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Articles published in
PLoS Comput Biol
    March 2024
  1. SHAO Y, Magee AF, Vasylyeva TI, Suchard MA, et al
    Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.
    PLoS Comput Biol. 2024;20:e1011640.
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  2. CASSIDY T, Stephenson KE, Barouch DH, Perelson AS, et al
    Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1.
    PLoS Comput Biol. 2024;20:e1011518.
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    December 2023
  3. HAKE A, Germann A, de Beer C, Thielen A, et al
    Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models.
    PLoS Comput Biol. 2023;19:e1010355.
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    August 2023
  4. ZHANG Z, Nishimura A, Trovao NS, Cherry JL, et al
    Accelerating Bayesian inference of dependency between mixed-type biological traits.
    PLoS Comput Biol. 2023;19:e1011419.
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  5. CODY JW, Ellis-Connell AL, O'Connor SL, Pienaar E, et al
    Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load.
    PLoS Comput Biol. 2023;19:e1011425.
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  6. LUBIANA T, Lopes R, Medeiros P, Silva JC, et al
    Ten quick tips for harnessing the power of ChatGPT in computational biology.
    PLoS Comput Biol. 2023;19:e1011319.
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    March 2023
  7. HARVEY WT, Davies V, Daniels RS, Whittaker L, et al
    A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.
    PLoS Comput Biol. 2023;19:e1010885.
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    January 2023
  8. GABRIELAITE M, Bennedbaek M, Rasmussen MS, Kan V, et al
    Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load.
    PLoS Comput Biol. 2023;19:e1010756.
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    December 2022
  9. JIANG Y, Zhang JX, Liu R
    Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing.
    PLoS Comput Biol. 2022;18:e1010744.
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  10. GOLDSTEIN IH, Bayer D, Barilar I, Kizito B, et al
    Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission.
    PLoS Comput Biol. 2022;18:e1010696.
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    November 2022
  11. CHATO C, Feng Y, Ruan Y, Xing H, et al
    Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.
    PLoS Comput Biol. 2022;18:e1010745.
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    October 2022
  12. ANDRESEN S, Balakrishna S, Mugglin C, Schmidt AJ, et al
    Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men.
    PLoS Comput Biol. 2022;18:e1010559.
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  13. LEE CY, Chen Y, Duan Z, Xu M, et al
    Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.
    PLoS Comput Biol. 2022;18:e1010636.
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  14. KUPPERMAN MD, Leitner T, Ke R
    A deep learning approach to real-time HIV outbreak detection using genetic data.
    PLoS Comput Biol. 2022;18:e1010598.
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  15. LEWITUS E, Hoang J, Li Y, Bai H, et al
    Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens.
    PLoS Comput Biol. 2022;18:e1010624.
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    September 2022
  16. 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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  17. 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
  18. 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
  19. 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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  20. 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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  21. 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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  22. 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
  23. 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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  24. 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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  25. 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
  26. 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
  27. 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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  28. 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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  29. 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
  30. 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
  31. 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.
    >> Share


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