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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
1125056 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
00
2812439 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
363771 2005 GENETICS 171 (4): 1455-1461
van Hoof A
Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication
00
4535124 2005 TRENDS IN GENETICS 21 (11): 602-607
Li WH; Yang J; Gu X
Expression divergence between duplicate genes
00
547374 2005 GENOME RESEARCH 15 (10): 1421-1430
Kuepfer L; Sauer U; Blank LM
Metabolic functions of duplicate genes in Saccharomyces cerevisiae
00
642975 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
7433131 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
832217 2004 GENOME BIOLOGY 5 (12): Art. No. 250
Van de Peer Y
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
06
9311540 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
00
1034046 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1133850 2005 CURRENT BIOLOGY 15 (11): 1016-1021
He XL; Zhang JZ
Gene complexity and gene duplicability
13
1235152 2005 CURRENT GENETICS 48 (2): 77-87
Zhang ZH; Dietrich FS
Identification and characterization of upstream open reading frames (uORF) in the 5 ' untranslated regions (UTR) of genes in Saccharomyces cerevisiae
00
1335259 2005 CURRENT OPINION IN PLANT BIOLOGY 8 (2): 135-141
Adams KL; Wendel JF
Polyploidy and genome evolution in plants
08
1435172 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
13
15311176 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
1637177 2005 GENOME RESEARCH 15 (12): 1675-1682
Crollius HR; Weissenbach J
Fish genomics and biology
00
1735987 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (5): 1337-1344
Rokas A; Carroll SB
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
04
1833095 2005 NATURE GENETICS 37 (7): 777-782
Wong S; Wolfe KH
Birth of a metabolic gene cluster in yeast by adaptive gene relocation
02
19312198 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
20359110 2005 PLANT MOLECULAR BIOLOGY 59 (1): 63-74
Wang HB; Yu LJ; Lai F; Liu LS; Wang JF
Molecular evidence for asymmetric evolution of sister duplicated blocks after cereal polyploidy
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
21382123 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
223133125 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
23341130 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 144-151
He XL; Zhang JZ
Higher duplicability of less important genes in yeast genomes
00
24353133 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
252199 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
2621028 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
24
2724535 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
2823836 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
2921442 2005 BIOFUTUR (254): 29-33
Robinson-Rechavi M
Fish, a successful genomic duplication
00
3025444 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31217447 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
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3227648 2005 COMPLEXITY 11 (2): 14-27
Zuckerkandl E
"Natural restoration" can generate biological complexity
00
3321849 2005 CURRENT BIOLOGY 15 (2): R52-R53
Presgraves DC
Evolutionary genomics: New genes for new jobs
01
3422153 2005 CURRENT GENETICS 48 (4): 247-255
Walther A; Wendland J
Initial molecular characterization of a novel Rho-type GTPase RhoH in the filamentous ascomycete Ashbya gossypii
00
3523754 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
01
3626257 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
3724558 2005 CURRENT OPINION IN MICROBIOLOGY 8 (5): 572-578
Lawrence JG; Hendrickson H
Genome evolution in bacteria: order beneath chaos
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3826061 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
3923862 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
4026263 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4125264 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
4222770 2005 GENETICS 171 (1): 63-69
Sugino RP; Innan H
Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast
00
4326281 2005 JOURNAL OF MOLECULAR EVOLUTION 60 (5): 665-676
Wagner GP; Takahashi K; Lynch V; Prohaska SJ; Fried C; et al.
Molecular evolution of duplicated ray finned fish HoxA clusters: Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences
01
4429986 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
4524489 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
4623391 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
4729892 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
4823093 2005 NATURE GENETICS 37 (3): 295-299
Kafri R; Bar-Even A; Pilpel Y
Transcription control reprogramming in genetic backup circuits
18
492699 2005 NATURE REVIEWS MICROBIOLOGY 3 (11): 832-833
Pain A
Genome watch - Fungi behaving badly
00
50225100 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51231101 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
52288102 2005 NUCLEIC ACIDS RESEARCH 33 (9): 2838-2851
Zhang ZH; Dietrich FS
Mapping of transcription start sites in Saccharomyces cerevisiae using 5 ' SAGE
22
53281103 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
54234104 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
55240106 2005 PLANT CELL 17 (1): 4-11
Veitia RA
Paralogs in polyploids: One for all and all for one?
05
56251111 2005 PLOS BIOLOGY 3 (10): 1700-1708
Dehal P; Boore JL
Two rounds of whole genome duplication in the ancestral vertebrate
00
57284112 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
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A surprisingly large RNase P RNA in Candida glabrata
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60220120 2005 TRENDS IN GENETICS 21 (1): 1-3
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A bunch of fun-guys: the whole-genome view of yeast evolution
02
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611241 2004 ALGORITHMS IN BIOINFORMATICS, PROCEEDINGS 3240: 326-337
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Taylor JS; Raes J
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641584 2004 BIOESSAYS 26 (11): 1225-1235
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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
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661386 2004 BMC EVOLUTIONARY BIOLOGY 4: Art. No. 51
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671597 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
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Wolfe K
Evolutionary genomics: Yeasts accelerate beyond BLAST
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6914110 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
7012211 2004 FEMS MICROBIOLOGY LETTERS 239 (1): 95-101
Sims AH; Dunn-Coleman NS; Robson GD; Oliver SG
Glutamic protease distribution is limited to filamentous fungi
02
#LCRNCRNode / Date / Journal / AuthorLCSGCS
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Alekseyev MA; Pevzner PA
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Veitia RA
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Incongruent patterns of local and global genome size evolution in cotton
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Castillo-Davis CI; Hartl DL; Achaz G
cis-Regulatory and protein evolution in orthologous and duplicate genes
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The evolutionary implications of knox-I gene duplications in conifers: Correlated evidence from phylogeny, gene mapping, and analysis of functional divergence
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Piskur J; Langkjaer RB
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Genome evolution in yeasts
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Computational approaches to unveiling ancient genome duplications
39
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Biological robustness
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Origins of variation in the fungal cell surface
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Conservation and evolution of cis-regulatory systems in ascomycete fungi
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9112637 2004 SCIENCE 306 (5700): 1367-1370
Gao LZ; Innan H
Very low gene duplication rate in the yeast genome
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Lynch M; Katju V
The altered evolutionary trajectories of gene duplicates
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The apology of bioinformatics
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Theoretical and practical advances in genome halving
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An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
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Sec16 is a determinant of transitional ER organization
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Computational methods for transcriptional regulation
02
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Echoes from the past - are we still in an RNP world?
03
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Rubio-Texeira M
A comparative analysis of the GAL genetic switch between not-so-distant cousins: Saccharomyces cerevisiae versus Kluyveromyces lactis
01
10018366 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

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