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Wed Mar 15 14:12:30 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
11241 2004 ALGORITHMS IN BIOINFORMATICS, PROCEEDINGS 3240: 326-337
Sundararajan M; Brudno M; Small K; Sidow A; Batzoglou S
Chaining algorithms for alignment of draft sequence
00
211452 2004 ANNUAL REVIEW OF GENETICS 38: 615-643
Taylor JS; Raes J
Duplication and divergence: The evolution of new genes and old ideas
212
3812439 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
4311540 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
00
51333 2004 BIOCHEMISTRY 43 (37): 11782-11789
Wang HH; Cronan JE
Only one of the two annotated Lactococcus lactis fabG genes encodes a functional beta-ketoacyl-acyl carrier protein reductase
01
61584 2004 BIOESSAYS 26 (11): 1225-1235
Simillion C; Vandepoele K; Van de Peer Y
Recent developments in computational approaches for uncovering genomic homology
02
7114741 2005 BIOFIZIKA 50 (4): 752-766
Gel'fand MS
The apology of bioinformatics
00
821442 2005 BIOFUTUR (254): 29-33
Robinson-Rechavi M
Fish, a successful genomic duplication
00
913543 2005 BIOINFORMATICS 21 (7): 869-879
Yin P; Hartemink AJ
Theoretical and practical advances in genome halving
00
1025444 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
111117127 2006 BIOTECHNOLOGY ADVANCES 24 (2): 210-223
Rubio-Texeira M
Endless versatility in the biotechnological applications of Kluyveromyces LAC genes
00
121555 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
131386 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
1416145 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
151597 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
1634046 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
17217447 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
00
1827648 2005 COMPLEXITY 11 (2): 14-27
Zuckerkandl E
"Natural restoration" can generate biological complexity
00
191208 2004 CURRENT BIOLOGY 14 (10): R392-R394
Wolfe K
Evolutionary genomics: Yeasts accelerate beyond BLAST
013
2021849 2005 CURRENT BIOLOGY 15 (2): R52-R53
Presgraves DC
Evolutionary genomics: New genes for new jobs
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2133850 2005 CURRENT BIOLOGY 15 (11): 1016-1021
He XL; Zhang JZ
Gene complexity and gene duplicability
13
2214251 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
2335152 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
2422153 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
2523754 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
01
2617455 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (2): 214-221
Siggia ED
Computational methods for transcriptional regulation
02
27125056 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
00
2826257 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
2924558 2005 CURRENT OPINION IN MICROBIOLOGY 8 (5): 572-578
Lawrence JG; Hendrickson H
Genome evolution in bacteria: order beneath chaos
00
3035259 2005 CURRENT OPINION IN PLANT BIOLOGY 8 (2): 135-141
Adams KL; Wendel JF
Polyploidy and genome evolution in plants
08
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31130260 2005 CYTOGENETIC AND GENOME RESEARCH 110 (1-4): 8-24
Brosius J
Echoes from the past - are we still in an RNP world?
03
322199 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
3326061 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
3423862 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
3526263 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
3614110 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
3712211 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
3825264 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
39113465 2005 FEMS YEAST RESEARCH 5 (12): 1115-1128
Rubio-Texeira M
A comparative analysis of the GAL genetic switch between not-so-distant cousins: Saccharomyces cerevisiae versus Kluyveromyces lactis
01
4011712 2004 FSTTCS 2004: FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE 3328: 1-15
Alekseyev MA; Pevzner PA
Genome halving problem revisited
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4112213 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
4213814 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
4313215 2004 GENETICS 168 (1): 569-574
Veitia RA
Gene dosage balance in cellular pathways: Implications for dominance and gene duplicability
15
4418366 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
4513667 2005 GENETICS 169 (2): 1157-1164
He XL; Zhang JZ
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
613
4617668 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
4712069 2005 GENETICS 170 (4): 1501-1513
Pyne S; Skiena S; Futcher B
Copy correction and concerted evolution in the conservation of yeast genes
00
4822770 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
4963771 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
5013516 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5132217 2004 GENOME BIOLOGY 5 (12): Art. No. 250
Van de Peer Y
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
06
5219518 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
5314019 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
5415720 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
00
5514921 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
5635172 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
13
5715373 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
5847374 2005 GENOME RESEARCH 15 (10): 1421-1430
Kuepfer L; Sauer U; Blank LM
Metabolic functions of duplicate genes in Saccharomyces cerevisiae
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5942975 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
60311176 2005 GENOME RESEARCH 15 (12): 1620-1631
Galagan JE; Henn MR; Ma LJ; Cuomo CA; Birren B
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Fish genomics and biology
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6312722 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279 (45): 46606-46613
Delplanque J; Delpierre G; Opperdoes FR; Van Schaftingen E
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6413979 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (14): 14097-14104
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6515480 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
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66143128 2006 JOURNAL OF CELL BIOLOGY 172 (3): 347-362
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6726281 2005 JOURNAL OF MOLECULAR EVOLUTION 60 (5): 665-676
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6812582 2005 JOURNAL OF MOLECULAR EVOLUTION 61 (6): 758-764
Hughes AL; Friedman R
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6911523 2004 MICROBIOLOGY-SGM 150: 1603-1606
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Genome Update: tRNAs in sequenced microbial genomes
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Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae
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Putnam CD; Pennaneach V; Kolodner RD
Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype
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Wagner GP; Fried C; Prohaska SJ; Stadler PF
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Higher duplicability of less important genes in yeast genomes
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Fares MA; Byrne KP; Wolfe KH
Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
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8116126 2004 MOLECULAR MICROBIOLOGY 53 (2): 381-389
Piskur J; Langkjaer RB
Yeast genome sequencing: the power of comparative genomics
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8224489 2005 MOLECULAR MICROBIOLOGY 56 (3): 696-707
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Zap1 activation domain 1 and its role in controlling gene expression in response to cellular zinc status
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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
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The genome of the social amoeba Dictyostelium discoideum
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Transcription control reprogramming in genetic backup circuits
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Thomson JM; Gaucher EA; Burgan MF; De Kee DW; Li T; et al.
Resurrecting ancestral alcohol dehydrogenases from yeast
02
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Wong S; Wolfe KH
Birth of a metabolic gene cluster in yeast by adaptive gene relocation
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9313096 2005 NATURE GENETICS 37 (12): 1372-1375
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Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
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94110231 2004 NATURE REVIEWS GENETICS 5 (10): 752-763
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Computational approaches to unveiling ancient genome duplications
39
95113332 2004 NATURE REVIEWS GENETICS 5 (11): 826-837
Kitano H
Biological robustness
119
9616333 2004 NATURE REVIEWS MICROBIOLOGY 2 (7): 533-540
Verstrepen KJ; Reynolds TB; Fink GR
Origins of variation in the fungal cell surface
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9717197 2005 NATURE REVIEWS MICROBIOLOGY 3 (5): 421-429
Wendland J; Walther A
Ashbya gossypii: A model for fungal developmental biology
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Deciphering the model pathogenic fungus Cryptococcus neoformans
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992699 2005 NATURE REVIEWS MICROBIOLOGY 3 (11): 832-833
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Genome watch - Fungi behaving badly
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Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
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