-
1
-
-
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
-
3
-
-
73349095713
-
Roles of Trans and Cis Variation in Yeast Intra-species Evolution of Gene Expression
-
Sung HM, Wang TY, Wang D, Huang YS, Wu JP, et al. (2009) Roles of Trans and Cis Variation in Yeast Intra-species Evolution of Gene Expression. Mol Biol Evol.
-
(2009)
Mol Biol Evol
-
-
Sung, H.M.1
Wang, T.Y.2
Wang, D.3
Huang, Y.S.4
Wu, J.P.5
-
4
-
-
41349098338
-
Evolution of eukaryotic transcription circuits
-
Tuch BB, Li H, Johnson AD (2008) Evolution of eukaryotic transcription circuits. Science 319: 1797-1799.
-
(2008)
Science
, vol.319
, pp. 1797-1799
-
-
Tuch, B.B.1
Li, H.2
Johnson, A.D.3
-
5
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
6
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20: 1377-1419.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
-
7
-
-
45349091096
-
The gene regulatory logic of transcription factor evolution
-
Wagner GP, Lynch VJ (2008) The gene regulatory logic of transcription factor evolution. Trends Ecol Evol 23: 377-385.
-
(2008)
Trends Ecol Evol
, vol.23
, pp. 377-385
-
-
Wagner, G.P.1
Lynch, V.J.2
-
8
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206-216.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
9
-
-
23944483135
-
Post-transcriptional control of gene expression: A genome-wide perspective
-
Mata J, Marguerat S, Bahler J (2005) Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 30: 506-514.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 506-514
-
-
Mata, J.1
Marguerat, S.2
Bahler, J.3
-
10
-
-
24644502657
-
From birth to death: The complex lives of eukaryotic mRNAs
-
Moore MJ (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309: 1514-1518.
-
(2005)
Science
, vol.309
, pp. 1514-1518
-
-
Moore, M.J.1
-
11
-
-
34250735674
-
RNA regulons: Coordination of post-transcriptional events
-
Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8: 533-543.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 533-543
-
-
Keene, J.D.1
-
12
-
-
39749083331
-
The birth and death of microRNA genes in Drosophila
-
Lu J, Shen Y, Wu Q, Kumar S, He B, et al. (2008) The birth and death of microRNA genes in Drosophila. Nat Genet 40: 351-355.
-
(2008)
Nat Genet
, vol.40
, pp. 351-355
-
-
Lu, J.1
Shen, Y.2
Wu, Q.3
Kumar, S.4
He, B.5
-
13
-
-
33751520430
-
Natural selection on human microRNA binding sites inferred from SNP data
-
Chen K, Rajewsky N (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38: 1452-1456.
-
(2006)
Nat Genet
, vol.38
, pp. 1452-1456
-
-
Chen, K.1
Rajewsky, N.2
-
14
-
-
70350510820
-
RNAi in budding yeast
-
Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, et al. (2009) RNAi in budding yeast. Science 326: 544-550.
-
(2009)
Science
, vol.326
, pp. 544-550
-
-
Drinnenberg, I.A.1
Weinberg, D.E.2
Xie, K.T.3
Mower, J.P.4
Wolfe, K.H.5
-
16
-
-
0142119568
-
The PUF family of RNA-binding proteins: Does evolutionarily conserved structure equal conserved function?
-
Spassov DS, Jurecic R (2003) The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function? IUBMB Life 55: 359-366.
-
(2003)
IUBMB Life
, vol.55
, pp. 359-366
-
-
Spassov, D.S.1
Jurecic, R.2
-
17
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
doi:10.1371/journal.pbio.0020079
-
Gerber AP, Herschlag D, Brown PO (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2: e79. doi:10.1371/journal.pbio.0020079.
-
(2004)
PLoS Biol
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
18
-
-
33645217973
-
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
-
Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D (2006) Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A 103: 4487-4492.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 4487-4492
-
-
Gerber, A.P.1
Luschnig, S.2
Krasnow, M.A.3
Brown, P.O.4
Herschlag, D.5
-
19
-
-
52349122355
-
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
-
doi:10.1371/journal.pone.0003164
-
Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, et al. (2008) Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One 3: e3164. doi:10.1371/journal.pone.0003164.
-
(2008)
PLoS One
, vol.3
-
-
Galgano, A.1
Forrer, M.2
Jaskiewicz, L.3
Kanitz, A.4
Zavolan, M.5
-
20
-
-
27944487902
-
Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
-
Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310: 1152-1158.
-
(2005)
Science
, vol.310
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
-
21
-
-
0028987223
-
Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos
-
Murata Y, Wharton RP (1995) Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos. Cell 80: 747-756.
-
(1995)
Cell
, vol.80
, pp. 747-756
-
-
Murata, Y.1
Wharton, R.P.2
-
22
-
-
0030755562
-
A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary
-
Lin H, Spradling AC (1997) A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 124: 2463-2476.
-
(1997)
Development
, vol.124
, pp. 2463-2476
-
-
Lin, H.1
Spradling, A.C.2
-
23
-
-
44949255018
-
Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
-
Morris AR, Mukherjee N, Keene JD (2008) Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol Cell Biol 28: 4093-4103.
-
(2008)
Mol Cell Biol
, vol.28
, pp. 4093-4103
-
-
Morris, A.R.1
Mukherjee, N.2
Keene, J.D.3
-
24
-
-
0343750650
-
Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae
-
Jacobs Anderson JS, Parker R (2000) Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res 28: 1604-1617.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1604-1617
-
-
Jacobs Anderson, J.S.1
Parker, R.2
-
25
-
-
34548093996
-
A catalog of stability-associated sequence elements in 39 UTRs of yeast mRNAs
-
Shalgi R, Lapidot M, Shamir R, Pilpel Y (2005) A catalog of stability-associated sequence elements in 39 UTRs of yeast mRNAs. Genome Biol 6: R86.
-
(2005)
Genome Biol
, vol.6
-
-
Shalgi, R.1
Lapidot, M.2
Shamir, R.3
Pilpel, Y.4
-
26
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
27
-
-
50649085041
-
Relaxation of yeast mitochondrial functions after whole-genome duplication
-
Jiang H, Guan W, Pinney D, Wang W, Gu Z (2008) Relaxation of yeast mitochondrial functions after whole-genome duplication. Genome Res 18: 1466-1471.
-
(2008)
Genome Res
, vol.18
, pp. 1466-1471
-
-
Jiang, H.1
Guan, W.2
Pinney, D.3
Wang, W.4
Gu, Z.5
-
28
-
-
33847305359
-
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
-
Man O, Pilpel Y (2007) Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet 39: 415-421.
-
(2007)
Nat Genet
, vol.39
, pp. 415-421
-
-
Man, O.1
Pilpel, Y.2
-
29
-
-
23244467882
-
Rewiring of the yeast transcriptional network through the evolution of motif usage
-
Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, et al. (2005) Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309: 938-940.
-
(2005)
Science
, vol.309
, pp. 938-940
-
-
Ihmels, J.1
Bergmann, S.2
Gerami-Nejad, M.3
Yanai, I.4
McClellan, M.5
-
30
-
-
63449135035
-
Gene expression divergence in yeast is coupled to evolution of DNAencoded nucleosome organization
-
Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, et al. (2009) Gene expression divergence in yeast is coupled to evolution of DNAencoded nucleosome organization. Nat Genet 41: 438-445.
-
(2009)
Nat Genet
, vol.41
, pp. 438-445
-
-
Field, Y.1
Fondufe-Mittendorf, Y.2
Moore, I.K.3
Mieczkowski, P.4
Kaplan, N.5
-
31
-
-
0034388021
-
The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast
-
Olivas W, Parker R (2000) The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. Embo J 19: 6602-6611.
-
(2000)
Embo J
, vol.19
, pp. 6602-6611
-
-
Olivas, W.1
Parker, R.2
-
32
-
-
0037162703
-
Modular recognition of RNA by a human pumilio-homology domain
-
Wang X, McLachlan J, Zamore PD, Hall TM (2002) Modular recognition of RNA by a human pumilio-homology domain. Cell 110: 501-512.
-
(2002)
Cell
, vol.110
, pp. 501-512
-
-
Wang, X.1
McLachlan, J.2
Zamore, P.D.3
Hall, T.M.4
-
33
-
-
41649092045
-
Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p
-
Miller MT, Higgin JJ, Hall TM (2008) Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nat Struct Mol Biol 15: 397-402.
-
(2008)
Nat Struct Mol Biol
, vol.15
, pp. 397-402
-
-
Miller, M.T.1
Higgin, J.J.2
Hall, T.M.3
-
34
-
-
0032568655
-
SMART, a simple modular architecture research tool: Identification of signaling domains
-
Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95: 5857-5864.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
37
-
-
48449096068
-
Yeast mitochondrial biogenesis: A role for the PUF RNA-binding protein Puf3p in mRNA localization
-
doi:10.1371/journal.pone.0002293
-
Saint-Georges Y, Garcia M, Delaveau T, Jourdren L, Le Crom S, et al. (2008) Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PLoS One 3: e2293. doi:10.1371/journal.pone.0002293.
-
(2008)
PLoS One
, vol.3
-
-
Saint-Georges, Y.1
Garcia, M.2
Delaveau, T.3
Jourdren, L.4
Le Crom, S.5
-
38
-
-
33846446777
-
Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast
-
Garcia-Rodriguez LJ, Gay AC, Pon LA (2007) Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast. J Cell Biol 176: 197-207.
-
(2007)
J Cell Biol
, vol.176
, pp. 197-207
-
-
Garcia-Rodriguez, L.J.1
Gay, A.C.2
Pon, L.A.3
-
39
-
-
0142184341
-
Global analysis of protein localization in budding yeast
-
Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
-
(2003)
Nature
, vol.425
, pp. 686-691
-
-
Huh, W.K.1
Falvo, J.V.2
Gerke, L.C.3
Carroll, A.S.4
Howson, R.W.5
-
40
-
-
19444380425
-
Nuclear genes and mitochondrial translation: A new class of genetic disease
-
Jacobs HT, Turnbull DM (2005) Nuclear genes and mitochondrial translation: a new class of genetic disease. Trends Genet 21: 312-314.
-
(2005)
Trends Genet
, vol.21
, pp. 312-314
-
-
Jacobs, H.T.1
Turnbull, D.M.2
-
41
-
-
0023650543
-
The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH (1987) The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
42
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H (2003) Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
43
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
-
44
-
-
0035254656
-
Post-transcriptional regulation through the HO 39-UTR by Mpt5, a yeast homolog of Pumilio and FBF
-
Tadauchi T, Matsumoto K, Herskowitz I, Irie K (2001) Post-transcriptional regulation through the HO 39-UTR by Mpt5, a yeast homolog of Pumilio and FBF. Embo J 20: 552-561.
-
(2001)
Embo J
, vol.20
, pp. 552-561
-
-
Tadauchi, T.1
Matsumoto, K.2
Herskowitz, I.3
Irie, K.4
-
45
-
-
4644284749
-
Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast
-
Jackson JS, Jr., Houshmandi SS, Lopez Leban F, Olivas WM (2004) Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast. Rna 10: 1625-1636.
-
(2004)
Rna
, vol.10
, pp. 1625-1636
-
-
Jackson Jr., J.S.1
Houshmandi, S.S.2
Lopez Leban, F.3
Olivas, W.M.4
-
46
-
-
29144500327
-
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
-
Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A 102: 17675-17680.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 17675-17680
-
-
Foat, B.C.1
Houshmandi, S.S.2
Olivas, W.M.3
Bussemaker, H.J.4
-
47
-
-
33846849322
-
Fermentative lifestyle in yeasts belonging to the Saccharomyces complex
-
Merico A, Sulo P, Piskur J, Compagno C (2007) Fermentative lifestyle in yeasts belonging to the Saccharomyces complex. Febs J 274: 976-989.
-
(2007)
Febs J
, vol.274
, pp. 976-989
-
-
Merico, A.1
Sulo, P.2
Piskur, J.3
Compagno, C.4
-
48
-
-
33645130011
-
Glucose signaling in Saccharomyces cerevisiae
-
Santangelo GM (2006) Glucose signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 70: 253-282.
-
(2006)
Microbiol Mol Biol Rev
, vol.70
, pp. 253-282
-
-
Santangelo, G.M.1
-
49
-
-
0017771466
-
Evolution and tinkering
-
Jacob F (1977) Evolution and tinkering. Science 196: 1161-1166.
-
(1977)
Science
, vol.196
, pp. 1161-1166
-
-
Jacob, F.1
-
50
-
-
22744439568
-
Evolution at two levels: On genes and form
-
doi:10.1371/journal.pbio.0030245
-
Carroll SB (2005) Evolution at two levels: on genes and form. PLoS Biol 3: e245. doi:10.1371/journal.pbio.0030245.
-
(2005)
PLoS Biol
, vol.3
-
-
Carroll, S.B.1
-
51
-
-
0035039018
-
Complexity and tinkering
-
Jacob F (2001) Complexity and tinkering. Ann N Y Acad Sci 929: 71-73.
-
(2001)
Ann N Y Acad Sci
, vol.929
, pp. 71-73
-
-
Jacob, F.1
-
52
-
-
0035546224
-
Evolution of novel genes
-
Long M (2001) Evolution of novel genes. Curr Opin Genet Dev 11: 673-680.
-
(2001)
Curr Opin Genet Dev
, vol.11
, pp. 673-680
-
-
Long, M.1
-
53
-
-
33845452848
-
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
-
Fitzpatrick DA, Logue ME, Stajich JE, Butler G (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 6: 99.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 99
-
-
Fitzpatrick, D.A.1
Logue, M.E.2
Stajich, J.E.3
Butler, G.4
-
54
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
56
-
-
0029461958
-
Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources
-
Chomczynski P, Mackey K (1995) Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19: 942-945.
-
(1995)
Biotechniques
, vol.19
, pp. 942-945
-
-
Chomczynski, P.1
Mackey, K.2
-
57
-
-
0036699060
-
Systematic screen for human disease genes in yeast
-
Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31: 400-404.
-
(2002)
Nat Genet
, vol.31
, pp. 400-404
-
-
Steinmetz, L.M.1
Scharfe, C.2
Deutschbauer, A.M.3
Mokranjac, D.4
Herman, Z.S.5
-
58
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
59
-
-
22344457014
-
enoLOGOS: A versatile web tool for energy normalized sequence logos
-
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, et al. (2005) enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res 33: W389-392.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Workman, C.T.1
Yin, Y.2
Corcoran, D.L.3
Ideker, T.4
Stormo, G.D.5
|