메뉴 건너뛰기




Volumn 7, Issue , 2016, Pages

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

(18)  Hacquard, Stéphane a   Kracher, Barbara a   Hiruma, Kei a,n   Münch, Philipp C b,c   Garrido Oter, Ruben a,d   Thon, Michael R e   Weimann, Aaron b,d   Damm, Ulrike f,o   Dallery, Jean Félix g   Hainaut, Matthieu h,i   Henrissat, Bernard h,i,j   Lespinet, Olivier k,l   Sacristán, Soledad m   Ver Loren Van Themaat, Emiel a,p   Kemen, Eric n   McHardy, Alice C a,b,d   Schulze Lefert, Paul a   O'Connell, Richard J a,g  


Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHATE; TRANSCRIPTION FACTOR WRKY33; TRANSCRIPTION FACTOR WRKY40; TRANSCRIPTOME; UNCLASSIFIED DRUG; CHITIN;

EID: 84962691880     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms11362     Document Type: Article
Times cited : (195)

References (72)
  • 1
    • 63449129221 scopus 로고    scopus 로고
    • Fungal endophytes: Diversity and functional roles
    • Rodriguez, R. J., White, Jr J. F., Arnold, A. E., Redman, R. S. Fungal endophytes: diversity and functional roles. New Phytol. 182, 314-330 (2009).
    • (2009) New Phytol , vol.182 , pp. 314-330
    • Rodriguez, R.J.1    White, J.F.2    Arnold, A.E.3    Redman, R.S.4
  • 2
    • 84865693932 scopus 로고    scopus 로고
    • Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses
    • O'Connell, R. J. et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat. Genet. 44, 1060-1065 (2012).
    • (2012) Nat. Genet , vol.44 , pp. 1060-1065
    • O'Connell, R.J.1
  • 3
    • 84920491130 scopus 로고    scopus 로고
    • Colletotrichum-names in current use
    • Hyde, K. D. et al. Colletotrichum-names in current use. Fungal Divers. 39, 147-182 (2009).
    • (2009) Fungal Divers , vol.39 , pp. 147-182
    • Hyde, K.D.1
  • 4
    • 38949185087 scopus 로고    scopus 로고
    • Root infection and systemic colonization of maize by Colletotrichum graminicola
    • Sukno, S. A., Garcia, V. M., Shaw, B. D., Thon, M. R. Root infection and systemic colonization of maize by Colletotrichum graminicola. Appl. Environ. Microbiol. 4, 823-832 (2008).
    • (2008) Appl. Environ. Microbiol , vol.4 , pp. 823-832
    • Sukno, S.A.1    Garcia, V.M.2    Shaw, B.D.3    Thon, M.R.4
  • 5
    • 33751018849 scopus 로고    scopus 로고
    • Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods
    • Go?tz, M. et al. Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods. FEMS Microbiol. Ecol. 58, 404-413 (2006).
    • (2006) FEMS Microbiol. Ecol , vol.58 , pp. 404-413
    • Gotz, M.1
  • 6
    • 84902675076 scopus 로고    scopus 로고
    • Root-associated fungi of Arabidopsis thaliana and Microthlaspi perfoliatum
    • Keim, J., Mishra, B., Sharma, R., Ploch, S., Thines, M. Root-associated fungi of Arabidopsis thaliana and Microthlaspi perfoliatum. Fungal Divers. 66, 99-111 (2014).
    • (2014) Fungal Divers , vol.66 , pp. 99-111
    • Keim, J.1    Mishra, B.2    Sharma, R.3    Ploch, S.4    Thines, M.5
  • 7
    • 84873248742 scopus 로고    scopus 로고
    • Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi
    • Gan, P. et al. Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol. 197, 1236-1249 (2012).
    • (2012) New Phytol , vol.197 , pp. 1236-1249
    • Gan, P.1
  • 8
    • 84961196851 scopus 로고    scopus 로고
    • Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status-dependent
    • Hiruma, K. et al. Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status-dependent. Cell 165, 1-11 (2016).
    • (2016) Cell , vol.165 , pp. 1-11
    • Hiruma, K.1
  • 9
    • 84905454834 scopus 로고    scopus 로고
    • Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution
    • Delaux, P. M. et al. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet. 10, e1004487 (2014).
    • (2014) PLoS Genet , vol.10 , pp. e1004487
    • Delaux, P.M.1
  • 11
    • 25444437473 scopus 로고    scopus 로고
    • Anthracnose of Japanese radish caused by Colletotrichum dematium
    • Sato, T. et al. Anthracnose of Japanese radish caused by Colletotrichum dematium. J. Gen. Plant Pathol. 71, 380-383 (2005).
    • (2005) J. Gen. Plant Pathol , vol.71 , pp. 380-383
    • Sato, T.1
  • 12
    • 84863593823 scopus 로고    scopus 로고
    • Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species
    • Stukenbrock, E. H., Christiansen, F. B., Hansen, T. T., Dutheil, J. Y., Schierup, M. H. Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc. Natl Acad. Sci. USA 109, 10954-10959 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 10954-10959
    • Stukenbrock, E.H.1    Christiansen, F.B.2    Hansen, T.T.3    Dutheil, J.Y.4    Schierup, M.H.5
  • 13
    • 84878969764 scopus 로고    scopus 로고
    • Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts
    • Hacquard, S. et al. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc. Natl Acad. Sci. USA 110, E2219-E2228 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. E2219-E2228
    • Hacquard, S.1
  • 15
    • 84925005930 scopus 로고    scopus 로고
    • Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
    • Kohler, A. et al. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat. Genet. 47, 410-415 (2015).
    • (2015) Nat. Genet , vol.47 , pp. 410-415
    • Kohler, A.1
  • 16
    • 77951144839 scopus 로고    scopus 로고
    • Pe?rigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
    • Martin, F. et al. Pe?rigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464, 1033-1038 (2010).
    • (2010) Nature , vol.464 , pp. 1033-1038
    • Martin, F.1
  • 17
    • 84936187728 scopus 로고    scopus 로고
    • Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity
    • Lahrmann, U. et al. Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity. New Phytol. 207, 841-857 (2015).
    • (2015) New Phytol , vol.207 , pp. 841-857
    • Lahrmann, U.1
  • 18
    • 84928892986 scopus 로고    scopus 로고
    • Fungal effectors and plant susceptibility
    • Lo Presti, L. et al. Fungal effectors and plant susceptibility. Annu. Rev. Plant Biol. 66, 513-545 (2015).
    • (2015) Annu. Rev. Plant Biol , vol.66 , pp. 513-545
    • Lo Presti, L.1
  • 19
    • 80055091319 scopus 로고    scopus 로고
    • Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica
    • Zuccaro, A. et al. Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog. 7, e1002290 (2011).
    • (2011) PLoS Pathog , vol.7 , pp. e1002290
    • Zuccaro, A.1
  • 20
    • 84904623639 scopus 로고    scopus 로고
    • The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte
    • Xu, X. H. et al. The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte. Sci. Rep. 4, 5783 (2014).
    • (2014) Sci. Rep , vol.4 , pp. 5783
    • Xu, X.H.1
  • 21
    • 84880296137 scopus 로고    scopus 로고
    • Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis
    • Bonfante, P., Genre, A. Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nat. Commun. 1, 48 (2010).
    • (2010) Nat. Commun , vol.1 , pp. 48
    • Bonfante, P.1    Genre, A.2
  • 22
    • 67650175435 scopus 로고    scopus 로고
    • Cis-element-and transcriptome-based screening of root hair-specific genes and their functional characterization in Arabidopsis
    • Won, S. K. et al. Cis-element-and transcriptome-based screening of root hair-specific genes and their functional characterization in Arabidopsis. Plant Physiol. 150, 1459-1473 (2009).
    • (2009) Plant Physiol , vol.150 , pp. 1459-1473
    • Won, S.K.1
  • 23
    • 68249143317 scopus 로고    scopus 로고
    • The role of WRKY transcription factors in plant immunity
    • Pandey, S. P., Somssich, I. E. The role of WRKY transcription factors in plant immunity. Plant Physiol. 150, 1648-1655 (2009).
    • (2009) Plant Physiol , vol.150 , pp. 1648-1655
    • Pandey, S.P.1    Somssich, I.E.2
  • 24
    • 33646832415 scopus 로고    scopus 로고
    • Genome-wide analysis of the ERF gene family in Arabidopsis and rice
    • Nakano, T., Suzuki, K., Fujimura, T., Shinshi, H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140, 411-432 (2006).
    • (2006) Plant Physiol , vol.140 , pp. 411-432
    • Nakano, T.1    Suzuki, K.2    Fujimura, T.3    Shinshi, H.4
  • 25
    • 34249809696 scopus 로고    scopus 로고
    • The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana
    • Gigolashvili, T. et al. The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant J. 50, 886-901 (2007).
    • (2007) Plant J , vol.50 , pp. 886-901
    • Gigolashvili, T.1
  • 26
    • 58149215723 scopus 로고    scopus 로고
    • A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense
    • Bednarek, P. et al. A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science 323, 101-106 (2009).
    • (2009) Science , vol.323 , pp. 101-106
    • Bednarek, P.1
  • 27
    • 58149242371 scopus 로고    scopus 로고
    • Glucosinolate metabolites required for an Arabidopsis innate immune response
    • Clay, N. K., Adio, A. M., Denoux, C., Jander, G., Ausubel, F. M. Glucosinolate metabolites required for an Arabidopsis innate immune response. Science 323, 95-101 (2009).
    • (2009) Science , vol.323 , pp. 95-101
    • Clay, N.K.1    Adio, A.M.2    Denoux, C.3    Jander, G.4    Ausubel, F.M.5
  • 28
    • 84929314503 scopus 로고    scopus 로고
    • Identification of primary and secondary metabolites with phosphorus status-dependent abundance in Arabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation
    • Pant, B. D. et al. Identification of primary and secondary metabolites with phosphorus status-dependent abundance in Arabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation. Plant Cell Environ. 38, 172-187 (2015).
    • (2015) Plant Cell Environ , vol.38 , pp. 172-187
    • Pant, B.D.1
  • 29
    • 0027416243 scopus 로고
    • Genetic conversion of a fungal plant pathogen to a nonpathogenic, endophytic mutualist
    • Freeman, S., Rodriguez, R. J. Genetic conversion of a fungal plant pathogen to a nonpathogenic, endophytic mutualist. Science 260, 75-78 (1993).
    • (1993) Science , vol.260 , pp. 75-78
    • Freeman, S.1    Rodriguez, R.J.2
  • 31
    • 84875741316 scopus 로고    scopus 로고
    • Transcriptome responses to combinations of stresses in Arabidopsis
    • Rasmussen, S. et al. Transcriptome responses to combinations of stresses in Arabidopsis. Plant Physiol. 161, 1783-1794 (2013).
    • (2013) Plant Physiol , vol.161 , pp. 1783-1794
    • Rasmussen, S.1
  • 32
    • 0027951885 scopus 로고
    • The development of mycorrhizal infection in cucumber: Effects of P supply on root growth, formation of entry points and growth of infection units
    • Bruce, A., Smith, S. E., Tester, M. The development of mycorrhizal infection in cucumber: effects of P supply on root growth, formation of entry points and growth of infection units. New Phytol. 127, 507-514 (1994).
    • (1994) New Phytol , vol.127 , pp. 507-514
    • Bruce, A.1    Smith, S.E.2    Tester, M.3
  • 33
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux, B. et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147-1159 (2004).
    • (2004) Genome Res , vol.14 , pp. 1147-1159
    • Chevreux, B.1
  • 34
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 35
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R., Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 36
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
    • (2004) Genome Biol , vol.5 , pp. R12
    • Kurtz, S.1
  • 37
    • 84878076144 scopus 로고    scopus 로고
    • REAPR: A universal tool for genome assembly evaluation
    • Hunt, M. et al. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14, R47 (2013).
    • (2013) Genome Biol , vol.14 , pp. R47
    • Hunt, M.1
  • 38
    • 34249848751 scopus 로고    scopus 로고
    • 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 23, 1061-1067 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 39
    • 84860513986 scopus 로고    scopus 로고
    • PILER: Identification and classification of genomic repeats
    • Edgar, R. C., Myers, E. W. PILER: identification and classification of genomic repeats. Bioinformatics 21, i152-i158 (2005).
    • (2005) Bioinformatics , vol.21 , pp. i152-i158
    • Edgar, R.C.1    Myers, E.W.2
  • 41
    • 23844525077 scopus 로고    scopus 로고
    • Repbase Update, a database of eukaryotic repetitive elements
    • Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
    • (2005) Cytogenet. Genome Res , vol.110 , pp. 462-467
    • Jurka, J.1
  • 42
    • 0037314098 scopus 로고    scopus 로고
    • R8S: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301-302 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 43
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.2
  • 44
    • 68549104404 scopus 로고    scopus 로고
    • The sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 45
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
    • (2009) Genome Res , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 46
    • 84055178433 scopus 로고    scopus 로고
    • MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects
    • Holt, C., Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12, 491 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 491
    • Holt, C.1    Yandell, M.2
  • 47
    • 33747830848 scopus 로고    scopus 로고
    • AUGUSTUS: Ab initio prediction of alternative transcripts
    • Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. W435-W439
    • Stanke, M.1
  • 48
    • 57149099395 scopus 로고    scopus 로고
    • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y., Borodovsky, M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18, 1979-1990 (2008).
    • (2008) Genome Res , vol.18 , pp. 1979-1990
    • Ter-Hovhannisyan, V.1    Lomsadze, A.2    Chernoff, Y.3    Borodovsky, M.4
  • 49
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 50
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater, G. S., Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 51
    • 79960264362 scopus 로고    scopus 로고
    • Full-Length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 52
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1
  • 53
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J., Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 54
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
    • (2011) Mol. Syst. Biol , vol.7 , pp. 539
    • Sievers, F.1
  • 55
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • So?ding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 56
    • 84891757311 scopus 로고    scopus 로고
    • Eggnog v4.0: Nested orthology inference across 3686 organisms
    • Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42, D231-D239 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D231-D239
    • Powell, S.1
  • 57
    • 84857156030 scopus 로고    scopus 로고
    • Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony-A simulation study
    • Ofir, C., Pupko, T. Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony-a simulation study. Genome Biol. Evol. 3, 1265-1275 (2011).
    • (2011) Genome Biol. Evol , vol.3 , pp. 1265-1275
    • Ofir, C.1    Pupko, T.2
  • 58
    • 33750983947 scopus 로고    scopus 로고
    • Clearcut: A fast implementation of relaxed neighbor joining
    • Sheneman, L., Evans, J., Foster, J. A. Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22, 2823-2824 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2823-2824
    • Sheneman, L.1    Evans, J.2    Foster, J.A.3
  • 59
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • Suyama, M., Torrents, D., Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609-W612 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. W609-W612
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 60
    • 84864719167 scopus 로고    scopus 로고
    • Detecting patches of protein sites of influenza A viruses under positive selection
    • Tusche, C., Steinbru?ck, L., McHardy, A. C. Detecting patches of protein sites of influenza A viruses under positive selection. Mol. Biol. Evol. 29, 2063-2071 (2012).
    • (2012) Mol. Biol. Evol , vol.29 , pp. 2063-2071
    • Tusche, C.1    Steinbruck, L.2    McHardy, A.C.3
  • 61
    • 34547560275 scopus 로고    scopus 로고
    • WoLF PSORT: Protein localization predictor
    • Horton, P. et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35, W585-W587 (2007).
    • (2007) Nucleic Acids Res , vol.35 , pp. W585-W587
    • Horton, P.1
  • 64
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1
  • 65
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-A Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P. T., Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2014).
    • (2014) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 66
    • 75249087100 scopus 로고    scopus 로고
    • Edger: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D., McCarthy, D. J., Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 67
    • 18744369640 scopus 로고    scopus 로고
    • Use of within-array replicate spots for assessing differential expression in microarray experiments
    • Smyth, G. K., Michaud, J., Scott, H. S. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21, 2067-2075 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 2067-2075
    • Smyth, G.K.1    Michaud, J.2    Scott, H.S.3
  • 68
    • 0036169031 scopus 로고    scopus 로고
    • Genesis: Cluster analysis of microarray data
    • Sturn, A., Quackenbush, J., Trajanoski, Z. Genesis: cluster analysis of microarray data. Bioinformatics 18, 207-208 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 207-208
    • Sturn, A.1    Quackenbush, J.2    Trajanoski, Z.3
  • 69
    • 33845873289 scopus 로고    scopus 로고
    • Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
    • Letunic, I., Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 70
    • 64549104807 scopus 로고    scopus 로고
    • ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
    • Bindea, G. et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25, 1091-1093 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1091-1093
    • Bindea, G.1
  • 71
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 72
    • 17344392308 scopus 로고    scopus 로고
    • A new mathematical model for relative quantification in real-time RT-PCR
    • Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).
    • (2001) Nucleic Acids Res , vol.29 , pp. e45
    • Pfaffl, M.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.