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Wed Mar 15 14:08:43 2006

Genome evolution in yeasts
DUJON B, SHERMAN D, FISCHER G, et al.
NATURE 430: 35-44 2004
and the citing papers

Nodes: 112, Authors: 620, Journals: 59, Outer References: 5059, Words: 574
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Collection span: 2004 - 2006
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
1122111 2005 ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 44 (42): 6828-6846
Bode HB; Muller R
The impact of bacterial genomics on natural product research
02
2312412 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
3111513 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
00
413214 2005 APPLIED AND ENVIRONMENTAL MICROBIOLOGY 71 (6): 2862-2869
Colussi PA; Specht CA; Taron CH
Characterization of a nucleus-encoded chitinase from the yeast Kluyveromyces lactis
01
512915 2005 APPLIED AND ENVIRONMENTAL MICROBIOLOGY 71 (12): 8249-8256
Jin YS; Alper H; Yang YT; Stephanopoulos G
Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach
00
6130102 2006 APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 69 (5): 564-572
Salani F; Bianchi MM
Production of glucoamylase in pyruvate decarboxylase deletion mutants of the yeast Kluyveromyces lactis
00
7110616 2005 BIOCHEMISTRY 44 (25): 8959-8975
Eilers M; Hornak V; Smith SO; Konopka JB
Comparison of Class A and D G protein-coupled receptors: Common features in structure and activation
06
812517 2005 BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION 1727 (1): 65-74
Trueb B; Neuhauss SCF; Baertschi S; Rieckmann T; Schild C; et al.
Fish possess multiple copies of fgfrll, the gene for a novel FGF receptor
00
91291 2004 BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 1742 (1-3): 133-140
Morgan RO; Martin-Almedina S; Iglesias JM; Gonzalez-Florez MI; Fernandez MP
Evolutionary perspective on annexin calcium-binding domains
01
1015418 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
111502 2004 BIOSCIENCE 54 (11): 991-1001
Delwiche CF
The genomic palimpsest: Genomics in evolution and ecology
01
121919 2005 BIOTECHNOLOGY LETTERS 27 (12): 859-864
Smit MS; Mokgoro MM; Setati E; Nicaud JM
alpha,omega-Dicarboxylic acid accumulation by acyl-CoA oxidase deficient mutants of Yarrowia lipolytica
00
1314420 2005 BMC BIOINFORMATICS 6: Art. No. 22
Novatchkova M; Bachmair A; Eisenhaber B; Eisenhaber F
Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family
00
1415921 2005 CANADIAN JOURNAL OF BOTANY-REVUE CANADIENNE DE BOTANIQUE 83 (8): 1001-1014
Reszka E; Chung KR; Tekauz A; Malkus A; Arseniuk E; et al.
Presence of beta-glucosidase (bgl1) gene in Phaeosphaeria nodorum and Phaeosphaeria avenaria f.sp triticea
01
1514022 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
16111523 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (11): 1182-1197
Andersson JO
Lateral gene transfer in eukaryotes
00
17117424 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
00
18312125 2005 CHROMOSOME RESEARCH 13 (5): 535-548
Teixeira MT; Gilson E
Telomere maintenance, function and evolution: the yeast paradigm
00
1914326 2005 CROP SCIENCE 45 (5): 1809-1816
Caetano-Anolles G
Evolution of genome size in the grasses
00
2014927 2005 CURRENT BIOLOGY 15 (3): 231-237
Joseph I; Jia DW; Lustig AJ
Ndj1p-dependent epigenetic resetting of telornere size in yeast meiosis
03
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2112328 2005 CURRENT GENETICS 47 (3): 172-181
Sybirna K; Guiard B; Li YF; Bao WG; Bolotin-Fukuhara M; et al.
A new Hansenula polymorpha HAP4 homologue which contains only the N-terminal conserved domain of the protein is fully functional in Saccharomyces cerevisiae
03
2225129 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
2312330 2005 CURRENT GENETICS 48 (2): 117-125
Edlind TD; Henry KW; Vermitsky JP; Edlind MP; Raj S; et al.
Promoter-dependent disruption of genes: simple, rapid, and specific PCR-based method with application to three different yeast
00
24113931 2005 CURRENT GENOMICS 6 (3): 157-187
de Vries RP; van Grieken C; vanKuyk PA; Wosten HAB
The value of genome sequences in the rapid identification of novel genes encoding specific plant cell wall degrading enzymes
00
2513732 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
01
2685033 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
00
271634 2005 CURRENT OPINION IN MICROBIOLOGY 8 (4): 359-361
Bussey H
Host-microbe interactions: fungi - Editorial overview
00
2846235 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
2915136 2005 CURRENT OPINION IN MICROBIOLOGY 8 (4): 385-392
Tekaia F; Latge JP
Aspergillus fumigatus: saprophyte or pathogen?
02
301193 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
3116037 2005 EUKARYOTIC CELL 4 (2): 356-364
Flores CL; Gancedo C
Yarrowia lipolytica mutants devoid of pyruvate carboxylase activity show an unusual growth phenotype
11
3213838 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
01
3314339 2005 EUKARYOTIC CELL 4 (3): 615-624
Neuveglise C; Chalvet F; Wincker P; Gaillardin C; Casaregola S
Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings
00
3416240 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
3516741 2005 EUKARYOTIC CELL 4 (8): 1364-1374
Krysan DJ; Ting EL; Abeijon C; Kroos L; Fuller RS
Yapsins are a family of aspartyl proteases required for cell wall integrity in Saccharomyces cerevisiae
00
36140103 2006 EUKARYOTIC CELL 5 (2): 262-271
Aggarwal M; Mondal AK
Role of N-terminal hydrophobic region in modulating the subcellular localization and enzyme activity of the bisphosphate nucleotidase from Debaryomyces hansenii
00
3714442 2005 EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 34 (5): 413-422
Zhou XL; Loukin SH; Coria R; Kung C; Saimi Y
Heterologously expressed fungal transient receptor potential channels retain mechanosensitivity in vitro and osmotic response in vivo
01
3813943 2005 FEBS LETTERS 579 (30): 6781-6785
Abdrakhmanova A; Dobrynin K; Zwicker K; Kerscher S; Brandt U
Functional sulfurtransferase is associated with mitochondrial complex I from Yarrowia lipolytica, but is not required for assembly of its iron-sulfur clusters
00
39111744 2005 FEMS YEAST RESEARCH 5 (6-7): 527-543
Fickers P; Benetti PH; Wache Y; Marty A; Mauersberger S; et al.
Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications
03
4015245 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4113446 2005 FEMS YEAST RESEARCH 5 (6-7): 595-604
Suleau A; Jacques N; Reitz-Ausseur J; Casaregola S
Intraspecific gene expression variability in the yeast Kluyveromyces lactis revealed by micro-array analysis
00
4216947 2005 FEMS YEAST RESEARCH 5 (8): 693-701
Prista C; Loureiro-Dias MC; Montiel V; Garcia R; Ramos J
Mechanisms underlying the halotolerant way of Debaryomyces hansenii
01
43115348 2005 FEMS YEAST RESEARCH 5 (11): 1079-1096
Gellissen G; Kunze G; Gaillardin C; Cregg JM; Berardi E; et al.
New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica - A comparison
00
4413249 2005 FUNGAL GENETICS AND BIOLOGY 42 (3): 264-274
Fickers P; Fudalej F; Le Dall MT; Casaregola S; Gaillardin C; et al.
Identification and characterisation of LIP7 and LIP8 genes encoding two extracellular triacylglycerol lipases in the yeast Yarrowia lipolytiea
01
4515550 2005 GENETICS 171 (1): 393-401
Tilburn J; Sanchez-Ferrero JC; Reoyo E; Arst HN; Penalva MA
Mutational analysis of the pH signal transduction component PalC of Aspergillus nidulans supports distant similarity to BRO1 domain family members
00
4611951 2005 GENOME BIOLOGY 6 (4): Art. No. R31
Liang H; Cavalcanti ARO; Landweber LF
Conservation of tandem stop codons in yeasts
01
4714852 2005 GENOME BIOLOGY 6 (4): Art. No. R35
Mazurie A; Bottani S; Vergassola M
An evolutionary and functional assessment of regulatory network motifs
02
4815153 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
23
4915254 2005 GENOME RESEARCH 15 (10): 1411-1420
Bekaert M; Richard H; Prum B; Rousset JP
Identification of programmed translational-1 frameshifting sites in the genome of Saccharomyces cerevisiae
00
5022955 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51111156 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
52121104 2006 INTERNATIONAL DAIRY JOURNAL 16 (3): 207-214
Becerra M; Gonzalez-Siso MI; Cerdan ME
A transcriptome analysis of Kluyveromyces lactic growing in cheese whey
00
5315257 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (7): 5169-5177
Novoseler M; Hershkovits G; Katcoff DJ
Functional domains of the yeast chromatin protein Sin1p/Spt2p can bind four-way junction and crossing DNA structures
01
5416858 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (34): 30638-30647
Kinclova-Zimmermannova O; Zavrel M; Sychrova H
Identification of conserved prolyl residue important for transport activity and the substrate specificity range of yeast plasma membrane Na+/H+ antiporters
00
55135105 2006 JOURNAL OF BIOLOGICAL CHEMISTRY 281 (7): 4446-4456
Saerens SMG; Verstrepen KJ; Van Laere SDM; Voet ARD; Van Dijck P; et al.
The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity
00
5613159 2005 JOURNAL OF CLINICAL MICROBIOLOGY 43 (9): 4574-4579
Foulet F; Nicolas N; Eloy O; Botterel F; Gantier JC; et al.
Microsatellite marker analysis as a typing system for Candida glabrata
00
57174 2004 MICROBIOLOGY-SGM 150: 2791-2793
Ussery DW; Tindbaek N; Hallin PF
Genome update: promoter profiles
00
5825960 2005 MICROBIOLOGY-SGM 151: 1465-1474
Flores CL; Martinez-Costa OH; Sanchez V; Gancedo C; Aragon JJ
The dimorphic yeast Yarrowia lipolytica possesses an atypical phosphofructokinase: characterization of the enzyme and its encoding gene
00
5917461 2005 MICROBIOLOGY-SGM 151: 1631-1644
Granger BL; Flenniken ML; Davis DA; Mitchell AP; Cutler JE
Yeast wall protein 1 of Candida albicans
01
6013762 2005 MICROBIOLOGY-SGM 151: 3627-3637
Blanchin-Roland S; Da Costa G; Gaillardin C
ESCRT-1 components of the endocytic machinery are required for Rim101-dependent ambient pH regulation in the yeast Yarrowia lipolytica
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
6119963 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
35
6215064 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (4): 1011-1023
Richard GF; Kerrest A; Lafontaine I; Dujon B
Comparative genomics of hemiascomycete yeasts: Genes involved in DNA replication, repair, and recombination
23
6325965 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
64345106 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 30-39
Prachumwat A; Li WH
Protein function, connectivity, and duplicability in yeast
00
65164107 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 189-202
Richard GF; Dujon B
Molecular evolution of minisatellites in hemiascomycetous yeasts
00
66233108 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
67170109 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (3): 513-522
Rocha EPC
Inference and analysis of the relative stability of bacterial chromosomes
00
6816566 2005 MOLECULAR BIOLOGY OF THE CELL 16 (10): 4636-4647
Uccelletti D; Farina F; Pinton P; Goffrini P; Mancini P; et al.
The Golgi Ca2+-ATPase KlPmr1p function is required for oxidative stress response by controlling the expression of the heat-shock element HSP60 in Kluyveromyces lactis
00
69210667 2005 MOLECULAR BIOLOGY OF THE CELL 16 (12): 5736-5748
Muller J; Oma Y; Vallar L; Friederich E; Poch O; et al.
Sequence and comparative genomic analysis of actin-related proteins
01
7013468 2005 MOLECULAR GENETICS AND GENOMICS 273 (1): 84-91
Mentel M; Piskur J; Neuveglise C; Rycovska A; Cellengova G; et al.
Triplicate genes for mitochondrial ADP/ATP carriers in the aerobic yeast Yarrowia lipolytica are regulated differentially in the absence of oxygen
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
7125069 2005 MOLECULAR GENETICS AND GENOMICS 274 (3): 205-216
Knoop V; Groth-Malonek M; Gebert M; Eifler K; Weyand K
Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily
00
7215070 2005 MOLECULAR MICROBIOLOGY 55 (4): 1259-1271
Iraqui I; Garcia-Sanchez S; Aubert S; Dromer F; Ghigo JM; et al.
The Yak1p kinase controls expression of adhesins and biofilm formation in Candida glabrata in a Sir4p-dependent pathway
24
7314471 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
7413372 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
75149110 2006 MOLECULAR PLANT PATHOLOGY 7 (1): 61-70
Soanes DM; Talbot NJ
Comparative genomic analysis of phytopathogenic fungi using expressed sequence tag (EST) collections
00
761105 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
14
770346 2004 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
111112
7811473 2005 NATURE 433 (7022): E4-E4
Pawlowska TE; Taylor JW
Arbuscular mycorrhizal fungi - Hyphal fusion and multigenomic structure - Reply
00
7919874 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
132
8014775 2005 NATURE 438 (7071): 1105-1115
Galagan JE; Calvo SE; Cuomo C; Ma LJ; Wortman JR; et al.
Sequencing of Aspergillus nidulans and comparative analysis with A-fumigatus and A-oryzae
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
8115976 2005 NATURE GENETICS 37 (6): 573-577
Francino MP
An adaptive radiation model for the origin of new gene functions
12
82211177 2005 NATURE REVIEWS GENETICS 6 (9): 699-708
Gregory TR
Synergy between sequence and size in large-scale genomics
00
83137 2004 NATURE REVIEWS MICROBIOLOGY 2 (11): 856-857
Pain A; Bentley S; Parkhill J
Eukaryotes: not beyond compare
00
841508 2004 NUCLEIC ACIDS RESEARCH 32 (17): 5076-5086
Fender A; Geslain R; Eriani G; Giege R; Sissler M; et al.
A yeast arginine specific tRNA is a remnant aspartate acceptor
00
8512578 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
8613179 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
8718880 2005 NUCLEIC ACIDS RESEARCH 33 (9): 2838-2851
Zhang ZH; Dietrich FS
Mapping of transcription start sites in Saccharomyces cerevisiae using 5 ' SAGE
22
8814581 2005 NUCLEIC ACIDS RESEARCH 33 (14): 4485-4495
Piccinelli P; Rosenblad MA; Samuelsson T
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes
00
8915982 2005 NUCLEIC ACIDS RESEARCH 33 (16): 5034-5044
Steigele S; Nieselt K
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes
00
901429 2004 ONCOGENE 23 (51): 8401-8409
Silva J; Chang K; Hannon GJ; Rivas FV
RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age
021
#LCRNCRNode / Date / Journal / AuthorLCSGCS
9115883 2005 PHYSICAL REVIEW E 72 (4): Art. No. 041915
Ouyang ZQ; Liu JK; She ZS
Hierarchical structure analysis describing abnormal base composition of genomes
00
92147111 2006 PHYTOPATHOLOGY 96 (1): 80-86
Massart S; Jijakli MH
Identification of differentially expressed genes by cDNA-amplified fragment length polymorphism in the biocontrol agent Pichia anomala (strain Kh5)
00
9315984 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
9416185 2005 PLOS COMPUTATIONAL BIOLOGY 1 (3): 202-211
Beltrao P; Serrano L
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
00
95113786 2005 PLOS GENETICS 1 (1): 36-57
Braun BR; Hoog MV; d'Enfert C; Martchenko M; Dungan J; et al.
A human-curated annotation of the Candida albicans genome
00
9614510 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
49
9718487 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
01
9813788 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (21): 7766-7771
Armstrong MR; Whisson SC; Pritchard L; Bos JIB; Venter E; et al.
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm
06
9912989 2005 PROTEOMICS 5 (7): 1838-1848
Stead D; Findon H; Yin ZK; Walker J; Selway L; et al.
Proteomic changes associated with inactivation of the Candida glabrata ACE2 virulence-moderating gene
11
10012390 2005 PROTEOMICS 5 (12): 3116-3119
Vergassola M; Vespignani A; Dujon B
Cooperative evolution in protein complexes of yeast from comparative analyses of its interaction network
00

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