Whaler B, Todd E, Shaw AB, Barr JN, Beauchemin CAA, Lythe G, Molina-París C, López-García M. (2026). Mechanistic mathematical model of the in vitro infection dynamics of Bunyamwera and Batai viruses including MOI-dependent shortening of the eclipse phase. ArXiv
D'Addiego J, Tishkova F, Mullojonova M, Dzhuraeva V, Lythe G, Dent S, Molina-París C, Leitner T, Hewson R. (2026). Genomic characterisation of Crimean-Congo haemorrhagic fever virus (CCHFV) in Tajikistan identifies a novel reassortant virus. PLoS neglected tropical diseases, 20(4)
Lin Q, Elaldi N, Yigit M, Yildiz B, Hewson R, López-García M, Lythe G, Pektas AN, Koksal B, Tasseten TN, Deniz A, Bedir H, Kiymaz YC, Vatansever Z, Molina-París C, Leitner T. (2026). Multiple Reassortments, Limited Geographic Spread, and Comparable Pathogenicity of Crimean-Congo Hemorrhagic Fever Viruses in Sivas Province, Türkiye. Journal of medical virology, 98(6)
Wilding KM, Molina-París C, Kubicek-Sutherland JZ, McMahon B, Perelson AS, Ribeiro RM. (2025). A consensus mathematical model of vaccine-induced antibody dynamics for multiple vaccine platforms and pathogens. Frontiers in immunology, (16)
Wigerblad G, Carruthers J, Ray S, Finnie T, Lythe G, Pyne S, Molina-París C, Kaplan MJ. (2025). A mathematical framework for human neutrophil state transitions inferred from single-cell RNA sequence data. Frontiers in immunology, (16)
Sambaturu N, Lapp Z, Tria FDK, Romero-Severson E, Molina-París C, Leitner T. (2025). wavess: An R package for simulation of adaptive within-host virus sequence evolution. PLoS computational biology, 21(9)
Mihalakakos EA, Ssempijja V, Ribeiro RM, Molina-Paris C, Katushabe G, Nalwadda J, Omooja J, Byarugaba DK, Rosenke K, Reynolds SJ, Grabowski MK, Galiwango RM, Ssekubugu R, Feldmann H, Hawman DW. (2025). Longitudinal seroprevalence of Crimean-Congo hemorrhagic fever virus in Southern Uganda. Emerging microbes & infections
Sambaturu N, Fray EJ, Hariharan V, Wu F, Zitzmann C, Simonetti FR, Barouch DH, Siliciano JD, Siliciano RF, Ribeiro RM, Perelson AS, Molina-París C, Leitner T. (2025). SIV proviruses seeded later in infection are harbored in short-lived CD4(+) T cells. Cell reports, 44(5)
Whaler B, Lythe G, Gillard JJ, Laws TR, Carruthers J, Finnie T, Molina-París C, López-García M. (2025). Mechanistic within-host mathematical model of inhalational anthrax. PLoS computational biology, 21(9)
Lin Q, Goldberg EE, Leitner T, Molina-París C, King AA, Romero-Severson EO. (2024). The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees. Molecular biology and evolution
Belluccini G, Lin Q, Williams B, Lou Y, Vatansever Z, López-García M, Lythe G, Leitner T, Romero-Severson E, Molina-París C. (2024). A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number. ArXiv
Harris DC, Shanker A, Montoya MM, Llewellyn TR, Matuszak AR, Lohar A, Kubicek-Sutherland JZ, Li YW, Wilding K, Mcmahon B, Gnanakaran S, Ribeiro RM, Perelson AS, Molina-París C. (2024). Quantification of heterogeneity in human CD8(+) T cell responses to vaccine antigens: an HLA-guided perspective. Frontiers in immunology, (15)
Dreiwi H, Feliciangeli F, Castro M, Lythe G, Molina-París C, López-García M. (2024). Stochastic journeys of cell progenies through compartments and the role of self-renewal, symmetric and asymmetric division. Scientific reports, 14(1)
Williams B, Carruthers J, Gillard JJ, Lythe G, Perelson AS, Ribeiro RM, Molina-París C, López-García M. (2024). The reproduction number and its probability distribution for stochastic viral dynamics. Journal of the Royal Society, Interface, 21(210)
Fray EJ, Wu F, Simonetti FR, Zitzmann C, Sambaturu N, Molina-Paris C, Bender AM, Liu PT, Ventura JD, Wiseman RW, O'Connor DH, Geleziunas R, Leitner T, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. (2023). Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell host & microbe, 31(3)
Luque Duque D, Gaevert JA, Thomas PG, López-García M, Lythe G, Molina-París C. (2023). Multi-variate model of T cell clonotype competition and homeostasis. Scientific reports, 13(1)
Sambaturu N, Fray EJ, Wu F, Zitzmann C, Simonetti FR, Barouch DH, Siliciano JD, Siliciano RF, Ribeiro RM, Perelson AS, Molina-París C, Leitner T. (2023). Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4(+) T cells. bioRxiv : the preprint server for biology
Belluccini G, López-García M, Lythe G, Molina-París C. (2022). Counting generations in birth and death processes with competing Erlang and exponential waiting times. Scientific reports, 12(1)
Feliciangeli F, Dreiwi H, López-García M, Castro Ponce M, Molina-París C, Lythe G. (2022). Why are cell populations maintained via multiple compartments?. Journal of the Royal Society, Interface, 19(196)
Barua N, Huang L, Li C, Yang Y, Luo M, Wei WI, Wong KT, Lo NWS, Kwok KO, Ip M. (2021). Comparative Study of Two-Dimensional (2D) vs. Three-Dimensional (3D) Organotypic Kertatinocyte-Fibroblast Skin Models for Staphylococcus aureus (MRSA) Infection. International journal of molecular sciences, 23(1)
Williams B, López-García M, Gillard JJ, Laws TR, Lythe G, Carruthers J, Finnie T, Molina-París C. (2021). A Stochastic Intracellular Model of Anthrax Infection With Spore Germination Heterogeneity. Frontiers in immunology, (12)
Wilmes S, Jeffrey PA, Martinez-Fabregas J, Hafer M, Fyfe PK, Pohler E, Gaggero S, López-García M, Lythe G, Taylor C, Guerrier T, Launay D, Mitra S, Piehler J, Molina-París C, Moraga I. (2021). Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses. eLife, (10)
Castro M, Lythe G, Smit J, Molina-París C. (2021). Fusion and fission events regulate endosome maturation and viral escape. Scientific reports, 11(1)
Gaevert JA, Luque Duque D, Lythe G, Molina-París C, Thomas PG. (2021). Quantifying T Cell Cross-Reactivity: Influenza and Coronaviruses. Viruses, 13(9)
Lin CY, Wolf J, Brice DC, Sun Y, Locke M, Cherry S, Castellaw AH, Wehenkel M, Crawford JC, Zarnitsyna VI, Duque D, Allison KJ, Allen EK, Brown SA, Mandarano AH, Estepp JH, , Taylor C, Molina-Paris C, Schultz-Cherry S, Tang L, Thomas PG, McGargill MA. (2021). Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response. Cell host & microbe
Locke M, Lythe G, López-García M, Muñoz-Fontela C, Carroll M, Molina-París C. (2021). Quantification of Type I Interferon Inhibition by Viral Proteins: Ebola Virus as a Case Study. Viruses, 13(12)
Carruthers J, Lythe G, López-García M, Gillard J, Laws TR, Lukaszewski R, Molina-París C. (2020). Stochastic dynamics of Francisella tularensis infection and replication. PLoS computational biology, 16(6)
Liao LE, Carruthers J, Smither SJ, , Weller SA, Williamson D, Laws TR, García-Dorival I, Hiscox J, Holder BP, Beauchemin CAA, Perelson AS, López-García M, Lythe G, Barr JN, Molina-París C. (2020). Quantification of Ebola virus replication kinetics in vitro. PLoS computational biology, 16(11)
de la Higuera L, López-García M, Castro M, Abourashchi N, Lythe G, Molina-París C. (2019). Fate of a Naive T Cell: A Stochastic Journey. Frontiers in immunology, (10)
Lythe G, Molina-París C. (2018). Some deterministic and stochastic mathematical models of naïve T-cell homeostasis. Immunological reviews, 285(1)
Castro M, López-García M, Lythe G, Molina-París C. (2018). First passage events in biological systems with non-exponential inter-event times. Scientific reports, 8(1)
Carruthers J, López-García M, Gillard JJ, Laws TR, Lythe G, Molina-París C. (2018). A Novel Stochastic Multi-Scale Model of Francisella tularensis Infection to Predict Risk of Infection in a Laboratory. Frontiers in microbiology, (9)
Gonçalves P, Ferrarini M, Molina-Paris C, Lythe G, Vasseur F, Lim A, Rocha B, Azogui O. (2017). A new mechanism shapes the naïve CD8(+) T cell repertoire: the selection for full diversity. Molecular immunology, (85)
Chu HH, Chan SW, Gosling JP, Blanchard N, Tsitsiklis A, Lythe G, Shastri N, Molina-París C, Robey EA. (2016). Continuous Effector CD8(+) T Cell Production in a Controlled Persistent Infection Is Sustained by a Proliferative Intermediate Population. Immunity, 45(1)
Castro M, Lythe G, Molina-París C, Ribeiro RM. (2016). Mathematics in modern immunology. Interface focus, 6(2)
Pham K, Shimoni R, Charnley M, Ludford-Menting MJ, Hawkins ED, Ramsbottom K, Oliaro J, Izon D, Ting SB, Reynolds J, Lythe G, Molina-Paris C, Melichar H, Robey E, Humbert PO, Gu M, Russell SM. (2015). Asymmetric cell division during T cell development controls downstream fate. The Journal of cell biology, 210(6)
Lythe G, Callard RE, Hoare RL, Molina-París C. (2016). How many TCR clonotypes does a body maintain?. Journal of theoretical biology, (389)
Castro M, van Santen HM, Férez M, Alarcón B, Lythe G, Molina-París C. (2014). Receptor Pre-Clustering and T cell Responses: Insights into Molecular Mechanisms. Frontiers in immunology, (5)
Sawicka M, Stritesky GL, Reynolds J, Abourashchi N, Lythe G, Molina-París C, Hogquist KA. (2014). From pre-DP, post-DP, SP4, and SP8 Thymocyte Cell Counts to a Dynamical Model of Cortical and Medullary Selection. Frontiers in immunology, (5)
Gillard JJ, Laws TR, Lythe G, Molina-París C. (2014). Modeling early events in Francisella tularensis pathogenesis. Frontiers in cellular and infection microbiology, (4)
Reynolds J, Amado IF, Freitas AA, Lythe G, Molina-París C. (2014). A mathematical perspective on CD4(+) T cell quorum-sensing. Journal of theoretical biology, (347)
Reynolds J, Coles M, Lythe G, Molina-París C. (2013). Mathematical Model of Naive T Cell Division and Survival IL-7 Thresholds. Frontiers in immunology, (4)
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