메뉴 건너뛰기




Volumn 11, Issue SUPPL. 4, 2010, Pages

Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 120;

EID: 78649778477     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S4-S22     Document Type: Article
Times cited : (6)

References (42)
  • 2
    • 0033919404 scopus 로고    scopus 로고
    • Oligomeric modeling and electrostatic analysis of the gp120 envelope glycoprotein of human immunodeficiency virus
    • 10.1128/JVI.74.4.1961-1972.2000, 111674, 10644369
    • Kwong PD, Wyatt R, Sattentau QJ, Sodroski J, Hendrickson WA. Oligomeric modeling and electrostatic analysis of the gp120 envelope glycoprotein of human immunodeficiency virus. J Virol 2000, 74(4):1961-72. 10.1128/JVI.74.4.1961-1972.2000, 111674, 10644369.
    • (2000) J Virol , vol.74 , Issue.4 , pp. 1961-1972
    • Kwong, P.D.1    Wyatt, R.2    Sattentau, Q.J.3    Sodroski, J.4    Hendrickson, W.A.5
  • 4
    • 33748925430 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection and these modifications affect antibody neutralization sensitivity
    • 10.1128/JVI.00141-06, 1617272, 16973562
    • Sagar M, Wu X, Lee S, Overbaugh J. Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection and these modifications affect antibody neutralization sensitivity. J Virol 2006, 80(19):9586-98. 10.1128/JVI.00141-06, 1617272, 16973562.
    • (2006) J Virol , vol.80 , Issue.19 , pp. 9586-9598
    • Sagar, M.1    Wu, X.2    Lee, S.3    Overbaugh, J.4
  • 5
    • 18144397438 scopus 로고    scopus 로고
    • Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels
    • 10.1128/JVI.79.10.6528-6531.2005, 1091724, 15858037
    • Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J. Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J Virol 2005, 79(10):6528-31. 10.1128/JVI.79.10.6528-6531.2005, 1091724, 15858037.
    • (2005) J Virol , vol.79 , Issue.10 , pp. 6528-6531
    • Chohan, B.1    Lang, D.2    Sagar, M.3    Korber, B.4    Lavreys, L.5    Richardson, B.6    Overbaugh, J.7
  • 7
    • 70449534963 scopus 로고    scopus 로고
    • Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes
    • 10.4049/jimmunol.0804287, 2808118, 19414790
    • Li H, Xu CF, Blais S, Wan Q, Zhang HT, Landry SJ, Hioe CE. Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes. J Immunol 2009, 182(10):6369-78. 10.4049/jimmunol.0804287, 2808118, 19414790.
    • (2009) J Immunol , vol.182 , Issue.10 , pp. 6369-6378
    • Li, H.1    Xu, C.F.2    Blais, S.3    Wan, Q.4    Zhang, H.T.5    Landry, S.J.6    Hioe, C.E.7
  • 8
    • 34247636624 scopus 로고    scopus 로고
    • Exploiting the defensive sugars of HIV-1 for drug and vaccine design
    • 10.1038/nature05818, 17460665
    • Scanlan CN, Offer J, Zitzmann N, Dwek RA. Exploiting the defensive sugars of HIV-1 for drug and vaccine design. Nature 2007, 446(7139):1038-45. 10.1038/nature05818, 17460665.
    • (2007) Nature , vol.446 , Issue.7139 , pp. 1038-1045
    • Scanlan, C.N.1    Offer, J.2    Zitzmann, N.3    Dwek, R.A.4
  • 9
    • 40549095374 scopus 로고    scopus 로고
    • HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments
    • 10.1186/1743-422X-5-14, 2265691, 18215327
    • Ho YS, Abecasis AB, Theys K, Deforche K, Dwyer DE, Charleston M, Vandamme AM, Saksena NK. HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments. Virol J 2008, 5:14. 10.1186/1743-422X-5-14, 2265691, 18215327.
    • (2008) Virol J , vol.5 , pp. 14
    • Ho, Y.S.1    Abecasis, A.B.2    Theys, K.3    Deforche, K.4    Dwyer, D.E.5    Charleston, M.6    Vandamme, A.M.7    Saksena, N.K.8
  • 10
    • 33846501408 scopus 로고    scopus 로고
    • Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope
    • Poon AF, Lewis FI, Pond SL, Frost SD. Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Bio 2007, 13(1):e11.
    • (2007) PLoS Comput Bio , vol.13 , Issue.1
    • Poon, A.F.1    Lewis, F.I.2    Pond, S.L.3    Frost, S.D.4
  • 11
    • 38749116607 scopus 로고    scopus 로고
    • Elite HIV controllers: myth or reality?
    • Saksena NK, Rodes B, Wang B, Soriano V. Elite HIV controllers: myth or reality?. AIDS Rev 2007, 9(4):195-207.
    • (2007) AIDS Rev , vol.9 , Issue.4 , pp. 195-207
    • Saksena, N.K.1    Rodes, B.2    Wang, B.3    Soriano, V.4
  • 12
    • 55449125185 scopus 로고    scopus 로고
    • Support vector machines and kernels for computational biology
    • 10.1371/journal.pcbi.1000173, 2547983, 18974822
    • Ben-Hur A, Ong CS, Sonnenburg S, Scholkopf B, Ratsch G. Support vector machines and kernels for computational biology. PLoS Comput Biol 2008, 4(10):e1000173. 10.1371/journal.pcbi.1000173, 2547983, 18974822.
    • (2008) PLoS Comput Biol , vol.4 , Issue.10
    • Ben-Hur, A.1    Ong, C.S.2    Sonnenburg, S.3    Scholkopf, B.4    Ratsch, G.5
  • 15
    • 0028392483 scopus 로고
    • Learning long-term dependencies with gradient descent is difficult
    • 10.1109/72.279181, 18267787
    • Bengio Y, Simard P, Frasconi P. Learning long-term dependencies with gradient descent is difficult. IEEE Trans Neural Netw 1994, 5(2):157-66. 10.1109/72.279181, 18267787.
    • (1994) IEEE Trans Neural Netw , vol.5 , Issue.2 , pp. 157-166
    • Bengio, Y.1    Simard, P.2    Frasconi, P.3
  • 16
    • 0000262562 scopus 로고
    • Hierarchical mixtures of experts and the EM algorithm
    • Jordan MI, Jacobs RA. Hierarchical mixtures of experts and the EM algorithm. Neural Comp 1994, 6:181-214.
    • (1994) Neural Comp , vol.6 , pp. 181-214
    • Jordan, M.I.1    Jacobs, R.A.2
  • 17
    • 0003450542 scopus 로고
    • The Nature of Statistical Learning Theory
    • Springer-Verlag, 0-387-98780-0
    • Vapnik V. The Nature of Statistical Learning Theory. 1995, Springer-Verlag, 0-387-98780-0.
    • (1995)
    • Vapnik, V.1
  • 19
    • 84983721794 scopus 로고    scopus 로고
    • Discovering Knowledge in Data
    • Larose DT. Discovering Knowledge in Data. Wiley 2005,
    • (2005) Wiley
    • Larose, D.T.1
  • 20
    • 0003760944 scopus 로고    scopus 로고
    • Spatial Tessellations - Concepts and Applications of Voronoi Diagrams
    • 2, 0-471-98635-6
    • Okabe A, Boots B, Sugihara K, Chiu SN. Spatial Tessellations - Concepts and Applications of Voronoi Diagrams. John Wiley 2000, 671. 2, 0-471-98635-6.
    • (2000) John Wiley , pp. 671
    • Okabe, A.1    Boots, B.2    Sugihara, K.3    Chiu, S.N.4
  • 22
    • 84880832861 scopus 로고    scopus 로고
    • In Constructing Diverse Classifier Ensembles using Artificial Training Examples
    • Melville P, Mooney RJ. In Constructing Diverse Classifier Ensembles using Artificial Training Examples. IJACI, Acapulco, Mexico 2003, 505-510.
    • (2003) IJACI, Acapulco, Mexico , pp. 505-510
    • Melville, P.1    Mooney, R.J.2
  • 23
    • 0003413187 scopus 로고    scopus 로고
    • Neural Networks: A Comprehensive Foundation
    • Prentice Hall, 2
    • Haykin S. Neural Networks: A Comprehensive Foundation. 1998, Prentice Hall, 2.
    • (1998)
    • Haykin, S.1
  • 24
    • 0003786273 scopus 로고    scopus 로고
    • Regularized Radial Basis Function Networks: Theory and Applications
    • John Wiley & Sons: Canada
    • Yee P, Haykin S. Regularized Radial Basis Function Networks: Theory and Applications. 2001, John Wiley & Sons: Canada.
    • (2001)
    • Yee, P.1    Haykin, S.2
  • 25
    • 33846516584 scopus 로고    scopus 로고
    • Pattern Recognition and Machine Learning (Information Science and Statistics)
    • Springer: Cambrridge UK
    • Bishop CM. Pattern Recognition and Machine Learning (Information Science and Statistics). 2007, Springer: Cambrridge UK.
    • (2007)
    • Bishop, C.M.1
  • 26
    • 33646769235 scopus 로고
    • C4.5: Programs for Machine Learning
    • Quinlan JR. C4.5: Programs for Machine Learning. Morgan Kaufmann 1992,
    • (1992) Morgan Kaufmann
    • Quinlan, J.R.1
  • 27
    • 0032543307 scopus 로고    scopus 로고
    • Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
    • 10.1038/31405, 9641677
    • Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 1998, 393(6686):648-59. 10.1038/31405, 9641677.
    • (1998) Nature , vol.393 , Issue.6686 , pp. 648-659
    • Kwong, P.D.1    Wyatt, R.2    Robinson, J.3    Sweet, R.W.4    Sodroski, J.5    Hendrickson, W.A.6
  • 28
    • 0030917941 scopus 로고    scopus 로고
    • In vivo sequence variability of human immunodeficiency virus type 1 envelope gp120: association of V2 extension with slow disease progression
    • 191717, 9188549
    • Shioda T, Oka S, Xin X, Liu H, Harukuni R, Kurotani A, Fukushima M, Hasan MK, Shiino T, Takebe Y, Iwamoto A, Nagai Y. In vivo sequence variability of human immunodeficiency virus type 1 envelope gp120: association of V2 extension with slow disease progression. J Virol 1997, 71(7):4871-81. 191717, 9188549.
    • (1997) J Virol , vol.71 , Issue.7 , pp. 4871-4881
    • Shioda, T.1    Oka, S.2    Xin, X.3    Liu, H.4    Harukuni, R.5    Kurotani, A.6    Fukushima, M.7    Hasan, M.K.8    Shiino, T.9    Takebe, Y.10    Iwamoto, A.11    Nagai, Y.12
  • 29
    • 0031298109 scopus 로고    scopus 로고
    • HIV entry and tropism: the chemokine receptor connection
    • Berger EA. HIV entry and tropism: the chemokine receptor connection. AIDS 1997, 11(SupplA):S3-16.
    • (1997) AIDS , vol.11 , Issue.SUPPL A
    • Berger, E.A.1
  • 30
    • 0033008471 scopus 로고    scopus 로고
    • Will multiple coreceptors need to be targeted by inhibitors of human immunodeficiency virus type 1 entry?
    • 104110, 10074200
    • Zhang YJ, Moore JP. Will multiple coreceptors need to be targeted by inhibitors of human immunodeficiency virus type 1 entry?. J Virol 1999, 73(4):3443-8. 104110, 10074200.
    • (1999) J Virol , vol.73 , Issue.4 , pp. 3443-3448
    • Zhang, Y.J.1    Moore, J.P.2
  • 31
    • 0037183931 scopus 로고    scopus 로고
    • Temporal relationship between V1V2 variation macrophage replication and coreceptor adaptation during HIV-1 disease progression
    • 10.1097/00002030-200209270-00005, 12351948
    • Masciotra S, Owen SM, Rudolph D, Yang C, Wang B, Saksena N, Spira T, Dhawan S, Lal RB. Temporal relationship between V1V2 variation macrophage replication and coreceptor adaptation during HIV-1 disease progression. AIDS 2002, 16(14):1887-98. 10.1097/00002030-200209270-00005, 12351948.
    • (2002) AIDS , vol.16 , Issue.14 , pp. 1887-1898
    • Masciotra, S.1    Owen, S.M.2    Rudolph, D.3    Yang, C.4    Wang, B.5    Saksena, N.6    Spira, T.7    Dhawan, S.8    Lal, R.B.9
  • 32
    • 0346365289 scopus 로고    scopus 로고
    • Intrapatient alterations in the human immunodeficiency virus type 1 gp120 V1V2 and V3 regions differentially modulate coreceptor usage virus inhibition by CC/CXC chemokines soluble CD4 and the b12 and 2G12 monoclonal antibodies
    • 10.1128/JVI.78.1.524-530.2004, 303404, 14671134
    • Nabatov AA, Pollakis G, Linnemann T, Kliphius A, Chalaby MI, Paxton WA. Intrapatient alterations in the human immunodeficiency virus type 1 gp120 V1V2 and V3 regions differentially modulate coreceptor usage virus inhibition by CC/CXC chemokines soluble CD4 and the b12 and 2G12 monoclonal antibodies. J Virol 2004, 78(1):524-30. 10.1128/JVI.78.1.524-530.2004, 303404, 14671134.
    • (2004) J Virol , vol.78 , Issue.1 , pp. 524-530
    • Nabatov, A.A.1    Pollakis, G.2    Linnemann, T.3    Kliphius, A.4    Chalaby, M.I.5    Paxton, W.A.6
  • 33
    • 0033942750 scopus 로고    scopus 로고
    • V2 loop glycosylation of the human immunodeficiency virus type 1 SF162 envelope facilitates interaction of this protein with CD4 and CCR5 receptors and protects the virus from neutralization by anti-V3 loop and anti-CD4 binding site antibodies
    • 10.1128/JVI.74.15.6769-6776.2000, 112193, 10888615
    • Ly A, Stamatatos L. V2 loop glycosylation of the human immunodeficiency virus type 1 SF162 envelope facilitates interaction of this protein with CD4 and CCR5 receptors and protects the virus from neutralization by anti-V3 loop and anti-CD4 binding site antibodies. J Virol 2000, 74(15):6769-76. 10.1128/JVI.74.15.6769-6776.2000, 112193, 10888615.
    • (2000) J Virol , vol.74 , Issue.15 , pp. 6769-6776
    • Ly, A.1    Stamatatos, L.2
  • 34
    • 0037213247 scopus 로고    scopus 로고
    • Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120
    • 10.1128/JVI.77.1.642-658.2003, 140633, 12477867
    • Pantophlet R, Ollmann E, Poignard P, Parren PW, Wilson IA, Burton DR. Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120. J Virol 2003, 77(1):642-58. 10.1128/JVI.77.1.642-658.2003, 140633, 12477867.
    • (2003) J Virol , vol.77 , Issue.1 , pp. 642-658
    • Pantophlet, R.1    Ollmann, E.2    Poignard, P.3    Parren, P.W.4    Wilson, I.A.5    Burton, D.R.6
  • 35
    • 1342306245 scopus 로고    scopus 로고
    • Biases and complex patterns in the residues flanking protein N-glycosylation sites
    • 10.1093/glycob/cwh004, 14514714
    • Ben-dor S, Esterman N, et al. Biases and complex patterns in the residues flanking protein N-glycosylation sites. Glycobiology 2004, 14:95-101. 10.1093/glycob/cwh004, 14514714.
    • (2004) Glycobiology , vol.14 , pp. 95-101
    • Ben-dor, S.1    Esterman, N.2
  • 36
    • 0029916898 scopus 로고    scopus 로고
    • Spitalnik SL: et al: The amino acid at the X position of an Asn-X-Ser sequon is an important determinant of N-linked core-glycosylation efficiency
    • 10.1074/jbc.271.11.6363, 8626433
    • Shakin-Eshleman SH. Spitalnik SL: et al: The amino acid at the X position of an Asn-X-Ser sequon is an important determinant of N-linked core-glycosylation efficiency. J Biol Chem 1996, 271:6363-6. 10.1074/jbc.271.11.6363, 8626433.
    • (1996) J Biol Chem , vol.271 , pp. 6363-6366
    • Shakin-Eshleman, S.H.1
  • 37
    • 46649097611 scopus 로고    scopus 로고
    • SiteSeek: Protein Post-Translational Modification Analysis Using Adaptive Locality-Effective Kernel Methods and New Profiles
    • 10.1186/1471-2105-9-272, 2442102, 18541042
    • Yoo PD, Ho S, Zhou BB, Zomaya AY. SiteSeek: Protein Post-Translational Modification Analysis Using Adaptive Locality-Effective Kernel Methods and New Profiles. BMC Bioinformatics 2008, 9:272. 10.1186/1471-2105-9-272, 2442102, 18541042.
    • (2008) BMC Bioinformatics , vol.9 , pp. 272
    • Yoo, P.D.1    Ho, S.2    Zhou, B.B.3    Zomaya, A.Y.4
  • 38
    • 78649797555 scopus 로고    scopus 로고
    • Bioinformatics: The machine learning approach 2nd ed MIT Press 2001 Cambridge Mass
    • 2
    • Baldi P, Brunak S. Bioinformatics: The machine learning approach 2nd ed MIT Press 2001 Cambridge Mass. 2.
    • Baldi, P.1    Brunak, S.2
  • 39
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Molecular Biology 1999, 292(2):195-202.
    • (1999) J Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 40
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: a simple approach to improve protein structure predictions
    • 10.1093/bioinformatics/btg124, 12761065
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003, 19(8):1015-1018. 10.1093/bioinformatics/btg124, 12761065.
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 41
    • 17844363963 scopus 로고    scopus 로고
    • PRODO: Prediction of Protein Domain Boundaries using Neural Networks
    • 10.1002/prot.20442, 15789433
    • Sim J, Kim SY, Lee J. PRODO: Prediction of Protein Domain Boundaries using Neural Networks. Proteins 2005, 59:627-632. 10.1002/prot.20442, 15789433.
    • (2005) Proteins , vol.59 , pp. 627-632
    • Sim, J.1    Kim, S.Y.2    Lee, J.3
  • 42
    • 33947385412 scopus 로고    scopus 로고
    • Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
    • 10.1186/1471-2105-7-S5-S6, 1764483, 17254311
    • Sikder AR, Zomaya AY. Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index. BMC Bioinformatics 2006, 7(5):S6. 10.1186/1471-2105-7-S5-S6, 1764483, 17254311.
    • (2006) BMC Bioinformatics , vol.7 , Issue.5
    • Sikder, A.R.1    Zomaya, A.Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.