-
1
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
DOI 10.1093/molbev/msg140
-
Wray GA, et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377-1419. (Pubitemid 37086669)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.9
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
-
3
-
-
0025647969
-
Human Hox-4.2 and Drosophila Deformed encode similar regulatory specificities in Drosophila embryos and larvae
-
McGinnis N, Kuziora MA, McGinnis W (1990) Human Hox-4.2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae. Cell 63:969-976. (Pubitemid 120034938)
-
(1990)
Cell
, vol.63
, Issue.5
, pp. 969-976
-
-
McGinnis, N.1
Kuziora, M.A.2
McGinnis, W.3
-
4
-
-
0028944665
-
Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila
-
Halder G, Callaerts P, Gehring WJ (1995) Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267:1788-1792.
-
(1995)
Science
, vol.267
, pp. 1788-1792
-
-
Halder, G.1
Callaerts, P.2
Gehring, W.J.3
-
5
-
-
14044252090
-
Conservation and evolution of cis-regulatory systems in ascomycete fungi
-
Gasch AP, et al. (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2:e398.
-
(2004)
PLoS Biol
, vol.2
-
-
Gasch, A.P.1
-
6
-
-
78650039587
-
Coevolution within a transcriptional network by compensatory trans and cis mutations
-
Kuo D, et al. (2010) Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res 20:1672-1678.
-
(2010)
Genome Res
, vol.20
, pp. 1672-1678
-
-
Kuo, D.1
-
7
-
-
0023666977
-
MAT alpha 1 protein, a yeast transcription activator, binds synergistically with a second protein to a set of cell-type-specific genes
-
Bender A, Sprague GF, Jr. (1987) MAT alpha 1 protein, a yeast transcription activator, binds synergistically with a second protein to a set of cell-type-specific genes. Cell 50:681-691.
-
(1987)
Cell
, vol.50
, pp. 681-691
-
-
Bender, A.1
Sprague Jr., G.F.2
-
8
-
-
0024693085
-
The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene
-
Jarvis EE, Clark KL, Sprague GF, Jr. (1989) The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene. Genes Dev 3:936-945.
-
(1989)
Genes Dev
, vol.3
, pp. 936-945
-
-
Jarvis, E.E.1
Clark, K.L.2
Sprague Jr., G.F.3
-
9
-
-
34247601439
-
Dating divergences in the Fungal Tree of Life: Review and new analyses
-
Taylor JW, Berbee ML (2006) Dating divergences in the Fungal Tree of Life: Review and new analyses. Mycologia 98:838-849. (Pubitemid 46683208)
-
(2006)
Mycologia
, vol.98
, Issue.6
, pp. 838-849
-
-
Taylor, J.W.1
Berbee, M.L.2
-
10
-
-
0344827287
-
Evolution of a Combinatorial Transcriptional Circuit: A Case Study in Yeasts
-
DOI 10.1016/S0092-8674(03)00885-7
-
Tsong AE, Miller MG, Raisner RM, Johnson AD (2003) Evolution of a combinatorial transcriptional circuit: A case study in yeasts. Cell 115:389-399. (Pubitemid 37456802)
-
(2003)
Cell
, vol.115
, Issue.4
, pp. 389-399
-
-
Tsong, A.E.1
Miller, M.G.2
Raisner, R.M.3
Johnson, A.D.4
-
11
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol 6:e38.
-
(2008)
PLoS Biol
, vol.6
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
12
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
DOI 10.1038/nature01644
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254. (Pubitemid 40852689)
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
13
-
-
66649105285
-
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
-
Butler G, et al. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459:657-662.
-
(2009)
Nature
, vol.459
, pp. 657-662
-
-
Butler, G.1
-
14
-
-
78650344876
-
Intercalation of a new tier of transcription regulation into an ancient circuit
-
Booth LN, Tuch BB, Johnson AD (2010) Intercalation of a new tier of transcription regulation into an ancient circuit. Nature 468:959-963.
-
(2010)
Nature
, vol.468
, pp. 959-963
-
-
Booth, L.N.1
Tuch, B.B.2
Johnson, A.D.3
-
15
-
-
70349645483
-
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
-
Sharpton TJ, et al. (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19:1722-1731.
-
(2009)
Genome Res
, vol.19
, pp. 1722-1731
-
-
Sharpton, T.J.1
-
16
-
-
0022386929
-
Changing the binding specificity of a repressor by redesigning an alpha-helix
-
DOI 10.1038/316601a0
-
Wharton RP, Ptashne M (1985) Changing the binding specificity of a repressor by redesigning an alpha-helix. Nature 316:601-605. (Pubitemid 16238377)
-
(1985)
Nature
, vol.316
, Issue.6029
, pp. 601-605
-
-
Wharton, R.P.1
Ptashne, M.2
-
18
-
-
58949084539
-
Adaptive evolution in zinc finger transcription factors
-
Emerson RO, Thomas JH (2009) Adaptive evolution in zinc finger transcription factors. PLoS Genet 5:e1000325.
-
(2009)
PLoS Genet
, vol.5
-
-
Emerson, R.O.1
Thomas, J.H.2
-
19
-
-
51549097146
-
Resurrecting the role of transcription factor change in developmental evolution
-
Lynch VJ, Wagner GP (2008) Resurrecting the role of transcription factor change in developmental evolution. Evolution 62:2131-2154.
-
(2008)
Evolution
, vol.62
, pp. 2131-2154
-
-
Lynch, V.J.1
Wagner, G.P.2
-
20
-
-
0031685432
-
Divergent roles for NK-2 class homeobox genes in cardiogenesis in flies and mice
-
Ranganayakulu G, Elliott DA, Harvey RP, Olson EN (1998) Divergent roles for NK-2 class homeobox genes in cardiogenesis in flies and mice. Development 125:3037-3048. (Pubitemid 28434404)
-
(1998)
Development
, vol.125
, Issue.16
, pp. 3037-3048
-
-
Ranganayakulu, G.1
Elliott, D.A.2
Harvey, R.P.3
Olson, E.N.4
-
21
-
-
13144257684
-
Differential rescue of visceral and cardiac defects in Drosophila by vertebrate tinman-related genes
-
DOI 10.1073/pnas.95.16.9366
-
Park M, et al. (1998) Differential rescue of visceral and cardiac defects in Drosophila by vertebrate tinman-related genes. Proc Natl Acad Sci USA 95:9366-9371. (Pubitemid 28506237)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.16
, pp. 9366-9371
-
-
Park, M.1
Lewis, C.2
Turbay, D.3
Chung, A.4
Chen, J.-N.5
Evans, S.6
Breitbart, R.E.7
Fishman, M.C.8
Izumo, S.9
Bodmer, R.10
-
22
-
-
16444377659
-
The floral regulator LEAFY evolves by substitutions in the DNA binding domain
-
DOI 10.1126/science.1108229
-
Maizel A, et al. (2005) The floral regulator LEAFY evolves by substitutions in the DNA binding domain. Science 308:260-263. (Pubitemid 40558863)
-
(2005)
Science
, vol.308
, Issue.5719
, pp. 260-263
-
-
Maizel, A.1
Busch, M.A.2
Tanahashi, T.3
Perkovic, J.4
Kato, M.5
Hasebe, M.6
Weigel, D.7
-
23
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
Xie X, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
-
24
-
-
34249723155
-
Frequent gain and loss of functional transcription factor binding sites
-
Doniger SW, Fay JC (2007) Frequent gain and loss of functional transcription factor binding sites. PLOS Comput Biol 3:e99.
-
(2007)
PLOS Comput Biol
, vol.3
-
-
Doniger, S.W.1
Fay, J.C.2
-
25
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li XY, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6:e27.
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.Y.1
-
26
-
-
34547396004
-
The frailty of adaptive hypotheses for the origins of organismal complexity
-
Lynch M (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104(Suppl 1):8597-8604.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.SUPPL. 1
, pp. 8597-8604
-
-
Lynch, M.1
-
27
-
-
0036862212
-
Speciation despite gene flow when developmental pathways evolve
-
Porter AH, Johnson NA (2002) Speciation despite gene flow when developmental pathways evolve. Evolution 56:2103-2111. (Pubitemid 35436819)
-
(2002)
Evolution
, vol.56
, Issue.11
, pp. 2103-2111
-
-
Porter, A.H.1
Johnson, N.A.2
-
29
-
-
11144355642
-
The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome
-
DOI 10.1126/science.1095781
-
Dietrich FS, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307. (Pubitemid 38452185)
-
(2004)
Science
, vol.304
, Issue.5668
, pp. 304-307
-
-
Dietrich, F.S.1
Voegeli, S.2
Brachat, S.3
Lerch, A.4
Gates, K.5
Steiner, S.6
Mohr, C.7
Pohlmann, R.8
Luedi, P.9
Choi, S.10
Wing, R.A.11
Flavier, A.12
Gaffney, T.D.13
Philippsen, P.14
-
30
-
-
3042720475
-
Genome evolution in yeasts
-
DOI 10.1038/nature02579
-
Dujon B, et al. (2004) Genome evolution in yeasts. Nature 430:35-44. (Pubitemid 38915217)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 35-44
-
-
Dujon, B.1
Sherman, D.2
Fischer, G.3
Durrens, P.4
Casaregela, S.5
Lafentaine, I.6
De Montigny, J.7
Marck, C.8
Neuveglise, C.9
Talla, E.10
Goffard, N.11
Frangeul, L.12
Algie, M.13
Anthouard, V.14
Babour, A.15
Barbe, V.16
Barnay, S.17
Blanchin, S.18
Beckerich, J.-M.19
Beyne, E.20
Bleykasten, C.21
Boisrame, A.22
Boyer, J.23
Cattolico, L.24
Confanioleri, F.25
De Daruvar, A.26
Despons, L.27
Fabre, E.28
Fairhead, C.29
Ferry-Dumazet, H.30
Groppi, A.31
Hantraye, F.32
Hennequin, C.33
Jauniaux, N.34
Joyot, P.35
Kachouri, R.36
Kerrest, A.37
Koszul, R.38
Lemaire, M.39
Lesur, I.40
Ma, L.41
Muller, H.42
Nicaud, J.-M.43
Nikolski, M.44
Oztas, S.45
Ozier-Kalogeropoulos, O.46
Pellenz, S.47
Potter, S.48
Richard, G.-F.49
Straub, M.-L.50
Suleau, A.51
Swennen, D.52
Tekai, F.53
Wesolowski-Louvel, M.54
Westhof, E.55
Wirth, B.56
Zeniou-Meyer, M.57
Zivanovic, I.58
Bolotin-Fukuhara, M.59
Thierry, A.60
Bouchter, C.61
Caudron, B.62
Scarpelli, C.63
Gaillardin, C.64
Weissebach, J.65
Wincker, P.66
Souciet, J.-L.67
more..
-
31
-
-
77951042893
-
MochiView: Versatile software for genome browsing and DNA motif analysis
-
Homann OR, Johnson AD (2010) MochiView: Versatile software for genome browsing and DNA motif analysis. BMC Biol 8:49.
-
(2010)
BMC Biol
, vol.8
, pp. 49
-
-
Homann, O.R.1
Johnson, A.D.2
-
33
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profiles
-
Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B (2004) JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32(Database issue):D91-D94. (Pubitemid 38081611)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
34
-
-
79956337102
-
SwissRegulon: A database of genome-wide annotations of regulatory sites
-
Pachkov M, et al. (2006) SwissRegulon: A database of genome-wide annotations of regulatory sites. Nucleic Acids Res 27(Database issue):D1-D5.
-
(2006)
Nucleic Acids Res
, vol.27
, Issue.DATABASE ISSUE
-
-
Pachkov, M.1
-
35
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
-
36
-
-
53749085875
-
MotifVoter: A novel ensemble method for fine-grained integration of generic motif finder
-
Wijaya E, et al. (2008) MotifVoter: A novel ensemble method for fine-grained integration of generic motif finder. Nucleic Acids Res 24:2288-2295.
-
(2008)
Nucleic Acids Res
, vol.24
, pp. 2288-2295
-
-
Wijaya, E.1
-
37
-
-
33645769260
-
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
-
MacIsaac KD, et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7:113.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 113
-
-
MacIsaac, K.D.1
-
38
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu C, et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19:556-566.
-
(2009)
Genome Res
, vol.19
, pp. 556-566
-
-
Zhu, C.1
-
39
-
-
0028953840
-
Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds
-
Mumberg D, Müller R, Funk M (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156:119-122.
-
(1995)
Gene
, vol.156
, pp. 119-122
-
-
Mumberg, D.1
Müller, R.2
Funk, M.3
-
40
-
-
0028586017
-
Regulatable promoters of Saccharomyces cerevisiae: Comparison of transcriptional activity and their use for heterologous expression
-
Mumberg D, Müller R, Funk M (1994) Regulatable promoters of Saccharomyces cerevisiae: Comparison of transcriptional activity and their use for heterologous expression. Nucleic Acids Res 22:5767-5768.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 5767-5768
-
-
Mumberg, D.1
Müller, R.2
Funk, M.3
-
42
-
-
11144221718
-
Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae
-
DOI 10.1073/pnas.0407611102
-
Galgoczy DJ, et al. (2004) Genomic dissection of the cell-type- specification circuit in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 101:18069-18074. (Pubitemid 40054075)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.52
, pp. 18069-18074
-
-
Galgoczy, D.J.1
Cassidy-Stone, A.2
Llinas, M.3
O'Rourke, S.M.4
Herskowitz, I.5
DeRisi, J.L.6
Johnson, A.D.7
-
43
-
-
0024396954
-
Yeast repressor alpha2 binds to its operator cooperatively with yeast protein Mcm1
-
Keleher CA, Passmore S, Johnson AD (1989) Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1. Mol Cell Biol 9:5228-5230. (Pubitemid 19275996)
-
(1989)
Molecular and Cellular Biology
, vol.9
, Issue.11
, pp. 5228-5230
-
-
Keleher, C.A.1
Passmore, S.2
Johnson, A.D.3
-
44
-
-
33749173831
-
Evolution of alternative transcriptional circuits with identical logic
-
DOI 10.1038/nature05099, PII NATURE05099
-
Tsong AE, Tuch BB, Li H, Johnson AD (2006) Evolution of alternative transcriptional circuits with identical logic. Nature 443:415-420. (Pubitemid 44477273)
-
(2006)
Nature
, vol.443
, Issue.7110
, pp. 415-420
-
-
Tsong, A.E.1
Tuch, B.B.2
Li, H.3
Johnson, A.D.4
-
45
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
46
-
-
0024234855
-
CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
-
DOI 10.1016/0378-1119(88)90330-7
-
Higgins DG, Sharp PM (1988) CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244. (Pubitemid 19033800)
-
(1988)
Gene
, vol.73
, Issue.1
, pp. 237-244
-
-
Higgins, D.G.1
Sharp, P.M.2
-
47
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
DOI 10.1126/science.1084337
-
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76. (Pubitemid 36801562)
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
48
-
-
34347209089
-
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
-
DOI 10.1073/pnas.0608218104
-
Scannell DR, et al. (2007) Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci USA 104:8397-8402. (Pubitemid 47175499)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.20
, pp. 8397-8402
-
-
Scannell, D.R.1
Frank, A.C.2
Conant, G.C.3
Byrne, K.P.4
Woolfit, M.5
Wolfe, K.H.6
|