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Wed Mar 15 14:12:31 2006

Proof and evolutionary analysis of ancient genome
duplication in the yeast Saccharomyces cerevisiae

KELLIS M, BIRREN BW, LANDER ES
NATURE 428: 617-624 2004
and the citing papers

Nodes: 134, Authors: 705, Journals: 59, Outer References: 5204, Words: 591
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Collection span: 2004 - 2006
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
135259 2005 CURRENT OPINION IN PLANT BIOLOGY 8 (2): 135-141
Adams KL; Wendel JF
Polyploidy and genome evolution in plants
08
211712 2004 FSTTCS 2004: FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE 3328: 1-15
Alekseyev MA; Pevzner PA
Genome halving problem revisited
00
313814 2004 GENETICS 167 (3): 1109-1121
Andalis AA; Storchova Z; Styles C; Galitski T; Pellman D; et al.
Defects arising from whole-genome duplications in Saacharomyces cerevisiae
36
4126126 2005 VIRUS GENES 31 (1): 65-72
Arav-Boger R; Zong JC; Foster CB
Loss of linkage disequilibrium and accelerated protein divergence in duplicated cytomegalovirus chemokine genes
01
534046 2005 CELL CYCLE 4 (1): 125-130
Archambault V; Buchler NE; Wilmes GM; Jacobson MD; Cross FR
Two-faced Cyclins with eyes on the targets
02
616090 2005 MOLECULAR MICROBIOLOGY 57 (1): 291-305
Avendano A; Riego L; DeLuna A; Aranda C; Romero G; et al.
Swi/SNF-GCN5-dependent chromatin remodelling determines induced expression of GDH3, one of the paralogous genes responsible for ammonium assimilation and glutamate biosynthesis in Saccharomyces cerevisiae
01
7153132 2006 NATURE STRUCTURAL & MOLECULAR BIOLOGY 13 (2): 168-176
Aviv T; Lin Z; Ben-Ari G; Smibert CA; Sicheri F
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
00
813516 2004 GENOME BIOLOGY 5 (10): Art. No. R76
Baudot A; Jacq B; Brun C
A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network
02
91386 2004 BMC EVOLUTIONARY BIOLOGY 4: Art. No. 51
Berg J; Lassig M; Wagner A
Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications
06
1025264 2005 FEMS YEAST RESEARCH 5 (6-7): 545-558
Blank LM; Lehmbeck F; Sauer U
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts
14
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1114110 2004 FEBS LETTERS 569 (1-3): 173-177
Boumann HA; de Kruijff B; Heck AJR; de Kroon AIPM
The selective utilization of substrates in vivo by the phosphatidylethanolamine and phosphatidylcholine biosynthetic enzymes Ept1p and Cpt1p in yeast
03
12130260 2005 CYTOGENETIC AND GENOME RESEARCH 110 (1-4): 8-24
Brosius J
Echoes from the past - are we still in an RNP world?
03
1342975 2005 GENOME RESEARCH 15 (10): 1456-1461
Byrne KP; Wolfe KH
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
11
1414019 2004 GENOME RESEARCH 14 (8): 1530-1536
Castillo-Davis CI; Hartl DL; Achaz G
cis-Regulatory and protein evolution in orthologous and duplicate genes
18
15156107 2005 PLANT CELL 17 (4): 1033-1045
Chantret N; Salse J; Sabot F; Rahman S; Bellec A; et al.
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and aegilops)
03
16353133 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (8): 2730-2735
Chapman BA; Bowers JE; Feltus FA; Paterson AH
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
00
17120129 2006 MOLECULAR AND BIOCHEMICAL PARASITOLOGY 146 (1): 24-29
Clark CG; Ali IKM; Zaki M; Loftus BJ; Hall N
Unique organisation of tRNA genes in Entamoeba histolytica
00
183133125 2005 TRENDS IN GENETICS 21 (12): 673-682
Coghlan A; Eichler EE; Oliver SG; Paterson AH; Stein L
Chromosome evolution in eukaryotes: a multi-kingdom perspective
00
1914251 2005 CURRENT BIOLOGY 15 (16): 1439-1447
Connerly PL; Esaki M; Montegna EA; Strongin DE; Levi S; et al.
Sec16 is a determinant of transitional ER organization
00
2037177 2005 GENOME RESEARCH 15 (12): 1675-1682
Crollius HR; Weissenbach J
Fish genomics and biology
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2118366 2005 GENETICS 169 (1): 215-229
Davidson CJ; Tirouvanziam R; Herzenberg LA; Lipsick JS
Functional evolution of the vertebrate Myb gene family: B-Myb, but neither A-Myb nor C-Myb, complements drosophila Myb in hemocytes
03
22133122 2005 TRENDS IN GENETICS 21 (10): 548-551
Davis JC; Petrov DA
Do disparate mechanisms of duplication add similar genes to the genome?
00
23251111 2005 PLOS BIOLOGY 3 (10): 1700-1708
Dehal P; Boore JL
Two rounds of whole genome duplication in the ancestral vertebrate
00
24217447 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
00
2512722 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279 (45): 46606-46613
Delplanque J; Delpierre G; Opperdoes FR; Van Schaftingen E
Tissue distribution and evolution of fructosamine 3-kinase and fructosamine 3-kinase-related protein
02
26150114 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (40): 14338-14343
Drummond DA; Bloom JD; Adami C; Wilke CO; Arnold FH
Why highly expressed proteins evolve slowly
01
2713429 2004 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
33112
28125056 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
00
2929892 2005 NATURE 435 (7038): 43-57
Eichinger L; Pachebat JA; Glockner G; Rajandream MA; Sucgang R; et al.
The genome of the social amoeba Dictyostelium discoideum
032
3029986 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (4): 856-873
Fabre E; Muller H; Therizols P; Lafontaine I; Dujon B; et al.
Comparative genomics in hemiascomycete yeasts: Evolution of sex, silencing, and subtelomeres
25
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31433131 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (2): 245-253
Fares MA; Byrne KP; Wolfe KH
Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
00
3226061 2005 EUKARYOTIC CELL 4 (2): 356-364
Flores CL; Gancedo C
Yarrowia lipolytica mutants devoid of pyruvate carboxylase activity show an unusual growth phenotype
01
3323862 2005 EUKARYOTIC CELL 4 (2): 401-406
Fraser JA; Huang JC; Pukkila-Worley R; Alspaugh JA; Mitchell TG; et al.
Chromosomal translocation and segmental duplication in Cryptococcus neoformans
11
3417668 2005 GENETICS 170 (2): 555-568
Friesen H; Colwill K; Robertson K; Schub O; Andrews B
Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle trafficking
01
35166109 2005 PLANT MOLECULAR BIOLOGY 58 (2): 229-245
Gachon CMM; Langlois-Meurinne M; Henry Y; Saindrenan P
Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications
02
36311176 2005 GENOME RESEARCH 15 (12): 1620-1631
Galagan JE; Henn MR; Ma LJ; Cuomo CA; Birren B
Genomics of the fungal kingdom: Insights into eukaryotic biology
01
372199 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
3812637 2004 SCIENCE 306 (5700): 1367-1370
Gao LZ; Innan H
Very low gene duplication rate in the yeast genome
612
39112434 2004 PLOS BIOLOGY 2 (12): Art. No. e398
Gasch AP; Moses AM; Chiang DY; Fraser HB; Berardini M; et al.
Conservation and evolution of cis-regulatory systems in ascomycete fungi
012
40114741 2005 BIOFIZIKA 50 (4): 752-766
Gel'fand MS
The apology of bioinformatics
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
41143128 2006 JOURNAL OF CELL BIOLOGY 172 (3): 347-362
Gladfelter AS; Hungerbuehler AK; Philippsen P
Asynchronous nuclear division cycles in multinucleated cells
00
4221028 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
24
4319518 2004 GENOME RESEARCH 14 (8): 1474-1482
Grover CE; Kim HR; Wing RA; Paterson AH; Wendel JF
Incongruent patterns of local and global genome size evolution in cotton
03
44132113 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (3): 707-712
Gu X; Zhang ZQ; Huang W
Rapid evolution of expression and regulatory divergences after yeast gene duplication
38
4516425 2004 MOLECULAR BIOLOGY AND EVOLUTION 21 (12): 2232-2245
Guillet-Claude C; Isabel N; Pelgas B; Bousquet J
The evolutionary implications of knox-I gene duplications in conifers: Correlated evidence from phylogeny, gene mapping, and analysis of functional divergence
03
46231101 2005 NUCLEIC ACIDS RESEARCH 33: D364-D368
Guldener U; Munsterkotter M; Kastenmuller G; Strack N; van Helden J; et al.
CYGD: the comprehensive Yeast Genome Database
010
4715373 2005 GENOME RESEARCH 15 (8): 1153-1160
Hahn MW; De Bie T; Stajich JE; Nguyen C; Cristianini N
Estimating the tempo and mode of gene family evolution from comparative genomic data
00
4826263 2005 EUKARYOTIC CELL 4 (6): 1102-1115
Hall C; Brachat S; Dietrich FS
Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
12
4933850 2005 CURRENT BIOLOGY 15 (11): 1016-1021
He XL; Zhang JZ
Gene complexity and gene duplicability
13
5013667 2005 GENETICS 169 (2): 1157-1164
He XL; Zhang JZ
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
613
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51341130 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 144-151
He XL; Zhang JZ
Higher duplicability of less important genes in yeast genomes
00
5223391 2005 MOLECULAR MICROBIOLOGY 57 (3): 834-846
Herbig A; Bird AJ; Swierczek S; McCall K; Mooney M; et al.
Zap1 activation domain 1 and its role in controlling gene expression in response to cellular zinc status
00
53225100 2005 NUCLEIC ACIDS RESEARCH 33: D348-D352
Hermida L; Brachat S; Voegeli S; Philippsen P; Primig M
The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists
00
5424489 2005 MOLECULAR MICROBIOLOGY 56 (3): 696-707
Heyken WT; Repenning A; Kumme J; Schuller HJ
Constitutive expression of yeast phospholipid biosynthetic genes by variants of Ino2 activator defective for interaction with Opi1 repressor
01
5515720 2004 GENOME RESEARCH 14 (10B): 2010-2014
Hill DE; Brasch MA; del Campo AA; Doucette-Stamm L; Garrels JI; et al.
Academia-industry collaboration: An integral element for building "omic" resources
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5624535 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (39): 14144-14149
Hittinger CT; Rokas A; Carroll SB
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts
59
5723754 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
01
5812213 2004 GENE 340 (2): 283-290
Hon-Nami K; Ueno S; Endo H; Nishimura H; Igarashi T; et al.
A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene
00
5912582 2005 JOURNAL OF MOLECULAR EVOLUTION 61 (6): 758-764
Hughes AL; Friedman R
Gene duplication and the properties of biological networks
00
60312198 2005 NATURE REVIEWS MICROBIOLOGY 3 (10): 753-764
Idnurm A; Bahn YS; Nielsen K; Lin XR; Fraser JA; et al.
Deciphering the model pathogenic fungus Cryptococcus neoformans
04
#LCRNCRNode / Date / Journal / AuthorLCSGCS
61214118 2005 SCIENCE 309 (5736): 938-940
Ihmels J; Bergmann S; Gerami-Nejad M; Yanai I; McClellan M; et al.
Rewiring of the yeast transcriptional network through the evolution of motif usage
04
6215730 2004 NATURE 431 (7011): 946-957
Jaillon O; Aury JM; Brunet F; Petit JL; Stange-Thomann N; et al.
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
780
63244116 2005 RNA-A PUBLICATION OF THE RNA SOCIETY 11 (7): 1064-1072
Kachouri R; Stribinskis S; Zhu YG; Ramos KS; Westhof E; et al.
A surprisingly large RNase P RNA in Candida glabrata
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6423093 2005 NATURE GENETICS 37 (3): 295-299
Kafri R; Bar-Even A; Pilpel Y
Transcription control reprogramming in genetic backup circuits
18
651555 2004 BMC EVOLUTIONARY BIOLOGY 4: Art. No. 32
Karev GP; Wolf YI; Berezovskaya FS; Koonin EV
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models
02
6626257 2005 CURRENT OPINION IN MICROBIOLOGY 8 (4): 378-384
Kaur R; Domergue R; Zupancic ML; Cormack BP
A yeast by any other name: Candida glabrata and its interaction with the host
00
6704527 2004 NATURE 428 (6983): 617-624
Kellis M; Birren BW; Lander ES
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
133133
68113332 2004 NATURE REVIEWS GENETICS 5 (11): 826-837
Kitano H
Biological robustness
119
69311540 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
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7047374 2005 GENOME RESEARCH 15 (10): 1421-1430
Kuepfer L; Sauer U; Blank LM
Metabolic functions of duplicate genes in Saccharomyces cerevisiae
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
7114921 2004 GENOME RESEARCH 14 (10A): 1924-1931
Lai JS; Ma JX; Swigonova Z; Ramakrishna W; Linton E; et al.
Gene loss and movement in the maize genome
322
7224558 2005 CURRENT OPINION IN MICROBIOLOGY 8 (5): 572-578
Lawrence JG; Hendrickson H
Genome evolution in bacteria: order beneath chaos
00
7316145 2005 BMC GENETICS 6: Art. No. 8
Lesage G; Shapiro J; Specht CA; Sdicu AM; Menard P; et al.
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
01
74535124 2005 TRENDS IN GENETICS 21 (11): 602-607
Li WH; Yang J; Gu X
Expression divergence between duplicate genes
00
75812439 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
76150121 2005 TRENDS IN GENETICS 21 (1): 60-65
Lockton S; Gaut BS
Plant conserved non-coding sequences and paralogue evolution
06
7713979 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (14): 14097-14104
Loewen CJR; Levine TP
A highly conserved binding site in vesicle-associated membrane protein-associated protein (VAP) for the FFAT motif of lipid-binding proteins
04
78113117 2005 SCIENCE 307 (5713): 1321-1324
Loftus BJ; Fung E; Roncaglia P; Rowley D; Amedeo P; et al.
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
431
7914438 2004 TRENDS IN GENETICS 20 (11): 544-549
Lynch M; Katju V
The altered evolutionary trajectories of gene duplicates
618
8015083 2005 MOLECULAR AND CELLULAR BIOLOGY 25 (14): 5920-5932
Lynch PJ; Fraser HB; Sevastopoulos E; Rine J; Rusche LN
Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae
02
#LCRNCRNode / Date / Journal / AuthorLCSGCS
81281103 2005 NUCLEIC ACIDS RESEARCH 33 (14): 4626-4638
Makarova KS; Wolf YI; Mekhedov SL; Mirkin BG; Koonin EV
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
01
82133115 2005 PROTEOMICS 5 (1): 67-75
Matis M; Zakelj-Mavric M; Peter-Katalinic J
Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus
02
83284112 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102: 6630-6635
Medina M
Genomes, phylogeny, and evolutionary systems biology
01
8423836 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (40): 14349-14354
Messing J; Bharti AK; Karlowski WM; Gundlach H; Kim HR; et al.
Sequence composition and genome organization of maize
126
85157108 2005 PLANT MOLECULAR BIOLOGY 57 (6): 907-924
Morimoto R; Kosugi T; Nakamura C; Takumi S
Intragenic diversity and functional conservation of the three homoeologous loci of the KN1-type homeobox gene Wknox1 in common wheat
00
8615480 2005 JOURNAL OF CELL BIOLOGY 170 (2): 225-235
Niepel M; Strambio-de-Castillia C; Fasolo J; Chait BT; Rout MP
The nuclear pore complex-associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly
03
871597 2004 CELL 119 (4): 491-502
Niessing D; Huttelmaier S; Zenklusen D; Singer RH; Burley SK
She2p is a novel RNA binding protein with a basic helical hairpin motif
04
88234104 2005 NUCLEIC ACIDS RESEARCH 33 (19): 6164-6171
Notebaart RA; Huynen MA; Teusink B; Siezen RJ; Snel B
Correlation between sequence conservation and the genomic context after gene duplication
01
89220120 2005 TRENDS IN GENETICS 21 (1): 1-3
Ochman H; Daubin V; Lerat E
A bunch of fun-guys: the whole-genome view of yeast evolution
02
90146134 2006 TRENDS IN GENETICS 22 (1): 56-63
Ooi SL; Pan XW; Peyser BD; Ye P; Meluh PB; et al.
Global synthetic-lethality analysis and yeast functional profiling
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
912699 2005 NATURE REVIEWS MICROBIOLOGY 3 (11): 832-833
Pain A
Genome watch - Fungi behaving badly
00
9213096 2005 NATURE GENETICS 37 (12): 1372-1375
Pal C; Papp B; Lercher MJ
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
00
93382123 2005 TRENDS IN GENETICS 21 (10): 559-567
Panopoulou G; Poustka AJ
Timing and mechanism of ancient vertebrate genome duplications - the adventure of a hypothesis
00
9413588 2005 MOLECULAR GENETICS AND GENOMICS 274 (6): 579-588
Park JY; Koo DH; Hong CP; Lee SJ; Jeon JW; et al.
Physical mapping and microsynteny of Brassica rapa ssp pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5
00
9535172 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
13
9625444 2005 BIOLOGY OF THE CELL 97 (7): 487-500
Pettersson N; Filipsson C; Becit E; Brive L; Hohmann S
Aquaporins in yeasts and filamentous fungi
00
9716126 2004 MOLECULAR MICROBIOLOGY 53 (2): 381-389
Piskur J; Langkjaer RB
Yeast genome sequencing: the power of comparative genomics
69
9821849 2005 CURRENT BIOLOGY 15 (2): R52-R53
Presgraves DC
Evolutionary genomics: New genes for new jobs
01
99111584 2005 MOLECULAR AND CELLULAR BIOLOGY 25 (16): 7226-7238
Putnam CD; Pennaneach V; Kolodner RD
Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype
01
10012069 2005 GENETICS 170 (4): 1501-1513
Pyne S; Skiena S; Futcher B
Copy correction and concerted evolution in the conservation of yeast genes
00

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