Shirai T, Mizukoshi F, Kimura R, Matsuoka R, Sada M, Shirato K
Microorganisms. 2025; 13(2).
PMID: 40005765
PMC: 11857903.
DOI: 10.3390/microorganisms13020399.
Manrique J, Maffia-Bizzozero S, Delpino M, Quarleri J, Jones L
J Med Virol. 2024; 96(12):e70107.
PMID: 39654307
PMC: 11656291.
DOI: 10.1002/jmv.70107.
Aguade-Gorgorio G, Anderson A, Sole R
iScience. 2024; 27(9):110699.
PMID: 39280631
PMC: 11402243.
DOI: 10.1016/j.isci.2024.110699.
Mainou E, Ribeiro R, Conway J
PLoS Comput Biol. 2024; 20(6):e1012129.
PMID: 38848426
PMC: 11189221.
DOI: 10.1371/journal.pcbi.1012129.
Ciupe S, Conway J
Microorganisms. 2024; 12(5).
PMID: 38792730
PMC: 11124127.
DOI: 10.3390/microorganisms12050900.
Modeling tumors as species-rich ecological communities.
Aguade-Gorgorio G, Anderson A, Sole R
bioRxiv. 2024; .
PMID: 38712062
PMC: 11071393.
DOI: 10.1101/2024.04.22.590504.
Mathematical Models of HIV-1 Dynamics, Transcription, and Latency.
DOrso I, Forst C
Viruses. 2023; 15(10).
PMID: 37896896
PMC: 10612035.
DOI: 10.3390/v15102119.
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.
Gabrielaite M, Bennedbaek M, Rasmussen M, Kan V, Furrer H, Flisiak R
PLoS Comput Biol. 2023; 19(1):e1010756.
PMID: 36595537
PMC: 9838853.
DOI: 10.1371/journal.pcbi.1010756.
SARS-CoV-2 Within-Host and Genomic Variability and Sub-Genomic RNA Levels Indicate Differences in Viral Expression Between Clinical Cohorts and Culture.
Agius J, Johnson-Mackinnon J, Fong W, Gall M, Lam C, Basile K
Front Microbiol. 2022; 13:824217.
PMID: 35663867
PMC: 9161297.
DOI: 10.3389/fmicb.2022.824217.
A multiscale model of virus pandemic: Heterogeneous interactive entities in a globally connected world.
Bellomo N, Bingham R, Chaplain M, Dosi G, Forni G, Knopoff D
Math Models Methods Appl Sci. 2022; 30(8):1591-1651.
PMID: 35309741
PMC: 8932953.
DOI: 10.1142/s0218202520500323.
Evolution during primary HIV infection does not require adaptive immune selection.
Swan D, Rolland M, Herbeck J, Schiffer J, Reeves D
Proc Natl Acad Sci U S A. 2022; 119(7).
PMID: 35145025
PMC: 8851487.
DOI: 10.1073/pnas.2109172119.
Benchmarking different approaches for Norovirus genome assembly in metagenome samples.
Fuentes-Trillo A, Monzo C, Manzano I, Santiso-Bellon C, de Andrade J, Gozalbo-Rovira R
BMC Genomics. 2021; 22(1):849.
PMID: 34819031
PMC: 8611953.
DOI: 10.1186/s12864-021-08067-2.
Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host.
Magalis B, Autissier P, Williams K, Chen X, Browne C, Salemi M
Front Immunol. 2021; 12:709962.
PMID: 34691023
PMC: 8527182.
DOI: 10.3389/fimmu.2021.709962.
Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences.
Olusola B, Olaleye D, Odaibo G
Front Microbiol. 2021; 11:615721.
PMID: 33505382
PMC: 7829476.
DOI: 10.3389/fmicb.2020.615721.
Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities.
Al Khatib H, Benslimane F, Elbashir I, Coyle P, Al Maslamani M, Al-Khal A
Front Cell Infect Microbiol. 2020; 10:575613.
PMID: 33123498
PMC: 7572854.
DOI: 10.3389/fcimb.2020.575613.
Leveraging Computational Modeling to Understand Infectious Diseases.
Jenner A, Aogo R, Davis C, Smith A, Craig M
Curr Pathobiol Rep. 2020; 8(4):149-161.
PMID: 32989410
PMC: 7511257.
DOI: 10.1007/s40139-020-00213-x.
Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials.
Reeves D, Huang Y, Duke E, Mayer B, Cardozo-Ojeda E, Boshier F
PLoS Comput Biol. 2020; 16(2):e1007626.
PMID: 32084132
PMC: 7055956.
DOI: 10.1371/journal.pcbi.1007626.
Inter- Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes.
Al Khatib H, Al Maslamani M, Coyle P, Thompson I, Farag E, Al Thani A
Microorganisms. 2020; 8(1).
PMID: 31963512
PMC: 7022955.
DOI: 10.3390/microorganisms8010133.
Immunological Paradigms, Mechanisms, and Models: Conceptual Understanding Is a Prerequisite to Effective Modeling.
Grossman Z
Front Immunol. 2019; 10:2522.
PMID: 31749803
PMC: 6848063.
DOI: 10.3389/fimmu.2019.02522.
Modeling the immune response to HIV infection.
Conway J, Ribeiro R
Curr Opin Syst Biol. 2019; 12:61-69.
PMID: 31463420
PMC: 6713454.
DOI: 10.1016/j.coisb.2018.10.006.