메뉴 건너뛰기




Volumn 48, Issue 2, 2016, Pages 167-175

Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; DNA BASE COMPOSITION; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HOST; LEGIONELLA; MACHINE LEARNING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTOZOON; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VALIDATION PROCESS; CLASSIFICATION; GENETICS; MOLECULAR EVOLUTION;

EID: 84961289935     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3481     Document Type: Article
Times cited : (217)

References (80)
  • 1
    • 78149443620 scopus 로고    scopus 로고
    • Bacterial contact-dependent delivery systems
    • Hayes, C.S., Aoki, S.K., & Low, D.A. Bacterial contact-dependent delivery systems. Annu. Rev. Genet. 44, 71-90 (2010
    • (2010) Annu. Rev. Genet , vol.44 , pp. 71-90
    • Hayes, C.S.1    Aoki, S.K.2    Low, D.A.3
  • 2
    • 0030200018 scopus 로고    scopus 로고
    • The molecular ecology of legionellae
    • Fields, B.S. The molecular ecology of legionellae. Trends Microbiol. 4, 286-290 (1996
    • (1996) Trends Microbiol , vol.4 , pp. 286-290
    • Fields, B.S.1
  • 3
    • 0036314980 scopus 로고    scopus 로고
    • Legionella and Legionnaires? Disease: 25 years of investigation
    • Fields, B.S., Benson, R.F., & Besser, R.E. Legionella and Legionnaires? disease: 25 years of investigation. Clin. Microbiol. Rev. 15, 506-526 (2002
    • (2002) Clin. Microbiol. Rev , vol.15 , pp. 506-526
    • Fields, B.S.1    Benson, R.F.2    Besser, R.E.3
  • 4
    • 37149000256 scopus 로고    scopus 로고
    • Legionella spp and Legionnaires? Disease
    • Diederen, B.M.W. Legionella spp. and Legionnaires? disease. J. Infect. 56, 1-12 (2008
    • (2008) J. Infect , vol.56 , pp. 1-12
    • Diederen, B.M.W.1
  • 5
    • 0032539674 scopus 로고    scopus 로고
    • Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome
    • Segal, G., Purcell, M., & Shuman, H.A. Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome. Proc. Natl. Acad. Sci. USA 95, 1669-1674 (1998
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1669-1674
    • Segal, G.1    Purcell, M.2    Shuman, H.A.3
  • 6
    • 0032488861 scopus 로고    scopus 로고
    • Conjugative transfer by the virulence system of Legionella pneumophila
    • Vogel, J.P., Andrews, H.L., Wong, S.K., & Isberg, R.R. Conjugative transfer by the virulence system of Legionella pneumophila. Science 279, 873-876 (1998
    • (1998) Science , vol.279 , pp. 873-876
    • Vogel, J.P.1    Andrews, H.L.2    Wong, S.K.3    Isberg, R.R.4
  • 7
    • 57649149094 scopus 로고    scopus 로고
    • The Legionella pneumophila replication vacuole: Making a cosy niche inside host cells
    • Isberg, R.R., O'Connor, T.J., & Heidtman, M. The Legionella pneumophila replication vacuole: making a cosy niche inside host cells. Nat. Rev. Microbiol. 7, 13-24 (2009
    • (2009) Nat. Rev. Microbiol , vol.7 , pp. 13-24
    • Isberg, R.R.1    O'Connor, T.J.2    Heidtman, M.3
  • 8
    • 24744441905 scopus 로고    scopus 로고
    • Coevolution between nonhomologous but functionally similar proteins and their conserved partners in the Legionella pathogenesis system
    • Feldman, M., Zusman, T., Hagag, S., & Segal, G. Coevolution between nonhomologous but functionally similar proteins and their conserved partners in the Legionella pathogenesis system. Proc. Natl. Acad. Sci. USA 102, 12206-12211 (2005
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 12206-12211
    • Feldman, M.1    Zusman, T.2    Hagag, S.3    Segal, G.4
  • 9
    • 3343000034 scopus 로고    scopus 로고
    • A specific genomic location within the icm/dot pathogenesis region of different Legionella species encodes functionally similar but nonhomologous virulence proteins
    • Feldman, M., & Segal, G A specific genomic location within the icm/dot pathogenesis region of different Legionella species encodes functionally similar but nonhomologous virulence proteins. Infect. Immun. 72, 4503-4511 (2004
    • (2004) Infect. Immun , vol.72 , pp. 4503-4511
    • Feldman, M.1    Segal, G.2
  • 10
    • 80052630257 scopus 로고    scopus 로고
    • Dot/Icm type IVB secretion system requirements for Coxiella burnetii growth in human macrophages
    • Beare P.A., et al. Dot/Icm type IVB secretion system requirements for Coxiella burnetii growth in human macrophages. MBio 2, e00175-11 (2011
    • (2011) MBio , vol.2 , pp. e00175-e00211
    • Beare, P.A.1
  • 11
    • 79958021807 scopus 로고    scopus 로고
    • The Coxiella burnetii Dot/Icm system delivers a unique repertoire of type IV effectors into host cells and is required for intracellular replication
    • Carey, K.L., Newton, H.J., Lührmann, A., & Roy, C.R. The Coxiella burnetii Dot/Icm system delivers a unique repertoire of type IV effectors into host cells and is required for intracellular replication. PLoS Pathog. 7, e1002056 (2011
    • (2011) PLoS Pathog , vol.7 , pp. e1002056
    • Carey, K.L.1    Newton, H.J.2    Lührmann, A.3    Roy, C.R.4
  • 12
    • 38349149732 scopus 로고    scopus 로고
    • Type IV secretion system components as phylogenetic markers of entomopathogenic bacteria of the genus Rickettsiella
    • Leclerque, A., & Kleespies, R.G. Type IV secretion system components as phylogenetic markers of entomopathogenic bacteria of the genus Rickettsiella. FEMS Microbiol. Lett. 279, 167-173 (2008
    • (2008) FEMS Microbiol. Lett , vol.279 , pp. 167-173
    • Leclerque, A.1    Kleespies, R.G.2
  • 13
    • 80052595488 scopus 로고    scopus 로고
    • Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion
    • O'Connor, T.J., Adepoju, Y., Boyd, D., & Isberg, R.R. Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion. Proc. Natl. Acad. Sci. USA 108, 14733-14740 (2011
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 14733-14740
    • O'Connor, T.J.1    Adepoju, Y.2    Boyd, D.3    Isberg, R.R.4
  • 14
    • 84871042527 scopus 로고    scopus 로고
    • Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen
    • O'Connor, T.J., Boyd, D., Dorer, M.S., & Isberg, R.R. Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen. Science 338, 1440-1444 (2012
    • (2012) Science , vol.338 , pp. 1440-1444
    • O'Connor, T.J.1    Boyd, D.2    Dorer, M.S.3    Isberg, R.R.4
  • 15
    • 68149093715 scopus 로고    scopus 로고
    • Search for a Tree of Life? in the thicket of the phylogenetic forest
    • Puigbò, P., Wolf, Y.I., & Koonin, E.V. Search for a Tree of Life? in the thicket of the phylogenetic forest. J. Biol. 8, 59 (2009
    • (2009) J. Biol , vol.8 , pp. 59
    • Puigbò, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 16
    • 0037108389 scopus 로고    scopus 로고
    • Infection due to Legionella species other than L pneumophila
    • Muder, R.R., & Yu, V.L. Infection due to Legionella species other than L. pneumophila. Clin. Infect. Dis. 35, 990-998 (2002
    • (2002) Clin. Infect. Dis , vol.35 , pp. 990-998
    • Muder, R.R.1    Yu, V.L.2
  • 17
    • 0036305718 scopus 로고    scopus 로고
    • Application of RNA polymerase β-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species
    • Ko K.S., et al. Application of RNA polymerase β-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J. Clin. Microbiol. 40, 2653-2658 (2002
    • (2002) J. Clin. Microbiol , vol.40 , pp. 2653-2658
    • Ko, K.S.1
  • 18
    • 11844273940 scopus 로고    scopus 로고
    • The Icm/Dot type-IV secretion systems of Legionella pneumophila and Coxiella burnetii
    • Segal, G., Feldman, M., & Zusman, T. The Icm/Dot type-IV secretion systems of Legionella pneumophila and Coxiella burnetii. FEMS Microbiol. Rev. 29, 65-81 (2005
    • (2005) FEMS Microbiol. Rev , vol.29 , pp. 65-81
    • Segal, G.1    Feldman, M.2    Zusman, T.3
  • 19
    • 84874280135 scopus 로고    scopus 로고
    • Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal
    • Lifshitz Z., et al. Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc. Natl. Acad. Sci. USA 110, E707-E715 (2013
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. E707-E715
    • Lifshitz, Z.1
  • 20
    • 84857771508 scopus 로고    scopus 로고
    • Comparative and functional genomics of Legionella identified eukaryotic like proteins as key players in host-pathogen interactions
    • Gomez-Valero, L., Rusniok, C., Cazalet, C., & Buchrieser, C. Comparative and functional genomics of Legionella identified eukaryotic like proteins as key players in host-pathogen interactions. Front. Microbiol. 2, 208 (2011
    • (2011) Front. Microbiol , vol.2 , pp. 208
    • Gomez-Valero, L.1    Rusniok, C.2    Cazalet, C.3    Buchrieser, C.4
  • 21
    • 70049110355 scopus 로고    scopus 로고
    • Genome-scale identification of Legionella pneumophila effectors using a machine learning approach
    • Burstein D., et al. Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog. 5, e1000508 (2009
    • (2009) PLoS Pathog , vol.5 , pp. e1000508
    • Burstein, D.1
  • 22
    • 84906070899 scopus 로고    scopus 로고
    • Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-Activated protein kinase pathway
    • Lifshitz Z., et al. Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-Activated protein kinase pathway. Infect. Immun. 82, 3740-3752 (2014
    • (2014) Infect. Immun , vol.82 , pp. 3740-3752
    • Lifshitz, Z.1
  • 23
    • 0027333330 scopus 로고
    • Hundreds of ankyrin-like repeats in functionally diverse proteins: Mobile modules that cross phyla horizontally?
    • Bork, P. Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally? Proteins 17, 363-374 (1993
    • (1993) Proteins , vol.17 , pp. 363-374
    • Bork, P.1
  • 24
    • 2442706456 scopus 로고    scopus 로고
    • The ankyrin repeat as molecular architecture for protein recognition
    • Mosavi, L.K., Cammett, T.J., Desrosiers, D.C., & Peng, Z.Y. The ankyrin repeat as molecular architecture for protein recognition. Protein Sci. 13, 1435-1448 (2004
    • (2004) Protein Sci , vol.13 , pp. 1435-1448
    • Mosavi, L.K.1    Cammett, T.J.2    Desrosiers, D.C.3    Peng, Z.Y.4
  • 25
    • 84926415727 scopus 로고    scopus 로고
    • IroT/mavN a new iron-regulated gene involved in Legionella pneumophila virulence against amoebae and macrophages
    • Portier, E., et al. IroT/mavN, a new iron-regulated gene involved in Legionella pneumophila virulence against amoebae and macrophages. Environ. Microbiol. 17, 1338-1350 (2015
    • (2015) Environ. Microbiol , vol.17 , pp. 1338-1350
    • Portier, E.1
  • 26
    • 84941696044 scopus 로고    scopus 로고
    • MavN is a Legionella pneumophila vacuole-Associated protein required for efficient iron acquisition during intracellular growth
    • Isaac, D.T., Laguna, R.K., Valtz, N., & Isberg, R.R. MavN is a Legionella pneumophila vacuole-Associated protein required for efficient iron acquisition during intracellular growth. Proc. Natl. Acad. Sci. USA 112, E5208-E5217 (2015
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. E5208-E5217
    • Isaac, D.T.1    Laguna, R.K.2    Valtz, N.3    Isberg, R.R.4
  • 27
    • 0025331420 scopus 로고
    • Nitrogen fixation genes involved in the Bradyrhizobium japonicum-soybean symbiosis
    • Hennecke, H. Nitrogen fixation genes involved in the Bradyrhizobium japonicum-soybean symbiosis. FEBS Lett. 268, 422-426 (1990
    • (1990) FEBS Lett , vol.268 , pp. 422-426
    • Hennecke, H.1
  • 28
    • 0036928484 scopus 로고    scopus 로고
    • Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110
    • Kaneko T., et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189-197 (2002
    • (2002) DNA Res , vol.9 , pp. 189-197
    • Kaneko, T.1
  • 29
    • 84895835195 scopus 로고    scopus 로고
    • Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla
    • Li, X.-Q., & Du, D. Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla. PLoS One 9, e88339 (2014
    • (2014) PLoS One , vol.9 , pp. e88339
    • Li, X.-Q.1    Du, D.2
  • 30
    • 26244463780 scopus 로고    scopus 로고
    • Candidatus Protochlamydia amoebophila? An endosymbiont of Acanthamoeba spp
    • Collingro, A., et al. Candidatus Protochlamydia amoebophila?, an endosymbiont of Acanthamoeba spp. Int. J. Syst. Evol. Microbiol. 55, 1863-1866 (2005
    • (2005) Int. J. Syst. Evol. Microbiol , vol.55 , pp. 1863-1866
    • Collingro, A.1
  • 31
    • 79960929331 scopus 로고    scopus 로고
    • Legionella pneumophila SidD is a deAMPylase that modifies Rab1
    • Tan, Y., & Luo, Z.-Q. Legionella pneumophila SidD is a deAMPylase that modifies Rab1. Nature 475, 506-509 (2011
    • (2011) Nature , vol.475 , pp. 506-509
    • Tan, Y.1    Luo, Z.-Q.2
  • 32
    • 79960699136 scopus 로고    scopus 로고
    • De-AMPylation of the small GTPase Rab1 by the pathogen Legionella pneumophila
    • Neunuebel M.R., et al. De-AMPylation of the small GTPase Rab1 by the pathogen Legionella pneumophila. Science 333, 453-456 (2011
    • (2011) Science , vol.333 , pp. 453-456
    • Neunuebel, M.R.1
  • 33
    • 36249027095 scopus 로고    scopus 로고
    • Legionella pneumophila proteins that regulate Rab1 membrane cycling
    • Ingmundson, A., Delprato, A., Lambright, D.G., & Roy, C.R. Legionella pneumophila proteins that regulate Rab1 membrane cycling. Nature 450, 365-369 (2007
    • (2007) Nature , vol.450 , pp. 365-369
    • Ingmundson, A.1    Delprato, A.2    Lambright, D.G.3    Roy, C.R.4
  • 34
    • 78651234971 scopus 로고    scopus 로고
    • Legionella metaeffector exploits host proteasome to temporally regulate cognate effector
    • Kubori, T., Shinzawa, N., Kanuka, H., & Nagai, H. Legionella metaeffector exploits host proteasome to temporally regulate cognate effector. PLoS Pathog. 6, e1001216 (2010
    • (2010) PLoS Pathog , vol.6 , pp. e1001216
    • Kubori, T.1    Shinzawa, N.2    Kanuka, H.3    Nagai, H.4
  • 35
    • 84926506077 scopus 로고    scopus 로고
    • Spatiotemporal regulation of a Legionella pneumophila T4SS substrate by the metaeffector SidJ
    • Jeong, K.C., Sexton, J.A., & Vogel, J.P. Spatiotemporal regulation of a Legionella pneumophila T4SS substrate by the metaeffector SidJ. PLoS Pathog. 11, e1004695 (2015
    • (2015) PLoS Pathog , vol.11 , pp. e1004695
    • Jeong, K.C.1    Sexton, J.A.2    Vogel, J.P.3
  • 36
    • 84939526529 scopus 로고    scopus 로고
    • Toxicity and sidj-mediated suppression of toxicity require distinct regions in the side family of legionella pneumophila effectors
    • Havey, J.C., & Roy, C.R. Toxicity and SidJ-mediated suppression of toxicity require distinct regions in the SidE family of Legionella pneumophila effectors. Infect. Immun. 83, 3506-3514 (2015
    • (2015) Infect. Immun , vol.83 , pp. 3506-3514
    • Havey, J.C.1    Roy, C.R.2
  • 37
    • 65549084822 scopus 로고    scopus 로고
    • Targeting eEF1A by a Legionella pneumophila effector leads to inhibition of protein synthesis and induction of host stress response
    • Shen X., et al. Targeting eEF1A by a Legionella pneumophila effector leads to inhibition of protein synthesis and induction of host stress response. Cell. Microbiol. 11, 911-926 (2009
    • (2009) Cell. Microbiol , vol.11 , pp. 911-926
    • Shen, X.1
  • 38
    • 79952203418 scopus 로고    scopus 로고
    • Secreted bacterial effectors that inhibit host protein synthesis are critical for induction of the innate immune response to virulent Legionella pneumophila
    • Fontana M.F., et al. Secreted bacterial effectors that inhibit host protein synthesis are critical for induction of the innate immune response to virulent Legionella pneumophila. PLoS Pathog. 7, e1001289 (2011
    • (2011) PLoS Pathog , vol.7 , pp. e1001289
    • Fontana, M.F.1
  • 39
    • 10044263696 scopus 로고    scopus 로고
    • Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity
    • Cazalet C., et al. Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat. Genet. 36, 1165-1173 (2004
    • (2004) Nat. Genet , vol.36 , pp. 1165-1173
    • Cazalet, C.1
  • 40
    • 27744546297 scopus 로고    scopus 로고
    • Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer
    • de Felipe K.S., et al. Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J. Bacteriol. 187, 7716-7726 (2005
    • (2005) J. Bacteriol , vol.187 , pp. 7716-7726
    • De Felipe, K.S.1
  • 41
    • 64149084796 scopus 로고    scopus 로고
    • Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila
    • Brombacher E., et al. Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila. J. Biol. Chem. 284, 4846-4856 (2009
    • (2009) J. Biol. Chem , vol.284 , pp. 4846-4856
    • Brombacher, E.1
  • 42
    • 33646915714 scopus 로고    scopus 로고
    • Legionella pneumophila exploits PI(4)P to anchor secreted effector proteins to the replicative vacuole
    • Weber, S.S., Ragaz, C., Reus, K., Nyfeler, Y., & Hilbi, H. Legionella pneumophila exploits PI(4)P to anchor secreted effector proteins to the replicative vacuole. PLoS Pathog. 2, e46 (2006
    • (2006) PLoS Pathog , vol.2 , pp. e46
    • Weber, S.S.1    Ragaz, C.2    Reus, K.3    Nyfeler, Y.4    Hilbi, H.5
  • 43
    • 84905372666 scopus 로고    scopus 로고
    • The machinery at endoplasmic reticulum-plasma membrane contact sites contributes to spatial regulation of multiple Legionella effector proteins
    • Hubber A., et al. The machinery at endoplasmic reticulum-plasma membrane contact sites contributes to spatial regulation of multiple Legionella effector proteins. PLoS Pathog. 10, e1004222 (2014
    • (2014) PLoS Pathog , vol.10 , pp. e1004222
    • Hubber, A.1
  • 45
    • 77955397296 scopus 로고    scopus 로고
    • Exploitation of conserved eukaryotic host cell farnesylation machinery by an F-box effector of Legionella pneumophila
    • Price, C.T.D., Al-Quadan, T., Santic, M., Jones, S.C., & Abu Kwaik, Y. Exploitation of conserved eukaryotic host cell farnesylation machinery by an F-box effector of Legionella pneumophila. J. Exp. Med. 207, 1713-1726 (2010
    • (2010) J. Exp. Med , vol.207 , pp. 1713-1726
    • Price, C.T.D.1    Al-Quadan, T.2    Santic, M.3    Jones, S.C.4    Abu Kwaik, Y.5
  • 46
    • 83855160757 scopus 로고    scopus 로고
    • Host proteasomal degradation generates amino acids essential for intracellular bacterial growth
    • Price, C.T.D., Al-Quadan, T., Santic, M., Rosenshine, I., & Abu Kwaik, Y. Host proteasomal degradation generates amino acids essential for intracellular bacterial growth. Science 334, 1553-1557 (2011
    • (2011) Science , vol.334 , pp. 1553-1557
    • Price, C.T.D.1    Al-Quadan, T.2    Santic, M.3    Rosenshine, I.4    Abu Kwaik, Y.5
  • 47
    • 84861196561 scopus 로고    scopus 로고
    • Domain organization of Legionella effector SetA
    • Jank T., et al. Domain organization of Legionella effector SetA. Cell. Microbiol. 14, 852-868 (2012
    • (2012) Cell. Microbiol , vol.14 , pp. 852-868
    • Jank, T.1
  • 48
    • 84882408124 scopus 로고    scopus 로고
    • The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism
    • Mishra, A.K., Del Campo, C.M., Collins, R.E., Roy, C.R., & Lambright, D.G. The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism. J. Biol. Chem. 288, 24000-24011 (2013
    • (2013) J. Biol. Chem , vol.288 , pp. 24000-24011
    • Mishra, A.K.1    Del Campo, C.M.2    Collins, R.E.3    Roy, C.R.4    Lambright, D.G.5
  • 50
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A.M., Lohse, M., & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 51
    • 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
  • 52
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt D., et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1
  • 53
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C.J. Jr., & 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
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M., & Eisen, J.A A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9, R151 (2008
    • (2008) Genome Biol , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 56
    • 34249761849 scopus 로고
    • Learning Bayesian networks: The combination of knowledge and statistical data
    • Heckerman, D., Geiger, D., & Chickering, D.M. Learning Bayesian networks: the combination of knowledge and statistical data. Mach. Learn. 20, 197-243 (1995
    • (1995) Mach. Learn , vol.20 , pp. 197-243
    • Heckerman, D.1    Geiger, D.2    Chickering, D.M.3
  • 57
    • 27144489164 scopus 로고    scopus 로고
    • A tutorial on support vector machines for pattern recognition
    • Burges, C.J.C A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Discov. 2, 121-167 (1998
    • (1998) Data Min. Knowl. Discov , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 58
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. Random forests. Mach. Learn. 45, 5-32 (2001
    • (2001) Mach. Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 60
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492-508 (2002
    • (2002) Syst. Biol , vol.51 , pp. 492-508
    • Shimodaira, H.1
  • 61
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289-300 (1995
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 62
    • 77249088623 scopus 로고    scopus 로고
    • Inference and characterization of horizontally transferred gene families using stochastic mapping
    • Cohen, O., & Pupko, T. Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol. Biol. Evol. 27, 703-713 (2010
    • (2010) Mol. Biol. Evol , vol.27 , pp. 703-713
    • Cohen, O.1    Pupko, T.2
  • 63
    • 75549088819 scopus 로고    scopus 로고
    • MicrobesOnline: An integrated portal for comparative and functional genomics
    • Dehal P.S., et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38, D396-D400 (2010
    • (2010) Nucleic Acids Res , vol.38 , pp. D396-D400
    • Dehal, P.S.1
  • 66
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-Analysis of large phylogenies
    • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-Analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 67
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira, H., & Hasegawa, M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247 (2001
    • (2001) Bioinformatics , vol.17 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 68
    • 1842406033 scopus 로고    scopus 로고
    • Characterization of a new region required for macrophage killing by Legionella pneumophila
    • Segal, G., & Shuman, H.A. Characterization of a new region required for macrophage killing by Legionella pneumophila. Infect. Immun. 65, 5057-5066 (1997
    • (1997) Infect. Immun , vol.65 , pp. 5057-5066
    • Segal, G.1    Shuman, H.A.2
  • 69
    • 0032932436 scopus 로고    scopus 로고
    • Legionella pneumophila utilizes the same genes to multiply within Acanthamoeba castellanii and human macrophages
    • Segal, G., & Shuman, H.A. Legionella pneumophila utilizes the same genes to multiply within Acanthamoeba castellanii and human macrophages. Infect. Immun. 67, 2117-2124 (1999
    • (1999) Infect. Immun , vol.67 , pp. 2117-2124
    • Segal, G.1    Shuman, H.A.2
  • 70
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K., & Standley, D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013
    • (2013) Mol. Biol. Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 71
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy, S.R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011
    • (2011) PLoS Comput. Biol , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 72
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert, M., Biegert, A., Hauser, A., & Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173-175 (2012
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Söding, J.4
  • 73
    • 0036087630 scopus 로고    scopus 로고
    • CDD: A database of conserved domain alignments with links to domain three-dimensional structure
    • Marchler-Bauer A., et al. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30, 281-283 (2002
    • (2002) Nucleic Acids Res , vol.30 , pp. 281-283
    • Marchler-Bauer, A.1
  • 74
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Punta M., et al. The Pfam protein families database. Nucleic Acids Res. 40, D290-D301 (2012
    • (2012) Nucleic Acids Res , vol.40 , pp. D290-D301
    • Punta, M.1
  • 75
    • 84862221167 scopus 로고    scopus 로고
    • SMART 7: Recent updates to the protein domain annotation resource
    • Letunic, I., Doerks, T., & Bork, P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40, D302-D305 (2012
    • (2012) Nucleic Acids Res , vol.40 , pp. D302-D305
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 76
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 77
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas, A., Van Dyke, M., & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162-1164 (1991
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 78
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi, G., & Nepusz, T. The igraph software package for complex network research. InterJournal Complex Syst. 1695, 1-9 (2006
    • (2006) InterJournal Complex Syst , vol.1695 , pp. 1-9
    • Csardi, G.1    Nepusz, T.2
  • 80
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree of Life v2: Online annotation and display of phylogenetic trees made easy
    • Letunic, I., & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011
    • (2011) Nucleic Acids Res , vol.39 , pp. W475-W478
    • Letunic, I.1    Bork, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.