-
1
-
-
0036500609
-
A genomic regulatory network for development
-
(doi:10.1126/science.1069883)
-
Davidson EH et al. 2002 A genomic regulatory network for development. Science 295, 1669-1678. (doi:10.1126/science.1069883)
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
-
2
-
-
77956520011
-
Functional roles for noise in genetic circuits
-
(doi:10.1038/nature09326)
-
Eldar A, Elowitz MB. 2010 Functional roles for noise in genetic circuits. Nature 467, 167-173. (doi:10.1038/nature09326)
-
(2010)
Nature
, vol.467
, pp. 167-173
-
-
Eldar, A.1
Elowitz, M.B.2
-
3
-
-
0037165942
-
Combinatorial synthesis of genetic networks
-
(doi:10.1126/science.1067407)
-
Guet CC, Elowitz MB, Hsing W, Leibler S. 2002 Combinatorial synthesis of genetic networks. Science 296, 1466-1470. (doi:10.1126/science.1067407)
-
(2002)
Science
, vol.296
, pp. 1466-1470
-
-
Guet, C.C.1
Elowitz, M.B.2
Hsing, W.3
Leibler, S.4
-
4
-
-
77956530755
-
Evolution of transcription networks-lessons from yeasts
-
(doi:10.1016/j.cub.2010.06.056)
-
Li H, Johnson AD. 2010 Evolution of transcription networks-lessons from yeasts. Curr. Biol. 20, R746-R753. (doi:10.1016/j.cub.2010.06.056)
-
(2010)
Curr. Biol.
, vol.20
-
-
Li, H.1
Johnson, A.D.2
-
5
-
-
77956545119
-
Evolution of complex gene regulatory circuits by addition of refinements
-
(doi:10.1016/j.cub.2010.06.028)
-
Little JW. 2010 Evolution of complex gene regulatory circuits by addition of refinements. Curr. Biol. 20, R724-R734. (doi:10.1016/j.cub.2010.06.028)
-
(2010)
Curr. Biol.
, vol.20
-
-
Little, J.W.1
-
6
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
(doi:10.1038/ng881)
-
Shen-Orr SS, Milo R, Mangan S, Alon U. 2002 Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68. (doi:10.1038/ng881)
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
7
-
-
33745583768
-
A genetic signature of interspecies variations in gene expression
-
(doi:10.1038/ ng1819)
-
Tirosh I, Weinberger A, Carmi M, Barkai N. 2006 A genetic signature of interspecies variations in gene expression. Nat. Genet. 38, 830-834. (doi:10.1038/ ng1819)
-
(2006)
Nat. Genet.
, vol.38
, pp. 830-834
-
-
Tirosh, I.1
Weinberger, A.2
Carmi, M.3
Barkai, N.4
-
8
-
-
41349098338
-
Evolution of eukaryotic transcription circuits
-
(doi:10.1126/science.1152398)
-
Tuch BB, Li H, Johnson AD. 2008 Evolution of eukaryotic transcription circuits. Science 319, 1797-1799. (doi:10.1126/science.1152398)
-
(2008)
Science
, vol.319
, pp. 1797-1799
-
-
Tuch, B.B.1
Li, H.2
Johnson, A.D.3
-
9
-
-
30744475434
-
The origins of eukaryotic gene structure
-
(doi:10. 1093/molbev/msj050)
-
Lynch M. 2006 The origins of eukaryotic gene structure. Mol. Biol. Evol. 23, 450-468. (doi:10. 1093/molbev/msj050)
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 450-468
-
-
Lynch, M.1
-
10
-
-
57349140010
-
Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
-
(doi:10.1073/pnas.0806317105)
-
Janga SC, Collado-Vides J, Babu MM. 2008 Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes. Proc. Natl Acad. Sci. USA 105, 15 761-15 766. (doi:10.1073/pnas.0806317105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 15761-15766
-
-
Janga, S.C.1
Collado-Vides, J.2
Babu, M.M.3
-
11
-
-
38449094866
-
From biophysics to evolutionary genetics: Statistical aspects of gene regulation
-
(doi:10.1186/1471-2105-8-S6-S7)
-
Lässig M. 2007 From biophysics to evolutionary genetics: statistical aspects of gene regulation. BMC Bioinform. 8(Suppl. 6), S7. (doi:10.1186/1471-2105-8-S6-S7)
-
(2007)
BMC Bioinform.
, vol.8
, Issue.SUPPL. 6
-
-
Lässig, M.1
-
12
-
-
84869056823
-
Why transcription factor binding sites are ten nucleotides long
-
(doi:10.1534/genetics.112. 143370)
-
Stewart AJ, Plotkin JB. 2012 Why transcription factor binding sites are ten nucleotides long. Genetics 192, 973-985. (doi:10.1534/genetics.112. 143370)
-
(2012)
Genetics
, vol.192
, pp. 973-985
-
-
Stewart, A.J.1
Plotkin, J.B.2
-
13
-
-
33746219660
-
The design of transcriptionfactor binding sites is affected by combinatorial regulation
-
(doi:10.1186/gb-2005-6-12-r103)
-
Bilu Y, Barkai N. 2005 The design of transcriptionfactor binding sites is affected by combinatorial regulation. Genome Biol. 6, R103. (doi:10.1186/gb-2005-6-12-r103)
-
(2005)
Genome Biol.
, vol.6
-
-
Bilu, Y.1
Barkai, N.2
-
14
-
-
33845503073
-
Adaptive evolution of transcription factor binding sites
-
(doi:10.1186/1471-2148-4-42)
-
Berg J, Willmann S, Lässig M. 2004 Adaptive evolution of transcription factor binding sites. BMC Evol. Biol. 4, 42. (doi:10.1186/1471-2148-4-42)
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 42
-
-
Berg, J.1
Willmann, S.2
Lässig, M.3
-
15
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
(doi:10.1186/1471-2148-3-19)
-
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. 2003 Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 3, 19. (doi:10.1186/1471-2148-3-19)
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
16
-
-
22144437325
-
The application of statistical physics to evolutionary biology
-
(doi:10.1073/pnas. 0501865102)
-
Sella G, Hirsh AE. 2005 The application of statistical physics to evolutionary biology. Proc. Natl Acad. Sci. USA 102, 9541-9546. (doi:10.1073/pnas. 0501865102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 9541-9546
-
-
Sella, G.1
Hirsh, A.E.2
-
17
-
-
0034598832
-
Evidence for stabilizing selection in a eukaryotic enhancer element
-
(doi:10.1038/35000615)
-
Ludwig MZ, Bergman CM, Patel NH, Kreitman M. 2000 Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403, 564-567. (doi:10.1038/35000615)
-
(2000)
Nature
, vol.403
, pp. 564-567
-
-
Ludwig, M.Z.1
Bergman, C.M.2
Patel, N.H.3
Kreitman, M.4
-
18
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
(doi:10.1126/science.1075090)
-
Lee TI et al. 2002 Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804. (doi:10.1126/science.1075090)
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
19
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
(doi:10.1038/nature02800)
-
Harbison CT et al. 2004 Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104. (doi:10.1038/nature02800)
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
20
-
-
38549096565
-
Jaspar, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update
-
(doi:10.1093/nar/gkm955)
-
Bryne JC, Valen E, Tang M-HE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. 2008 Jaspar, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 36, D102-D106. (doi:10.1093/nar/gkm955)
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.-H.E.3
Marstrand, T.4
Winther, O.5
da Piedade, I.6
Krogh, A.7
Lenhard, B.8
Sandelin, A.9
-
21
-
-
1542328960
-
Identification and distinct regulation of yeast TATA box-containing genes
-
(doi:10. 1016/S0092-8674(04)00205-3)
-
Basehoar AD, Zanton SJ, Pugh BF. 2004 Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709. (doi:10. 1016/S0092-8674(04)00205-3)
-
(2004)
Cell
, vol.116
, pp. 699-709
-
-
Basehoar, A.D.1
Zanton, S.J.2
Pugh, B.F.3
-
22
-
-
84857427738
-
Chromatin and transcription in yeast
-
(doi:10.1534/genetics.111.132266)
-
Rando OJ, Winston F. 2012 Chromatin and transcription in yeast. Genetics 190, 351-387. (doi:10.1534/genetics.111.132266)
-
(2012)
Genetics
, vol.190
, pp. 351-387
-
-
Rando, O.J.1
Winston, F.2
-
23
-
-
78651299341
-
Regulondb version 7.0: Transcriptional regulation of Escherichia coli k-12 integrated within genetic sensory response units (gensor units)
-
(doi:10.1093/nar/gkq1110)
-
Gama-Castro S et al. 2011 Regulondb version 7.0: transcriptional regulation of Escherichia coli k-12 integrated within genetic sensory response units (gensor units). Nucleic Acids Res. 39, D98-D105. (doi:10.1093/nar/gkq1110)
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Gama-Castro, S.1
-
24
-
-
15744387380
-
Transcriptional regulation by the numbers: Models
-
(doi:10.1016/j.gde.2005.02.007)
-
Bintu L, Buchler N, Garcia H, Gerland U, Hwa T, Kondev J, Phillips R. 2005 Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116-124. (doi:10.1016/j.gde.2005.02.007)
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.2
Garcia, H.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
25
-
-
0037965981
-
On schemes of combinatorial transcription logic
-
(doi:10.1073/pnas.0930314100)
-
Buchler NE, Gerland U, Hwa T. 2003 On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. USA 100, 5136-5141. (doi:10.1073/pnas.0930314100)
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
26
-
-
61449155349
-
Models of transcription factor binding: Sensitivity of activation functions to model assumptions
-
(doi:10.1016/j.jtbi.2008.11.026)
-
Chu D, Zabet NR, Mitavskiy B. 2009 Models of transcription factor binding: sensitivity of activation functions to model assumptions. J. Theor. Biol. 257, 419-429. (doi:10.1016/j.jtbi.2008.11.026)
-
(2009)
J. Theor. Biol.
, vol.257
, pp. 419-429
-
-
Chu, D.1
Zabet, N.R.2
Mitavskiy, B.3
-
27
-
-
0036787402
-
On the selection and evolution of regulatory DNA motifs
-
(doi:10.1007/s00239-002-2335-z)
-
Gerland U, Hwa T. 2002 On the selection and evolution of regulatory DNA motifs. J. Mol. Evol. 55, 386-400. (doi:10.1007/s00239-002-2335-z)
-
(2002)
J. Mol. Evol.
, vol.55
, pp. 386-400
-
-
Gerland, U.1
Hwa, T.2
-
28
-
-
50449102853
-
Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites
-
(doi:10.1073/pnas.0805909105)
-
Mustonen V, Kinney J, Callan Jr CG, Lässig M. 2008 Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc. Natl Acad. Sci. USA 105, 12 376-12 381. (doi:10.1073/pnas.0805909105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 12376-12381
-
-
Mustonen, V.1
Kinney, J.2
Callan Jr., C.G.3
Lässig, M.4
-
29
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interaction
-
(doi:10.1073/ pnas.192693599)
-
Gerland U, Moroz JD, Hwa T. 2002 Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl Acad. Sci. USA 99, 12 015-12 020. (doi:10.1073/ pnas.192693599)
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, J.D.2
Hwa, T.3
-
30
-
-
33645748095
-
What are DNA sequence motifs?
-
(doi:10.1038/ nbt0406-423)
-
D'haeseleer P. 2006 What are DNA sequence motifs? Nat. Biotechnol. 24, 423-425. (doi:10.1038/ nbt0406-423)
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 423-425
-
-
D'Haeseleer, P.1
-
31
-
-
0037133207
-
Specificity and robustness in transcription control networks
-
(doi:10.1073/pnas.022388499)
-
Sengupta AM, Djordjevic M, Shraiman BI. 2002 Specificity and robustness in transcription control networks. Proc. Natl Acad. Sci. USA 99, 2072-2077. (doi:10.1073/pnas.022388499)
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 2072-2077
-
-
Sengupta, A.M.1
Djordjevic, M.2
Shraiman, B.I.3
-
32
-
-
79955623470
-
Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis regulatory modules
-
(doi:10.1371/journal.pgen.1002053)
-
He BZ, Holloway AK, Maerkl SJ, Kreitman M. 2011 Does positive selection drive transcription factor binding site turnover? a test with Drosophila cis regulatory modules. PLoS Genet. 7, e1002053. (doi:10.1371/journal.pgen.1002053)
-
(2011)
PLoS Genet.
, vol.7
-
-
He, B.Z.1
Holloway, A.K.2
Maerkl, S.J.3
Kreitman, M.4
-
33
-
-
33749173831
-
Evolution of alternative transcriptional circuits with identical logic
-
(doi:10.1038/nature05099)
-
Tsong AE, Tuch BB, Li H, Johnson AD. 2006 Evolution of alternative transcriptional circuits with identical logic. Nature 443, 415-420. (doi:10.1038/nature05099)
-
(2006)
Nature
, vol.443
, pp. 415-420
-
-
Tsong, A.E.1
Tuch, B.B.2
Li, H.3
Johnson, A.D.4
-
34
-
-
76249107162
-
Ctcf binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features
-
(doi:10.1186/gb-2009-10-11-r131)
-
Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S. 2009 Ctcf binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol. 10, R131. (doi:10.1186/gb-2009-10-11-r131)
-
(2009)
Genome Biol.
, vol.10
-
-
Essien, K.1
Vigneau, S.2
Apreleva, S.3
Singh, L.N.4
Bartolomei, M.S.5
Hannenhalli, S.6
-
35
-
-
84863404645
-
Evolutionary origins of transcription factor binding site clusters
-
(doi:10.1093/ molbev/msr277)
-
He X, Duque TSPC, Sinha S. 2012 Evolutionary origins of transcription factor binding site clusters. Mol. Biol. Evol. 29, 1059-1070. (doi:10.1093/ molbev/msr277)
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1059-1070
-
-
He, X.1
Duque, T.S.P.C.2
Sinha, S.3
-
36
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
(doi:10.1101/gr.5113606)
-
Tanay A. 2006 Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 16, 962-972. (doi:10.1101/gr.5113606)
-
(2006)
Genome Res.
, vol.16
, pp. 962-972
-
-
Tanay, A.1
-
37
-
-
78049233382
-
Redundancy and the evolution of cis-regulatory element multiplicity
-
(doi:10.1371/ journal.pcbi.1000848)
-
Paixão T, Azevedo RBR. 2010 Redundancy and the evolution of cis-regulatory element multiplicity. PLoS Comput. Biol. 6, e1000848. (doi:10.1371/ journal.pcbi.1000848)
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Paixão, T.1
Azevedo, R.B.R.2
-
38
-
-
34548724489
-
The evolution of genetic networks by non-adaptive processes
-
(doi:10.1038/nrg2192)
-
Lynch M. 2007 The evolution of genetic networks by non-adaptive processes. Nat. Rev. Genet. 8, 803-813. (doi:10.1038/nrg2192)
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 803-813
-
-
Lynch, M.1
-
39
-
-
79961191133
-
RIP: The regulatory interaction predictor-a machine learning-based approach for predicting target genes of transcription factors
-
(doi:10. 1093/bioinformatics/btr366)
-
Bauer T, Eils R, König R. 2011 RIP: the regulatory interaction predictor-a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 27, 2239-2247. (doi:10. 1093/bioinformatics/btr366)
-
(2011)
Bioinformatics
, vol.27
, pp. 2239-2247
-
-
Bauer, T.1
Eils, R.2
König, R.3
-
40
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
(doi:10.1016/j.molcel.2006.11.003)
-
Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. 2006 Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 24, 853-865. (doi:10.1016/j.molcel.2006.11.003)
-
(2006)
Mol. Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
Balázsi, G.2
Kohanski, M.A.3
Isaacs, F.J.4
Murphy, K.F.5
Kuang, Y.6
Cantor, C.R.7
Walt, D.R.8
Collins, J.J.9
|