Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ: Identification of host proteins required for HIV infection through a functional genomic screen. Science. 2008, 319 (5865): 921-926. 10.1126/science.1152725.
Article
CAS
PubMed
Google Scholar
Konig R, Zhou YY, Elleder D, Diamond TL, Bonamy GMC, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE: Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008, 135 (1): 49-60. 10.1016/j.cell.2008.07.032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou HL, Xu M, Huang Q, Gates AT, Zhang XHD, Castle JC, Stec E, Ferrer M, Strulovici B, Hazuda DJ: Genome-Scale RNAi Screen for Host Factors Required for HIV Replication. Cell Host Microbe. 2008, 4 (5): 495-504. 10.1016/j.chom.2008.10.004.
Article
CAS
PubMed
Google Scholar
Yeung ML, Houzet L, Yedavalli VSRK, Jeang KT: A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. J Biol Chem. 2009, 284 (29): 19463-19473. 10.1074/jbc.M109.010033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bushman FD, Malani N, Fernandes J, D’Orso I, Cagney G, Diamond TL, Zhou HL, Hazuda DJ, Espeseth AS, Konig R: Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies. PLoS Pathog. 2009, 5 (5): e1000437-10.1371/journal.ppat.1000437.
Article
PubMed
PubMed Central
Google Scholar
Mehla R, Ayyavoo V: Gene Array Studies in HIV-1 Infection. Curr HIV/AIDS Rep. 2012, 9: 34-43. 10.1007/s11904-011-0100-x.
Article
PubMed
PubMed Central
Google Scholar
Giri MS, Nebozhyn M, Showe L, Montaner LJ: Microarray data on gene modulation by HIV-1 in immune cells: 2000–2006. J Leukoc Biol. 2006, 80 (5): 1031-1043. 10.1189/jlb.0306157.
Article
CAS
PubMed
Google Scholar
Li QS, Smith AJ, Schacker TW, Carlis JV, Duan L, Reilly CS, Haase AT: Microarray Analysis of Lymphatic Tissue Reveals Stage-Specific, Gene Expression Signatures in HIV-1 Infection. J Immunol. 2009, 183 (3): 1975-1982. 10.4049/jimmunol.0803222.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith AJ, Li QS, Wietgrefe SW, Schacker TW, Reilly CS, Haase AT: Host Genes Associated with HIV-1 Replication in Lymphatic Tissue. J Immunol. 2010, 185 (9): 5417-5424. 10.4049/jimmunol.1002197.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K: Global landscape of HIV-human protein complexes. Nature. 2012, 481 (7381): 365-370.
Google Scholar
Zhang L, Zhang X, Ma Q, Zhou H: Host Proteome Research in HIV Infection. Genomics Proteomics Bioinformatics. 2010, 8 (1): 1-9. 10.1016/S1672-0229(10)60001-0.
Article
CAS
PubMed
Google Scholar
Kontijevskis A, Wikberg JES, Komorowski J: Computational proteomics analysis of HIV‒1 protease interactome. Proteins Struct Function Bioinformatics. 2007, 68 (1): 305-312. 10.1002/prot.21415.
Article
CAS
Google Scholar
Limou S, Le Clerc S, Coulonges C, Carpentier W, Dina C, Delaneau O, Labib T, Taing L, Sladek R, Deveau C: Genomewide Association Study of an AIDS-Nonprogression Cohort Emphasizes the Role Played by HLA Genes (ANRS Genomewide Association Study 02). J Infect Dis. 2009, 199 (3): 419-426. 10.1086/596067.
Article
PubMed
Google Scholar
Le Clerc S, Limou S, Coulonges C, Carpentier W, Dina C, Taing L, Delaneau O, Labib T, Sladek R, Deveau C: Genomewide Association Study of a Rapid Progression Cohort Identifies New Susceptibility Alleles for AIDS (ANRS Genomewide Association Study 03). J Infect Dis. 2009, 200 (8): 1194-1201. 10.1086/605892.
Article
CAS
PubMed
Google Scholar
Guergnon J, Theodorou I: What did we learn on host’s genetics by studying large cohorts of HIV-1-infected patients in the genome-wide association era?. Curr Opin HIV AIDS. 2011, 6 (4): 290-296. 10.1097/COH.0b013e3283478449.
Article
PubMed
Google Scholar
Sheehy AM, Gaddis NC, Choi JD, Malim MH: Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002, 418 (6898): 646-650. 10.1038/nature00939.
Article
CAS
PubMed
Google Scholar
Stremlau M, Owens CM, Perron MJ, Kiessling M, Autissier P, Sodroski J: The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys. Nature. 2004, 427 (6977): 848-853. 10.1038/nature02343.
Article
CAS
PubMed
Google Scholar
Neil SJD, Zang T, Bieniasz PD: Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature. 2008, 451 (7177): 425-430. 10.1038/nature06553.
Article
CAS
PubMed
Google Scholar
Tyagi M, Kashanchi F: New and novel intrinsic host repressive factors against HIV-1: PAF1 complex, HERC5 and others. Retrovirology. 2012, 9 (1): 19-10.1186/1742-4690-9-19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu L, Oliveira NMM, Cheney KM, Pade C, Dreja H, Bergin AMH, Borgdorff V, Beach DH, Bishop CL, Dittmar MT: A whole genome screen for HIV restriction factors. Retrovirology. 2011, 8: 94-10.1186/1742-4690-8-94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levy JA: Pathogenesis of human-immunodeficiency-virus infection. Microbiol Rev. 1993, 57 (1): 183-289.
CAS
PubMed
PubMed Central
Google Scholar
Ho M, Armstrong J, McMahon D, Pazin G, Huang XL, Rinaldo C, Whiteside T, Tripoli C, Levine G, Moody D: A phase-1 study of adoptive transfer of autologous CD8+ T-lymphocytes in patients with acquired-immunodeficiency-syndrome (AIDS)-related complex or AIDS. Blood. 1993, 81 (8): 2093-2101.
CAS
PubMed
Google Scholar
Roederer M, Raju PA, Mitra DK, Herzenberg LA: HIV does not replicate in naive CD4 T cells stimulated with CD3/CD28. J Clin Invest. 1997, 99 (7): 1555-10.1172/JCI119318.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mengozzi M, Malipatlolla M, De Rosa SC, Herzenberg LA, Roederer M: Naive CD4 T cells inhibit CD28-costimulated R5 HIV replication in memory CD4 T cells. Proc Natl Acad Sci. 2001, 98 (20): 11644-10.1073/pnas.211205098.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barker E, Bossart KN, Levy JA: Differential effects of CD28 costimulation on HIV production by CD4+ cells. J Immunol. 1998, 161 (11): 6223.
CAS
PubMed
Google Scholar
Spina CA, Prince HE, Richman DD: Preferential replication of HIV-1 in the CD45RO memory cell subset of primary CD4 lymphocytes in vitro. J Clin Invest. 1997, 99 (7): 1774-1785. 10.1172/JCI119342.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levine BL, Mosca JD, Riley JL, Carroll RG, Vahey MT, Jagodzinski LL, Wagner KF, Mayers DL, Burke DS, Weislow OS: Antiviral effect and ex vivo CD4+ T cell proliferation in HIV-positive patients as a result of CD28 costimulation. Science. 1996, 272 (5270): 1939-10.1126/science.272.5270.1939.
Article
CAS
PubMed
Google Scholar
Carroll RG, Riley JL, Levine BL, Feng Y, Kaushal S, Ritchey DW, Bernstein W, Weislow OS, Brown CR, Berger EA: Differential regulation of HIV-1 fusion cofactor expression by CD28 costimulation of CD4+ T cells. Science. 1997, 276 (5310): 273-276. 10.1126/science.276.5310.273.
Article
CAS
PubMed
Google Scholar
Wright GW, Simon RM: A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics. 2003, 19 (18): 2448-10.1093/bioinformatics/btg345.
Article
CAS
PubMed
Google Scholar
Yang H, Crawford N, Lukes L, Finney R, Lancaster M, Hunter KW: Metastasis predictive signature profiles pre-exist in normal tissues. Clin Exper Meta. 2005, 22 (7): 593-603. 10.1007/s10585-005-6244-6.
Article
CAS
Google Scholar
Clarke R, Ressom HW, Wang A, Xuan J, Liu MC, Gehan EA, Wang Y: The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer. 2008, 8 (1): 37-49. 10.1038/nrc2294.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramoni MF, Sebastiani P, Kohane IS: Cluster analysis of gene expression dynamics. Proc Natl Acad Sci. 2002, 99 (14): 9121-10.1073/pnas.132656399.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller LD, Long PM, Wong L, Mukherjee S, McShane LM, Liu ET: Optimal gene expression analysis by microarrays. Cancer Cell. 2002, 2 (5): 353-361. 10.1016/S1535-6108(02)00181-2.
Article
CAS
PubMed
Google Scholar
Harris MA, Clark JI, Ireland A, Lomax J, Ashburner M, Collins R, Eilbeck K, Lewis S, Mungall C, Richter J: The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006, 34: D322-D326.
Article
Google Scholar
Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B: Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007, 39 (11): 1338-1349. 10.1038/ng.2007.2.
Article
CAS
PubMed
Google Scholar
Prieto C, Risueno A, Fontanillo C, De las Rivas J: Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One. 2008, 3 (12): e3911-10.1371/journal.pone.0003911.
Article
PubMed
PubMed Central
Google Scholar
Barabasi AL, Oltvai ZN: Network biology: understanding the cell’s functional organization. Nat rev. 2004, 5 (2): 101-113. 10.1038/nrg1272.
Article
CAS
Google Scholar
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical organization of modularity in metabolic networks. Science. 2002, 297 (5586): 1551-1555. 10.1126/science.1073374.
Article
CAS
PubMed
Google Scholar
Chen F, Zhu HH, Zhou LF, Li J, Zhao LY, Wu SS, Wang J, Liu W, Chen Z: Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model. BMC Genomics. 2010, 11 (1): 240-10.1186/1471-2164-11-240.
Article
PubMed
PubMed Central
Google Scholar
Chen L, Xu W-w, Han M-j, Guo Y, Wang J, Cui W-q, Jia M-h, Ma Y-l, Lu L, Zhang H-T: CD3/CD28 costimulation-induced resistance to HIV-1 and cell subsets analysis. Int J Immunol. 2011, 34 (5): 297-301.
Google Scholar
Zheng Q, Wang XJ: GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 2008, 36 (suppl 2): W358-W363.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jonathan D, John P, David R: The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Syst Biol. 2010, 4: 80-10.1186/1752-0509-4-80.
Article
Google Scholar
Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature. 2001, 411 (6833): 41-42. 10.1038/35075138.
Article
CAS
PubMed
Google Scholar
Oswald-Richter K, Grill SM, Leelawong M, Tseng M, Kalams SA, Hulgan T, Haas DW, Unutmaz D: Identification of a CCR5-expressing T cell subset that is resistant to R5-tropic HIV infection. PLoS Pathog. 2007, 3 (4): e58-10.1371/journal.ppat.0030058.
Article
PubMed
PubMed Central
Google Scholar
Creson JR, Lin AA, Li Q, Broad DF, Roberts MR, Anderson SJ: The mode and duration of anti-CD28 costimulation determine resistance to infection by macrophage-tropic strains of human immunodeficiency virus type 1 in vitro. J Virol. 1999, 73 (11): 9337-9347.
CAS
PubMed
PubMed Central
Google Scholar
Riley JL, Levine BL, Craighead N, Francomano T, Kim D, Carroll RG, June CH: Native and memory CD4 T cells differ in their susceptibilities to human immunodeficiency virus type 1 infection following CD28 costimulation: Implications for transmission and pathogenesis. J Virol. 1998, 72 (10): 8273-8280.
CAS
PubMed
PubMed Central
Google Scholar
Naghavi MH, Goff SP: Retroviral proteins that interact with the host cell cytoskeleton. Curr Opin Immunol. 2007, 19 (4): 402-407. 10.1016/j.coi.2007.07.003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Belkina NV, Shaw S: HIV Infection of T Cells: Actin-in and Actin-out. Sci Signal. 2009, 2 (66): pe23-10.1126/scisignal.266pe23.
Article
PubMed
Google Scholar
Foley JF, Yu CR, Solow R, Yacobucci M, Peden KWC, Farber JM: Roles for CXC chemokine ligands 10 and 11 in recruiting CD4+ T cells to HIV-1-infected monocyte-derived macrophages, dendritic cells, and lymph nodes. J Immunol. 2005, 174 (8): 4892.
Article
CAS
PubMed
Google Scholar
Butler SL, Johnson EP, Bushman FD: Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles. J Virol. 2002, 76 (8): 3739-3747. 10.1128/JVI.76.8.3739-3747.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwartz O, Maréchal V, Friguet B, Arenzana-Seisdedos F, Heard JM: Antiviral activity of the proteasome on incoming human immunodeficiency virus type 1. J Virol. 1998, 72 (5): 3845-3850.
CAS
PubMed
PubMed Central
Google Scholar
Baumeister W, Walz J, Proteolysis C: The proteasome: paradigm review of a self-compartmentalizing protease. Cell. 1998, 92: 367-380. 10.1016/S0092-8674(00)80929-0.
Article
CAS
PubMed
Google Scholar
Coux O, Tanaka K, Goldberg AL: Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem. 1996, 65 (1): 801-847. 10.1146/annurev.bi.65.070196.004101.
Article
CAS
PubMed
Google Scholar
Wei BL, Denton PW, O’Neill E, Luo T, Foster JL, Garcia JV: Inhibition of lysosome and proteasome function enhances human immunodeficiency virus type 1 infection. J Virol. 2005, 79 (9): 5705-5712. 10.1128/JVI.79.9.5705-5712.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sankaran S, Guadalupe M, Reay E, George MD, Flamm J, Prindiville T, Dandekar S: Gut mucosal T cell responses and gene expression correlate with protection against disease in long-term HIV-1-infected nonprogressors. Proc Natl Acad Sci USA. 2005, 102 (28): 9860-9865. 10.1073/pnas.0503463102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salgado M, Lopez-Romero P, Callejas S, Lopez M, Labarga P, Dopazo A, Soriano V, Rodes B: Characterization of host genetic expression patterns in HIV-infected individuals with divergent disease progression. Virology. 2011, 411 (1): 103-112. 10.1016/j.virol.2010.12.037.
Article
CAS
PubMed
Google Scholar
Varbanov M, Espert L, Biard-Piechaczyk M: Mechanisms of CD4 T-cell depletion triggered by HIV-1 viral proteins. AIDS Rev. 2006, 8 (4): 221-236.
PubMed
Google Scholar
MacPherson JI, Dickerson JE, Pinney JW, Robertson DL: Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Comput Biol. 2010, 6 (7): e1000863-10.1371/journal.pcbi.1000863.
Article
PubMed
PubMed Central
Google Scholar
Krishnan V, Zeichner SL: Host cell gene expression during human immunodeficiency virus type I latency and reactivation and effects of targeting genes that are differentially expressed in viral latency. J Virol. 2004, 78 (17): 9458-9473. 10.1128/JVI.78.17.9458-9473.2004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chun TW, Justement JS, Lempicki RA, Yang J, Dennis G, Hallahan CW, Sanford C, Pandya P, Liu S, McLaughlin M: Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci. 2003, 100 (4): 1908-1913. 10.1073/pnas.0437640100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang T, Xu Z, Chen L, Cai YD, Kong X: Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network. PLoS One. 2011, 6 (3): e17291-10.1371/journal.pone.0017291.
Article
CAS
PubMed
PubMed Central
Google Scholar