The evolution of antibiotic resistance in Europe, 1998–2019.

Authors: Emons, Martin^1,2,3 (AUTHOR), Blanquart, François⁴ (AUTHOR), Lehtinen, Sonja^1,3,5 (AUTHOR) sonja.lehtinen@unil.ch

Source: PLoS Pathogens. 4/3/2025, Vol. 21 Issue 4, p1-22. 22p.

Subject Terms: *DRUG resistance in bacteria, *NATURAL selection, *ANTIBIOTICS, *EQUILIBRIUM, *PUBLIC health

The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection

Authors: Czuppon, Peter, Schertzer, Emmanuel, Blanquart, François, Débarre, Florence

Subject Terms: Quantitative Biology - Populations and Evolution

Access URL: http://arxiv.org/abs/2011.08966

From individual-based epidemic models to McKendrick-von Foerster PDEs: A guide to modeling and inferring COVID-19 dynamics

Authors: Foutel-Rodier, Félix, Blanquart, François, Courau, Philibert, Czuppon, Peter, Duchamps, Jean-Jil, Gamblin, Jasmine, Kerdoncuff, Élise, Kulathinal, Rob, Régnier, Léo, Vuduc, Laura, Lambert, Amaury, Schertzer, Emmanuel

Subject Terms: Quantitative Biology - Populations and Evolution, Mathematics - Probability, Primary: 92D30, Secondary: 60J80, 60J85, 35Q92

Access URL: http://arxiv.org/abs/2007.09622

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

Authors: Blanquart, François, Abad, Clémence, Ambroise, Joevin, Bernard, Mathieu, Débarre, Florence, Giannoli, Jean-Marc, Rey, Thomas, Vieillefond, Vincent

Source: In International Journal of Infectious Diseases August 2023 133:89-96

Influenza vaccine effectiveness against detected infection in the community, France, October 2024 to February 2025.

Authors: Blanquart, François, Vieillefond, Vincent, Visseaux, Benoit, Chakra, Claire Nour Abou, Nunes, Marta C., Jacques, Alexandra, Haim-Boukobza, Stephanie, Josset, Laurence, Wehrle, Valentin, Deleglise, Guillaume, Duret, Thomas, Rameix-Welti, Marie Anne, Lina, Bruno, Enouf, Vincent, Bal, Antonin

Source: Eurosurveillance (15607917); 2/20/2025, Vol. 30 Issue 7, p1-8, 8p

Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020

Authors: Belloir, Antoine, Blanquart, François ^*

Source: In Epidemics June 2021 35

Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher's Geometric model?

Authors: Blanquart, François, Bataillon, Thomas

Subject Terms: Quantitative Biology - Populations and Evolution

Access URL: http://arxiv.org/abs/1507.08245

Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.

Authors: Gamblin, Jasmine, Lambert, Amaury, Blanquart, François

Source: Molecular Biology & Evolution; Jan2025, Vol. 42 Issue 1, p1-16, 16p

Subject Terms: LOCUS (Genetics), GENE frequency, BACTERIAL evolution, PHYLOGENETIC models, PAN-genome, HORIZONTAL gene transfer

Properties of selected mutations and genotypic landscapes under Fisher's Geometric Model

Authors: Blanquart, François, Achaz, Guillaume, Bataillon, Thomas, Tenaillon, Olivier

Subject Terms: Quantitative Biology - Populations and Evolution

Access URL: http://arxiv.org/abs/1405.3504

Bottlenecks can constrain and channel evolutionary paths.

Authors: Gamblin, Jasmine¹, jasmine.gamblin@polytechnique.org, Gandon, Sylvain², Blanquart, François^1,3, Lambert, Amaury^1,4

Source: Genetics; Jun2023, Vol. 224 Issue 2, p1-9, 9p

The evolution of subtype B HIV-1 tat in the Netherlands during 1985–2012

Authors: van der Kuyl, Antoinette C., Vink, Monique, Zorgdrager, Fokla, Bakker, Margreet, Wymant, Chris, Hall, Matthew, Gall, Astrid, Blanquart, François, Berkhout, Ben, Fraser, Christophe, Cornelissen, Marion

Source: In Virus Research 2 May 2018 250:51-64

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.

Authors: Burgaya, Judit^1,2, Marin, Julie³, Royer, Guilhem^4,5,6, Condamine, Bénédicte⁴, Gachet, Benoit⁴, Clermont, Olivier⁴, Jaureguy, Françoise³, Burdet, Charles⁴, Lefort, Agnès⁴, de Lastours, Victoire⁴, Denamur, Erick^4,7, erick.denamur@inserm.fr, Galardini, Marco^1,2, Blanquart, François⁸

Source: PLoS Genetics; 8/2/2023, Vol. 19 Issue 8, p1-28, 28p

An evolutionary model topredict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae

Authors: Blanquart, François, Lehtinen, Sonja, Fraser, Christophe

Source: Proceedings: Biological Sciences, 2017 May . 284(1855), 1-10.

Access URL: https://www.jstor.org/stable/44683413

Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study.

Authors: Zeeb, Marius, Pasin, Chloé, Cavassini, Matthias, Bieler-Aeschlimann, Mélanie, Frischknecht, Paul, Kusejko, Katharina, Fellay, Jacques, Blanquart, François, Metzner, Karin J, Neumann, Kathrin, Jörimann, Lisa, Tschumi, Jasmin, Bernasconi, Enos, Huber, Michael, Kovari, Helen, Leuzinger, Karoline, Notter, Julia, Perreau, Matthieu, Rauch, Andri, Ramette, Alban

Source: Brain Communications; 2024, Vol. 6 Issue 4, p1-12, 12p

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Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

Authors: Lehtinen, Sonja, Blanquart, François, Croucher, Nicholas J., Turner, Paul, Lipsitch, Marc, Fraser, Christophe

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Jan . 114(5), 1075-1080.

Access URL: https://www.jstor.org/stable/26479138

Evidence for parasite-mediated selection during short-lasting toxic algal blooms

Authors: Blanquart, François, Valero, Myriam, Alves-de-Souza, Catharina, Dia, Aliou, Lepelletier, Frédéric, Bigeard, Estelle, Jeanthon, Christian, Destombe, Christophe, Guillou, Laure

Source: Proceedings: Biological Sciences, 2016 Oct . 283(1841), 1-9.

Access URL: http://www.jstor.org/stable/26159079

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha.

Authors: Faucher, Benjamin, Sabbatini, Chiara E., Czuppon, Peter, Kraemer, Moritz U. G., Lemey, Philippe, Colizza, Vittoria, Blanquart, François, Boëlle, Pierre-Yves, Poletto, Chiara

Source: Nature Communications; 3/9/2024, Vol. 15 Issue 1, p1-13, 13p

Subject Terms: SARS-CoV-2, EPIDEMICS, LOGARITHMS

Geographic Terms: UNITED Kingdom

Using early detection data to estimate the date of emergence of an epidemic outbreak.

Authors: Jijón, Sofía, Czuppon, Peter, Blanquart, François, Débarre, Florence

Source: PLoS Computational Biology; 3/8/2024, Vol. 20 Issue 3, p1-19, 19p

Subject Terms: SARS-CoV-2, EMERGING infectious diseases, EPIDEMICS, COVID-19 pandemic, POPULATION dynamics

Geographic Terms: WUHAN (China)

The demography of a metapopulation in an environment changing in time and space

Authors: Blanquart, François

Source: In Theoretical Population Biology June 2014 94:1-9