메뉴 건너뛰기




Volumn 8, Issue 12, 2013, Pages

Effective identification of gram-negative bacterial type III secreted effectors using position-specific residue conservation profiles

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; CHAPERONE;

EID: 84896707996     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084439     Document Type: Article
Times cited : (24)

References (83)
  • 1
    • 63549137674 scopus 로고    scopus 로고
    • Secretion and subcellular localizations of bacterial proteins: A semantic awareness issue
    • Desvaux M, Hebraud M, Talon R, Henderson IR (2009) Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 17: 139-145.
    • (2009) Trends Microbiol , vol.17 , pp. 139-145
    • Desvaux, M.1    Hebraud, M.2    Talon, R.3    Henderson, I.R.4
  • 2
    • 0033016809 scopus 로고    scopus 로고
    • Bacterial secreted proteins are required for the internalization of Campylobacter jejuni into cultured mammalian cells
    • DOI 10.1046/j.1365-2958.1999.01376.x
    • Konkel ME, Kim BJ, Rivera-Amill V, Garvis SG (1999) Bacterial secreted proteins are required for the internalization of Campylobacter jejuni into cultured mammalian cells. Mol Microbiol 32: 691-701. (Pubitemid 29241511)
    • (1999) Molecular Microbiology , vol.32 , Issue.4 , pp. 691-701
    • Konkel, M.E.1    Kim, B.J.2    Rivera-Amill, V.3    Garvis, S.G.4
  • 3
    • 8844275498 scopus 로고    scopus 로고
    • Type III protein secretion mechanism in mammalian and plant pathogens
    • DOI 10.1016/j.bbamcr.2004.03.011, PII S0167488904000874
    • He SY, Nomura K, Whittam TS (2004) Type III protein secretion mechanism in mammalian and plant pathogens. BBA-Mol Cell Res 1694: 181-206. (Pubitemid 39535069)
    • (2004) Biochimica et Biophysica Acta - Molecular Cell Research , vol.1694 , Issue.1-3 SPEC.ISS. , pp. 181-206
    • He, S.Y.1    Nomura, K.2    Whittam, T.S.3
  • 4
    • 84896710923 scopus 로고    scopus 로고
    • The type-III secretion injectisome
    • Cornelis GR (2007) The type-III secretion injectisome. Int J Medical Microbiol 297: 28-28.
    • (2007) Int J Medical Microbiol , vol.297 , pp. 28-28
    • Cornelis, G.R.1
  • 5
    • 79960719451 scopus 로고    scopus 로고
    • Functional domains and motifs of bacterial type III effector proteins and their roles in infection
    • Dean P (2011) Functional domains and motifs of bacterial type III effector proteins and their roles in infection. Fems Microbiol Rev 35: 1100-1125.
    • (2011) Fems Microbiol Rev , vol.35 , pp. 1100-1125
    • Dean, P.1
  • 6
    • 48049108686 scopus 로고    scopus 로고
    • Evolution of prokaryotic and eukaryotic virulence effectors
    • Ma W, Guttman DS (2008) Evolution of prokaryotic and eukaryotic virulence effectors. Curr Opin Plant Biol 11: 412-419.
    • (2008) Curr Opin Plant Biol , vol.11 , pp. 412-419
    • Ma, W.1    Guttman, D.S.2
  • 8
    • 77955668989 scopus 로고    scopus 로고
    • SecretP: Identifying bacterial secreted proteins by fusing Chou's pseudo-amino acid composition
    • Yu LZ, Guo YZ, Li YZ, Li GB, Li ML, et al. (2010) SecretP: Identifying bacterial secreted proteins by fusing Chou's pseudo-amino acid composition. J Theor Biol 267: 1-6.
    • (2010) J Theor Biol , vol.267 , pp. 1-6
    • Yu, L.Z.1    Guo, Y.Z.2    Li, Y.Z.3    Li, G.B.4    Li, M.L.5
  • 9
    • 0033044637 scopus 로고    scopus 로고
    • Machine learning approaches for the prediction of signal peptides and other protein sorting signals
    • Nielsen H, Brunak S, von Heijne G (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng 12: 3-9. (Pubitemid 29050535)
    • (1999) Protein Engineering , vol.12 , Issue.1 , pp. 3-9
    • Nielsen, H.1    Brunak, S.2    Von Heijne, G.3
  • 10
    • 0031240609 scopus 로고    scopus 로고
    • A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst 8: 581-599.
    • (1997) Int J Neural Syst , vol.8 , pp. 581-599
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 11
    • 15844431346 scopus 로고    scopus 로고
    • PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
    • DOI 10.1093/bioinformatics/bti057
    • Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, et al. (2005) PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21: 617-623. (Pubitemid 40424787)
    • (2005) Bioinformatics , vol.21 , Issue.5 , pp. 617-623
    • Gardy, J.L.1    Laird, M.R.2    Chen, F.3    Rey, S.4    Walsh, C.J.5    Ester, M.6    Brinkman, F.S.L.7
  • 12
    • 77649238490 scopus 로고    scopus 로고
    • SecretP: A new method for predicting mammalian secreted proteins
    • Yu LZ, Guo YZ, Zhang Z, Li YZ, Li ML, et al. (2010) SecretP: A new method for predicting mammalian secreted proteins. Peptides 31: 574-578.
    • (2010) Peptides , vol.31 , pp. 574-578
    • Yu, L.Z.1    Guo, Y.Z.2    Zhang, Z.3    Li, Y.Z.4    Li, M.L.5
  • 13
    • 83655167415 scopus 로고    scopus 로고
    • Functional classification of secreted proteins by position specific scoring matrix and auto covariance
    • Luo JS, Yu LZ, Guo YZ, Li ML (2012) Functional classification of secreted proteins by position specific scoring matrix and auto covariance. Chemometrics and Intell Lab Syst 110: 163-167.
    • (2012) Chemometrics and Intell Lab Syst , vol.110 , pp. 163-167
    • Luo, J.S.1    Yu, L.Z.2    Guo, Y.Z.3    Li, M.L.4
  • 14
    • 26244460966 scopus 로고    scopus 로고
    • A genome-wide screen identifies a Bordetella type III secretion effector and candidate effectors in other species
    • DOI 10.1111/j.1365-2958.2005.04823.x
    • Panina EM, Mattoo S, Griffith N, Kozak NA, Yuk MH, et al. (2005) A genome-wide screen identifies a Bordetella type III secretion effector and candidate effectors in other species. Mol Microbiol 58: 267-279. (Pubitemid 41415046)
    • (2005) Molecular Microbiology , vol.58 , Issue.1 , pp. 267-279
    • Panina, E.M.1    Mattoo, S.2    Griffith, N.3    Kozak, N.A.4    Yuk, M.H.5    Miller, J.F.6
  • 17
    • 27144559247 scopus 로고    scopus 로고
    • Chaperone release and unfolding of substrates in type III secretion
    • DOI 10.1038/nature03992, PII N03992
    • Akeda Y, Galan JE (2005) Chaperone release and unfolding of substrates in type III secretion. Nature 437: 911-915. (Pubitemid 41486769)
    • (2005) Nature , vol.437 , Issue.7060 , pp. 911-915
    • Akeda, Y.1    Galan, J.E.2
  • 18
    • 10344249890 scopus 로고    scopus 로고
    • Process of protein transport by the type III secretion system
    • Ghosh P (2004) Process of protein transport by the type III secretion system. Microbiol Mol Biol Rev 68: 771-795.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 771-795
    • Ghosh, P.1
  • 20
    • 67149131853 scopus 로고    scopus 로고
    • Identification and characterization of a type III secretion-associated chaperone in the type III secretion system 1 of Vibrio parahaemolyticus
    • Akeda Y, Okayama K, Kimura T, Dryselius R, Kodama T, et al. (2009) Identification and characterization of a type III secretion-associated chaperone in the type III secretion system 1 of Vibrio parahaemolyticus. FEMS Microbiol Lett 296: 18-25.
    • (2009) FEMS Microbiol Lett , vol.296 , pp. 18-25
    • Akeda, Y.1    Okayama, K.2    Kimura, T.3    Dryselius, R.4    Kodama, T.5
  • 22
    • 1842413699 scopus 로고    scopus 로고
    • A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica
    • Anderson DM, Schneewind O (1997) A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica. Science 278: 1140-1143.
    • (1997) Science , vol.278 , pp. 1140-1143
    • Anderson, D.M.1    Schneewind, O.2
  • 23
    • 70350181746 scopus 로고    scopus 로고
    • Identification of a Campylobacter jejuni-secreted protein required for maximal invasion of host cells
    • Christensen JE, Pacheco SA, Konkel ME (2009) Identification of a Campylobacter jejuni-secreted protein required for maximal invasion of host cells. Mol Microbiol 73: 650-662.
    • (2009) Mol Microbiol , vol.73 , pp. 650-662
    • Christensen, J.E.1    Pacheco, S.A.2    Konkel, M.E.3
  • 24
    • 0036267324 scopus 로고    scopus 로고
    • Yersinia enterocolitica type III secretion: Mutational analysis of the yopQ secretion signal
    • DOI 10.1128/JB.184.12.3321-3328.2002
    • Ramamurthi KS, Schneewind O (2002) Yersinia enterocolitica type III secretion: mutational analysis of the yopQ secretion signal. J Bacteriol 184: 3321-3328. (Pubitemid 34568942)
    • (2002) Journal of Bacteriology , vol.184 , Issue.12 , pp. 3321-3328
    • Ramamurthi, K.S.1    Schneewind, O.2
  • 25
    • 0344826585 scopus 로고    scopus 로고
    • Yersinia yopQ mRNa encodes a bipartite type III secretion signal in the first 15 codons
    • DOI 10.1046/j.1365-2958.2003.03772.x
    • Ramamurthi KS, Schneewind O (2003) Yersinia yopQ mRNA encodes a bipartite type III secretion signal in the first 15 codons. Mol Microbiol 50: 1189-1198. (Pubitemid 37475852)
    • (2003) Molecular Microbiology , vol.50 , Issue.4 , pp. 1189-1198
    • Ramamurthi, K.S.1    Schneewind, O.2
  • 26
    • 0028105015 scopus 로고
    • Translocation of a hybrid YopE-adenylate cyclase from Yersinia enterocolitica into HeLa cells
    • Sory MP, Cornelis GR (1994) Translocation of a hybrid YopE-adenylate cyclase from Yersinia enterocolitica into HeLa cells. Mol Microbiol 14: 583-594.
    • (1994) Mol Microbiol , vol.14 , pp. 583-594
    • Sory, M.P.1    Cornelis, G.R.2
  • 27
    • 66349123567 scopus 로고    scopus 로고
    • Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems
    • doi:10.1371/journal.-ppat.1000375
    • Samudrala R, Heffron F, McDermott JE (2009) Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems. PLoS Pathog 5: e1000375. doi:10.1371/journal.- ppat.1000375.
    • (2009) PLoS Pathog , vol.5
    • Samudrala, R.1    Heffron, F.2    McDermott, J.E.3
  • 28
    • 84857874120 scopus 로고    scopus 로고
    • A new means to identify type 3 secreted effectors: Functionally interchangeable class IB chaperones recognize a conserved sequence
    • Costa SCP, Schmitz AM, Jahufar FF, Boyd JD, Cho MY, et al. (2012) A new means to identify type 3 secreted effectors: functionally interchangeable class IB chaperones recognize a conserved sequence. mBio, 3: e00243-11.
    • (2012) mBio , vol.3
    • Costa, S.C.P.1    Schmitz, A.M.2    Jahufar, F.F.3    Boyd, J.D.4    Cho, M.Y.5
  • 29
    • 0036500995 scopus 로고    scopus 로고
    • A functional screen for the type III (Hrp) secretome of the plant pathogen Pseudomonas syringae
    • DOI 10.1126/science.295.5560.1722
    • Guttman DS, Vinatzer BA, Sarkar SF, Ranall MV, Kettler G, et al. (2002) A functional screen for the type III (Hrp) secretome of the plant pathogen Pseudomonas syringae. Science 295: 1722-1726. (Pubitemid 34202909)
    • (2002) Science , vol.295 , Issue.5560 , pp. 1722-1726
    • Guttman, D.S.1    Vinatzer, B.A.2    Sarkar, S.F.3    Ranall, M.V.4    Kettler, G.5    Greenberg, J.T.6
  • 30
    • 66349124179 scopus 로고    scopus 로고
    • Sequence-Based Prediction of Type III Secreted Proteins
    • doi:10.1371/journal.ppat.1000376
    • Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, et al. (2009) Sequence-Based Prediction of Type III Secreted Proteins. PLoS Pathog 5: e1000376. doi:10.1371/journal.ppat.1000376.
    • (2009) PLoS Pathog , vol.5
    • Arnold, R.1    Brandmaier, S.2    Kleine, F.3    Tischler, P.4    Heinz, E.5
  • 31
    • 67650151451 scopus 로고    scopus 로고
    • Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria
    • doi:10.1371/journal.pone.0005917
    • Loewer M, Schneider G (2009) Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria. PloS One 4: e5917. doi:10.1371/journal.pone. 0005917.
    • (2009) PloS One , vol.4
    • Loewer, M.1    Schneider, G.2
  • 32
    • 81055131616 scopus 로고    scopus 로고
    • Meta-analytic approach to the accurate prediction of secreted virulence effectors in Gram-negative bacteria
    • Sato Y, Takaya A, Yamamoto T (2011) Meta-analytic approach to the accurate prediction of secreted virulence effectors in Gram-negative bacteria. BMC Bioinformatics 12: 442.
    • (2011) BMC Bioinformatics , vol.12 , pp. 442
    • Sato, Y.1    Takaya, A.2    Yamamoto, T.3
  • 33
    • 75149124497 scopus 로고    scopus 로고
    • Computational prediction of type III secreted proteins from Gram-negative bacteria
    • Yang Y, Zhao J, Morgan RL, Ma W, Jiang T (2010) Computational prediction of type III secreted proteins from Gram-negative bacteria. BMC Bioinformatics 11: S47.
    • (2010) BMC Bioinformatics , vol.11
    • Yang, Y.1    Zhao, J.2    Morgan, R.L.3    Ma, W.4    Jiang, T.5
  • 34
    • 79952594050 scopus 로고    scopus 로고
    • High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
    • Wang Y, Zhang Q, Sun MA, Guo D (2011) High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 27: 777-784.
    • (2011) Bioinformatics , vol.27 , pp. 777-784
    • Wang, Y.1    Zhang, Q.2    Sun, M.A.3    Guo, D.4
  • 35
    • 84874234583 scopus 로고    scopus 로고
    • Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes
    • Dong X, Zhang YJ, Zhang Z (2013) Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes. PLoS One 8: e56632.
    • (2013) PLoS One , vol.8
    • Dong, X.1    Zhang, Y.J.2    Zhang, Z.3
  • 37
    • 0034700171 scopus 로고    scopus 로고
    • Molecular signals required for type III secretion and translocation of the Xanthomonas campestris AvrBs2 protein to pepper plants
    • Mudgett MB, Chesnokova O, Dahlbeck D, Clark ET, Rossier O, et al. (2000) Molecular signals required for type III secretion and translocation of the Xanthomonas campestris AvrBs2 protein to pepper plants. Proc Natl Acad Sci U S A 97: 13324-13329.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 13324-13329
    • Mudgett, M.B.1    Chesnokova, O.2    Dahlbeck, D.3    Clark, E.T.4    Rossier, O.5
  • 39
    • 77957902441 scopus 로고    scopus 로고
    • T3SEdb: Data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
    • Tay DMM, Govindarajan KR, Khan AM, Ong TYR, Samad HM, et al. (2010) T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics 11: S4.
    • (2010) BMC Bioinformatics , vol.11
    • Tay, D.M.M.1    Govindarajan, K.R.2    Khan, A.M.3    Ong, T.Y.R.4    Samad, H.M.5
  • 40
    • 0036440902 scopus 로고    scopus 로고
    • The N-terminus of enteropathogenic Escherichia coli (EPEC) Tir mediates transport across bacterial and eukaryotic cell membranes
    • DOI 10.1046/j.1365-2958.2002.03214.x
    • Crawford JA, Kaper JB (2002) The N-terminus of enteropathogenic Escherichia coli (EPEC) Tir mediates transport across bacterial and eukaryotic cell membranes. Mol Microbiol 46: 855-68. (Pubitemid 35365619)
    • (2002) Molecular Microbiology , vol.46 , Issue.3 , pp. 855-868
    • Crawford, J.A.1    Kaper, J.B.2
  • 41
    • 84871018385 scopus 로고    scopus 로고
    • A translocator-specific export signal establishes the translocator-effector secretion hierarchy that is important for type III secretion system function
    • Tomalka AG, Stopford CM, Lee PC, Rietsch A (2012) A translocator-specific export signal establishes the translocator-effector secretion hierarchy that is important for type III secretion system function. Mol Microbiol 86: 1464-81.
    • (2012) Mol Microbiol , vol.86 , pp. 1464-1481
    • Tomalka, A.G.1    Stopford, C.M.2    Lee, P.C.3    Rietsch, A.4
  • 42
    • 0029608720 scopus 로고
    • Identification of the YopE and YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach
    • DOI 10.1073/pnas.92.26.11998
    • Sory MP, Boland A, Lambermont I, Cornelis GR (1995) Identification of the YopE and YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach. Proc Natl Acad Sci U S A 92: 11998-12002. (Pubitemid 26013998)
    • (1995) Proceedings of the National Academy of Sciences of the United States of America , vol.92 , Issue.26 , pp. 11998-12002
    • Sory, M.-P.1    Boland, A.2    Lambermont, I.3    Cornelis, G.R.4
  • 43
    • 0030474296 scopus 로고    scopus 로고
    • Delineation and mutational analysis of the Yersinia pseudotuberculosis YopE domains which mediate translocation across bacterial and eukaryotic cellular membranes
    • Schesser K, Frithz-Lindsten E, Wolf-Watz H (1996) Delineation and mutational analysis of the Yersinia pseudotuberculosis YopE domains which mediate translocation across bacterial and eukaryotic cellular membranes. J Bacteriol 178: 7227-7233. (Pubitemid 26424638)
    • (1996) Journal of Bacteriology , vol.178 , Issue.24 , pp. 7227-7233
    • Schesser, K.1    Frithz-Lindsten, E.2    Wolf-Watz, H.3
  • 44
    • 0942279512 scopus 로고    scopus 로고
    • Salmonella type III secretion-associated chaperones confer secretion-pathway specificity
    • Sang HL, Jorge EG (2004) Salmonella type III secretion-associated chaperones confer secretion-pathway specificity. Mol Microbiol 51: 483-495.
    • (2004) Mol Microbiol , vol.51 , pp. 483-495
    • Sang, H.L.1    Jorge, E.G.2
  • 46
    • 0029944323 scopus 로고    scopus 로고
    • The cytosolic SycE and SycH chaperones of Yersinia protect the region of YopE and YopH involved in translocation across eukaryotic cell membranes
    • DOI 10.1111/j.1365-2958.1996.tb02645.x
    • Woestyn S, Sory MP, Boland A, Lequenne O, Cornelis GR (1996) The cytosolic SycE and SycH chaperones of Yersinia protect the region of YopE and YopH involved in translocation across eukaryotic cell membranes. Mol Microbiol 20: 1261-1271. (Pubitemid 26225433)
    • (1996) Molecular Microbiology , vol.20 , Issue.6 , pp. 1261-1271
    • Woestyn, S.1    Sory, M.-P.2    Boland, A.3    Lequenne, O.4    Cornelis, G.R.5
  • 47
    • 0344666692 scopus 로고    scopus 로고
    • InvB Is a Type III Secretion-Associated Chaperone for the Salmonella enterica Effector Protein SopE
    • DOI 10.1128/JB.185.24.7279-7284.2003
    • Lee SH, Jorge EG (2003) InvB is a type III secretion-associated chaperone for the Salmonella enterica effector protein SopE. J Bacteriol 185: 7279-7284. (Pubitemid 37509846)
    • (2003) Journal of Bacteriology , vol.185 , Issue.24 , pp. 7279-7284
    • Lee, S.H.1    Galan, J.E.2
  • 48
    • 0347915662 scopus 로고    scopus 로고
    • Pseudomonas syringae Type III Secretion System Targeting Signals and Novel Effectors Studied with a Cya Translocation Reporter
    • DOI 10.1128/JB.186.2.543-555.2004
    • Schechter LM, Roberts KA, Jamir Y, Alfano JR, Collmer A (2004) Pseudomonas sytingae type III secretion system targeting signals and novel effectors studied with a Cya translocation reporter. J Bacteriol 186: 543-555. (Pubitemid 38076444)
    • (2004) Journal of Bacteriology , vol.186 , Issue.2 , pp. 543-555
    • Schechter, L.M.1    Roberts, K.A.2    Jamir, Y.3    Alfano, J.R.4    Collmer, A.5
  • 49
    • 14244263014 scopus 로고    scopus 로고
    • Type III secretion of the Salmonella effector protein SopE is mediated via an N-terminal amino acid signal and not an mRNA sequence
    • DOI 10.1128/JB.187.5.1559-1567.2005
    • Karavolos MH, Wilson M, Henderson J, Lee JJ, Khan CMA (2005) Type III secretion of the Salmonella effector protein SopE is mediated via an N-terminal amino acid signal and not an mRNA sequence. J Bacteriol 187: 1559-1567. (Pubitemid 40289356)
    • (2005) Journal of Bacteriology , vol.187 , Issue.5 , pp. 1559-1567
    • Karavolos, M.H.1    Wilson, M.2    Henderson, J.3    Lee, J.J.4    Khan, C.M.A.5
  • 50
    • 0035151519 scopus 로고    scopus 로고
    • Yersinia YopE is targeted for type III secretion by N-terminal, not mRNA, signals
    • DOI 10.1046/j.1365-2958.2001.02271.x
    • Lloyd SA, Norman M, Rosqvist R, Wolf-Watz H (2001) Yersinia YopE is targeted for type III secretion by N-terminal, not mRNA, signals. Mol Microbiol 39: 520-531. (Pubitemid 32113521)
    • (2001) Molecular Microbiology , vol.39 , Issue.2 , pp. 520-531
    • Lloyd, S.A.1    Norman, M.2    Rosqvist, R.3    Wolf-Watz, H.4
  • 51
    • 0036197569 scopus 로고    scopus 로고
    • Molecular characterization of type III secretion signals via analysis of synthetic N-terminal amino acid sequences
    • DOI 10.1046/j.1365-2958.2002.02738.x
    • Lloyd SA, Sjostrom M, Andersson S, Wolf-Watz H (2002) Molecular characterization of type III secretion signals via analysis of synthetic N-terminal amino acid sequences. Mol Microbiol 43: 51-59. (Pubitemid 34212190)
    • (2002) Molecular Microbiology , vol.43 , Issue.1 , pp. 51-59
    • Lloyd, S.A.1    Sjostrom, M.2    Andersson, S.3    Wolf-Watz, H.4
  • 52
    • 42149084419 scopus 로고    scopus 로고
    • Discrimination of outer membrane proteins with improved performance
    • Yan CH, Hu J, Wang YF (2008) Discrimination of outer membrane proteins with improved performance. BMC Bioinformatics 9: 47.
    • (2008) BMC Bioinformatics , vol.9 , pp. 47
    • Yan, C.H.1    Hu, J.2    Wang, Y.F.3
  • 53
    • 77954168567 scopus 로고    scopus 로고
    • SPA: Short peptide analyzer of intrinsic disorder status of short peptides
    • Xue B, Hsu WL, Lee JH, Lu H, Dunker AK, et al. (2010) SPA: Short peptide analyzer of intrinsic disorder status of short peptides. Genes Cells, 15: 635-646.
    • (2010) Genes Cells , vol.15 , pp. 635-646
    • Xue, B.1    Hsu, W.L.2    Lee, J.H.3    Lu, H.4    Dunker, A.K.5
  • 54
    • 79955638463 scopus 로고    scopus 로고
    • Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
    • Zhao HY, Yang YD, Zhou YQ (2010) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res, 39: 3017-3025.
    • (2010) Nucleic Acids Res , vol.39 , pp. 3017-3025
    • Zhao, H.Y.1    Yang, Y.D.2    Zhou, Y.Q.3
  • 55
    • 84861324339 scopus 로고    scopus 로고
    • Extent of structural asymmetry in homodimeric proteins: Prevalence and relevance
    • Swapna LS, Srikeerthana K, Srinivasan N (2012) Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PLoS ONE 7: e36688.
    • (2012) PLoS ONE , vol.7
    • Swapna, L.S.1    Srikeerthana, K.2    Srinivasan, N.3
  • 56
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: A web server for clustering and comparing biological sequences
    • Huang Y, Niu BF, Gao Y, Fu LM, Li WZ (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.F.2    Gao, Y.3    Fu, L.M.4    Li, W.Z.5
  • 58
    • 49749109156 scopus 로고    scopus 로고
    • PRINTR: Prediction of RNA binding sites in proteins using SVM and profiles
    • Wang Y, Xue Z, Shen G, Xu J (2008) PRINTR: Prediction of RNA binding sites in proteins using SVM and profiles. Amino Acids 35: 295-302.
    • (2008) Amino Acids , vol.35 , pp. 295-302
    • Wang, Y.1    Xue, Z.2    Shen, G.3    Xu, J.4
  • 59
    • 53749083563 scopus 로고    scopus 로고
    • Accurate sequence-based prediction of catalytic residues
    • Zhang T, Zhang H, Chen K, Shen S, Ruan J, et al. (2008) Accurate sequence-based prediction of catalytic residues. Bioinformatics 24: 2329-2338.
    • (2008) Bioinformatics , vol.24 , pp. 2329-2338
    • Zhang, T.1    Zhang, H.2    Chen, K.3    Shen, S.4    Ruan, J.5
  • 61
    • 25444524842 scopus 로고    scopus 로고
    • PSSM-based prediction of DNA binding sites in proteins
    • Ahmad S, Sarai A (2005) PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 6: 33.
    • (2005) BMC Bioinformatics , vol.6 , pp. 33
    • Ahmad, S.1    Sarai, A.2
  • 62
    • 77950471248 scopus 로고    scopus 로고
    • Identification of ATP binding residues of a protein from its primary sequence
    • Chauhan JS, Mishra NK, Raghava GPS (2009) Identification of ATP binding residues of a protein from its primary sequence. BMC Bioinformatics 10: 434.
    • (2009) BMC Bioinformatics , vol.10 , pp. 434
    • Chauhan, J.S.1    Mishra, N.K.2    Raghava, G.P.S.3
  • 63
    • 84862782308 scopus 로고    scopus 로고
    • Predicting deleterious nonsynonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes
    • Qin WL, Li YZ, Li J, Yu LZ, Wu D, et al. (2012) Predicting deleterious nonsynonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes. Comput Biol Chem 36: 31-35.
    • (2012) Comput Biol Chem , vol.36 , pp. 31-35
    • Qin, W.L.1    Li, Y.Z.2    Li, J.3    Yu, L.Z.4    Wu, D.5
  • 64
    • 0037372098 scopus 로고    scopus 로고
    • Prediction of beta-turns in proteins from multiple alignment using neural network
    • DOI 10.1110/ps.0228903
    • Kaur H, Raghava GPS (2003) Prediction of beta-turns in proteins from multiple alignment using neural network. Protein Sci 12: 627-634. (Pubitemid 36241119)
    • (2003) Protein Science , vol.12 , Issue.3 , pp. 627-634
    • Kaur, H.1    Raghava, G.P.S.2
  • 65
    • 26444473604 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
    • DOI 10.1002/prot.20630
    • Garg A, Kaur H, Raghava GPS (2005) Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure. Proteins 61: 318-324. (Pubitemid 41429139)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.2 , pp. 318-324
    • Garg, A.1    Kaur, H.2    Raghava, G.P.S.3
  • 67
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • DOI 10.1093/bioinformatics/btf877
    • Reiner A, Yekutieli D, Benjamini Y (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19: 368-375. (Pubitemid 36284936)
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 368-375
    • Reiner, A.1    Yekutieli, D.2    Benjamini, Y.3
  • 68
    • 79959875910 scopus 로고    scopus 로고
    • DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer
    • Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, et al. (2011) DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res 21: 1017-1027.
    • (2011) Genome Res , vol.21 , pp. 1017-1027
    • Kobayashi, Y.1    Absher, D.M.2    Gulzar, Z.G.3    Young, S.R.4    McKenney, J.K.5
  • 69
    • 66249109653 scopus 로고    scopus 로고
    • Characterization of a Naturally Occurring Breast Cancer Subset Enriched in Epithelial-to-Mesenchymal Transition and Stem Cell Characteristics
    • Hennessy BT, Gonzalez-Angulo A-M, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, et al. (2009) Characterization of a Naturally Occurring Breast Cancer Subset Enriched in Epithelial-to-Mesenchymal Transition and Stem Cell Characteristics. Cancer Res 69: 4116-4124.
    • (2009) Cancer Res , vol.69 , pp. 4116-4124
    • Hennessy, B.T.1    Gonzalez-Angulo, A.-M.2    Stemke-Hale, K.3    Gilcrease, M.Z.4    Krishnamurthy, S.5
  • 70
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks-based regression
    • DOI 10.1002/prot.20176
    • Adamczak R, Porollo A, Meller J (2004) Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 56: 753-767. (Pubitemid 39063318)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.4 , pp. 753-767
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 71
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • DOI 10.1002/prot.20441
    • Adamczak R, Porollo A, Meller J (2005) Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59: 467-475. (Pubitemid 40594291)
    • (2005) Proteins: Structure, Function and Genetics , vol.59 , Issue.3 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 72
    • 17844381893 scopus 로고    scopus 로고
    • Linear regression models for solvent accessibility prediction in proteins
    • DOI 10.1089/cmb.2005.12.355
    • Wagner M, Adamczak R, Porollo A, Meller J (2005) Linear regression models for solvent accessibility prediction in proteins. J Comput Biol 12: 355-369. (Pubitemid 40586438)
    • (2005) Journal of Computational Biology , vol.12 , Issue.3 , pp. 355-369
    • Wagner, M.1    Adamczak, R.2    Porollo, A.3    Meller, J.4
  • 74
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L (2001) Random forests. Machine Learning 45: 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 75
    • 75149167094 scopus 로고    scopus 로고
    • In silico method for systematic analysis of feature importance in microRNA-mRNA interactions
    • Xiao J, Li Y, Wang K, Wen Z, Li M, et al. (2009) In silico method for systematic analysis of feature importance in microRNA-mRNA interactions. BMC Bioinformatics 10: 427.
    • (2009) BMC Bioinformatics , vol.10 , pp. 427
    • Xiao, J.1    Li, Y.2    Wang, K.3    Wen, Z.4    Li, M.5
  • 76
    • 79955948344 scopus 로고    scopus 로고
    • Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure
    • Xiao J, Tang X, Li Y, Fang Z, Ma D, et al. (2011) Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure. BMC Bioinformatics 12: 165.
    • (2011) BMC Bioinformatics , vol.12 , pp. 165
    • Xiao, J.1    Tang, X.2    Li, Y.3    Fang, Z.4    Ma, D.5
  • 77
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • Jiang P, Wu H, Wang W, Ma W, Sun X, et al. (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 35: W339-W344.
    • (2007) Nucleic Acids Res , vol.35
    • Jiang, P.1    Wu, H.2    Wang, W.3    Ma, W.4    Sun, X.5
  • 78
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • Breiman L (1996) Bagging predictors. Machine Learning 24: 123-140.
    • (1996) Machine Learning , vol.24 , pp. 123-140
    • Breiman, L.1
  • 79
    • 77952814988 scopus 로고    scopus 로고
    • Permutation importance: A corrected feature importance measure
    • Altmann A, Tolosi L, Sander O, Lengauer T (2010) Permutation importance: a corrected feature importance measure. Bioinformatics 26: 1340-1347.
    • (2010) Bioinformatics , vol.26 , pp. 1340-1347
    • Altmann, A.1    Tolosi, L.2    Sander, O.3    Lengauer, T.4
  • 80
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • Swets JA (1988) Measuring the accuracy of diagnostic systems. Science 240: 1285-1293.
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 81
    • 84867288210 scopus 로고    scopus 로고
    • Identification of novel type III effectors using latent dirichlet allocation
    • ID
    • Yang Y (2012) Identification of novel type III effectors using latent dirichlet allocation. Comput Math Method M, ID: 696190.
    • (2012) Comput Math Method M , pp. 696190
    • Yang, Y.1
  • 82
    • 84893143909 scopus 로고    scopus 로고
    • Computational Identification of Discriminating Features of Pathogenic and Symbiotic Type III Secreted Effector Proteins
    • Yahara K, Jiang Y, Yanagawa T (2011) Computational Identification of Discriminating Features of Pathogenic and Symbiotic Type III Secreted Effector Proteins. Inform Media Tech 6: 39-51.
    • (2011) Inform Media Tech , vol.6 , pp. 39-51
    • Yahara, K.1    Jiang, Y.2    Yanagawa, T.3
  • 83
    • 84865760673 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of type III secretome of enteropathogenic escherichia coli reveals an expanded effector repertoire for attaching/effacing bacterial pathogens
    • Deng W, Yu HB, de Hoog CL, Stoynov N, Li Y, et al. (2012) Quantitative proteomic analysis of type III secretome of enteropathogenic escherichia coli reveals an expanded effector repertoire for attaching/effacing bacterial pathogens. Mol Cell Proteomics 11: 692-709.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 692-709
    • Deng, W.1    Yu, H.B.2    De Hoog, C.L.3    Stoynov, N.4    Li, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.