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Articles published in
PLoS Comput Biol
    September 2022
  1. WALTARI E, Nafees S, McCutcheon KM, Wong J, et al
    AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses.
    PLoS Comput Biol. 2022;18:e1010052.
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  2. BULLOCK ME, Moreno-Martinez N, Miller-Jensen K
    A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription.
    PLoS Comput Biol. 2022;18:e1010152.
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    August 2022
  3. LUNDGREN E, Romero-Severson E, Albert J, Leitner T, et al
    Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.
    PLoS Comput Biol. 2022;18:e1009741.
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    April 2022
  4. MAYER BT, deCamp AC, Huang Y, Schiffer JT, et al
    Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention.
    PLoS Comput Biol. 2022;18:e1010003.
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  5. CONTI S, Ovchinnikov V, Faris JG, Chakraborty AK, et al
    Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.
    PLoS Comput Biol. 2022;18:e1009391.
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  6. HOEHN KB, Pybus OG, Kleinstein SH
    Phylogenetic analysis of migration, differentiation, and class switching in B cells.
    PLoS Comput Biol. 2022;18:e1009885.
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  7. KUMATA R, Iwanami S, Mar KB, Kakizoe Y, et al
    Antithetic effect of interferon-alpha on cell-free and cell-to-cell HIV-1 infection.
    PLoS Comput Biol. 2022;18:e1010053.
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    February 2022
  8. KLINK GV, Kalinina OV, Bazykin GA
    Phylogenetic inference of changes in amino acid propensities with single-position resolution.
    PLoS Comput Biol. 2022;18:e1009878.
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  9. CHAI H, Gu Q, Hughes J, Robertson DL, et al
    In silico prediction of HIV-1-host molecular interactions and their directionality.
    PLoS Comput Biol. 2022;18:e1009720.
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  10. ZELNER J, Masters NB, Naraharisetti R, Mojola SA, et al
    There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.
    PLoS Comput Biol. 2022;18:e1009795.
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    January 2022
  11. BRYER AJ, Reddy T, Lyman E, Perilla JR, et al
    Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.
    PLoS Comput Biol. 2022;18:e1009781.
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    December 2021
  12. ZHANG L, Wang J, von Kleist M
    Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes.
    PLoS Comput Biol. 2021;17:e1009295.
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  13. KREGER J, Komarova NL, Wodarz D
    A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV.
    PLoS Comput Biol. 2021;17:e1009713.
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  14. THINDWA D, Wolter N, Pinsent A, Carrim M, et al
    Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study.
    PLoS Comput Biol. 2021;17:e1009680.
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    October 2021
  15. BALAKRISHNA S, Salazar-Vizcaya L, Schmidt AJ, Kachalov V, et al
    Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study.
    PLoS Comput Biol. 2021;17:e1009529.
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    September 2021
  16. GOSCE L, Abou Jaoude GJ, Kedziora DJ, Benedikt C, et al
    Optima TB: A tool to help optimally allocate tuberculosis spending.
    PLoS Comput Biol. 2021;17:e1009255.
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  17. 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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  18. 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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  19. 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
  20. 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
  21. 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
  22. 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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  23. 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
  24. 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
  25. 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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  26. 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
  27. 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
  28. 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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  29. BARKER CT, Vaidya NK
    Modeling HIV-1 infection in the brain.
    PLoS Comput Biol. 2020;16:e1008305.
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    October 2020
  30. 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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  31. 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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  32. 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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