-
1
-
-
1942453302
-
Predicting gene expression from sequence
-
DOI 10.1016/S0092-8674(04)00304-6, PII S0092867404003046
-
Beer M A and Tavazoie S 2004 Predicting gene expression from sequence Cell 117 185-98 (Pubitemid 38496239)
-
(2004)
Cell
, vol.117
, Issue.2
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
2
-
-
15744387380
-
Transcriptional regulation by the numbers: Applications
-
DOI 10.1016/j.gde.2005.02.006, Chromosomes and Expression Mechanisms
-
Bintu L, Buchler N E, Garcia H G, Gerland U, Hwa T, Kondev J, Kuhlman T and Phillips R 2005a Transcriptional regulation by the numbers: applications Curr. Opin. Genet. Dev. 15 125-35 (Pubitemid 40410660)
-
(2005)
Current Opinion in Genetics and Development
, vol.15
, Issue.2
, pp. 125-135
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Kuhlman, T.7
Phillips, R.8
-
3
-
-
15744394192
-
Transcriptional regulation by the numbers: Models
-
DOI 10.1016/j.gde.2005.02.007, Chromosomes and Expression Mechanisms
-
Bintu L, Buchler N E, Garcia H G, Gerland U, Hwa T, Kondev J and Phillips R 2005b Transcriptional regulation by the numbers: models Curr. Opin. Genet. Dev. 15 116-24 (Pubitemid 40410659)
-
(2005)
Current Opinion in Genetics and Development
, vol.15
, Issue.2
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
4
-
-
77956848161
-
Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription
-
Dowell N L, Sperling A S, Mason M J and Johnson R C 2010 Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription Genes Dev. 24 2031-42
-
(2010)
Genes Dev.
, vol.24
, Issue.18
, pp. 2031-2042
-
-
Dowell, N.L.1
Sperling, A.S.2
Mason, M.J.3
Johnson, R.C.4
-
5
-
-
76149087772
-
Deciphering a transcriptional regulatory code: Modeling short-range repression in the Drosophila embryo
-
Fakhouri W D, Ay A, Sayal R, Dresch J, Dayringer E and Arnosti D N 2010 Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo Mol. Syst. Biol. 6 341
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 341
-
-
Fakhouri, W.D.1
Ay, A.2
Sayal, R.3
Dresch, J.4
Dayringer, E.5
Arnosti, D.N.6
-
6
-
-
78650216734
-
Transcription by the numbers redux: Experiments and calculations that surprise
-
Garcia H G, Sanchez A, Kuhlman T, Kondev J and Phillips R 2010 Transcription by the numbers redux: experiments and calculations that surprise Trends Cell Biol. 20 723-33
-
(2010)
Trends Cell Biol.
, vol.20
, Issue.12
, pp. 723-733
-
-
Garcia, H.G.1
Sanchez, A.2
Kuhlman, T.3
Kondev, J.4
Phillips, R.5
-
7
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz J, Siggia E D and Cohen B A 2009 Analysis of combinatorial cis-regulation in synthetic and genomic promoters Nature 457 215-8
-
(2009)
Nature
, vol.457
, Issue.7226
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
8
-
-
78049450019
-
Thermodynamics-based models of transcriptional regulation by enhancers: The roles of synergistic activation, cooperative binding and short-range repression
-
He X, Samee M A, Blatti C and Sinha S 2010 Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression PLoS Comput. Biol. 6 e1000935
-
(2010)
PLoS Comput. Biol.
, vol.6
, Issue.9
, pp. 1000935
-
-
He, X.1
Samee, M.A.2
Blatti, C.3
Sinha, S.4
-
9
-
-
3142734333
-
Dynamic control of positional information in the early Drosophila embryo
-
DOI 10.1038/nature02678
-
Jaeger J et al 2004 Dynamic control of positional information in the early Drosophila embryo Nature 430 368-71 (Pubitemid 38937746)
-
(2004)
Nature
, vol.430
, Issue.6997
, pp. 368-371
-
-
Jaeger, J.1
Surkova, S.2
Blagov, M.3
Janssens, H.4
Kosman, D.5
Kozlov, K.H.6
Manu7
Myasnikova, E.8
Vanario-Alonso, C.E.9
Samsonova, M.10
Sharp, D.H.11
Reinitz, J.12
-
10
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
-
DOI 10.1038/ng1886, PII NG1886
-
Janssens H, Hou S, Jaeger J, Kim A R, Myasnikova E, Sharp D and Reinitz J 2006 Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene Nat. Genet 38 1159-65 (Pubitemid 44470361)
-
(2006)
Nature Genetics
, vol.38
, Issue.10
, pp. 1159-1165
-
-
Janssens, H.1
Hou, S.2
Jaeger, J.3
Kim, A.-R.4
Myasnikova, E.5
Sharp, D.6
Reinitz, J.7
-
11
-
-
79952273012
-
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
-
Kaplan T, Li X Y, Sabo P J, Thomas S, Stamatoyannopoulos J A, Biggin M D and Eisen M B 2011 Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development PLoS Genet 7 e1001290
-
(2011)
PLoS Genet
, vol.7
, Issue.2
, pp. 1001290
-
-
Kaplan, T.1
Li, X.Y.2
Sabo, P.J.3
Thomas, S.4
Stamatoyannopoulos, J.A.5
Biggin, M.D.6
Eisen, M.B.7
-
12
-
-
79952360918
-
Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes
-
Li L M and Arnosti D N 2011 Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes Curr. Biol. 21 406-12
-
(2011)
Curr. Biol.
, vol.21
, Issue.5
, pp. 406-412
-
-
Li, L.M.1
Arnosti, D.N.2
-
13
-
-
0344442419
-
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
-
DOI 10.1093/nar/gkg799
-
Makeev V J, Lifanov A P, Nazina A G and Papatsenko D A 2003 Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information Nucleic Acids Res. 31 6016-26 (Pubitemid 37442327)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.20
, pp. 6016-6026
-
-
Makeev, V.J.1
Lifanov, A.P.2
Nazina, A.G.3
Papatsenko, D.A.4
-
14
-
-
0016175370
-
Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice
-
McGhee J D and von Hippel P H 1974 Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice J. Mol. Biol. 86 469-89
-
(1974)
J. Mol. Biol.
, vol.86
, Issue.2
, pp. 469-489
-
-
McGhee, J.D.1
Von Hippel, P.H.2
-
15
-
-
0037369952
-
Collaborative competition mechanism for gene activation in vivo
-
DOI 10.1128/MCB.23.5.1623-1632.2003
-
Miller J A and Widom J 2003 Collaborative competition mechanism for gene activation in vivo Mol. Cell Biol. 23 1623-32 (Pubitemid 36246044)
-
(2003)
Molecular and Cellular Biology
, vol.23
, Issue.5
, pp. 1623-1632
-
-
Miller, J.A.1
Widom, J.2
-
16
-
-
70549090448
-
Organization of developmental enhancers in the Drosophila embryo
-
Papatsenko D, Goltsev Y and Levine M 2009 Organization of developmental enhancers in the Drosophila embryo Nucleic Acids Res. 37 5665-77
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.17
, pp. 5665-5677
-
-
Papatsenko, D.1
Goltsev, Y.2
Levine, M.3
-
17
-
-
0035668536
-
Making contacts on a nucleic acid polymer
-
DOI 10.1016/S0968-0004(01)01978-8, PII S0968000401019788
-
Rippe K 2001 Making contacts on a nucleic acid polymer Trends Biochem. Sci. 26 733-40 (Pubitemid 34014840)
-
(2001)
Trends in Biochemical Sciences
, vol.26
, Issue.12
, pp. 733-740
-
-
Rippe, K.1
-
19
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
DOI 10.1038/nature06496, PII NATURE06496
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U and Gaul U 2008 Predicting expression patterns from regulatory sequence in Drosophila segmentation Nature 451 535-40 (Pubitemid 351186263)
-
(2008)
Nature
, vol.451
, Issue.7178
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
20
-
-
34547128905
-
R operator of phage λ
-
R operator of phage λ Nucleic Acids Res. 35 e80
-
(2007)
Nucleic Acids Res.
, vol.35
, Issue.11
, pp. 80
-
-
Teif, V.B.1
-
21
-
-
77950669526
-
Predicting gene-regulation functions: Lessons from temperate bacteriophages
-
Teif V B 2010 Predicting gene-regulation functions: lessons from temperate bacteriophages Biophys. J. 98 1247-56
-
(2010)
Biophys. J.
, vol.98
, Issue.7
, pp. 1247-1256
-
-
Teif, V.B.1
-
22
-
-
78049343481
-
A lattice model for transcription factor access to nucleosomal DNA
-
Teif V B, Ettig R and Rippe K 2010 A lattice model for transcription factor access to nucleosomal DNA Biophys. J. 99 2597-607
-
(2010)
Biophys. J.
, vol.99
, Issue.8
, pp. 2597-2607
-
-
Teif, V.B.1
Ettig, R.2
Rippe, K.3
-
23
-
-
78049327377
-
Statistical-mechanical lattice models for protein-DNA binding in chromatin
-
Teif V B and Rippe K 2010 Statistical-mechanical lattice models for protein-DNA binding in chromatin J. Phys.: Condens. Matter 22 414105
-
(2010)
J. Phys.: Condens. Matter
, vol.22
, Issue.41
, pp. 414105
-
-
Teif, V.B.1
Rippe, K.2
-
24
-
-
36949030484
-
Predicting gene expression from sequence: A reexamination
-
Yuan Y, Guo L, Shen L and Liu J S 2007 Predicting gene expression from sequence: a reexamination PLoS Comput. Biol. 3 e243
-
(2007)
PLoS Comput. Biol.
, vol.3
, Issue.11
, pp. 243
-
-
Yuan, Y.1
Guo, L.2
Shen, L.3
Liu, J.S.4
-
25
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
DOI 10.1126/science.279.5358.1896
-
Yuh C H, Bolouri H and Davidson E H 1998 Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene Science 279 1896-902 (Pubitemid 28168638)
-
(1998)
Science
, vol.279
, Issue.5358
, pp. 1896-1902
-
-
Yuh, C.-H.1
Bolouri, H.2
Davidson, E.H.3
-
26
-
-
33745658106
-
Computational models for neurogenic gene expression in the Drosophila embryo
-
DOI 10.1016/j.cub.2006.05.044, PII S0960982206016277
-
Zinzen R P, Senger K, Levine M and Papatsenko D 2006 Computational models for neurogenic gene expression in the Drosophila embryo Curr. Biol. 16 1358-65 (Pubitemid 43975367)
-
(2006)
Current Biology
, vol.16
, Issue.13
, pp. 1358-1365
-
-
Zinzen, R.P.1
Senger, K.2
Levine, M.3
Papatsenko, D.4
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