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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
104527 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
213429 2004 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
33112
315730 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
416126 2004 MOLECULAR MICROBIOLOGY 53 (2): 381-389
Piskur J; Langkjaer RB
Yeast genome sequencing: the power of comparative genomics
69
512637 2004 SCIENCE 306 (5700): 1367-1370
Gao LZ; Innan H
Very low gene duplication rate in the yeast genome
612
614438 2004 TRENDS IN GENETICS 20 (11): 544-549
Lynch M; Katju V
The altered evolutionary trajectories of gene duplicates
618
713667 2005 GENETICS 169 (2): 1157-1164
He XL; Zhang JZ
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
613
824535 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
9113117 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
1013814 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1114921 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
12110231 2004 NATURE REVIEWS GENETICS 5 (10): 752-763
Van de Peer Y
Computational approaches to unveiling ancient genome duplications
39
13132113 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
1411452 2004 ANNUAL REVIEW OF GENETICS 38: 615-643
Taylor JS; Raes J
Duplication and divergence: The evolution of new genes and old ideas
212
1521028 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
24
1629986 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
17288102 2005 NUCLEIC ACIDS RESEARCH 33 (9): 2838-2851
Zhang ZH; Dietrich FS
Mapping of transcription start sites in Saccharomyces cerevisiae using 5 ' SAGE
22
1813215 2004 GENETICS 168 (1): 569-574
Veitia RA
Gene dosage balance in cellular pathways: Implications for dominance and gene duplicability
15
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
2013624 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
21113332 2004 NATURE REVIEWS GENETICS 5 (11): 826-837
Kitano H
Biological robustness
119
2223836 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
2333850 2005 CURRENT BIOLOGY 15 (11): 1016-1021
He XL; Zhang JZ
Gene complexity and gene duplicability
13
2423862 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
2526263 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
2625264 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
2735172 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
13
2842975 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
2923093 2005 NATURE GENETICS 37 (3): 295-299
Kafri R; Bar-Even A; Pilpel Y
Transcription control reprogramming in genetic backup circuits
18
3017197 2005 NATURE REVIEWS MICROBIOLOGY 3 (5): 421-429
Wendland J; Walther A
Ashbya gossypii: A model for fungal developmental biology
13
#LCRNCRNode / Date / Journal / AuthorLCSGCS
311241 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
321333 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
331584 2004 BIOESSAYS 26 (11): 1225-1235
Simillion C; Vandepoele K; Van de Peer Y
Recent developments in computational approaches for uncovering genomic homology
02
341555 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
351386 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
361597 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
371208 2004 CURRENT BIOLOGY 14 (10): R392-R394
Wolfe K
Evolutionary genomics: Yeasts accelerate beyond BLAST
013
382199 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
3914110 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
4012211 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
4111712 2004 FSTTCS 2004: FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE 3328: 1-15
Alekseyev MA; Pevzner PA
Genome halving problem revisited
00
4212213 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
4313516 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
4432217 2004 GENOME BIOLOGY 5 (12): Art. No. 250
Van de Peer Y
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
06
4519518 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
4615720 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
4712722 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
4811523 2004 MICROBIOLOGY-SGM 150: 1603-1606
Ussery DW; Hallin PF; Lagesen K; Wassenaar TM
Genome Update: tRNAs in sequenced microbial genomes
01
4916425 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
5016333 2004 NATURE REVIEWS MICROBIOLOGY 2 (7): 533-540
Verstrepen KJ; Reynolds TB; Fink GR
Origins of variation in the fungal cell surface
08
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51112434 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
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Liti G; Louis EJ
Yeast evolution and comparative genomics
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Kohn LM
Mechanisms of fungal speciation
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54114741 2005 BIOFIZIKA 50 (4): 752-766
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The apology of bioinformatics
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5521442 2005 BIOFUTUR (254): 29-33
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Fish, a successful genomic duplication
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5613543 2005 BIOINFORMATICS 21 (7): 869-879
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Theoretical and practical advances in genome halving
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5725444 2005 BIOLOGY OF THE CELL 97 (7): 487-500
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An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
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Hemiascomycetous yeasts at the forefront of comparative genomics
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