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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
11291 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
21502 2004 BIOSCIENCE 54 (11): 991-1001
Delwiche CF
The genomic palimpsest: Genomics in evolution and ecology
01
31193 2004 ENVIRONMENTAL MICROBIOLOGY 6 (10): 1001-1004
Galperin MY
The bugs that came in from the cold
00
4174 2004 MICROBIOLOGY-SGM 150: 2791-2793
Ussery DW; Tindbaek N; Hallin PF
Genome update: promoter profiles
00
51105 2004 NATURE 430 (6995): 25-26
Goffeau A
Evolutionary genomics - Seeing double
14
60346 2004 NATURE 430 (6995): 35-44
Dujon B; Sherman D; Fischer G; Durrens P; Casaregola S; et al.
Genome evolution in yeasts
111112
7137 2004 NATURE REVIEWS MICROBIOLOGY 2 (11): 856-857
Pain A; Bentley S; Parkhill J
Eukaryotes: not beyond compare
00
81508 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
91429 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
1014510 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
11122111 2005 ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 44 (42): 6828-6846
Bode HB; Muller R
The impact of bacterial genomics on natural product research
02
12312412 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 135-153
Liti G; Louis EJ
Yeast evolution and comparative genomics
02
13111513 2005 ANNUAL REVIEW OF PHYTOPATHOLOGY 43: 279-308
Kohn LM
Mechanisms of fungal speciation
00
1413214 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
1512915 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
16110616 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
1712517 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
1815418 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
191919 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
2014420 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2115921 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
2214022 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
23111523 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (11): 1182-1197
Andersson JO
Lateral gene transfer in eukaryotes
00
24117424 2005 CELLULAR AND MOLECULAR LIFE SCIENCES 62 (19-20): 2204-2227
del Arco A; Satrustegui J
New mitochondrial carriers: an overview
00
25312125 2005 CHROMOSOME RESEARCH 13 (5): 535-548
Teixeira MT; Gilson E
Telomere maintenance, function and evolution: the yeast paradigm
00
2614326 2005 CROP SCIENCE 45 (5): 1809-1816
Caetano-Anolles G
Evolution of genome size in the grasses
00
2714927 2005 CURRENT BIOLOGY 15 (3): 231-237
Joseph I; Jia DW; Lustig AJ
Ndj1p-dependent epigenetic resetting of telornere size in yeast meiosis
03
2812328 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
2925129 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
3012330 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31113931 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
3213732 2005 CURRENT OPINION IN BIOTECHNOLOGY 16 (3): 356-360
Hohmann S
The Yeast Systems Biology Network: mating communities
01
3385033 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 614-620
Dujon B
Hemiascomycetous yeasts at the forefront of comparative genomics
00
341634 2005 CURRENT OPINION IN MICROBIOLOGY 8 (4): 359-361
Bussey H
Host-microbe interactions: fungi - Editorial overview
00
3546235 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
3615136 2005 CURRENT OPINION IN MICROBIOLOGY 8 (4): 385-392
Tekaia F; Latge JP
Aspergillus fumigatus: saprophyte or pathogen?
02
3716037 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
3813838 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
3914339 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
4016240 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4116741 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
4214442 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
4313943 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
44111744 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
4515245 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
4613446 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
4716947 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
48115348 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
4913249 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
5015550 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5111951 2005 GENOME BIOLOGY 6 (4): Art. No. R31
Liang H; Cavalcanti ARO; Landweber LF
Conservation of tandem stop codons in yeasts
01
5214852 2005 GENOME BIOLOGY 6 (4): Art. No. R35
Mazurie A; Bottani S; Vergassola M
An evolutionary and functional assessment of regulatory network motifs
02
5315153 2005 GENOME RESEARCH 15 (4): 552-559
Pereira-Leal JB; Teichmann SA
Novel specificities emerge by stepwise duplication of functional modules
23
5415254 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
5522955 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
56111156 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
5715257 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
5816858 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
5913159 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
6025960 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
6117461 2005 MICROBIOLOGY-SGM 151: 1631-1644
Granger BL; Flenniken ML; Davis DA; Mitchell AP; Cutler JE
Yeast wall protein 1 of Candida albicans
01
6213762 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
6319963 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
6415064 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
6525965 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
6616566 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
67210667 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
6813468 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
6925069 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
7015070 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
7114471 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
7213372 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
7311473 2005 NATURE 433 (7022): E4-E4
Pawlowska TE; Taylor JW
Arbuscular mycorrhizal fungi - Hyphal fusion and multigenomic structure - Reply
00
7419874 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
7514775 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
7615976 2005 NATURE GENETICS 37 (6): 573-577
Francino MP
An adaptive radiation model for the origin of new gene functions
12
77211177 2005 NATURE REVIEWS GENETICS 6 (9): 699-708
Gregory TR
Synergy between sequence and size in large-scale genomics
00
7812578 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
7913179 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
8018880 2005 NUCLEIC ACIDS RESEARCH 33 (9): 2838-2851
Zhang ZH; Dietrich FS
Mapping of transcription start sites in Saccharomyces cerevisiae using 5 ' SAGE
22
#LCRNCRNode / Date / Journal / AuthorLCSGCS
8114581 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
8215982 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
8315883 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
8415984 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
8516185 2005 PLOS COMPUTATIONAL BIOLOGY 1 (3): 202-211
Beltrao P; Serrano L
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
00
86113786 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
8718487 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
8813788 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
8912989 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
9012390 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
9115891 2005 RESEARCH IN MICROBIOLOGY 156 (7): 822-829
Knechtle P; Goyard S; Brachat S; Ibrahim-Granet O; d'Enfert C
Phosphatidylinositol-dependent phospholipases C Plc2 and Plc3 of Candida albicans are dispensable for morphogenesis and host-pathogen interaction
01
9213492 2005 RNA-A PUBLICATION OF THE RNA SOCIETY 11 (6): 928-938
Torchet C; Badis G; Devaux F; Costanzo G; Werner M; et al.
The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae
03
9314493 2005 RNA-A PUBLICATION OF THE RNA SOCIETY 11 (7): 1064-1072
Kachouri R; Stribinskis S; Zhu YG; Ramos KS; Westhof E; et al.
A surprisingly large RNase P RNA in Candida glabrata
00
9422794 2005 SCIENCE 308 (5723): 866-870
Domergue R; Castano I; De las Penas A; Zupancic M; Lockatell V; et al.
Nicotinic acid limitation regulates silecing of Candida adhesins during UTI
11
9512095 2005 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
22
96213396 2005 TRENDS IN GENETICS 21 (12): 673-682
Coghlan A; Eichler EE; Oliver SG; Paterson AH; Stein L
Chromosome evolution in eukaryotes: a multi-kingdom perspective
00
9711997 2005 YEAST 22 (5): 337-342
Durrens P; Sherman DJ
A systematic nomenclature of chromosomal elements for hemiascomycete yeasts
00
9812998 2005 YEAST 22 (6): 493-501
Butler MI; Goodwin TJD; Poulter RTM
Two new fungal inteins
00
9915699 2005 YEAST 22 (8): 659-668
Bowen S; Roberts C; Wheals AE
Patterns of polymorphism and divergence in stress-related yeast proteins
00
100138100 2005 YEAST 22 (12): 947-956
Kawasaki L; Savinon-Tejeda AL; Ongay-Larios L; Ramirez J; Coria R
The G beta(KISte4p) subunit of the heterotrimeric G protein has a positive and essential role in the induction of mating in the yeast Kluyveromyces lactis
00

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