Dekaj E. and Gjini E. Pneumococcus and the stress-gradient hypothesis: a trade-off links R0 and susceptibility to co-colonization across countries submitted arXiv (preprint pdf)

Le T.M.T., Gjini E. and Madec S. (2021) Quasi-neutral Dynamics in a Coinfection System with N Strains and Asymmetries along Multiple Traits submitted – arXiv (preprint)

Gjini E. and Madec S. (2021) Towards a mathematical understanding of colonization resistance submitted, bioRxiv (preprint)


28. Trindade, S., De Niz, M., Sequeira, M., Bizarra-Rebelo, T., Bento, F., Dejung, M., … Gjini, E. & Figueiredo, L. (2022). Slow growing behavior in African trypanosomes during adipose tissue colonization. Nat Commun 13, 7548 – (pdf)

27. Le, T. M. T., Madec, S., & Gjini, E. (2022). Disentangling how multiple traits drive 2 strain frequencies in SIS dynamics with coinfection. Journal of Theoretical Biology, 538 – (bioRxiv pdf)


26. Ramos G, Gjini E, Coelho L, Silveira M. (2021) Unsupervised learning approach for predicting sepsis onset in ICU patients. Annu Int Conf IEEE Eng Med Biol Soc. 2021 Nov;2021:1916-1919. doi: 10.1109/EMBC46164.2021.9629559. PMID: 34891661.

25. Gjini E. and Wood K. B. (2021) Price equation captures the role of drug interactions and collateral effects in the evolution of multidrug resistance, eLife, doi: 10.7554/eLife.64851

24. Gjini E, and Madec, S. (2021) The ratio of single to co-colonization is key to complexity in interacting systems with multiple strainsEcology and Evolution,

23. Singh, S., Thompson, J.A., Weis, S., Sobral, D., Truglio, M., Yilmaz, B., Rebelo, S., Cardoso, S., Gjini, E., Nuñez, G. and Soares, M.P., (2021). Loss of α-gal during primate evolution enhanced antibody-effector function and resistance to bacterial sepsisCell Host & Microbe


22. Madec S. and Gjini, E. (2020) Predicting N-strain coexistence from co-colonization interactions: epidemiology meets ecology and the replicator equation Bulletin of Mathematical Biology 82142. (pdf)

21. Gjini E., Pauperio F.F.S. and Ganusov V.V. (2020) Treatment timing shifts the benefits of short vs. long antibiotic treatment over infection Evolution, Medicine, and Public Health, eoaa033

20. Dimas Martins A. and Gjini E. (2020) Modeling competitive mixtures with the Lotka-Volterra framework for more complex fitness assessment between strains Frontiers in Microbiology | doi: 10.3389/fmicb.2020.572487

19. Ramos, C.V., Ballesteros-Arias, L., Silva, J.G., Paiva, R.A., Nogueira, M.F., Carneiro, J., Gjini, E. and Martins, V.C., (2020) Cell Competition, the Kinetics of Thymopoiesis, and Thymus Cellularity Are Regulated by Double-Negative 2 to 3 Early Thymocytes. Cell Reports, 32(3), p.107910. (pdf)

18. Gjini E. (2020) Perspektiva matematike për të kuptuar ecurinë e një epidemie (Report on Covid-19 dynamics in Albania)

17. Gjini E. (2020) Modeling Covid-10 dynamics for real-time estimates and projections: an application to Albanian data (medRxiv preprint)


16. Pauperio F.S. and Gjini, E. (2019) Quantifying bacterial fitness in intracellular dynamics in Conference Proceedings 2019 IEEE 6th Portuguese Meeting on Bioengineering (ENBENG) DOI:10.1109/ENBENG.2019.8692528 (pdf)

15. Ramos S. et al. (2019) Renal control of disease tolerance to malaria Proceedings of the National Academy of Sciences doi:10.1073/pnas.1822024116 (pdf)


14. Azevedo M., Dionisio F., Gjini E. (2017) Transmission fitness in co-colonization and the persistence of bacterial pathogens Bulletin of Mathematical Biology, doi: 10.1007/s11538-017-0320-3 (pdf)

13. Gjini E. (2017) Geographic variation in pneumococcal vaccine efficacy estimated from dynamic modeling of epidemiological data post-PCV7 Nature Scientific Reports 7: 3049 | DOI:10.1038/s41598-017-02955-y (pdf)

12. Gjini E. (2017) Human African Trypanosomiasis: What are the prospects for control? Human Parasitic Diseases (9) DOI: 1179570017700644 (pdf)


11. Gjini E. and Madec S. (2016) A slow-fast dynamic decomposition links neutral and non-neutral coexistence in interacting multi-strain pathogens.Theoretical Ecology  pp:1-13, doi:10.1007/s12080-016-0320-1 (pdf)

10. Gjini E. and Brito P.H. (2016) Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive treatment. PLoS Computational Biology 12(4), e1004857. DOI:10.1371/journal.pcbi.1004857 (pdf)                                   

Work from my Post-Doc

9. Gomes M.G.M., Gjini E., Lopes J.S.,Souto-Maior C., Rebelo C. (2016) A theoretical framework to identify invariant thresholds in infectious disease epidemiology. Journal of Theoretical Biology 395:97-102 doi: 10.1016/j.jtbi.2016.01.029 (pdf)

8. Gjini E., and Gomes M.G.M. (2016) Expanding vaccine efficacy estimation with dynamic models fitted to cross-sectional prevalence data post-licensure. Epidemics 14: 71-82 DOI: 10.1016/j.epidem.2015.11.001 (pdf)

7. Gjini E., Valente C., Sa-Leao R., Gomes, M.G.M. (2016) How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems. Journal of Theoretical Biology  388:50-60, DOI: 10.1016/j.jtbi.2015.09.031 (pdf)

6. Mendes CSM, Lopes J.S., Gjini E., Struchiner C.J., Teixeira L., Gomes M.G.M. (2014) Heterogeneity in symbiotic effects facilitates Wolbachia establishment in insect populations. Theoretical Ecology 8 (1), 53-65 (pdf)

5. Pessoa D.,Mendes CSM,Lopes J.S., Gjini E., Ceña B., Codeco, CT, Gomes M.G.M. (2014) Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens, PLoS Computational Biology 10(8): e1003773.(pdf)

Work from my Phd

4. Gjini, E., Haydon, D.T., Barry, J.D. and Cobbold, C.A. (2014) Revisiting the difffusion approximation to estimate evolutionary rates of gene family diversification. Journal of Theoretical Biology. 341:111-22.(pdf)

3. Gjini, E., Haydon, D.T., Barry, J.D. and Cobbold, C.A. (2013) Linking the antigen archive structure to pathogen fitness in African trypanosomes Proceedings of the Royal Society B, 280 (1753). pp. 21-29 (pdf)

2.  Gjini, E., Haydon, D., Barry, J. and Cobbold, C. (2012) The Impact of Mutation and Gene Conversion on the Local Diversification of Antigen Genes in African Trypanosomes Molecular Biology and Evolution 29 (11): 3321-3331 (pdf)

1. Gjini, E., Haydon, D., Barry, J. and Cobbold, C. (2010) Critical Interplay between Parasite Differentiation, Host Immunity, and Antigenic Variation in Trypanosome Infections.The American Naturalist, 176 (4). pp. 424-439.(pdf)