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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. doi: 10.1186/1755-8794-2-27.


HIV protein sequence hotspots for crosstalk with host hub proteins.

Sarmady M, Dampier W, Tozeren A.

PLoS One. 2011;6(8):e23293. doi: 10.1371/journal.pone.0023293. Epub 2011 Aug 15.


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. doi: 10.1371/journal.pone.0020735. Epub 2011 Jun 28.


Computational prediction of host-pathogen protein-protein interactions.

Dyer MD, Murali TM, Sobral BW.

Bioinformatics. 2007 Jul 1;23(13):i159-66.


Evidence for the concerted evolution between short linear protein motifs and their flanking regions.

Chica C, Diella F, Gibson TJ.

PLoS One. 2009 Jul 8;4(7):e6052. doi: 10.1371/journal.pone.0006052.


Host sequence motifs shared by HIV predict response to antiretroviral therapy.

Dampier W, Evans P, Ungar L, Tozeren A.

BMC Med Genomics. 2009 Jul 23;2:47. doi: 10.1186/1755-8794-2-47.


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. doi: 10.1186/1752-0509-4-96.


Strategies for inhibiting function of HIV-1 accessory proteins: a necessary route to AIDS therapy?

Richter SN, Frasson I, Pal├╣ G.

Curr Med Chem. 2009;16(3):267-86. Review.


Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

Garamszegi S, Franzosa EA, Xia Y.

PLoS Pathog. 2013;9(12):e1003778. doi: 10.1371/journal.ppat.1003778. Epub 2013 Dec 5.


Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting.

Kim J, Huang DS, Han K.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S57. doi: 10.1186/1471-2105-10-S1-S57.


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.


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.


The role of peptide motifs in the evolution of a protein network.

Saito H, Kashida S, Inoue T, Shiba K.

Nucleic Acids Res. 2007;35(19):6357-66. Epub 2007 Sep 18.


Modular composition predicts kinase/substrate interactions.

Liu Y, Tozeren A.

BMC Bioinformatics. 2010 Jun 25;11:349. doi: 10.1186/1471-2105-11-349.


Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.

Makarova KS, Wolf YI, van der Oost J, Koonin EV.

Biol Direct. 2009 Aug 25;4:29. doi: 10.1186/1745-6150-4-29.


Interaction between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network.

Shimizu K, Toh H.

J Mol Biol. 2009 Oct 9;392(5):1253-65. doi: 10.1016/j.jmb.2009.07.088. Epub 2009 Aug 3.


[Genetic analysis of the complete env genes of HIV-1 from paid blood donors in Henan province].

Feng X, Yang HR, Yu SQ, Zhou L, Li HX, Li ZL, Zeng Y.

Bing Du Xue Bao. 2009 Mar;25(2):88-94. Chinese.


Identification of a novel tobacco DnaJ-like protein that interacts with the movement protein of tobacco mosaic virus.

Shimizu T, Yoshii A, Sakurai K, Hamada K, Yamaji Y, Suzuki M, Namba S, Hibi T.

Arch Virol. 2009;154(6):959-67. doi: 10.1007/s00705-009-0397-6. Epub 2009 May 21.


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. doi: 10.1016/j.meegid.2011.02.022. Epub 2011 Mar 5.


Human immunodeficiency virus type 1 Vpr: functions and molecular interactions.

Romani B, Engelbrecht S.

J Gen Virol. 2009 Aug;90(Pt 8):1795-805. doi: 10.1099/vir.0.011726-0. Epub 2009 May 20. Review.

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