Retroviruses

Publications about this resource

• HIV-1, human interaction database: current status and new features. Ako-Adjei D, Fu W, Wallin C, Katz KS, Song G, Darji D, Brister JR, Ptak RG,Pruitt KD. Nucleic Acids Res. 2015; 43(Database issue):D566-70 DOI:10.1093/nar/gku1126. PMID: 25378338
• HIV-host interactions: a map of viral perturbation of the host system Pinney, J.W.; Dickerson, J.E.; Fu, W.; Sanders-Beer, B.E.; Ptak, R.G.; Robertson, D.L. AIDS 2009; 23(5):549-554. DOI:10.1097/QAD.0b013e328325a495. PubMed ID: 19262354
• Human immunodeficiency virus type 1, human protein interaction database at NCBI. Fu, W., Sanders-Beer, B.E., Katz, K.S., Maglott, D.R., Pruitt, K.D., Ptak, R.G. Nucleic Acids Research 2009; 37(Database issue):D417-22 DOI: 10.1093/nar/gkn708. PubMed ID: 18927109
• Cataloguing the HIV-1 Human Protein Interaction Network Ptak, R.G., Fu, W., Sanders-Beer, B.E., Dickerson, J.E., Pinney, J.W., Robertson, D.L., Rozanov, M.N., Katz, K.S., Maglott, D.R., Pruitt, K.D., Dieffenbach, C.W. AIDS Research and Human Retroviruses 2008; 24(12):1497-502 DOI:10.1089/aid.2008.0113. PubMed ID: 19025396. Supplemental Information

Publications citing use of this resource

• HIV, Tat and dopamine transmission. Gaskill PJ, Miller DR, Gamble-George J, Yano H, Khoshbouei H. Neurobiol Dis. 2017 Sep;105:51-73. doi: 10.1016/j.nbd.2017.04.015. Epub 2017 Apr 27. Review. PMID: 28457951

• HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. Li C, Ramarathinam SH, Revote J, Khoury G, Song J, Purcell AW. Sci Rep. 2017 Mar 30;7:45509. doi: 10.1038/srep45509. PMID: 28358052

• HIV Genome-Wide Protein Associations: a Review of 30 Years of Research. Li G, De Clercq E. Microbiol Mol Biol Rev. 2016 Jun 29;80(3):679-731. doi: 10.1128/MMBR.00065-15. Print 2016 Sep. Review. PMID: 27357278

• HPIDB 2.0: a curated database for host-pathogen interactions.Ammari MG, Gresham CR, McCarthy FM, Nanduri B.  Database (Oxford). 2016 Jul 3. PMID: 27374121

• Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.Druce M, Hulo C, Masson P, Sommer P, Xenarios I, Le Mercier P, De Oliveira T. Database (Oxford). 2016 Apr 17. PMID: 27087306

• A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs. Ray S, Bandyopadhyay S. BMC Bioinformatics. 2016 Mar 8;17:121. doi: 10.1186/s12859-016-0952-6. PMID: 26956556

• Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity.Cui T, Li W, Liu L, Huang Q, He ZG. PLoS One. 2016 Jan 22;11(1):e0147612. doi: 10.1371/journal.pone.0147612. PMID:26799490

• Database resources of the National Center for Biotechnology Information. NCBI Resource Coordinators. Nucleic Acids Res. 2016 Jan 4;44(D1):D7-19. doi: 10.1093/nar/gkv1290. Epub 2015 Nov 28. PMID: 26615191

• Identification of novel HIV-1 dependency factors in primary CCR4(+)CCR6(+)Th17 cells via a genome-wide transcriptional approach. Cleret-Buhot A, Zhang Y, Planas D, Goulet JP, Monteiro P, Gosselin A, Wacleche VS, Tremblay CL, Jenabian MA, Routy JP, El-Far M, Chomont N, Haddad EK, Sekaly RP, Ancuta P. Retrovirology. 2015 Dec 10;12:102. doi: 10.1186/s12977-015-0226-9. PMID: 26654242

• A review on computational systems biology of pathogen-host interactions. Durmuş S, Çakır T, Özgür A, Guthke R. Front Microbiol. 2015 Apr 9;6:235. PMID: 25914674

• A logical model of HIV-1 interactions with the T-cell activation signalling pathway.Oyeyemi OJ, Davies O, Robertson DL, Schwartz JM. Bioinformatics. 2015 Apr 1;31(7):1075-83. doi: 10.1093/bioinformatics/btu787. Epub 2014 Nov 26. PMID: 25431332

• An integrated map of HIV genome-wide variation from a population perspective.Li G, Piampongsant S, Faria NR, Voet A, Pineda-Peña AC, Khouri R, Lemey P, Vandamme AM, Theys K. Retrovirology. 2015 Feb 15;12:18. PMID: 25808207

• An integrative approach for a network based meta-analysis of viral RNAi screens. Amberkar SS and Kaderali L. Algorithms Mol Biol. 2015 Feb 13;10:6. PMID: 25691914

• Unraveling the web of viroinformatics: computational tools and databases in virus research. Sharma D, Priyadarshini P, Vrati S. . J Virol. 2015 Feb;89(3):1489-501. PMID: 25428870

• Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. Nandal UK, Vlietstra WJ, Byrman C, Jeeninga RE, Ringrose JH, van Kampen AH, Speijer D, Moerland PD. BMC Bioinformatics. 2015 Jan 28;16(1):25. PMID: 25627479
• The domain landscape of virus-host interactomes. Zheng LL, Li C, Ping J, Zhou Y, Li Y, Hao P. Biomed Res Int. 2014;2014:867235. PMID: 24991570
• Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Zhou H, Gao S, Nguyen NN, Fan M, Jin J, Liu B, Zhao L, Xiong G, Tan M, Li S, Wong L. Biol Direct. 2014 Apr 8;9:5. PMID:24708540
• Incorporating the type and direction information in predicting novel regulatory    interactions between HIV-1 and human proteins using a biclustering approach. Mukhopadhyay A, Ray S, Maulik U. BMC Bioinformatics. 2014 Jan 24;15:26. doi: 10.1186/1471-2105-15-26.PMID: 24460683
• Roles and functions of HIV-1 Tat protein in the CNS: an overview. Bagashev A, Sawaya BE. Virol J. 2013 Dec 21;10:358. doi: 10.1186/1743-422X-10-358. Review. PMID: 24359561
• Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Zhou H, Rezaei J, Hugo W, Gao S, Jin J, Fan M, Yong CH, Wozniak M, Wong L. BMC Syst Biol. 2013;7 Suppl 6:S6. PMID: 24564941
• Tanscriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy. Wu JQ, Sassé TR, Saksena MM, Saksena NK. Virol J. 2013 Dec 27;10:361. doi: 10.1186/1743-422X-10-361. PMID: 24370116
• Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. Mei S. PLoS One. 2013 Nov 18;8(11):e79606. doi: 10.1371/journal.pone.0079606. eCollection 2013. PMID: 24260261
• A viral-human interactome based on structural motif-domain interactions captures the human infectome. Segura-Cabrera A, García-Pérez CA, Guo X, Rodríguez-Pérez MA. PLoS One. 2013 Aug 8;8(8):e71526. doi: 10.1371/journal.pone.0071526. eCollection 2013. PMID: 23951184
• Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network. Li BQ, Niu B, Chen L, Wei ZJ, Huang T, Jiang M, Lu J, Zheng MY, Kong XY, Cai YD. PLoS One. 2013 Jun 6;8(6):e65207. doi: 10.1371/journal.pone.0065207. Print 2013. PMID: 23762317
• Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry. Wojcechowskyj JA, Didigu CA, Lee JY, Parrish NF, Sinha R, Hahn BH, Bushman FD, Jensen ST, Seeholzer SH, Doms RW. Cell Host Microbe. 2013 May 15;13(5):613-23. doi: 10.1016/j.chom.2013.04.011. PMID: 23684312
• The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types. Linde ME, Colquhoun DR, Ubaida Mohien C, Kole T, Aquino V, Cotter R, Edwards N, Hildreth JE, Graham DR. J Proteome Res. 2013 May 3;12(5):2045-54. PMID: 23432411
• Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. Mairiang D, Zhang H, Sodja A, Murali T, Suriyaphol P, Malasit P, Limjindaporn T, Finley RL Jr. PLoS One. 2013;8(1):e53535. PMID: 23326450
• Quantitative proteomic analysis of exosomes from HIV-1-infected lymphocytic cells. Li M, Aliotta JM, Asara JM, Tucker L, Quesenberry P, Lally M, Ramratnam B. Proteomics. 2012 Jul;12(13):2203-11. doi: 10.1002/pmic.201100376. PMID: 22807456
• Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: protein synthesis, cell proliferation, and T-cell activation. Navare AT, Sova P, Purdy DE, Weiss JM, Wolf-Yadlin A, Korth MJ, Chang ST, Proll SC, Jahan TA, Krasnoselsky AL, Palermo RE, Katze MG. Virology. 2012 Jul 20;429(1):37-46. doi: 10.1016/j.virol.2012.03.026. Epub 2012 Apr 26. PMID: 22542004
• Determining confidence of predicted interactions between hiv-1 and human proteins using conformal method. Nouretdinov I, Gammerman A, Qi Y, Klein-Seetharaman J. Pac Symp Biocomput. 2012:311-22. PMID: 22174286
• A novel biclustering approach to association rule mining for predicting HIV-1-human protein interactions. Mukhopadhyay A, Maulik U, Bandyopadhyay S. PLoS One. 2012;7(4):e32289. Epub 2012 Apr 23. PMID: 22539940
• Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Jamieson DG, Gerner M, Sarafraz F, Nenadic G, Robertson DL. Database (Oxford). 2012 Apr 23;2012:bas023. Print 2012. PMID: 22529179
• Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles. Chen KC, Wang TY, Chan CH. PLoS One. 2012;7(3):e34240. doi: 10.1371/journal.pone.0034240. Epub 2012 Mar 27. PMID: 22479575
• Building an HIV data mashup using Bio2RDF. Nolin MA, Dumontier M, Belleau F, Corbeil J. Brief Bioinform. 2012 Jan;13(1):98-106. doi: 10.1093/bib/bbr003. Epub 2011 Mar 24. PMID: 22223742
• Proteomic signatures of human oral epithelial cells in HIV-infected subjects. Yohannes E, Ghosh SK, Jiang B, McCormick TS, Weinberg A, Hill E, Faddoul F, Chance MR. PLoS One. 2011;6(11):e27816. Epub 2011 Nov 16. PMID: 22114700
• Genome-wide association study implicates PARD3B-based AIDS restriction. Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson SL, Li G, Pontius J, Tang M, An P, Winkler CA, Limou S, Le Clerc S, Delaneau O, Zagury JF, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O'Brien SJ. J Infect Dis. 2011 May 15;203(10):1491-502. PMID: 21502085
• Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef. Sarmady M, Dampier W, Tozeren A. PLoS One. 2011;6(6):e20735. Epub 2011 Jun 28. PMID: 21738584
• HIV protein sequence hotspots for crosstalk with host hub proteins. Sarmady M, Dampier W, Tozeren A. PLoS One. 2011;6(8):e23293. Epub 2011 Aug 15. PMID: 21858059
• HIVToolbox, an integrated web application for investigating HIV. Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR. PLoS One. 2011;6(5):e20122. Epub 2011 May 25. PMID: 21647445
• HIV-1 remodels the nuclear pore complex. Monette A, Pante N, Mouland AJ. J Cell Biol. 2011 May 16;193(4):619-31. doi: 10.1083/jcb.201008064. PMID: 21576391
• Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network. Huang T, Xu Z, Chen L, Cai YD, Kong X. PLoS One. 2011 Mar 4;6(3):e17291. doi: 10.1371/journal.pone.0017291. PMID: 21394196
• Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. Qian X, Yoon BJ. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S19. PMID: 21342548
• Dominating biological networks.Milenković T, Memišević V, Bonato A, Pržulj N. PLoS One. 2011;6(8):e23016. Epub 2011 Aug 26. PMID: 21887225
• GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. BMC Bioinformatics. 2011 Jul 22;12:298. PMID: 21777475
• Supervised learning and prediction of physical interactions between human and HIV proteins. Dyer MD, Murali TM, Sobral BW. Infect Genet Evol. 2011 Jul;11(5):917-23. Epub 2011 Mar 5. PMID: 21382517
• Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB. PLoS One. 2011 Feb 25;6(2):e17190. PMID: 21364930
• Functional comparison of innate immune signaling pathways in primates. Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. PLoS Genet. 2010 Dec 16;6(12):e1001249. PMID: 21187902
• Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. Chinn LW, Tang M, Kessing BD, Lautenberger JA, Troyer JL, Malasky MJ, McIntosh C, Kirk GD, Wolinsky SM, Buchbinder SP, Gomperts ED, Goedert JJ, O'Brien SJ. J Infect Dis. 2010 Dec 15;202(12):1836-45. PMID: 21083371
• Viral organization of human proteins. Wuchty S, Siwo G, Ferdig MT. PLoS One. 2010 Aug 25;5(8):e11796. PMID: 20827298
• Gene expression variability within and between human populations and implications toward disease susceptibility. Li J, Liu Y, Kim T, Min R, Zhang Z. PLoS Comput Biol. 2010 Aug 26;6(8). pii: e1000910. doi: 10.1371/journal.pcbi.1000910. PMID: 20865155
• Purification and characterization of HIV-human protein complexes. Jager S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. Methods. 2011 Jan;53(1):13-9. doi: 10.1016/j.ymeth.2010.08.007. Epub 2010 Aug 12. Review. PMID: 20708689
• Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. van Dijk D, Ertaylan G, Boucher CA, Sloot PM. BMC Syst Biol. 2010 Jul 15;4:96. PMID: 20633292
• Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells. Rato S, Maia S, Brito PM, Resende L, Pereira CF, Moita C, Freitas RP, Moniz-Pereira J, Hacohen N, Moita LF, Goncalves J. PLoS One. 2010 Feb 17;5(2):e9276. PMID: 20174665
• Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins. Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J, Weston J. Bioinformatics. 2010 Sep 15;26(18):i645-52. PMID: 20823334
• Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. MacPherson JI, Dickerson JE, Pinney JW, Robertson DL. PLoS Comput Biol. 2010 Jul 29;6(7):e1000863. PMID: 20686668
• Inference of surface membrane factors of HIV-1 infection through functional interaction networks. Jaeger S, Ertaylan G, van Dijk D, Leser U, Sloot P. PLoS One. 2010 Oct 12;5(10):e13139. PMID: 20967291
• Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach. Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. PLoS Genet. 2010 Feb 19;6(2):e1000849. PMID: 20174570
• Positive selection of HIV host factors and the evolution of lentivirus genes. Bozek K, Lengauer T. BMC Evol Biol. 2010 Jun 18;10:186. PMID: 20565842
• The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. Dickerson JE, Pinney JW, Robertson DL. BMC Syst Biol. 2010 Jun 7;4:80. PMID: 20529270
• Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Doolittle JM, Gomez SM. Virol J. 2010 Apr 28;7:82. PMID: 20426868
• Alternative paths in HIV-1 targeted human signal transduction pathways. Balakrishnan S, Tastan O, Carbonell J, Klein-Seetharaman J. BMC Genomics. 2009 Dec 3;10 Suppl 3:S30. doi: 10.1186/1471-2164-10-S3-S30. PMID: 19958495
• Evolutionary trajectories of primate genes involved in HIV pathogenesis. Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L, Telenti A. Mol Biol Evol. 2009 Dec;26(12):2865-75. doi: 10.1093/molbev/msp197. Epub 2009 Sep 2. PMID: 19726537
• CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. Lin FK, Pan CL, Yang JM, Chuang TJ, Chen FC. BMC Microbiol. 2009 Aug 12;9:164. PMID: 19674441
• Dynamic host energetics and cytoskeletal proteomes in human immunodeficiency virus type 1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry. Chan EY, Sutton JN, Jacobs JM, Bondarenko A, Smith RD, Katze MG. J Virol. 2009 Sep;83(18):9283-95. Epub 2009 Jul 8. PMID: 19587052
• Host cell factors in HIV replication: meta-analysis of genome-wide studies. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. PLoS Pathog. 2009 May;5(5):e1000437. Epub 2009 May 29. Review. PMID: 19478882
• Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. Evans P, Dampier W, Ungar L, Tozeren A. BMC Med Genomics. 2009 May 18;2:27. PMID: 19450270
• JNets: exploring networks by integrating annotation. Macpherson JI, Pinney JW, Robertson DL. BMC Bioinformatics. 2009 Mar 26;10:95. PMID: 19323810
• Prediction of interactions between HIV-1 and human proteins by information integration. Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J. Pac Symp Biocomput. 2009:516-27. PMID: 19209727