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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 APR 8 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
21208 2004 MAY 25 CURRENT BIOLOGY 14 (10): R392-R394
Wolfe K
Evolutionary genomics: Yeasts accelerate beyond BLAST
013
311523 2004 JUN [15] MICROBIOLOGY-SGM 150: 1603-1606
Ussery DW; Hallin PF; Lagesen K; Wassenaar TM
Genome Update: tRNAs in sequenced microbial genomes
01
41241 2004 [JUN 30] 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
511452 2004 [JUN 30] ANNUAL REVIEW OF GENETICS 38: 615-643
Taylor JS; Raes J
Duplication and divergence: The evolution of new genes and old ideas
212
611712 2004 [JUN 30] FSTTCS 2004: FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE 3328: 1-15
Alekseyev MA; Pevzner PA
Genome halving problem revisited
00
713516 2004 [JUN 30] 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
832217 2004 [JUN 30] GENOME BIOLOGY 5 (12): Art. No. 250
Van de Peer Y
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
06
921028 2004 JUL 1 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
24
1013429 2004 JUL 1 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
33112
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1114110 2004 JUL 2 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
1213814 2004 JUL [15] 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
1316126 2004 JUL [15] MOLECULAR MICROBIOLOGY 53 (2): 381-389
Piskur J; Langkjaer RB
Yeast genome sequencing: the power of comparative genomics
69
1416333 2004 JUL [15] NATURE REVIEWS MICROBIOLOGY 2 (7): 533-540
Verstrepen KJ; Reynolds TB; Fink GR
Origins of variation in the fungal cell surface
08
1519518 2004 AUG [15] 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
1614019 2004 AUG [15] GENOME RESEARCH 14 (8): 1530-1536
Castillo-Davis CI; Hartl DL; Achaz G
cis-Regulatory and protein evolution in orthologous and duplicate genes
18
171555 2004 SEP 9 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
1813215 2004 SEP [15] GENETICS 168 (1): 569-574
Veitia RA
Gene dosage balance in cellular pathways: Implications for dominance and gene duplicability
15
191333 2004 SEP 21 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
2024535 2004 SEP 28 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2112211 2004 OCT 1 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
2223836 2004 OCT 5 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
2312213 2004 OCT 13 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
242199 2004 OCT [15] ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
2515720 2004 OCT [15] 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
2614921 2004 OCT [15] 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
27110231 2004 OCT [15] NATURE REVIEWS GENETICS 5 (10): 752-763
Van de Peer Y
Computational approaches to unveiling ancient genome duplications
39
2815730 2004 OCT 21 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
2912722 2004 NOV 5 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
301597 2004 NOV 12 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
311584 2004 NOV [15] BIOESSAYS 26 (11): 1225-1235
Simillion C; Vandepoele K; Van de Peer Y
Recent developments in computational approaches for uncovering genomic homology
02
3213624 2004 NOV [15] 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
33113332 2004 NOV [15] NATURE REVIEWS GENETICS 5 (11): 826-837
Kitano H
Biological robustness
119
3414438 2004 NOV [15] TRENDS IN GENETICS 20 (11): 544-549
Lynch M; Katju V
The altered evolutionary trajectories of gene duplicates
618
3512637 2004 NOV 19 SCIENCE 306 (5700): 1367-1370
Gao LZ; Innan H
Very low gene duplication rate in the yeast genome
612
361386 2004 NOV 27 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
3716425 2004 DEC [15] 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
38112434 2004 DEC [15] 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
39225100 2005 JAN 1 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
40231101 2005 JAN 1 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4134046 2005 JAN [15] 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
4218366 2005 JAN [15] 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
43240106 2005 JAN [15] PLANT CELL 17 (1): 4-11
Veitia RA
Paralogs in polyploids: One for all and all for one?
05
44133115 2005 JAN [15] 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
45220120 2005 JAN [15] 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
46150121 2005 JAN [15] TRENDS IN GENETICS 21 (1): 60-65
Lockton S; Gaut BS
Plant conserved non-coding sequences and paralogue evolution
06
47132113 2005 JAN 18 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
4821849 2005 JAN 26 CURRENT BIOLOGY 15 (2): R52-R53
Presgraves DC
Evolutionary genomics: New genes for new jobs
01
4926061 2005 FEB [15] EUKARYOTIC CELL 4 (2): 356-364
Flores CL; Gancedo C
Yarrowia lipolytica mutants devoid of pyruvate carboxylase activity show an unusual growth phenotype
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Fraser JA; Huang JC; Pukkila-Worley R; Alspaugh JA; Mitchell TG; et al.
Chromosomal translocation and segmental duplication in Cryptococcus neoformans
11
#LCRNCRNode / Date / Journal / AuthorLCSGCS
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He XL; Zhang JZ
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
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Origins of Chagas disease: Didelphis species are natural hosts of Trypanosoma cruzi I and armadillos hosts of Trypanosoma cruzi II, including hybrids
04
5316145 2005 FEB 16 BMC GENETICS 6: Art. No. 8
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The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
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Divergence pattern of duplicate genes in protein-protein interactions follows the power law
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Theoretical and practical advances in genome halving
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5813979 2005 APR 8 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (14): 14097-14104
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A highly conserved binding site in vesicle-associated membrane protein-associated protein (VAP) for the FFAT motif of lipid-binding proteins
04
5921442 2005 APR [15] BIOFUTUR (254): 29-33
Robinson-Rechavi M
Fish, a successful genomic duplication
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Siggia ED
Computational methods for transcriptional regulation
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
6135259 2005 APR [15] CURRENT OPINION IN PLANT BIOLOGY 8 (2): 135-141
Adams KL; Wendel JF
Polyploidy and genome evolution in plants
08
6225264 2005 APR [15] FEMS YEAST RESEARCH 5 (6-7): 545-558
Blank LM; Lehmbeck F; Sauer U
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts
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Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
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Comparative genomics in hemiascomycete yeasts: Evolution of sex, silencing, and subtelomeres
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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
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Gene complexity and gene duplicability
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The Yeast Systems Biology Network: mating communities
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Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
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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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Mechanisms of fungal speciation
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