Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002;74(20):5383–92.
Article
CAS
PubMed
Google Scholar
Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol. 2010;28(7):710–21.
Article
CAS
PubMed
Google Scholar
Codrea MC, Nahnsen S. Platforms and pipelines for proteomics data analysis and management. Modern Proteomics - Sample Preparation, Analysis and Practical Applications. 2016;919:203–15.
Article
CAS
Google Scholar
Kentaro Kawata AH, Yugi K, Kubota H, Sano T, Fujii M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Yutaka S, Matsumoto M, Nakayama KI, Saitoh K, Kato K, Ueno A, Ohishi M, Hirayama A, Kuroda S. Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience. 2018;7:1–18.
Article
CAS
Google Scholar
Koberlin MS, Snijder B, Heinz LX, Baumann CL, Fauster A, Vladimer GI, Gavin AC, Superti-Furga G. A conserved circular network of Coregulated lipids modulates innate immune responses. Cell. 2015;162(1):170–83.
Article
PubMed
PubMed Central
CAS
Google Scholar
Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH. Functional organization of the transcriptome in human brain. Nat Neurosci. 2008;11(11):1271–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li D, Li YP, Li YX, Zhu XH, Du XG, Zhou M, Li WB, Deng HY. Effect of regulatory network of exosomes and microRNAs on neurodegenerative diseases. Chin Med J. 2018;131(18):2216–25.
Article
PubMed
PubMed Central
Google Scholar
Szilagyi A, Nussinov R, Csermely P. Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks. Curr Top Med Chem. 2013;13(1):64–77.
Article
CAS
PubMed
Google Scholar
Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, et al. Global landscape of HIV-human protein complexes. Nature. 2011;481(7381):365–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Miozzo F, Veres DV, Piazza F, Nussinov R. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. Curr Protein Pept Sci. 2012;13(1):19–33.
Article
CAS
PubMed
Google Scholar
Dai LY, Zhao TY, Bisteau X, Sun WD, Prabhu N, Lim YT, Sobota RM, Kaldis P, Nordlund P. Modulation of Protein-Interaction States through the Cell Cycle. Cell. 2018;173(6):1481.
Article
CAS
PubMed
Google Scholar
Weiss RA. The discovery of endogenous retroviruses. Retrovirology. 2006;3:67.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kirchhoff F: HIV Life Cycle: Overview. In: Encyclopedia of AIDS. Edited by Hope TJ, Stevenson M, Richman D. New York, NY: Springer New York; 2013: 1–9.
Google Scholar
Lehmann-Che J, Saib A. Early stages of HIV replication: how to hijack cellular functions for a successful infection. AIDS Rev. 2004;6(4):199–207.
PubMed
Google Scholar
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):921–6.
Article
CAS
PubMed
Google Scholar
Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008;135(1):49–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res. 2009;37:D417–22.
Article
CAS
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.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dickerson JE, Pinney JW, Robertson DL. The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Syst Biol. 2010;4:80.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pinney JW, Dickerson JE, Fu W, Sanders-Beer BE, Ptak RG, Robertson DL. HIV-host interactions: a map of viral perturbation of the host system. Aids. 2009;23(5):549–54.
PubMed
Google Scholar
Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, Dianes JA, Sun Z, Farrah T, Bandeira N, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;32(3):223–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–8.
Article
CAS
PubMed
Google Scholar
Zhou HL, Xu M, Huang Q, Gates AT, Zhang XHD, Castle JC, Stec E, Ferrer M, Strulovici B, Hazuda DJ, et al. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe. 2008;4(5):495–504.
Article
CAS
PubMed
Google Scholar
Arhel N, Kirchhoff F. Host proteins involved in HIV infection: new therapeutic targets. Bba-Mol Basis Dis. 2010;1802(3):313–21.
Article
CAS
Google Scholar
Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Munoz M, Gunthard HF, Beerenwinkel N, Telenti A, Ciuffi A. 24 hours in the life of HIV-1 in a T cell line. PLoS Pathog. 2013;9(1):e1003161.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nemeth J, Vongrad V, Metzner KJ, Strouvelle VP, Weber R, Pedrioli P, Aebersold R, Gunthard HF, Collins B. In vivo and in vitro proteome analysis of human immunodeficiency virus (HIV)-1-infected, human CD4(+) T cells. Mol Cell Proteomics. 2017;16(4):S108–23.
Article
PubMed
PubMed Central
Google Scholar
Goff SP. Knockdown screens to knockout HIV-1. Cell. 2008;135(3):417–20.
Article
CAS
PubMed
PubMed Central
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):19463–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science. 2005;307(5710):724–7.
Article
PubMed
CAS
Google Scholar
Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, et al. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. 2015;47(6):569–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, et al. Quantitative analysis of protein interaction network dynamics in yeast. Mol Syst Biol. 2017;13(7):934.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP. Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A. 2008;105(5):1454–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU. Complex networks: structure and dynamics. Phys Rep. 2006;424(4–5):175–308.
Article
Google Scholar
Kleinman CL, Doria M, Orecchini E, Giuliani E, Galardi S, De Jay N, Michienzi A. HIV-1 infection causes a down-regulation of genes involved in ribosome biogenesis. PloS one. 2014;9(12):e113908.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dowling D, Nasr-Esfahani S, Tan CH, O'Brien K, Howard JL, Jans DA, Purcell DF, Stoltzfus CM, Sonza S. HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splicing and virus production in macrophages. Retrovirology. 2008;5:18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet. Virology. 2018;516:176–188.
Article
CAS
PubMed
Google Scholar
Garcia-Moreno M, Noerenberg M, Ni S, Jarvelin AI, Gonzalez-Almela E, Lenz CE, Bach-Pages M, Cox V, Avolio R, Davis T, et al. System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection. Molecular cell. 2019;74(1):196–211, e111.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lum JJ, Badley AD: Resistance to apoptosis: mechanism for the development of HIV reservoirs. Current HIV research. 2003;1(3):261–274.
Article
CAS
PubMed
Google Scholar
Antoni BA, Sabbatini P, Rabson AB, White E. Inhibition of apoptosis in human immunodeficiency virus-infected cells enhances virus production and facilitates persistent infection. J Virol. 1995;69(4):2384–392.
Badley AD, Sainski A, Wightman F, Lewin SR. Altering cell death pathways as an approach to cure HIV infection. Cell death & disease. 2013;4:e718.
Stricher F, Macri C, Ruff M, Muller S. HSPA8/HSC70 chaperone protein: structure, function, and chemical targeting. Autophagy. 2013;9(12):1937–54.
Article
CAS
PubMed
Google Scholar
Sherman MP, Greene WC. Slipping through the door: HIV entry into the nucleus. Microbes and infection / Institut Pasteur. 2002;4(1):67–73.
Article
CAS
PubMed
Google Scholar
Chang ST, Sova P, Peng X, Weiss J, Law GL, Palermo RE, Katze MG. Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and regulation of noncoding RNA expression in a CD4+ T cell line. mBio. 2011;2(5).
Rato S, Rausell A, Munoz M, Telenti A, Ciuffi A. Single-cell analysis identifies cellular markers of the HIV permissive cell. Plos Pathog. 2017;13(10):e1006678.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rao S, Amorim R, Niu M, Breton Y, Tremblay MJ, Mouland AJ. Host mRNA decay proteins influence HIV-1 replication and viral gene expression in primary monocyte-derived macrophages. Retrovirology. 2019;16(1):3.
Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. Journal of proteome research. 2010;9(2):761–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heaven MR, Funk AJ, Cobbs AL, Haffey WD, Norris JL, McCullumsmith RE, Greis KD. Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics-a prototype design for a single injection assay. J Mass Spectrom : JMS. 2016;51(1):1–11.
Article
CAS
Google Scholar
Miklossy G, Tozser J, Kadas J, Ishima R, Louis JM, Bagossi P. Novel macromolecular inhibitors of human immunodeficiency virus-1 protease. Protein engineering, design & selection : PEDS. 2008;21(7):453–61.
Article
CAS
PubMed Central
Google Scholar
Dull T, Zufferey R, Kelly M, Mandel RJ, Nguyen M, Trono D, Naldini L. A third-generation lentivirus vector with a conditional packaging system. J Virol. 1998;72(11):8463–71.
CAS
PubMed
PubMed Central
Google Scholar
Csosz E, Markus B, Darula Z, Medzihradszky KF, Nemes J, Szabo E, Tozser J, Kiss C, Marton I. Salivary proteome profiling of oral squamous cell carcinoma in a Hungarian population. FEBS open bio. 2018;8(4):556–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andon NL, Hollingworth S, Koller A, Greenland AJ, Yates JR 3rd, Haynes PA. Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry. Proteomics. 2002;2(9):1156–68.
Article
CAS
PubMed
Google Scholar
Qian WJ, Liu T, Monroe ME, Strittmatter EF, Jacobs JM, Kangas LJ, Petritis K, Camp DG 2nd, Smith RD. Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res. 2005;4(1):53–62.
Article
CAS
PubMed
Google Scholar
Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Analytical chemistry. 2003;75(17):4646–58.
Article
CAS
PubMed
Google Scholar
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41(Database issue):D808–15.
CAS
PubMed
Google Scholar
W.N. Venables BDR. Modern applied statistics with S. New York: Springer-Verlag; 2002.
Book
Google Scholar
Lenth RV. Least-squares means: the R package lsmeans. J Stat Softw. 2016;69(1):1–33.
Article
Google Scholar
matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors). R package version 0.52.2 [https://github.com/HenrikBengtsson/matrixStats].
Wickham H. Reshaping data with the reshape package. J Stat Softw. 2007;21(12):1–20.
Article
Google Scholar
Ginestet C. ggplot2: elegant graphics for data analysis. J R Stat Soc a Stat. 2011;174:245.
Article
Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18(9):1509–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:3.
Article
Google Scholar
Searle SR, Speed FM, Milliken GA. Population marginal means in the linear-model - an alternative to least-squares means. Am Stat. 1980;34(4):216–21.
Google Scholar
MHaDA W. Nonparametric statistical methods. New York: John Wiley & Sons; 1999.
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995;57(1):289–300.
Google Scholar