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Drug resistance emergence in macaques administered cabotegravir long-acting for pre-exposure prophylaxis during acute SHIV infection.

Radzio-Basu J, Council O, Cong ME, Ruone S, Newton A, Wei X, Mitchell J, Ellis S, Petropoulos CJ, Huang W, Spreen W, Heneine W, García-Lerma JG.

Nat Commun. 2019 May 1;10(1):2005. doi: 10.1038/s41467-019-10047-w.


Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens.

Mesa KA, Yu B, Wrin T, Petropoulos CJ, Pogson GH, Alexander DL, Perez G, O'Rourke SM, Sinangil F, Robinson J, Conant MA, Berman PW.

PLoS One. 2019 Apr 10;14(4):e0213409. doi: 10.1371/journal.pone.0213409. eCollection 2019.


Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease.

Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA.

Structure. 2018 Oct 2;26(10):1360-1372.e5. doi: 10.1016/j.str.2018.07.004. Epub 2018 Aug 23.


Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants.

Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.

ACS Med Chem Lett. 2018 May 17;9(7):691-696. doi: 10.1021/acsmedchemlett.8b00150. eCollection 2018 Jul 12.


p95HER2 Methionine 611 Carboxy-Terminal Fragment Is Predictive of Trastuzumab Adjuvant Treatment Benefit in the FinHer Trial.

Sperinde J, Huang W, Vehtari A, Chenna A, Kellokumpu-Lehtinen PL, Winslow J, Bono P, Lie YS, Petropoulos CJ, Weidler J, Joensuu H.

Clin Cancer Res. 2018 Jul 1;24(13):3046-3052. doi: 10.1158/1078-0432.CCR-17-3250. Epub 2018 Mar 13.


High p95HER2/HER2 Ratio Associated With Poor Outcome in Trastuzumab-Treated HER2-Positive Metastatic Breast Cancer NCCTG N0337 and NCCTG 98-32-52 (Alliance).

Chumsri S, Sperinde J, Liu H, Gligorov J, Spano JP, Antoine M, Moreno Aspitia A, Tan W, Winslow J, Petropoulos CJ, Chenna A, Bates M, Weidler JM, Huang W, Dueck A, Perez EA.

Clin Cancer Res. 2018 Jul 1;24(13):3053-3058. doi: 10.1158/1078-0432.CCR-17-1864. Epub 2018 Mar 12.


Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.

Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt-Yilmaz N, Schiffer CA, Ali A.

J Med Chem. 2017 Jul 13;60(13):5699-5716. doi: 10.1021/acs.jmedchem.7b00426. Epub 2017 Jun 19.


Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1.

Polster R, Petropoulos CJ, Bonhoeffer S, Guillaume F.

Mol Biol Evol. 2016 Dec;33(12):3213-3225. Epub 2016 Sep 27.


Elucidation of the Molecular Mechanism Driving Duplication of the HIV-1 PTAP Late Domain.

Martins AN, Waheed AA, Ablan SD, Huang W, Newton A, Petropoulos CJ, Brindeiro RD, Freed EO.

J Virol. 2015 Oct 28;90(2):768-79. doi: 10.1128/JVI.01640-15. Print 2016 Jan 15.


Five Antiretroviral Drug Class-Resistant HIV-1 in a Treatment-Naïve Patient Successfully Suppressed with Optimized Antiretroviral Drug Selection.

Volpe JM, Ward DJ, Napolitano L, Phung P, Toma J, Solberg O, Petropoulos CJ, Walworth CM.

J Int Assoc Provid AIDS Care. 2015 Sep-Oct;14(5):398-401. doi: 10.1177/2325957415596229. Epub 2015 Jul 17.


Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1.

Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, Engelstädter J, Bonhoeffer S.

PLoS Genet. 2014 Jun 26;10(6):e1004439. doi: 10.1371/journal.pgen.1004439. eCollection 2014 Jun.


Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method.

Evans MC, Phung P, Paquet AC, Parikh A, Petropoulos CJ, Wrin T, Haddad M.

BMC Bioinformatics. 2014 Mar 19;15:77. doi: 10.1186/1471-2105-15-77.


A decade of HIV-1 drug resistance in the United States: trends and characteristics in a large protease/reverse transcriptase and co-receptor tropism database from 2003 to 2012.

Paquet AC, Solberg OD, Napolitano LA, Volpe JM, Walworth C, Whitcomb JM, Petropoulos CJ, Haddad M.

Antivir Ther. 2014;19(4):435-41. doi: 10.3851/IMP2748. Epub 2014 Feb 12.


Role of the K101E substitution in HIV-1 reverse transcriptase in resistance to rilpivirine and other nonnucleoside reverse transcriptase inhibitors.

Xu HT, Colby-Germinario SP, Huang W, Oliveira M, Han Y, Quan Y, Petropoulos CJ, Wainberg MA.

Antimicrob Agents Chemother. 2013 Nov;57(11):5649-57. doi: 10.1128/AAC.01536-13. Epub 2013 Sep 3.


HER3, p95HER2, and HER2 protein expression levels define multiple subtypes of HER2-positive metastatic breast cancer.

Lipton A, Goodman L, Leitzel K, Cook J, Sperinde J, Haddad M, Köstler WJ, Huang W, Weidler JM, Ali S, Newton A, Fuchs EM, Paquet A, Singer CF, Horvat R, Jin X, Banerjee J, Mukherjee A, Tan Y, Shi Y, Chenna A, Larson J, Lie Y, Sherwood T, Petropoulos CJ, Williams S, Winslow J, Parry G, Bates M.

Breast Cancer Res Treat. 2013 Aug;141(1):43-53.


A case-based reasoning system for genotypic prediction of HIV-1 co-receptor tropism.

Evans MC, Paquet AC, Huang W, Napolitano L, Frantzell A, Toma J, Stawiski EW, Goetz MB, Petropoulos CJ, Whitcomb J, Coakley E, Haddad M.

J Bioinform Comput Biol. 2013 Aug;11(4):1350006. doi: 10.1142/S0219720013500066. Epub 2013 Apr 7.


Evaluating the role of macrocycles in the susceptibility of hepatitis C virus NS3/4A protease inhibitors to drug resistance.

Ali A, Aydin C, Gildemeister R, Romano KP, Cao H, Ozen A, Soumana D, Newton A, Petropoulos CJ, Huang W, Schiffer CA.

ACS Chem Biol. 2013 Jul 19;8(7):1469-78. doi: 10.1021/cb400100g. Epub 2013 May 1.


Viral fitness cost prevents HIV-1 from evading dolutegravir drug pressure.

Mesplède T, Quashie PK, Osman N, Han Y, Singhroy DN, Lie Y, Petropoulos CJ, Huang W, Wainberg MA.

Retrovirology. 2013 Feb 22;10:22. doi: 10.1186/1742-4690-10-22.


Novel method to assess antiretroviral target trough concentrations using in vitro susceptibility data.

Acosta EP, Limoli KL, Trinh L, Parkin NT, King JR, Weidler JM, Ofotokun I, Petropoulos CJ.

Antimicrob Agents Chemother. 2012 Nov;56(11):5938-45. doi: 10.1128/AAC.00691-12. Epub 2012 Sep 10.


The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors.

Romano KP, Ali A, Aydin C, Soumana D, Ozen A, Deveau LM, Silver C, Cao H, Newton A, Petropoulos CJ, Huang W, Schiffer CA.

PLoS Pathog. 2012;8(7):e1002832. doi: 10.1371/journal.ppat.1002832. Epub 2012 Jul 26.


Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.

Mostowy R, Kouyos RD, Hoof I, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Keşmir C, Bonhoeffer S.

PLoS Comput Biol. 2012;8(5):e1002525. doi: 10.1371/journal.pcbi.1002525. Epub 2012 May 24.


Substitutions at amino acid positions 143, 148, and 155 of HIV-1 integrase define distinct genetic barriers to raltegravir resistance in vivo.

Fransen S, Gupta S, Frantzell A, Petropoulos CJ, Huang W.

J Virol. 2012 Jul;86(13):7249-55. doi: 10.1128/JVI.06618-11. Epub 2012 May 2.


Exploring the complexity of the HIV-1 fitness landscape.

Kouyos RD, Leventhal GE, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Bonhoeffer S.

PLoS Genet. 2012;8(3):e1002551. doi: 10.1371/journal.pgen.1002551. Epub 2012 Mar 8.


Assessing predicted HIV-1 replicative capacity in a clinical setting.

Kouyos RD, von Wyl V, Hinkley T, Petropoulos CJ, Haddad M, Whitcomb JM, Böni J, Yerly S, Cellerai C, Klimkait T, Günthard HF, Bonhoeffer S; Swiss HIV Cohort Study.

PLoS Pathog. 2011 Nov;7(11):e1002321. doi: 10.1371/journal.ppat.1002321. Epub 2011 Nov 3.


The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment.

Fessel WJ, Anderson B, Follansbee SE, Winters MA, Lewis ST, Weinheimer SP, Petropoulos CJ, Shafer RW.

Antiviral Res. 2011 Dec;92(3):484-7. doi: 10.1016/j.antiviral.2011.09.010. Epub 2011 Oct 4.


A directed molecular evolution approach to improved immunogenicity of the HIV-1 envelope glycoprotein.

Du SX, Xu L, Zhang W, Tang S, Boenig RI, Chen H, Mariano EB, Zwick MB, Parren PW, Burton DR, Wrin T, Petropoulos CJ, Ballantyne JA, Chambers M, Whalen RG.

PLoS One. 2011;6(6):e20927. doi: 10.1371/journal.pone.0020927. Epub 2011 Jun 29.


Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing.

Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, Frantzell A, Petropoulos CJ, Coakley E, Schuitemaker H, Harrigan PR, van 't Wout AB.

PLoS Pathog. 2011 Jun;7(6):e1002106. doi: 10.1371/journal.ppat.1002106. Epub 2011 Jun 23.


Connection domain mutations in HIV-1 reverse transcriptase do not impact etravirine susceptibility and virologic responses to etravirine-containing regimens.

Gupta S, Vingerhoets J, Fransen S, Tambuyzer L, Azijn H, Frantzell A, Paredes R, Coakley E, Nijs S, Clotet B, Petropoulos CJ, Schapiro J, Huang W, Picchio G.

Antimicrob Agents Chemother. 2011 Jun;55(6):2872-9. doi: 10.1128/AAC.01695-10. Epub 2011 Apr 4.


Transmission of integrase strand-transfer inhibitor multidrug-resistant HIV-1: case report and response to raltegravir-containing antiretroviral therapy.

Young B, Fransen S, Greenberg KS, Thomas A, Martens S, St Clair M, Petropoulos CJ, Ha B.

Antivir Ther. 2011;16(2):253-6. doi: 10.3851/IMP1748.


A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase.

Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb JM, Petropoulos CJ, Bonhoeffer S.

Nat Genet. 2011 May;43(5):487-9. doi: 10.1038/ng.795. Epub 2011 Mar 27.


Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments.

Martins JZ, Chappey C, Haddad M, Whitcomb JM, Stawiski E, Petropoulos CJ, Bonhoeffer S.

Epidemics. 2010 Jun;2(2):85-91. doi: 10.1016/j.epidem.2010.03.003. Epub 2010 Mar 31.


Loss of asparagine-linked glycosylation sites in variable region 5 of human immunodeficiency virus type 1 envelope is associated with resistance to CD4 antibody ibalizumab.

Toma J, Weinheimer SP, Stawiski E, Whitcomb JM, Lewis ST, Petropoulos CJ, Huang W.

J Virol. 2011 Apr;85(8):3872-80. doi: 10.1128/JVI.02237-10. Epub 2011 Feb 2.


Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens.

Larson JS, Goodman LJ, Tan Y, Defazio-Eli L, Paquet AC, Cook JW, Rivera A, Frankson K, Bose J, Chen L, Cheung J, Shi Y, Irwin S, Kiss LD, Huang W, Utter S, Sherwood T, Bates M, Weidler J, Parry G, Winslow J, Petropoulos CJ, Whitcomb JM.

Patholog Res Int. 2010 Jun 28;2010:814176. doi: 10.4061/2010/814176.


Mutational pathways and genetic barriers to CXCR4-mediated entry by human immunodeficiency virus type 1.

Huang W, Frantzell A, Toma J, Fransen S, Whitcomb JM, Stawiski E, Petropoulos CJ.

Virology. 2011 Jan 20;409(2):308-18. doi: 10.1016/j.virol.2010.09.026. Epub 2010 Nov 10.


Dual-tropic HIV type 1 isolates vary dramatically in their utilization of CCR5 and CXCR4 coreceptors.

Toma J, Whitcomb JM, Petropoulos CJ, Huang W.

AIDS. 2010 Sep 10;24(14):2181-6. doi: 10.1097/QAD.0b013e32833c543f.


Combinations of mutations in the connection domain of human immunodeficiency virus type 1 reverse transcriptase: assessing the impact on nucleoside and nonnucleoside reverse transcriptase inhibitor resistance.

Gupta S, Fransen S, Paxinos EE, Stawiski E, Huang W, Petropoulos CJ.

Antimicrob Agents Chemother. 2010 May;54(5):1973-80. doi: 10.1128/AAC.00870-09. Epub 2010 Mar 1.


Immune escape mutations detected within HIV-1 epitopes associated with viral control during treatment interruption.

Schweighardt B, Wrin T, Meiklejohn DA, Spotts G, Petropoulos CJ, Nixon DF, Hecht FM.

J Acquir Immune Defic Syndr. 2010 Jan;53(1):36-46. doi: 10.1097/QAI.0b013e3181c4b885.


Effect of trimerization motifs on quaternary structure, antigenicity, and immunogenicity of a noncleavable HIV-1 gp140 envelope glycoprotein.

Du SX, Idiart RJ, Mariano EB, Chen H, Jiang P, Xu L, Ostrow KM, Wrin T, Phung P, Binley JM, Petropoulos CJ, Ballantyne JA, Whalen RG.

Virology. 2009 Dec 5;395(1):33-44. doi: 10.1016/j.virol.2009.07.042. Epub 2009 Oct 8.


Loss of raltegravir susceptibility by human immunodeficiency virus type 1 is conferred via multiple nonoverlapping genetic pathways.

Fransen S, Gupta S, Danovich R, Hazuda D, Miller M, Witmer M, Petropoulos CJ, Huang W.

J Virol. 2009 Nov;83(22):11440-6. doi: 10.1128/JVI.01168-09. Epub 2009 Sep 16.


Comparison of human immunodeficiency virus type 1 tropism profiles in clinical samples by the Trofile and MT-2 assays.

Coakley E, Reeves JD, Huang W, Mangas-Ruiz M, Maurer I, Harskamp AM, Gupta S, Lie Y, Petropoulos CJ, Schuitemaker H, van 't Wout AB.

Antimicrob Agents Chemother. 2009 Nov;53(11):4686-93. doi: 10.1128/AAC.00229-09. Epub 2009 Aug 17.


Characterization of human immunodeficiency virus type 1 populations containing CXCR4-using variants from recently infected individuals.

Huang W, Toma J, Stawiski E, Fransen S, Wrin T, Parkin N, Whitcomb JM, Coakley E, Hecht FM, Deeks SG, Gandhi RT, Eshleman SH, Petropoulos CJ.

AIDS Res Hum Retroviruses. 2009 Aug;25(8):795-802. doi: 10.1089/aid.2008.0252.


Longitudinal analysis of raltegravir susceptibility and integrase replication capacity of human immunodeficiency virus type 1 during virologic failure.

Fransen S, Karmochkine M, Huang W, Weiss L, Petropoulos CJ, Charpentier C.

Antimicrob Agents Chemother. 2009 Oct;53(10):4522-4. doi: 10.1128/AAC.00651-09. Epub 2009 Aug 10.


Vertical transmission of X4-tropic and dual-tropic HIV-1 in five Ugandan mother-infant pairs.

Huang W, Eshleman SH, Toma J, Stawiski E, Whitcomb JM, Jackson JB, Guay L, Musoke P, Parkin N, Petropoulos CJ.

AIDS. 2009 Sep 10;23(14):1903-8. doi: 10.1097/QAD.0b013e32832f1802.


Broad neutralization of human immunodeficiency virus type 1 (HIV-1) elicited from human rhinoviruses that display the HIV-1 gp41 ELDKWA epitope.

Arnold GF, Velasco PK, Holmes AK, Wrin T, Geisler SC, Phung P, Tian Y, Resnick DA, Ma X, Mariano TM, Petropoulos CJ, Taylor JW, Katinger H, Arnold E.

J Virol. 2009 May;83(10):5087-100. doi: 10.1128/JVI.00184-09. Epub 2009 Mar 11.


In vivo fitness cost of the M184V mutation in multidrug-resistant human immunodeficiency virus type 1 in the absence of lamivudine.

Paredes R, Sagar M, Marconi VC, Hoh R, Martin JN, Parkin NT, Petropoulos CJ, Deeks SG, Kuritzkes DR.

J Virol. 2009 Feb;83(4):2038-43. doi: 10.1128/JVI.02154-08. Epub 2008 Nov 19.


Suppression of dualtropic human immunodeficiency virus type 1 by the CXCR4 antagonist AMD3100 is associated with efficiency of CXCR4 use and baseline virus composition.

Fransen S, Bridger G, Whitcomb JM, Toma J, Stawiski E, Parkin N, Petropoulos CJ, Huang W.

Antimicrob Agents Chemother. 2008 Jul;52(7):2608-15. doi: 10.1128/AAC.01226-07. Epub 2008 Apr 28.


Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection.

Little SJ, Frost SD, Wong JK, Smith DM, Pond SL, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD.

J Virol. 2008 Jun;82(11):5510-8. doi: 10.1128/JVI.02579-07. Epub 2008 Mar 19.


Coreceptor tropism can be influenced by amino acid substitutions in the gp41 transmembrane subunit of human immunodeficiency virus type 1 envelope protein.

Huang W, Toma J, Fransen S, Stawiski E, Reeves JD, Whitcomb JM, Parkin N, Petropoulos CJ.

J Virol. 2008 Jun;82(11):5584-93. doi: 10.1128/JVI.02676-07. Epub 2008 Mar 19.


Genetic and immunologic heterogeneity among persons who control HIV infection in the absence of therapy.

Pereyra F, Addo MM, Kaufmann DE, Liu Y, Miura T, Rathod A, Baker B, Trocha A, Rosenberg R, Mackey E, Ueda P, Lu Z, Cohen D, Wrin T, Petropoulos CJ, Rosenberg ES, Walker BD.

J Infect Dis. 2008 Feb 15;197(4):563-71. doi: 10.1086/526786.


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