Publications

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Articles

(In gray, preprints)

COVID-19

Origin & early dynamics

Hensel, Z., & Débarre, F. (2025). An updated dataset of early SARS-CoV-2 diversity supports a wildlife market origin. bioRxiv. https://doi.org/10.1101/2025.04.05.647275

Débarre, F., & Hensel, Z. (2025). Theories of the origin of SARS-CoV-2 in the light of its continuing evolution. C R Biol., 348(G1), 189–209. https://doi.org/10.5802/crbiol.183

Débarre, F., & Hensel, Z. (2025). A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data. Molecular Biology and Evolution, 42(6), msaf109. https://doi.org/10.1093/molbev/msaf109

Pekar, J. E., Moshiri, N., Lemey, P., Crits-Christoph, A., Débarre, F., Goldstein, S. A., Hensel, Z., Rambaut, A., Worobey, M., Holmes, E. C., & Wertheim, J. O. (2025). Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived. Virus Evolution, 11(1), veaf008. https://doi.org/10.1093/ve/veaf008

Crits-Christoph, A., Levy, J. I., Pekar, J. E., Goldstein, S. A., Singh, R., Hensel, Z., Gangavarapu, K., Rogers, M. B., Moshiri, N., Garry, R. F., Holmes, E. C., Koopmans, M. P. G., Lemey, P., Peacock, T. P., Popescu, S., Rambaut, A., Robertson, D. L., Suchard, M. A., Wertheim, J. O., … Débarre, F. (2024). Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. Cell, 187(19), 5468–5482.e11. https://doi.org/10.1016/j.cell.2024.08.010

Débarre, F., & Worobey, M. (2024). No evidence of systematic proximity ascertainment bias in early COVID-19 cases in Wuhan Reply to Weissman (2024). arXiv. https://doi.org/10.48550/arXiv.2405.08040

Débarre, F., & Worobey, M. (2024). Confirmation of the centrality of the Huanan market among early COVID-19 cases. arXiv. https://doi.org/10.48550/arXiv.2403.05859

Débarre, F. (2024). What we can and cannot learn from SARS-CoV-2 and animals in metagenomic samples from the Huanan market. Virus Evolution, 10(1), vead077. https://doi.org/10.1093/ve/vead077

Jijón, S., Czuppon, P., Blanquart, F., & Débarre, F. (2024). Using early detection data to estimate the date of emergence of an epidemic outbreak. PLOS Computational Biology, 20(3), e1011934. https://doi.org/10.1371/journal.pcbi.1011934

Czuppon, P., Schertzer, E., Blanquart, F., & Débarre, F. (2021). The stochastic dynamics of early epidemics: Probability of establishment, initial growth rate, and infection cluster size at first detection. Journal of The Royal Society Interface, 18(184), 20210575. https://doi.org/10.1098/rsif.2021.0575

Vaccination

Blanquart, F., Abad, C., Ambroise, J., Bernard, M., Débarre, F., Giannoli, J.-M., Rey, T., & Vieillefond, V. (2023). Temporal, age, and geographical variation in vaccine efficacy against infection by the Delta and Omicron variants in the community in France, December 2021 to March 2022. International Journal of Infectious Diseases, 133, 89–96. https://doi.org/10.1016/j.ijid.2023.04.410

Débarre, F., Lecoeur, E., Guimier, L., Jauffret-Roustide, M., & Jannot, A.-S. (2022). The French Covid-19 vaccination policy did not solve vaccination inequities: A nationwide study on 64.5 million people. European Journal of Public Health, 32(5), 825–830. https://doi.org/10.1093/eurpub/ckac125

Blanquart, F., Abad, C., Ambroise, J., Bernard, M., Cosentino, G., Giannoli, J.-M., & Débarre, F. (2021). Characterisation of vaccine breakthrough infections of SARS-CoV-2 Delta and Alpha variants and within-host viral load dynamics in the community, France, June to July 2021. Eurosurveillance, 26(37). https://doi.org/10.2807/1560-7917.ES.2021.26.37.2100824

Variants

Blanquart, F., Hozé, N., Cowling, B. J., Débarre, F., & Cauchemez, S. (2022). Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants. eLife, 11, e75791. https://doi.org/10.7554/eLife.75791

Cosentino, G., Bernard, M., Ambroise, J., Giannoli, J.-M., Guedj, J., Débarre, F., & Blanquart, F. (2021). SARS-CoV-2 viral dynamics in infections with Alpha and Beta variants of concern in the French community. Journal of Infection, S0163445321003741. https://doi.org/10.1016/j.jinf.2021.07.031

Within-host dynamics

Czuppon, P., Débarre, F., Gonçalves, A., Tenaillon, O., Perelson, A. S., Guedj, J., & Blanquart, F. (2021). Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action. PLOS Computational Biology, 17(3), e1008752. https://doi.org/10.1371/journal.pcbi.1008752

Gene drives

Kläy, L., Girardin, L., Débarre, F., & Calvez, V. (2025). Stochastic dynamics at the back of a gene drive propagation wave. arXiv. https://doi.org/10.48550/arXiv.2502.21268

Kläy, L., Girardin, L., Calvez, V., & Débarre, F. (2025). The Spatial Spread and the Persistence of Gene Drives Are Affected by Demographic Feedbacks, Density Dependence and Allee Effects. Molecular Ecology, 34(16), e70028. https://doi.org/10.1111/mec.70028

De Haas, F. J. H., Kläy, L., Débarre, F., & Otto, S. P. (2024). Modelling daisy quorum drive: A short-term bridge across engineered fitness valleys. PLOS Genetics, 20(5), e1011262. https://doi.org/10.1371/journal.pgen.1011262

Kläy, L., Girardin, L., Calvez, V., & Débarre, F. (2023). Pulled, pushed or failed: The demographic impact of a gene drive can change the nature of its spatial spread. Journal of Mathematical Biology, 87(2), 30. https://doi.org/10.1007/s00285-023-01926-4

Girardin, L., & Débarre, F. (2021). Demographic feedbacks can hamper the spatial spread of a gene drive. Journal of Mathematical Biology, 83(6–7), 67. https://doi.org/10.1007/s00285-021-01702-2

Rode, N. O., Courtier-Orgogozo, V., & Débarre, F. (2020). Can a Population Targeted by a CRISPR-Based Homing Gene Drive Be Rescued? G3 Genes|Genomes|Genetics, 10(9), 3403–3415. https://doi.org/10.1534/g3.120.401484

Rode, N. O., Estoup, A., Bourguet, D., Courtier-Orgogozo, V., & Débarre, F. (2019). Population management using gene drive: Molecular design, models of spread dynamics and assessment of ecological risks. Conservation Genetics, 20(4), 671–690. https://doi.org/10.1007/s10592-019-01165-5

Girardin, L., Calvez, V., & Débarre, F. (2019). Catch Me If You Can: A Spatial Model for a Brake-Driven Gene Drive Reversal. Bulletin of Mathematical Biology, 81(12), 5054–5088. https://doi.org/10.1007/s11538-019-00668-z

Evolutionary epidemiology

Jacopin, E., Lehtinen, S., Débarre, F., & Blanquart, F. (2020). Factors favouring the evolution of multidrug resistance in bacteria. Journal of The Royal Society Interface, 17(168), 20200105. https://doi.org/10.1098/rsif.2020.0105

Gascuel, F., Choisy, M., Duplantier, J.-M., Débarre, F., & Brouat, C. (2013). Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus. PLoS Computational Biology, 9(5), e1003039. https://doi.org/10.1371/journal.pcbi.1003039

Débarre, F., Lion, S., van Baalen, M., & Gandon, S. (2012). Evolution of Host Life-History Traits in a Spatially Structured Host-Parasite System. The American Naturalist, 179(1), 52–63. https://doi.org/10.1086/663199

Débarre, F., Lenormand, T., & Gandon, S. (2009). Evolutionary Epidemiology of Drug-Resistance in Space. PLoS Computational Biology, 5(4), e1000337. https://doi.org/10.1371/journal.pcbi.1000337

Débarre, F., Bonhoeffer, S., & Regoes, R. R. (2007). The effect of population structure on the emergence of drug resistance during influenza pandemics. Journal of The Royal Society Interface, 4(16), 893–906. https://doi.org/10.1098/rsif.2007.1126

Social evolution

Débarre, F. (2020). Imperfect Strategy Transmission Can Reverse the Role of Population Viscosity on the Evolution of Altruism. Dynamic Games and Applications, 10(3), 732–763. https://doi.org/10.1007/s13235-019-00326-y

Estrela, S., Libby, E., Van Cleve, J., Débarre, F., Deforet, M., Harcombe, W. R., Peña, J., Brown, S. P., & Hochberg, M. E. (2019). Environmentally Mediated Social Dilemmas. Trends in Ecology & Evolution, 34(1), 6–18. https://doi.org/10.1016/j.tree.2018.10.004

Débarre, F. (2017). Fidelity of parent-offspring transmission and the evolution of social behavior in structured populations. Journal of Theoretical Biology, 420, 26–35. https://doi.org/10.1016/j.jtbi.2017.02.027

Débarre, F., Hauert, C., & Doebeli, M. (2014). Social evolution in structured populations. Nature Communications, 5(1), 3409. https://doi.org/10.1038/ncomms4409

Evolutionary ecology

Local adaptation

Czuppon, P., Blanquart, F., Uecker, H., & Débarre, F. (2021). The Effect of Habitat Choice on Evolutionary Rescue in Subdivided Populations. The American Naturalist, 197(6), 625–643. https://doi.org/10.1086/714034

Andrello, M., Noirot, C., Débarre, F., & Manel, S. (2021). MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size. Molecular Ecology Resources, 21(2), 596–608. https://doi.org/10.1111/1755-0998.13270

Connallon, T., Débarre, F., & Li, X.-Y. (2018). Linking local adaptation with the evolution of sex differences. Philosophical Transactions of the Royal Society B: Biological Sciences, 373(1757), 20170414. https://doi.org/10.1098/rstb.2017.0414

Débarre, F., Yeaman, S., & Guillaume, F. (2015). Evolution of Quantitative Traits under a Migration-Selection Balance: When Does Skew Matter? The American Naturalist, 186(S1), S37–S47. https://doi.org/10.1086/681717

Débarre, F., Ronce, O., & Gandon, S. (2013). Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments. Journal of Evolutionary Biology, 26(6), 1185–1202. https://doi.org/10.1111/jeb.12132

Débarre, F., & Gandon, S. (2011). Evolution in Heterogeneous Environments: Between Soft and Hard Selection. The American Naturalist, 177(3), E84–E97. https://doi.org/10.1086/658178

Débarre, F., & Lenormand, T. (2011). Distance-limited dispersal promotes coexistence at habitat boundaries: Reconsidering the competitive exclusion principle: Distance-limited dispersal promotes coexistence at habitat boundaries. Ecology Letters, 14(3), 260–266. https://doi.org/10.1111/j.1461-0248.2010.01580.x

Débarre, F., & Gandon, S. (2010). Evolution of specialization in a spatially continuous environment. Journal of Evolutionary Biology, 23(5), 1090–1099. https://doi.org/10.1111/j.1420-9101.2010.01966.x

Speciation, diversification

Bienvenu, F., Débarre, F., & Lambert, A. (2019). The split-and-drift random graph, a null model for speciation. Stochastic Processes and Their Applications, 129(6), 2010–2048. https://doi.org/10.1016/j.spa.2018.06.009

Débarre, F., & Otto, S. P. (2016). Evolutionary dynamics of a quantitative trait in a finite asexual population. Theoretical Population Biology, 108, 75–88. https://doi.org/10.1016/j.tpb.2015.12.002

Débarre, F., Nuismer, S. L., & Doebeli, M. (2014). Multidimensional (Co)Evolutionary Stability. The American Naturalist, 184(2), 158–171. https://doi.org/10.1086/677137

Other

Harmon, L. J., Andreazzi, C. S., Débarre, F., Drury, J., Goldberg, E. E., Martins, A. B., Melián, C. J., Narwani, A., Nuismer, S. L., Pennell, M. W., Rudman, S. M., Seehausen, O., Silvestro, D., Weber, M., & Matthews, B. (2019). Detecting the macroevolutionary signal of species interactions. Journal of Evolutionary Biology, 32(8), 769–782. https://doi.org/10.1111/jeb.13477

Rego‐Costa, A., Débarre, F., & Chevin, L. (2018). Chaos and the (un)predictability of evolution in a changing environment. Evolution, 72(2), 375–385. https://doi.org/10.1111/evo.13407

Débarre, F. (2015). Fitness costs in spatially structured environments. Evolution, 69(5), 1329–1335. https://doi.org/10.1111/evo.12646

Massol, F., & Débarre, F. (2015). Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles. Evolution, 69(7), 1925–1937. https://doi.org/10.1111/evo.12699

Metascience

Débarre, F., Rode, N. O., & Ugelvig, L. V. (2018). Gender equity at scientific events. Evolution Letters, 2(3), 148–158. https://doi.org/10.1002/evl3.49

Vines, T. H., Albert, A. Y. K., Andrew, R. L., Débarre, F., Bock, D. G., Franklin, M. T., Gilbert, K. J., Moore, J.-S., Renaut, S., & Rennison, D. J. (2014). The Availability of Research Data Declines Rapidly with Article Age. Current Biology, 24(1), 94–97. https://doi.org/10.1016/j.cub.2013.11.014

Books

Edited books

Débarre, F., & Praz, F. (2024). Covid: l’ère des pandémies les avancées de la recherche. CNRS éditions le Cherche midi.

Book chapters

Débarre, F., & Gandon, S. (2008). Épidémiologie évolutive des maladies infectieuses. In J.-F. Guégan & M. Choisy (Eds.), Introduction à l’Épidémiologie intégrative des maladies infectieuses et parasitaires (pp. 347–374). De Boeck Université Collection Masters, Louvain-la-Neuve, Belgique. https://www.normalesup.org/~fdebarre/papers/Debarre-Gandon_2008.pdf

Dissertations

Débarre, F. (2019). Some models in Evolutionary Ecology [Habilitation à Diriger des Recherches]. Sorbonne Université.

Débarre, F. (2010). Persistance, compétition et évolution dans un environnement hétérogène [PhD thesis]. http://www.theses.fr/2010MON20067/document

Other

Technical reports

Crits-Christoph, A., Gangavarapu, K., Pekar, J. E., Moshiri, N., Singh, R., Levy, J. I., Goldstein, S. A., Suchard, M. A., Popescu, S., Robertson, D. L., Lemey, P., Wertheim, J. O., Garry, R. F., Rasmussen, A. L., Andersen, K. G., Holmes, E. C., Rambaut, A., Worobey, M., & Débarre, F. (2023). Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control. Zenodo. https://doi.org/10.5281/ZENODO.7754299

Editorials

Fitzpatrick, C. L., Alter, S. E., Boughman, J. W., Débarre, F., Edmands, S., Moehring, A., Moyle, L., Otto, S. P., Ronce, O., Rubin, M. J., & Sweigart, A. L. (2021). The virus evolves: Four public health priorities for reducing the evolutionary potential of SARS-CoV-2. BioScience, 71(4), 319–319. https://doi.org/10.1093/biosci/biab037

Bolnick, D. I., Fox, J. W., Débarre, F., Dietrich, E. I., Phelps, S. M., Jordan, A., & Sorbus torminalis (2021). Editorial Expression of Concern. The American Naturalist, 198(2), 313–316. https://doi.org/10.1086/714867

Meeting reports

Giese, B., Frieß, J. L., Barton, N. H., Messer, P. W., Débarre, F., Schetelig, M. F., Windbichler, N., Meimberg, H., & Boëte, C. (2019). Gene Drives: Dynamics and Regulatory Matters—A Report from the Workshop “Evaluation of Spatial and Temporal Control of Gene Drives,” April 4–5, 2019, Vienna. BioEssays, 41(11), 1900151. https://doi.org/10.1002/bies.201900151

Courses

Débarre, F. (2007). SIR models of epidemics. ETH. https://ethz.ch/content/dam/ethz/special-interest/usys/ibz/theoreticalbiology/education/learningmaterials/701-1424-00L/sir.pdf

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