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HIV Infection

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 28 articles: HTML format

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March 2026
1. OVERSTI S, Boumasmoud M, Gunthard HF, Sax H, et al
   Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.
   PLoS Comput Biol. 2026;22:e1013982.
   PubMed     Abstract available
   
   
   January 2026
2. AGGARWAL M, Periwal V
   Forecasting drug resistant HIV protease evolution.
   PLoS Comput Biol. 2026;22:e1013913.
   PubMed     Abstract available
   
   
   December 2025
3. LONGLEY H, Fraser C, Wymant C, Lythgoe K, et al
   Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution.
   PLoS Comput Biol. 2025;21:e1013131.
   PubMed     Abstract available
   
   
   November 2025
4. GUANG A, Dunn CW, Novitsky V, Howison M, et al
   T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.
   PLoS Comput Biol. 2025;21:e1013676.
   PubMed     Abstract available
   
   
   
5. PARKER NT, Hong V, Davis GS, Pomichowski M, et al
   Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population.
   PLoS Comput Biol. 2025;21:e1013723.
   PubMed     Abstract available
   
   
   
6. DANKWA EA, Cavalli L, Balasubramanian R, Can MH, et al
   Calibration of transmission-dynamic infectious disease models: A scoping review and reporting framework.
   PLoS Comput Biol. 2025;21:e1013647.
   PubMed     Abstract available
   
   
   
7. XU S, Hudson A, Janes HE, Tomaras GD, et al
   Candidate correlates of protection in the HVTN505 HIV-1 vaccine efficacy trial identified by positive-unlabeled learning.
   PLoS Comput Biol. 2025;21:e1013705.
   PubMed     Abstract available
   
   
   October 2025
8. JOUBBI S, Micheli A, Milazzo P, Ciano G, et al
   Enhancing antibody-antigen interaction prediction with atomic flexibility.
   PLoS Comput Biol. 2025;21:e1013576.
   PubMed     Abstract available
   
   
   September 2025
9. MULLER NF, Bouckaert RR, Wu CH, Bedford T, et al
   MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.
   PLoS Comput Biol. 2025;21:e1013421.
   PubMed     Abstract available
   
   
   
10. SAMBATURU N, Lapp Z, Tria FDK, Romero-Severson E, et al
    wavess: An R package for simulation of adaptive within-host virus sequence evolution.
    PLoS Comput Biol. 2025;21:e1013437.
    PubMed     Abstract available
    
    
    
11. GARCIA NOCEDA M, Kher G, Uttam S, Barton JP, et al
    Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV.
    PLoS Comput Biol. 2025;21:e1013433.
    PubMed     Abstract available
    
    
    
12. BURBACH SM, Briney B
    A curriculum learning approach to training antibody language models.
    PLoS Comput Biol. 2025;21:e1013473.
    PubMed     Abstract available
    
    
    July 2025
13. NGANDU NK, Fielding BC, van Heusden P, Mcinga K, et al
    Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region.
    PLoS Comput Biol. 2025;21:e1013261.
    PubMed     Abstract available
    
    
    June 2025
14. YAMAMOTO N, Citron DT, Mwalili SM, Gathungu DK, et al
    Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study.
    PLoS Comput Biol. 2025;21:e1013178.
    PubMed     Abstract available
    
    
    May 2025
15. ZHUKOVA A, Gascuel O
    Accounting for contact tracing in epidemiological birth-death models.
    PLoS Comput Biol. 2025;21:e1012461.
    PubMed     Abstract available
    
    
    
16. DENG Q, Woldegerima WA, Zhang W, Asgary A, et al
    Uncovering the impact of infection routes on within-host MPXV dynamics: Insights from a mathematical modeling study.
    PLoS Comput Biol. 2025;21:e1013073.
    PubMed     Abstract available
    
    
    February 2025
17. TESLYA A, Heijne JCM, van der Loeff MFS, van Sighem A, et al
    Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands.
    PLoS Comput Biol. 2025;21:e1012055.
    PubMed     Abstract available
    
    
    
18. BANHOLZER N, Middelkoop K, Leukes J, Weingartner E, et al
    Estimating Mycobacterium tuberculosis transmission in a South African clinic: Spatiotemporal model based on person movements.
    PLoS Comput Biol. 2025;21:e1012823.
    PubMed     Abstract available
    
    
    December 2024
19. ABRAHAM AA, Tan ZC, Shrestha P, Bozich ER, et al
    A multivalent binding model infers antibody Fc species from systems serology.
    PLoS Comput Biol. 2024;20:e1012663.
    PubMed     Abstract available
    
    
    November 2024
20. IGIRANEZA AB, Zacharopoulou P, Hinch R, Wymant C, et al
    Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning.
    PLoS Comput Biol. 2024;20:e1012618.
    PubMed     Abstract available
    
    
    September 2024
21. VEMPARALA B, Madelain V, Passaes C, Millet A, et al
    Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data.
    PLoS Comput Biol. 2024;20:e1012434.
    PubMed     Abstract available
    
    
    July 2024
22. TATARA E, Lin Q, Ozik J, Kolak M, et al
    Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios.
    PLoS Comput Biol. 2024;20:e1012307.
    PubMed     Abstract available
    
    
    June 2024
23. ADOLF-BRYFOGLE J, Labonte JW, Kraft JC, Shapovalov M, et al
    Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.
    PLoS Comput Biol. 2024;20:e1011895.
    PubMed     Abstract available
    
    
    
24. MAINOU E, Ribeiro RM, Conway JM
    Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection.
    PLoS Comput Biol. 2024;20:e1012129.
    PubMed     Abstract available
    
    
    April 2024
25. ZITZMANN C, Ke R, Ribeiro RM, Perelson AS, et al
    How robust are estimates of key parameters in standard viral dynamic models?
    PLoS Comput Biol. 2024;20:e1011437.
    PubMed     Abstract available
    
    
    
26. SUN C, Fang R, Salemi M, Prosperi M, et al
    DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.
    PLoS Comput Biol. 2024;20:e1011351.
    PubMed     Abstract available
    
    
    March 2024
27. 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.
    PubMed     Abstract available
    
    
    
28. 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.
    PubMed     Abstract available
    
    

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