-
1
-
-
0000898584
-
Phaffia, a new yeast genus in the deuteromycotina (Blastomycetes)
-
M. W. Miller MY, Masami S. Phaffia, a new yeast genus in the deuteromycotina (Blastomycetes). Int J Syst Evol Microbiol. 1976;26(2):286-91.
-
(1976)
Int J Syst Evol Microbiol
, vol.26
, Issue.2
, pp. 286-291
-
-
Miller, M.Y.1
Masami, S.2
-
4
-
-
84893416665
-
Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe
-
David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol. 2014;23(4):921-32.
-
(2014)
Mol Ecol
, vol.23
, Issue.4
, pp. 921-932
-
-
David-Palma, M.1
Libkind, D.2
Sampaio, J.P.3
-
5
-
-
0031947064
-
Homothallic life cycle in the diploid red yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma)
-
Kucsera J, Pfeiffer I, Ferenczy L. Homothallic life cycle in the diploid red yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma). Antonie Van Leeuwenhoek. 1998;73(2):163-8.
-
(1998)
Antonie Van Leeuwenhoek
, vol.73
, Issue.2
, pp. 163-168
-
-
Kucsera, J.1
Pfeiffer, I.2
Ferenczy, L.3
-
6
-
-
0028817338
-
Perfect state of Rhodomyces dendrorhous (Phaffia rhodozyma)
-
Golubev WI. Perfect state of Rhodomyces dendrorhous (Phaffia rhodozyma). Yeast. 1995;11(2):101-10.
-
(1995)
Yeast
, vol.11
, Issue.2
, pp. 101-110
-
-
Golubev, W.I.1
-
7
-
-
0242690297
-
Genetic determination of ploidy level in Xanthophyllomyces dendrorhous
-
Hermosilla G, Martinez C, Retamales P, Leon R, Cifuentes V. Genetic determination of ploidy level in Xanthophyllomyces dendrorhous. Antonie Van Leeuwenhoek. 2003;84(4):279-87.
-
(2003)
Antonie Van Leeuwenhoek
, vol.84
, Issue.4
, pp. 279-287
-
-
Hermosilla, G.1
Martinez, C.2
Retamales, P.3
Leon, R.4
Cifuentes, V.5
-
8
-
-
0031015587
-
High copy number integration into the ribosomal DNA of the yeast Phaffia rhodozyma
-
Wery J, Gutker D, Renniers AC, Verdoes JC, van Ooyen AJ. High copy number integration into the ribosomal DNA of the yeast Phaffia rhodozyma. Gene. 1997;184(1):89-97.
-
(1997)
Gene
, vol.184
, Issue.1
, pp. 89-97
-
-
Wery, J.1
Gutker, D.2
Renniers, A.C.3
Verdoes, J.C.4
Ooyen, A.J.5
-
9
-
-
0030907076
-
Demonstration of the Crabtree effect in Phaffia rhodozyma during continuous and fed-batch cultivation
-
Reynders MB, Rawlings DE, Harrison STL. Demonstration of the Crabtree effect in Phaffia rhodozyma during continuous and fed-batch cultivation. Biotechnol Lett. 1997;19(6):549-52.
-
(1997)
Biotechnol Lett
, vol.19
, Issue.6
, pp. 549-552
-
-
Reynders, M.B.1
Rawlings, D.E.2
Harrison, S.T.L.3
-
10
-
-
0027193037
-
Antioxidant role of carotenoids in Phaffia rhodozyma
-
William A, Schroeder EAJ. Antioxidant role of carotenoids in Phaffia rhodozyma. Microbiology. 1993;139(5):907-12.
-
(1993)
Microbiology
, vol.139
, Issue.5
, pp. 907-912
-
-
William, A.1
Schroeder, E.A.J.2
-
11
-
-
0029085902
-
Carotenoids protectPhaffia rhodozyma against singlet oxygen damage
-
William A, Schroeder EAJ. Carotenoids protectPhaffia rhodozyma against singlet oxygen damage. J Ind Microbiol. 1995;14(6):502-7.
-
(1995)
J Ind Microbiol
, vol.14
, Issue.6
, pp. 502-507
-
-
William, A.1
Schroeder, E.A.J.2
-
12
-
-
4143116359
-
The mycota X industrial applications
-
In: Karl Esser PAL, Bennett JW, Heinz D, editors. Osiewacz: Springer Verlag Berlin
-
Sandmann G MN. The mycota X industrial applications. In: Karl Esser PAL, Bennett JW, Heinz D, editors. The Mycota X industrial applications. Osiewacz: Springer Verlag Berlin; 2002.
-
(2002)
The Mycota X industrial applications
-
-
Sandmann, G.M.N.1
-
13
-
-
32444444375
-
Cloning of the astaxanthin synthase gene from Xanthophyllomyces dendrorhous (Phaffia rhodozyma) and its assignment as a beta-carotene 3-hydroxylase/4-ketolase
-
Ojima K, Breitenbach J, Visser H, Setoguchi Y, Tabata K, Hoshino T, et al. Cloning of the astaxanthin synthase gene from Xanthophyllomyces dendrorhous (Phaffia rhodozyma) and its assignment as a beta-carotene 3-hydroxylase/4-ketolase. Mol Genet Genomics. 2006;275(2):148-58.
-
(2006)
Mol Genet Genomics
, vol.275
, Issue.2
, pp. 148-158
-
-
Ojima, K.1
Breitenbach, J.2
Visser, H.3
Setoguchi, Y.4
Tabata, K.5
Hoshino, T.6
-
14
-
-
55149109484
-
Cloning of the cytochrome p450 reductase (crtR) gene and its involvement in the astaxanthin biosynthesis of Xanthophyllomyces dendrorhous
-
Alcaino J, Barahona S, Carmona M, Lozano C, Marcoleta A, Niklitschek M, et al. Cloning of the cytochrome p450 reductase (crtR) gene and its involvement in the astaxanthin biosynthesis of Xanthophyllomyces dendrorhous. BMC Microbiol. 2008;8:169.
-
(2008)
BMC Microbiol
, vol.8
, pp. 169
-
-
Alcaino, J.1
Barahona, S.2
Carmona, M.3
Lozano, C.4
Marcoleta, A.5
Niklitschek, M.6
-
15
-
-
84891857645
-
Genetic engineering of the complete carotenoid pathway towards enhanced astaxanthin formation in Xanthophyllomyces dendrorhous starting from a high-yield mutant
-
Gassel S, Breitenbach J, Sandmann G. Genetic engineering of the complete carotenoid pathway towards enhanced astaxanthin formation in Xanthophyllomyces dendrorhous starting from a high-yield mutant. Appl Microbiol Biotechnol. 2014;98(1):345-50.
-
(2014)
Appl Microbiol Biotechnol
, vol.98
, Issue.1
, pp. 345-350
-
-
Gassel, S.1
Breitenbach, J.2
Sandmann, G.3
-
16
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
18
-
-
0033239250
-
Isolation of the isopentenyl diphosphate isomerase encoding gene of Phaffia rhodozyma; improved carotenoid production in Escherichia coli
-
Verdoesa JC, Ooyenab AJJ. Isolation of the isopentenyl diphosphate isomerase encoding gene of Phaffia rhodozyma; improved carotenoid production in Escherichia coli. Acta Botanica Gallica: Botany Lett. 1999;146(1):43-53.
-
(1999)
Acta Botanica Gallica: Botany Lett
, vol.146
, Issue.1
, pp. 43-53
-
-
Verdoesa, J.C.1
Ooyenab, A.J.J.2
-
19
-
-
79952763038
-
Engineering of geranylgeranyl pyrophosphate synthase levels and physiological conditions for enhanced carotenoid and astaxanthin synthesis in Xanthophyllomyces dendrorhous
-
Breitenbach J, Visser H, Verdoes JC, van Ooyen AJ, Sandmann G. Engineering of geranylgeranyl pyrophosphate synthase levels and physiological conditions for enhanced carotenoid and astaxanthin synthesis in Xanthophyllomyces dendrorhous. Biotechnol Lett. 2011;33(4):755-61.
-
(2011)
Biotechnol Lett
, vol.33
, Issue.4
, pp. 755-761
-
-
Breitenbach, J.1
Visser, H.2
Verdoes, J.C.3
Ooyen, A.J.4
Sandmann, G.5
-
20
-
-
84900439259
-
Functional characterization of the Xanthophyllomyces dendrorhous farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase encoding genes that are involved in the synthesis of isoprenoid precursors
-
Alcaino J, Romero I, Niklitschek M, Sepulveda D, Rojas MC, Baeza M, et al. Functional characterization of the Xanthophyllomyces dendrorhous farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase encoding genes that are involved in the synthesis of isoprenoid precursors. PLoS One. 2014;9(5):e96626.
-
(2014)
PLoS One
, vol.9
, Issue.5
, pp. e96626
-
-
Alcaino, J.1
Romero, I.2
Niklitschek, M.3
Sepulveda, D.4
Rojas, M.C.5
Baeza, M.6
-
21
-
-
77956283840
-
Phylogenetic distribution of fungal sterols
-
Weete JD, Abril M, Blackwell M. Phylogenetic distribution of fungal sterols. PLoS One. 2010;5(5):e10899.
-
(2010)
PLoS One
, vol.5
, Issue.5
, pp. e10899
-
-
Weete, J.D.1
Abril, M.2
Blackwell, M.3
-
22
-
-
84867527941
-
Enhancement of carotenoid production by disrupting the C22-sterol desaturase gene (CYP61) in Xanthophyllomyces dendrorhous
-
Loto I, Gutierrez MS, Barahona S, Sepulveda D, Martinez-Moya P, Baeza M, et al. Enhancement of carotenoid production by disrupting the C22-sterol desaturase gene (CYP61) in Xanthophyllomyces dendrorhous. BMC Microbiol. 2012;12:235.
-
(2012)
BMC Microbiol
, vol.12
, pp. 235
-
-
Loto, I.1
Gutierrez, M.S.2
Barahona, S.3
Sepulveda, D.4
Martinez-Moya, P.5
Baeza, M.6
-
23
-
-
0032722810
-
Isolation and functional characterisation of a novel type of carotenoid biosynthetic gene from Xanthophyllomyces dendrorhous
-
Verdoes JC, Krubasik KP, Sandmann G, van Ooyen AJ. Isolation and functional characterisation of a novel type of carotenoid biosynthetic gene from Xanthophyllomyces dendrorhous. Mol Gen Genet. 1999;262(3):453-61.
-
(1999)
Mol Gen Genet
, vol.262
, Issue.3
, pp. 453-461
-
-
Verdoes, J.C.1
Krubasik, K.P.2
Sandmann, G.3
Ooyen, A.J.4
-
24
-
-
0033587374
-
Cloning and characterization of the astaxanthin biosynthetic gene encoding phytoene desaturase of Xanthophyllomyces dendrorhous
-
Verdoes JC, Misawa N, van Ooyen AJ. Cloning and characterization of the astaxanthin biosynthetic gene encoding phytoene desaturase of Xanthophyllomyces dendrorhous. Biotechnol Bioeng. 1999;63(6):750-5.
-
(1999)
Biotechnol Bioeng
, vol.63
, Issue.6
, pp. 750-755
-
-
Verdoes, J.C.1
Misawa, N.2
Ooyen, A.J.3
-
25
-
-
4544275674
-
Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems
-
Schweizer E, Hofmann J. Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems. Microbiol Mol Biol Rev. 2004;68(3):501-17. table of contents.
-
(2004)
Microbiol Mol Biol Rev
, vol.68
, Issue.3
, pp. 501-517
-
-
Schweizer, E.1
Hofmann, J.2
-
26
-
-
0030915349
-
Mitochondrial fatty acid synthesis: a relic of endosymbiontic origin and a specialized means for respiration
-
Schneider R, Brors B, Massow M, Weiss H. Mitochondrial fatty acid synthesis: a relic of endosymbiontic origin and a specialized means for respiration. FEBS Lett. 1997;407(3):249-52.
-
(1997)
FEBS Lett
, vol.407
, Issue.3
, pp. 249-252
-
-
Schneider, R.1
Brors, B.2
Massow, M.3
Weiss, H.4
-
27
-
-
77955274600
-
SMURF: genomic mapping of fungal secondary metabolite clusters
-
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, et al. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 2010;47(9):736-41.
-
(2010)
Fungal Genet Biol
, vol.47
, Issue.9
, pp. 736-741
-
-
Khaldi, N.1
Seifuddin, F.T.2
Turner, G.3
Haft, D.4
Nierman, W.C.5
Wolfe, K.H.6
-
28
-
-
84901315116
-
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation
-
Janbon G, Ormerod KL, Paulet D, Byrnes 3rd EJ, Yadav V, Chatterjee G, et al. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014;10(4):e1004261.
-
(2014)
PLoS Genet
, vol.10
, Issue.4
, pp. e1004261
-
-
Janbon, G.1
Ormerod, K.L.2
Paulet, D.3
Byrnes, E.J.4
Yadav, V.5
Chatterjee, G.6
-
29
-
-
84896547853
-
Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae
-
Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, et al. Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. New Phytol. 2014;202(2):554-64.
-
(2014)
New Phytol
, vol.202
, Issue.2
, pp. 554-564
-
-
Toome, M.1
Ohm, R.A.2
Riley, R.W.3
James, T.Y.4
Lazarus, K.L.5
Henrissat, B.6
-
30
-
-
84896135582
-
Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids
-
Morita T, Koike H, Hagiwara H, Ito E, Machida M, Sato S, et al. Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids. PLoS One. 2014;9(2):e86490.
-
(2014)
PLoS One
, vol.9
, Issue.2
, pp. e86490
-
-
Morita, T.1
Koike, H.2
Hagiwara, H.3
Ito, E.4
Machida, M.5
Sato, S.6
-
31
-
-
84862977387
-
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes
-
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012;336(6089):1715-9.
-
(2012)
Science
, vol.336
, Issue.6089
, pp. 1715-1719
-
-
Floudas, D.1
Binder, M.2
Riley, R.3
Barry, K.4
Blanchette, R.A.5
Henrissat, B.6
-
32
-
-
84926528832
-
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum
-
Sharma R, Mishra B, Runge F, Thines M. Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum. Genome Biol Evol. 2014;6:2034-49.
-
(2014)
Genome Biol Evol
, vol.6
, pp. 2034-2049
-
-
Sharma, R.1
Mishra, B.2
Runge, F.3
Thines, M.4
-
33
-
-
20244366844
-
The genome sequence of the rice blast fungus Magnaporthe grisea
-
Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 2005;434(7036):980-6.
-
(2005)
Nature
, vol.434
, Issue.7036
, pp. 980-986
-
-
Dean, R.A.1
Talbot, N.J.2
Ebbole, D.J.3
Farman, M.L.4
Mitchell, T.K.5
Orbach, M.J.6
-
34
-
-
24044440773
-
Aflatoxin biosynthesis gene clusters and flanking regions
-
Ehrlich KC, Yu J, Cotty PJ. Aflatoxin biosynthesis gene clusters and flanking regions. J Appl Microbiol. 2005;99(3):518-27.
-
(2005)
J Appl Microbiol
, vol.99
, Issue.3
, pp. 518-527
-
-
Ehrlich, K.C.1
Yu, J.2
Cotty, P.J.3
-
35
-
-
36749090098
-
Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens
-
Xu J, Saunders CW, Hu P, Grant RA, Boekhout T, Kuramae EE, et al. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci U S A. 2007;104(47):18730-5.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.47
, pp. 18730-18735
-
-
Xu, J.1
Saunders, C.W.2
Hu, P.3
Grant, R.A.4
Boekhout, T.5
Kuramae, E.E.6
-
36
-
-
1842850621
-
Completed sequence of aflatoxin pathway gene cluster in Aspergillus parasiticus
-
Yu J, Bhatnagar D, Cleveland TE. Completed sequence of aflatoxin pathway gene cluster in Aspergillus parasiticus. FEBS Lett. 2004;564(1-2):126-30.
-
(2004)
FEBS Lett
, vol.564
, Issue.1-2
, pp. 126-130
-
-
Yu, J.1
Bhatnagar, D.2
Cleveland, T.E.3
-
37
-
-
12144286398
-
Clustered pathway genes in aflatoxin biosynthesis
-
Yu J, Chang PK, Ehrlich KC, Cary JW, Bhatnagar D, Cleveland TE, et al. Clustered pathway genes in aflatoxin biosynthesis. Appl Environ Microbiol. 2004;70(3):1253-62.
-
(2004)
Appl Environ Microbiol
, vol.70
, Issue.3
, pp. 1253-1262
-
-
Yu, J.1
Chang, P.K.2
Ehrlich, K.C.3
Cary, J.W.4
Bhatnagar, D.5
Cleveland, T.E.6
-
38
-
-
84884567083
-
Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
-
Zajc J, Liu Y, Dai W, Yang Z, Hu J, Gostincar C, et al. Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. BMC Genomics. 2013;14:617.
-
(2013)
BMC Genomics
, vol.14
, pp. 617
-
-
Zajc, J.1
Liu, Y.2
Dai, W.3
Yang, Z.4
Hu, J.5
Gostincar, C.6
-
39
-
-
84862831566
-
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
-
Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, et al. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol. 2012;49(3):217-26.
-
(2012)
Fungal Genet Biol
, vol.49
, Issue.3
, pp. 217-226
-
-
Padamsee, M.1
Kumar, T.K.2
Riley, R.3
Binder, M.4
Boyd, A.5
Calvo, A.M.6
-
40
-
-
84872419320
-
Cell-to-cell communication in plants, animals, and fungi: a comparative review
-
Bloemendal S, Kuck U. Cell-to-cell communication in plants, animals, and fungi: a comparative review. Naturwissenschaften. 2013;100(1):3-19.
-
(2013)
Naturwissenschaften
, vol.100
, Issue.1
, pp. 3-19
-
-
Bloemendal, S.1
Kuck, U.2
-
42
-
-
34247558244
-
Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota
-
Matheny PBGJ, Zalar P, Arun Kumar TK, Hibbett DS. Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Can J Bot. 2006;84:1794-805.
-
(2006)
Can J Bot
, vol.84
, pp. 1794-1805
-
-
Matheny, P.B.G.J.1
Zalar, P.2
Arun Kumar, T.K.3
Hibbett, D.S.4
-
43
-
-
79960569713
-
Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)
-
Millanes AM, Diederich P, Ekman S, Wedin M. Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi). Mol Phylogenet Evol. 2011;61(1):12-28.
-
(2011)
Mol Phylogenet Evol
, vol.61
, Issue.1
, pp. 12-28
-
-
Millanes, A.M.1
Diederich, P.2
Ekman, S.3
Wedin, M.4
-
44
-
-
84857556426
-
A consistent phylogenetic backbone for the fungi
-
Ebersberger I, de Matos SR, Kupczok A, Gube M, Kothe E, Voigt K, et al. A consistent phylogenetic backbone for the fungi. Mol Biol Evol. 2012;29(5):1319-34.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.5
, pp. 1319-1334
-
-
Ebersberger, I.1
Matos, S.R.2
Kupczok, A.3
Gube, M.4
Kothe, E.5
Voigt, K.6
-
45
-
-
34250341823
-
A higher-level phylogenetic classification of the Fungi
-
Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, et al. A higher-level phylogenetic classification of the Fungi. Mycol Res. 2007;111(Pt 5):509-47.
-
(2007)
Mycol Res
, vol.111
, pp. 509-547
-
-
Hibbett, D.S.1
Binder, M.2
Bischoff, J.F.3
Blackwell, M.4
Cannon, P.F.5
Eriksson, O.E.6
-
46
-
-
34247647914
-
A phylogenetic overview of the Agaricomycotina
-
Hibbett DS. A phylogenetic overview of the Agaricomycotina. Mycologia. 2006;98(6):917-25.
-
(2006)
Mycologia
, vol.98
, Issue.6
, pp. 917-925
-
-
Hibbett, D.S.1
-
47
-
-
84873263109
-
Production of alpha-cuprenene in Xanthophyllomyces dendrorhous: a step closer to a potent terpene biofactory
-
Melillo E, Setroikromo R, Quax WJ, Kayser O. Production of alpha-cuprenene in Xanthophyllomyces dendrorhous: a step closer to a potent terpene biofactory. Microb Cell Fact. 2013;12:13.
-
(2013)
Microb Cell Fact
, vol.12
, pp. 13
-
-
Melillo, E.1
Setroikromo, R.2
Quax, W.J.3
Kayser, O.4
-
48
-
-
79961215645
-
Functional analysis of the Phycomyces carRA gene encoding the enzymes phytoene synthase and lycopene cyclase
-
Sanz C, Velayos A, Alvarez MI, Benito EP, Eslava AP. Functional analysis of the Phycomyces carRA gene encoding the enzymes phytoene synthase and lycopene cyclase. PLoS One. 2011;6(8):e23102.
-
(2011)
PLoS One
, vol.6
, Issue.8
, pp. e23102
-
-
Sanz, C.1
Velayos, A.2
Alvarez, M.I.3
Benito, E.P.4
Eslava, A.P.5
-
49
-
-
0036329644
-
A carotenoid biosynthesis gene cluster in Fusarium fujikuroi: the genes carB and carRA
-
Linnemannstons P, Prado MM, Fernandez-Martin R, Tudzynski B, Avalos J. A carotenoid biosynthesis gene cluster in Fusarium fujikuroi: the genes carB and carRA. Mol Genet Genomics. 2002;267(5):593-602.
-
(2002)
Mol Genet Genomics
, vol.267
, Issue.5
, pp. 593-602
-
-
Linnemannstons, P.1
Prado, M.M.2
Fernandez-Martin, R.3
Tudzynski, B.4
Avalos, J.5
-
50
-
-
65549103832
-
Fatty acid metabolism in the ectomycorrhizal fungus Laccaria bicolor
-
Reich M, Gobel C, Kohler A, Buee M, Martin F, Feussner I, et al. Fatty acid metabolism in the ectomycorrhizal fungus Laccaria bicolor. New Phytol. 2009;182(4):950-64.
-
(2009)
New Phytol
, vol.182
, Issue.4
, pp. 950-964
-
-
Reich, M.1
Gobel, C.2
Kohler, A.3
Buee, M.4
Martin, F.5
Feussner, I.6
-
51
-
-
79954424714
-
Differential carotenoid production and gene expression in Xanthophyllomyces dendrorhous grown in a nonfermentable carbon source
-
Wozniak A, Lozano C, Barahona S, Niklitschek M, Marcoleta A, Alcaino J, et al. Differential carotenoid production and gene expression in Xanthophyllomyces dendrorhous grown in a nonfermentable carbon source. FEMS Yeast Res. 2011;11(3):252-62.
-
(2011)
FEMS Yeast Res
, vol.11
, Issue.3
, pp. 252-262
-
-
Wozniak, A.1
Lozano, C.2
Barahona, S.3
Niklitschek, M.4
Marcoleta, A.5
Alcaino, J.6
-
52
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15)):2114-20.
-
(2014)
Bioinformatics
, vol.30
, Issue.15
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
53
-
-
34249848751
-
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
-
Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23(9):1061-7.
-
(2007)
Bioinformatics
, vol.23
, Issue.9
, pp. 1061-1067
-
-
Parra, G.1
Bradnam, K.2
Korf, I.3
-
54
-
-
0036673472
-
Automated de novo identification of repeat sequence families in sequenced genomes
-
Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002;12(8):1269-76.
-
(2002)
Genome Res
, vol.12
, Issue.8
, pp. 1269-1276
-
-
Bao, Z.1
Eddy, S.R.2
-
55
-
-
29144455282
-
De novo identification of repeat families in large genomes
-
Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21 Suppl 1:i351-8.
-
(2005)
Bioinformatics
, vol.21
, pp. i351-i358
-
-
Price, A.L.1
Jones, N.C.2
Pevzner, P.A.3
-
56
-
-
23844525077
-
Repbase update, a database of eukaryotic repetitive elements
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1-4):462-7.
-
(2005)
Cytogenet Genome Res
, vol.110
, Issue.1-4
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
57
-
-
0033555906
-
Tandem repeats finder: a program to analyze DNA sequences
-
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573-80.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.2
, pp. 573-580
-
-
Benson, G.1
-
58
-
-
84857623318
-
Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES
-
Chapter 4, Unit 4 6 1-10
-
Borodovsky M, Lomsadze A. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Curr Protoc Bioinformatics. 2011;Chapter 4:Unit 4 6 1-10.
-
(2011)
Curr Protoc Bioinformatics
-
-
Borodovsky, M.1
Lomsadze, A.2
-
59
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
60
-
-
33645161645
-
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
-
Stanke M, Schoffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006;7:62.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 62
-
-
Stanke, M.1
Schoffmann, O.2
Morgenstern, B.3
Waack, S.4
-
61
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
-
(2013)
Genome Biol
, vol.14
, Issue.4
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
62
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511-5.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.5
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Baren, M.J.6
-
63
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith Jr RK, Hannick LI, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003;31(19):5654-66.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.19
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith, R.K.5
Hannick, L.I.6
-
64
-
-
18744383071
-
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
-
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21(9):1859-75.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
65
-
-
42949086676
-
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
-
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9(1):R7.
-
(2008)
Genome Biol
, vol.9
, Issue.1
, pp. R7
-
-
Haas, B.J.1
Salzberg, S.L.2
Zhu, W.3
Pertea, M.4
Allen, J.E.5
Orvis, J.6
-
66
-
-
24644503098
-
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674-6.
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3674-3676
-
-
Conesa, A.1
Gotz, S.2
Garcia-Gomez, J.M.3
Terol, J.4
Talon, M.5
Robles, M.6
-
67
-
-
38549146894
-
The Pfam protein families database
-
Database issue
-
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, et al. The Pfam protein families database. Nucleic Acids Res. 2008;36(Database issue):D281-8.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D281-D288
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.R.6
-
68
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
69
-
-
34547588704
-
KAAS: an automatic genome annotation and pathway reconstruction server
-
Web Server issue
-
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35(Web Server issue)):W182-5.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W182-W185
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.C.4
Kanehisa, M.5
-
70
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 2004;5(2):R7.
-
(2004)
Genome Biol
, vol.5
, Issue.2
, pp. R7
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Krylov, D.M.5
Makarova, K.S.6
-
71
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
72
-
-
23144458473
-
InterProScan: protein domains identifier
-
Web Server issue
-
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33(Web Server issue):W116-20.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W116-W120
-
-
Quevillon, E.1
Silventoinen, V.2
Pillai, S.3
Harte, N.4
Mulder, N.5
Apweiler, R.6
-
73
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30(7):1575-84.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Dongen, S.2
Ouzounis, C.A.3
-
74
-
-
80053345905
-
SignalP 4.0: discriminating signal peptides from transmembrane regions
-
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785-6.
-
(2011)
Nat Methods
, vol.8
, Issue.10
, pp. 785-786
-
-
Petersen, T.N.1
Brunak, S.2
Heijne, G.3
Nielsen, H.4
-
75
-
-
0034697980
-
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
-
Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000;300(4):1005-16.
-
(2000)
J Mol Biol
, vol.300
, Issue.4
, pp. 1005-1016
-
-
Emanuelsson, O.1
Nielsen, H.2
Brunak, S.3
Heijne, G.4
-
76
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567-80.
-
(2001)
J Mol Biol
, vol.305
, Issue.3
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Heijne, G.3
Sonnhammer, E.L.4
-
77
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert Jr CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178-89.
-
(2003)
Genome Res
, vol.13
, Issue.9
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
78
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
-
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-80.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.4
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
79
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21):2688-90.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
80
-
-
84860109324
-
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
-
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539-42.
-
(2012)
Syst Biol
, vol.61
, Issue.3
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
Mark, P.3
Ayres, D.L.4
Darling, A.5
Hohna, S.6
|