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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
31333 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
41584 2004 BIOESSAYS 26 (11): 1225-1235
Simillion C; Vandepoele K; Van de Peer Y
Recent developments in computational approaches for uncovering genomic homology
02
51555 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
61386 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
71597 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
81208 2004 CURRENT BIOLOGY 14 (10): R392-R394
Wolfe K
Evolutionary genomics: Yeasts accelerate beyond BLAST
013
92199 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
1014110 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1112211 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
1211712 2004 FSTTCS 2004: FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE 3328: 1-15
Alekseyev MA; Pevzner PA
Genome halving problem revisited
00
1312213 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
1413814 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
1513215 2004 GENETICS 168 (1): 569-574
Veitia RA
Gene dosage balance in cellular pathways: Implications for dominance and gene duplicability
15
1613516 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
1732217 2004 GENOME BIOLOGY 5 (12): Art. No. 250
Van de Peer Y
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
06
1819518 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
1914019 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
2015720 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2114921 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
2212722 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
2311523 2004 MICROBIOLOGY-SGM 150: 1603-1606
Ussery DW; Hallin PF; Lagesen K; Wassenaar TM
Genome Update: tRNAs in sequenced microbial genomes
01
2413624 2004 MOLECULAR BIOLOGY AND EVOLUTION 21 (11): 2116-2121
Wagner GP; Fried C; Prohaska SJ; Stadler PF
Divergence of conserved non-coding sequences: rate estimates and relative rate tests
15
2516425 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
2616126 2004 MOLECULAR MICROBIOLOGY 53 (2): 381-389
Piskur J; Langkjaer RB
Yeast genome sequencing: the power of comparative genomics
69
2704527 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
2821028 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
24
2913429 2004 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
33112
3015730 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31110231 2004 NATURE REVIEWS GENETICS 5 (10): 752-763
Van de Peer Y
Computational approaches to unveiling ancient genome duplications
39
32113332 2004 NATURE REVIEWS GENETICS 5 (11): 826-837
Kitano H
Biological robustness
119
3316333 2004 NATURE REVIEWS MICROBIOLOGY 2 (7): 533-540
Verstrepen KJ; Reynolds TB; Fink GR
Origins of variation in the fungal cell surface
08
34112434 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
3524535 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
3623836 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
3712637 2004 SCIENCE 306 (5700): 1367-1370
Gao LZ; Innan H
Very low gene duplication rate in the yeast genome
612
3814438 2004 TRENDS IN GENETICS 20 (11): 544-549
Lynch M; Katju V
The altered evolutionary trajectories of gene duplicates
618
39812439 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
40311540 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
41114741 2005 BIOFIZIKA 50 (4): 752-766
Gel'fand MS
The apology of bioinformatics
00
4221442 2005 BIOFUTUR (254): 29-33
Robinson-Rechavi M
Fish, a successful genomic duplication
00
4313543 2005 BIOINFORMATICS 21 (7): 869-879
Yin P; Hartemink AJ
Theoretical and practical advances in genome halving
00
4425444 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
4516145 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
4634046 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
47217447 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
00
4827648 2005 COMPLEXITY 11 (2): 14-27
Zuckerkandl E
"Natural restoration" can generate biological complexity
00
4921849 2005 CURRENT BIOLOGY 15 (2): R52-R53
Presgraves DC
Evolutionary genomics: New genes for new jobs
01
5033850 2005 CURRENT BIOLOGY 15 (11): 1016-1021
He XL; Zhang JZ
Gene complexity and gene duplicability
13
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5114251 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
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5235152 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
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5322153 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
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5423754 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
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5517455 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (2): 214-221
Siggia ED
Computational methods for transcriptional regulation
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56125056 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
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5726257 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
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5824558 2005 CURRENT OPINION IN MICROBIOLOGY 8 (5): 572-578
Lawrence JG; Hendrickson H
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5935259 2005 CURRENT OPINION IN PLANT BIOLOGY 8 (2): 135-141
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Polyploidy and genome evolution in plants
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60130260 2005 CYTOGENETIC AND GENOME RESEARCH 110 (1-4): 8-24
Brosius J
Echoes from the past - are we still in an RNP world?
03
#LCRNCRNode / Date / Journal / AuthorLCSGCS
6126061 2005 EUKARYOTIC CELL 4 (2): 356-364
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6326263 2005 EUKARYOTIC CELL 4 (6): 1102-1115
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6425264 2005 FEMS YEAST RESEARCH 5 (6-7): 545-558
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Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle trafficking
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Novel specificities emerge by stepwise duplication of functional modules
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Estimating the tempo and mode of gene family evolution from comparative genomic data
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Metabolic functions of duplicate genes in Saccharomyces cerevisiae
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The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
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Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype
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Divergence pattern of duplicate genes in protein-protein interactions follows the power law
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The genome of the social amoeba Dictyostelium discoideum
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Resurrecting ancestral alcohol dehydrogenases from yeast
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Birth of a metabolic gene cluster in yeast by adaptive gene relocation
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Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
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Ashbya gossypii: A model for fungal developmental biology
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Deciphering the model pathogenic fungus Cryptococcus neoformans
04
992699 2005 NATURE REVIEWS MICROBIOLOGY 3 (11): 832-833
Pain A
Genome watch - Fungi behaving badly
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100225100 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
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