp. 936-942
    • Sharpee, T.1    Sugihara, H.2    Kurgansky, A.3    Rebrik, S.4    Stryker, M.5    Miller, K.6
  • 33
    • 70649100413 scopus 로고    scopus 로고
    • Estimating linear-nonlinear models using Rényi divergences
    • Kouh, M., Sharpee, T.O.: Estimating linear-nonlinear models using Rényi divergences. Network-Comput. Neural 20(2), 49–68 (2009)
    • (2009) Network-Comput. Neural , vol.20 , Issue.2 , pp. 49-68
    • Kouh, M.1    Sharpee, T.O.2
  • 34
    • 84881003399 scopus 로고    scopus 로고
    • Learning quadratic receptive fields from neural responses to natural signals: information theoretic and likelihood methods
    • Rajan, K., Marre, O., Tkacik, G.: Learning quadratic receptive fields from neural responses to natural signals: information theoretic and likelihood methods. Neural Comput. 25(7), 1661–1692 (2013)
    • (2013) Neural Comput. , vol.25 , Issue.7 , pp. 1661-1692
    • Rajan, K.1    Marre, O.2    Tkacik, G.3
  • 36
    • 0024365536 scopus 로고
    • Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein
    • Oliphant, A., Brandl, C., Struhl, K.: Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9(7), 2944–2949 (1989)
    • (1989) Mol. Cell. Biol. , vol.9 , Issue.7 , pp. 2944-2949
    • Oliphant, A.1    Brandl, C.2    Struhl, K.3
  • 37
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C., Gold, L.: Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968), 505–510 (1990)
    • (1990) Science , vol.249 , Issue.4968 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 38
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A.D., Szostak, J.W.: In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287), 818–822 (1990)
    • (1990) Nature , vol.346 , Issue.6287 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 39
    • 0025572707 scopus 로고
    • Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection
    • Blackwell, T.K., Weintraub, H.: Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science 250(4984), 1104–1110 (1990)
    • (1990) Science , vol.250 , Issue.4984 , pp. 1104-1110
    • Blackwell, T.K.1    Weintraub, H.2
  • 40
    • 0025822948 scopus 로고
    • Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site
    • Wright, W., Binder, M., Funk, W.: Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site. Mol. Cell. Biol. 11(8), 4104–4110 (1991)
    • (1991) Mol. Cell. Biol. , vol.11 , Issue.8 , pp. 4104-4110
    • Wright, W.1    Binder, M.2    Funk, W.3
  • 41
    • 0016927159 scopus 로고
    • Fluorescence-activated cell sorting
    • Herzenberg, L., Sweet, R., Herzenberg, L.: Fluorescence-activated cell sorting. Sci. Am. 234(3), 108–117 (1976)
    • (1976) Sci. Am. , vol.234 , Issue.3 , pp. 108-117
    • Herzenberg, L.1    Sweet, R.2    Herzenberg, L.3
  • 42
    • 84905217368 scopus 로고    scopus 로고
    • Deep mutational scanning: a new style of protein science
    • Fowler, D.M., Fields, S.: Deep mutational scanning: a new style of protein science. Nat. Methods 11(8), 801–807 (2014)
    • (2014) Nat. Methods , vol.11 , Issue.8 , pp. 801-807
    • Fowler, D.M.1    Fields, S.2
  • 43
    • 84895815806 scopus 로고    scopus 로고
    • Equitability, mutual information, and the maximal information coefficient
    • Kinney, J.B., Atwal, G.S.: Equitability, mutual information, and the maximal information coefficient. Proc. Natl. Acad. Sci. USA 111(9), 3354–3359 (2014)
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , Issue.9 , pp. 3354-3359
    • Kinney, J.B.1    Atwal, G.S.2
  • 44
    • 34547962800 scopus 로고    scopus 로고
    • Relative performance of mutual information estimation methods for quantifying the dependence among short and noisy data
    • Khan, S., Bandyopadhyay, S., Ganguly, A., Saigal, S., Erickson III, D., Protopopescu, V., Ostrouchov, G.: Relative performance of mutual information estimation methods for quantifying the dependence among short and noisy data. Phys. Rev. E 76(2), 026209 (2007)
    • (2007) Phys. Rev. E , vol.76 , Issue.2 , pp. 026209
    • Khan, S.1    Bandyopadhyay, S.2    Ganguly, A.3    Saigal, S.4    Erickson, D.5    Protopopescu, V.6    Ostrouchov, G.7
  • 45
    • 0000395622 scopus 로고    scopus 로고
    • Field theories for learning probability distributions
    • Bialek, W., Callan, C., Strong, S.: Field theories for learning probability distributions. Phys. Rev. Lett. 77(23), 4693–4697 (1996)
    • (1996) Phys. Rev. Lett. , vol.77 , Issue.23 , pp. 4693-4697
    • Bialek, W.1    Callan, C.2    Strong, S.3
  • 46
    • 84904181988 scopus 로고    scopus 로고
    • Estimation of probability densities using scale-free field theories
    • Kinney, J.B.: Estimation of probability densities using scale-free field theories. Phys. Rev. E 90(1), 011301(R) (2014)
    • (2014) Phys. Rev. E , vol.90 , Issue.1 , pp. 11301
    • Kinney, J.B.1
  • 47
    • 85203733788 scopus 로고    scopus 로고
    • Kinney, J.B.: Unification of field theory and maximum entropy methods for learning probability densities. Phys. Rev. E 92(3), 032107 (2015)
    • Kinney, J.B.: Unification of field theory and maximum entropy methods for learning probability densities. Phys. Rev. E 92(3), 032107 (2015)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.