-
1
-
-
65249143921
-
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
-
Fawcett JA, Maere S, Van de Peer Y (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA 106:5737-5742.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 5737-5742
-
-
Fawcett, J.A.1
Maere, S.2
Van de Peer, Y.3
-
2
-
-
33745610025
-
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
-
Freeling M, Thomas BC (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16:805-814.
-
(2006)
Genome Res
, vol.16
, pp. 805-814
-
-
Freeling, M.1
Thomas, B.C.2
-
4
-
-
33645023614
-
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
-
Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.
-
(2006)
Nature
, vol.440
, pp. 341-345
-
-
Scannell, D.R.1
Byrne, K.P.2
Gordon, J.L.3
Wong, S.4
Wolfe, K.H.5
-
5
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
6
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
Maere S, et al. (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102:5454-5459.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
-
7
-
-
24644486450
-
Do disparate mechanisms of duplication add similar genes to the genome?
-
Davis JC, Petrov DA (2005) Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet 21:548-551.
-
(2005)
Trends Genet
, vol.21
, pp. 548-551
-
-
Davis, J.C.1
Petrov, D.A.2
-
8
-
-
35548954250
-
The evolutionary consequences of polyploidy
-
Otto SP (2007) The evolutionary consequences of polyploidy. Cell 131:452-462.
-
(2007)
Cell
, vol.131
, pp. 452-462
-
-
Otto, S.P.1
-
9
-
-
33646859550
-
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
-
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 7:R13.
-
(2006)
Genome Biol
, vol.7
-
-
Casneuf, T.1
De Bodt, S.2
Raes, J.3
Maere, S.4
Van de Peer, Y.5
-
10
-
-
26444488575
-
Expression divergence between duplicate genes
-
Li WH, Yang J, Gu X (2005) Expression divergence between duplicate genes. Trends Genet 21:602-607.
-
(2005)
Trends Genet
, vol.21
, pp. 602-607
-
-
Li, W.H.1
Yang, J.2
Gu, X.3
-
11
-
-
44149105911
-
PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
-
Gnad F, et al. (2007) PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 8:R250.
-
(2007)
Genome Biol
, vol.8
-
-
Gnad, F.1
-
12
-
-
2342473198
-
The importance of intrinsic disorder for protein phosphorylation
-
Iakoucheva LM, et al. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32:1037-1049.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1037-1049
-
-
Iakoucheva, L.M.1
-
13
-
-
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
-
14
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
15
-
-
47849125967
-
A multidimensional chromatography technology for indepth phosphoproteome analysis
-
Albuquerque CP, et al. (2008) A multidimensional chromatography technology for indepth phosphoproteome analysis. Mol Cell Proteomics 7:1389-1396.
-
(2008)
Mol Cell Proteomics
, vol.7
, pp. 1389-1396
-
-
Albuquerque, C.P.1
-
16
-
-
57449105428
-
PhosphoPep - A database of protein phosphorylation sites in model organisms
-
Bodenmiller B, et al. (2008) PhosphoPep - A database of protein phosphorylation sites in model organisms. Nat Biotechnol 26:1339-1340.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1339-1340
-
-
Bodenmiller, B.1
-
17
-
-
33847778786
-
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry
-
Chi A, et al. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 104:2193-2198.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2193-2198
-
-
Chi, A.1
-
18
-
-
15944377809
-
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway
-
Gruhler A, et al. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4:310-327.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 310-327
-
-
Gruhler, A.1
-
19
-
-
33947584417
-
Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae
-
Li X, et al. (2007) Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. J Proteome Res 6:1190-1197.
-
(2007)
J Proteome Res
, vol.6
, pp. 1190-1197
-
-
Li, X.1
-
20
-
-
36749053957
-
Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase
-
Reinders J, et al. (2007) Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol Cell Proteomics 6:1896-1906.
-
(2007)
Mol Cell Proteomics
, vol.6
, pp. 1896-1906
-
-
Reinders, J.1
-
21
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15:1456-1461.
-
(2005)
Genome Res
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
22
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102:10930-10935.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
23
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp B, Pál C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pál, C.2
Hurst, L.D.3
-
24
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425:737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
-
25
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
-
26
-
-
68449090023
-
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
-
Pache RA, Babu MM, Aloy P (2009) Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions. BMC Syst Biol 3:74.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 74
-
-
Pache, R.A.1
Babu, M.M.2
Aloy, P.3
-
28
-
-
0036699060
-
Systematic screen for human disease genes in yeast
-
Steinmetz LM, 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
-
29
-
-
50949092459
-
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality. PLoS Comput Biol 4:e1000140.
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality. PLoS Comput Biol 4:e1000140.
-
-
-
-
30
-
-
33750238153
-
Stratus not altocumulus: A new view of the yeast protein interaction network
-
Batada NN, et al. (2006) Stratus not altocumulus: A new view of the yeast protein interaction network. PLoS Biol 4:e317.
-
(2006)
PLoS Biol
, vol.4
-
-
Batada, N.N.1
-
31
-
-
3042593155
-
Functional evolution of the yeast protein interaction network
-
Kunin V, Pereira-Leal JB, Ouzounis CA (2004) Functional evolution of the yeast protein interaction network. Mol Biol Evol 21:1171-1176.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1171-1176
-
-
Kunin, V.1
Pereira-Leal, J.B.2
Ouzounis, C.A.3
-
32
-
-
11144355642
-
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
-
Dietrich FS, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307.
-
(2004)
Science
, vol.304
, pp. 304-307
-
-
Dietrich, F.S.1
-
33
-
-
3042720475
-
Genome evolution in yeasts
-
Dujon B, et al. (2004) Genome evolution in yeasts. Nature 430:35-44.
-
(2004)
Nature
, vol.430
, pp. 35-44
-
-
Dujon, B.1
-
34
-
-
65349155149
-
Weak functional constraints on phosphoproteomes
-
Landry CR, Levy ED, Michnick SW (2009)Weak functional constraints on phosphoproteomes. Trends Genet 25:193-197.
-
(2009)
Trends Genet
, vol.25
, pp. 193-197
-
-
Landry, C.R.1
Levy, E.D.2
Michnick, S.W.3
-
35
-
-
48149087568
-
Non-functional phosphorylations?
-
Lienhard GE (2008) Non-functional phosphorylations? Trends Biochem Sci 33:351-352.
-
(2008)
Trends Biochem Sci
, vol.33
, pp. 351-352
-
-
Lienhard, G.E.1
-
36
-
-
0033972072
-
The probability of duplicate gene preservation by subfunctionalization
-
Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
-
(2000)
Genetics
, vol.154
, pp. 459-473
-
-
Lynch, M.1
Force, A.2
-
37
-
-
70349546862
-
Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
-
Holt LJ, et al. (2009) Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325:1682-1686.
-
(2009)
Science
, vol.325
, pp. 1682-1686
-
-
Holt, L.J.1
-
38
-
-
15544389841
-
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
-
He X, Zhang J (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164.
-
(2005)
Genetics
, vol.169
, pp. 1157-1164
-
-
He, X.1
Zhang, J.2
-
39
-
-
34548527460
-
Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
-
BarkaiN
-
Tirosh I, BarkaiN(2007) Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 8:R50.
-
(2007)
Genome Biol
, vol.8
-
-
Tirosh, I.1
-
40
-
-
57149116929
-
Tight regulation of unstructured proteins: From transcript synthesis to protein degradation
-
Gsponer J, Futschik ME, Teichmann SA, Babu MM (2008) Tight regulation of unstructured proteins: From transcript synthesis to protein degradation. Science 322:1365-1368.
-
(2008)
Science
, vol.322
, pp. 1365-1368
-
-
Gsponer, J.1
Futschik, M.E.2
Teichmann, S.A.3
Babu, M.M.4
-
41
-
-
34247847827
-
Functional analysis of gene duplications in Saccharomyces cerevisiae
-
Guan Y, Dunham MJ, Troyanskaya OG (2007) Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 175:933-943.
-
(2007)
Genetics
, vol.175
, pp. 933-943
-
-
Guan, Y.1
Dunham, M.J.2
Troyanskaya, O.G.3
-
42
-
-
38049133600
-
All duplicates are not equal: The difference between small-scale and genome duplication
-
Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL (2007) All duplicates are not equal: The difference between small-scale and genome duplication. Genome Biol 8:R209.
-
(2007)
Genome Biol
, vol.8
-
-
Hakes, L.1
Pinney, J.W.2
Lovell, S.C.3
Oliver, S.G.4
Robertson, D.L.5
-
44
-
-
34250632677
-
The gene balance hypothesis: From classical genetics to modern genomics
-
Birchler JA, Veitia RA (2007) The gene balance hypothesis: From classical genetics to modern genomics. Plant Cell 19:395-402.
-
(2007)
Plant Cell
, vol.19
, pp. 395-402
-
-
Birchler, J.A.1
Veitia, R.A.2
-
45
-
-
20144374141
-
Gene complexity and gene duplicability
-
He X, Zhang J (2005) Gene complexity and gene duplicability. Curr Biol 15:1016-1021.
-
(2005)
Curr Biol
, vol.15
, pp. 1016-1021
-
-
He, X.1
Zhang, J.2
-
46
-
-
33847616949
-
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
-
Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R (2007) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 4:231-237.
-
(2007)
Nat Methods
, vol.4
, pp. 231-237
-
-
Bodenmiller, B.1
Mueller, L.N.2
Mueller, M.3
Domon, B.4
Aebersold, R.5
-
47
-
-
34248576306
-
NetPhosYeast: Prediction of protein phosphorylation sites in yeast
-
Ingrell CR, Miller ML, Jensen ON, Blom N (2007) NetPhosYeast: Prediction of protein phosphorylation sites in yeast. Bioinformatics 23:895-897.
-
(2007)
Bioinformatics
, vol.23
, pp. 895-897
-
-
Ingrell, C.R.1
Miller, M.L.2
Jensen, O.N.3
Blom, N.4
-
48
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
49
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A, et al. (1996) Life with 6000 genes. Science 274:546, 563-567.
-
(1996)
Science
, vol.274
, Issue.546
, pp. 563-567
-
-
Goffeau, A.1
-
50
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217.
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
|