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HIV Infection

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PLoS Comput Biol
    February 2021
  1. FISCON G, Conte F, Farina L, Paci P, et al
    SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19.
    PLoS Comput Biol. 2021;17:e1008686.
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  2. DEARLOVE B, Tovanabutra S, Owen CL, Lewitus E, et al
    Factors influencing estimates of HIV-1 infection timing using BEAST.
    PLoS Comput Biol. 2021;17:e1008537.
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    January 2021
  3. TESEI G, Martins JM, Kunze MBA, Wang Y, et al
    DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.
    PLoS Comput Biol. 2021;17:e1008551.
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    November 2020
  4. SAHA A, Dixit NM
    Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection.
    PLoS Comput Biol. 2020;16:e1008434.
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  5. BARKER CT, Vaidya NK
    Modeling HIV-1 infection in the brain.
    PLoS Comput Biol. 2020;16:e1008305.
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    October 2020
  6. MAGEE AF, Hohna S, Vasylyeva TI, Leache AD, et al
    Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts.
    PLoS Comput Biol. 2020;16:e1007999.
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  7. DORIGATTI E, Schubert B
    Graph-theoretical formulation of the generalized epitope-based vaccine design problem.
    PLoS Comput Biol. 2020;16:e1008237.
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  8. VAN DORP CH, Conway JM, Barouch DH, Whitney JB, et al
    Models of SIV rebound after treatment interruption that involve multiple reactivation events.
    PLoS Comput Biol. 2020;16:e1008241.
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    September 2020
  9. ZHANG Y, Leitner T, Albert J, Britton T, et al
    Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention.
    PLoS Comput Biol. 2020;16:e1008122.
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    August 2020
  10. DESIKAN R, Raja R, Dixit NM
    Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection.
    PLoS Comput Biol. 2020;16:e1008064.
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  11. DHAR A, Ralph DK, Minin VN, Matsen FA 4th, et al
    A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.
    PLoS Comput Biol. 2020;16:e1008030.
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    May 2020
  12. HAZELBAG CM, Dushoff J, Dominic EM, Mthombothi ZE, et al
    Calibration of individual-based models to epidemiological data: A systematic review.
    PLoS Comput Biol. 2020;16:e1007893.
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    February 2020
  13. REEVES DB, Huang Y, Duke ER, Mayer BT, et al
    Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials.
    PLoS Comput Biol. 2020;16:e1007626.
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  14. MOYANO A, Lustig G, Rodel HE, Antal T, et al
    Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition.
    PLoS Comput Biol. 2020;16:e1007482.
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    December 2019
  15. MITTLER JE, Murphy JT, Stansfield SE, Peebles KC, et al
    Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model.
    PLoS Comput Biol. 2019;15:e1007561.
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    November 2019
  16. ZHELTKOVA V, Argilaguet J, Peligero C, Bocharov G, et al
    Prediction of PD-L1 inhibition effects for HIV-infected individuals.
    PLoS Comput Biol. 2019;15:e1007401.
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    September 2019
  17. SKITTRALL JP, Ingemarsdotter CK, Gog JR, Lever AML, et al
    A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.
    PLoS Comput Biol. 2019;15:e1007345.
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    August 2019
  18. DHARMAVARAM S, She SB, Lazaro G, Hagan MF, et al
    Gaussian curvature and the budding kinetics of enveloped viruses.
    PLoS Comput Biol. 2019;15:e1006602.
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    July 2019
  19. CONWAY JM, Perelson AS, Li JZ
    Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers.
    PLoS Comput Biol. 2019;15:e1007229.
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    June 2019
  20. HAUSER A, Kusejko K, Johnson LF, Wandeler G, et al
    Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa.
    PLoS Comput Biol. 2019;15:e1007083.
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  21. GOODSELL DS, Jewett A, Olson AJ, Forli S, et al
    Integrative modeling of the HIV-1 ribonucleoprotein complex.
    PLoS Comput Biol. 2019;15:e1007150.
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  22. BAI H, Li Y, Michael NL, Robb ML, et al
    The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes.
    PLoS Comput Biol. 2019;15:e1007056.
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  23. Correction: Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection.
    PLoS Comput Biol. 2019;15:e1007138.
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  24. KIBLAWI S, Chasman D, Henning A, Park E, et al
    Augmenting subnetwork inference with information extracted from the scientific literature.
    PLoS Comput Biol. 2019;15:e1006758.
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    April 2019
  25. ROSENBLOOM DIS, Bacchetti P, Stone M, Deng X, et al
    Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size.
    PLoS Comput Biol. 2019;15:e1006849.
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  26. MAGARET CA, Benkeser DC, Williamson BD, Borate BR, et al
    Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.
    PLoS Comput Biol. 2019;15:e1006952.
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  27. CONTI S, Karplus M
    Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.
    PLoS Comput Biol. 2019;15:e1006954.
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    February 2019
  28. METZIG C, Ratmann O, Bezemer D, Colijn C, et al
    Phylogenies from dynamic networks.
    PLoS Comput Biol. 2019;15:e1006761.
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    January 2019
  29. DUWAL S, Dickinson L, Khoo S, von Kleist M, et al
    Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis.
    PLoS Comput Biol. 2019;15:e1006740.
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    December 2018
  30. EREN K, Weaver S, Ketteringham R, Valentyn M, et al
    Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.
    PLoS Comput Biol. 2018;14:e1006498.
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    October 2018
  31. WODARZ D, Skinner PJ, Levy DN, Connick E, et al
    Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques.
    PLoS Comput Biol. 2018;14:e1006461.
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    September 2018
  32. NA H, Song G
    All-atom normal mode dynamics of HIV-1 capsid.
    PLoS Comput Biol. 2018;14:e1006456.
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  33. QUADEER AA, Morales-Jimenez D, McKay MR
    Co-evolution networks of HIV/HCV are modular with direct association to structure and function.
    PLoS Comput Biol. 2018;14:e1006409.
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    August 2018
  34. AMITAI A, Chakraborty AK, Kardar M
    The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation.
    PLoS Comput Biol. 2018;14:e1006408.
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    June 2018
  35. DUWAL S, Dickinson L, Khoo S, von Kleist M, et al
    Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes.
    PLoS Comput Biol. 2018;14:e1006155.
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    April 2018
  36. BYRNE CM, Gantt S, Coombs D
    Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition.
    PLoS Comput Biol. 2018;14:e1006129.
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  37. YU WH, Zhao P, Draghi M, Arevalo C, et al
    Exploiting glycan topography for computational design of Env glycoprotein antigenicity.
    PLoS Comput Biol. 2018;14:e1006093.
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    March 2018
  38. GAHBAUER S, Pluhackova K, Bockmann RA
    Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol.
    PLoS Comput Biol. 2018;14:e1006062.
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  39. FRYER HR, Wolinsky SM, McLean AR
    Increased T cell trafficking as adjunct therapy for HIV-1.
    PLoS Comput Biol. 2018;14:e1006028.
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    February 2018
  40. SEVY AM, Panda S, Crowe JE Jr, Meiler J, et al
    Integrating linear optimization with structural modeling to increase HIV neutralization breadth.
    PLoS Comput Biol. 2018;14:e1005999.
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  41. GUPTA V, Dixit NM
    Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents.
    PLoS Comput Biol. 2018;14:e1006004.
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  42. NEAGU IA, Olejarz J, Freeman M, Rosenbloom DIS, et al
    Life cycle synchronization is a viral drug resistance mechanism.
    PLoS Comput Biol. 2018;14:e1005947.
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    November 2017
    A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.
    PLoS Comput Biol. 2017;13:e1005868.
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    October 2017
  44. HAKE A, Pfeifer N
    Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time.
    PLoS Comput Biol. 2017;13:e1005789.
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  45. PULLER V, Neher R, Albert J
    Estimating time of HIV-1 infection from next-generation sequence diversity.
    PLoS Comput Biol. 2017;13:e1005775.
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    September 2017
  46. LIU Y, Zou X
    Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization.
    PLoS Comput Biol. 2017;13:e1005733.
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