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Articles published in
PLoS Comput Biol
    September 2021
  1. POSADA-CESPEDES S, Van Zyl G, Montazeri H, Kuipers J, et al
    Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.
    PLoS Comput Biol. 2021;17:e1008363.
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  2. PICKLES M, Cori A, Probert WJM, Sauter R, et al
    PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial.
    PLoS Comput Biol. 2021;17:e1009301.
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  3. MAZROUEE S, Little SJ, Wertheim JO
    Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.
    PLoS Comput Biol. 2021;17:e1009336.
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    August 2021
  4. BLASSEL L, Tostevin A, Villabona-Arenas CJ, Peeters M, et al
    Using machine learning and big data to explore the drug resistance landscape in HIV.
    PLoS Comput Biol. 2021;17:e1008873.
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    July 2021
  5. CODY JW, Ellis-Connell AL, O'Connor SL, Pienaar E, et al
    Mathematical modeling of N-803 treatment in SIV-infected non-human primates.
    PLoS Comput Biol. 2021;17:e1009204.
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    June 2021
  6. BYRNE CM, Johnston C, Orem J, Okuku F, et al
    Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads.
    PLoS Comput Biol. 2021;17:e1009072.
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  7. WELLS CR, Cao Y, Durham DP, Byrareddy SN, et al
    Mechanistic basis of post-treatment control of SIV after anti-alpha4beta7 antibody therapy.
    PLoS Comput Biol. 2021;17:e1009031.
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    March 2021
  8. RIPOLL DR, Chaudhury S, Wallqvist A
    Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.
    PLoS Comput Biol. 2021;17:e1008864.
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    February 2021
  9. 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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  10. 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
  11. 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
  12. 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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  13. BARKER CT, Vaidya NK
    Modeling HIV-1 infection in the brain.
    PLoS Comput Biol. 2020;16:e1008305.
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    October 2020
  14. 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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  15. 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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  16. 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
  17. 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
  18. 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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  19. 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
  20. 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
  21. 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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  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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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  29. 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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  30. 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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  31. 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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  32. 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
  33. 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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  34. 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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  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. NA H, Song G
    All-atom normal mode dynamics of HIV-1 capsid.
    PLoS Comput Biol. 2018;14:e1006456.
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  41. 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
  42. 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
  43. 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
  44. 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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  45. 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
  46. 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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  47. 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
  48. 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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  49. 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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  50. 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.
    >> Share

    November 2017
  51. MCCLOSKEY RM, Poon AFY
    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
  52. 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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  53. 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
  54. LIU Y, Zou X
    Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization.
    PLoS Comput Biol. 2017;13:e1005733.
    >> Share


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