Publications

Stochastic models in population genetics and evolution:

Coalescent processes in subdivided populations subject to recurrent mass extinctions. Jay Taylor and A.V. (2009). Electron. J. Probab., 14: 242-288.

A new model for evolution in a spatial continuum. Nick Barton, Alison Etheridge and A.V. (2010). Electron. J. Probab., 15: 162-216.

The spatial Lambda-Fleming-Viot process on a large torus: genealogies in the presence of recombination. Alison Etheridge and A.V. (2012). Ann. Applied Probab., 22: 2165-2209.

Large scale behaviour of the spatial Lambda-Fleming-Viot process. Nathanaël Berestycki, Alison Etheridge and A.V. (2013). Ann. Inst. H. Poincaré Probab. Statist., 49: 374-401.

Modelling evolution in a spatial continuum. Nick Barton, Alison Etheridge and A.V. (2013). Journal of Statistical Mechanics, P01002.

Genetic hitchhiking in spatially extended populations. Nick Barton, Alison Etheridge, Jerome Kelleher and A.V. (2013). Theor. Popul. Biol., 87: 75-89.

The spatial Lambda-Fleming-Viot process: an event-based construction and a lookdown representation. A.V. and Anton Wakolbinger (2015). Ann. Inst. H. Poincaré Probab. Statist., 51: 570-598.

Ancestries of a recombining diploid population. Raazesh Sainudiin, Balchandra Thatte and A.V. (2016). J. Math. Biol., 72: 363-408.

Spread of pedigree versus genetic ancestry in spatially distributed populations. Nick Barton, Alison Etheridge, Jerome Kelleher and A.V. (2016). Theor. Popul. Biol., 108: 1-12.

A Beta-splitting model for evolutionary trees. Raazesh Sainudiin and A.V. (2016). R. Soc. open sci., 3: 160016.

The infinitesimal model: definition, derivation and implications. Nick Barton, Alison Etheridge and A.V. (2017). Theor. Popul. Biol., 118: 50-73.

Rescaling limits of the spatial Lambda-Fleming-Viot process with selection. Alison Etheridge, A.V. and Feng Yu (2020). Electron. J. Probab., 25(120): 1-89.
Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. Paul Jay, Emilie Tezenas, A.V. and Tatiana Giraud (2022). Formerly : PLOS Biol., 20(7): e3001698, now Retracted. Indeed, after its publication in PLOS Biology, part of our methodology was questioned in a bioRxiv preprint and in a subsequent review paper using the material presented in the bioRxiv preprint. In order to clarify the different points of misunderstanding that have led to these criticisms, in this document we have provided a response that, we hope, demonstrates the validity of our approach. This debate is grounded on the very interesting question of which control scenario is appropriate to assess the efficiency of the sheltering effect, and we still hope to contribute to this discussion with sound logical arguments and relevant biological concepts. The preprint Jay, Véber and Giraud (2024) below also offers supplementary analyses which reinforce our conclusions. The preprint Jay, Véber and Giraud (2026) combines the results of the former PLOS Biol. article and the supplementary analyses.
The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing. Emilie Tezenas, Tatiana Giraud, A.V. and Sylvain Billiard (2023). Peer Community Journal, 3: e14.
Drosophilids with darker cuticle have higher body temperature under light. Laurent Freoa, Luis-Miguel Chevin, Philippe Christol, Sylvie Méléard, Michaël Rera, A.V. and Jean-Michel Gibert (2023). Scientific Reports, 13: 3513, 2023.
The infinitesimal model with dominance. Nick Barton, Alison Etheridge and A.V. (2023). Genetics, 225(2): iyad133.
Measure-valued growth processes in continuous space and growth properties starting from an infinite interface. Apolline Louvet and A.V. (2024). Stochastic Process. Appl., 170: 104291.
Why do sex chromosomes progressively lose recombination? Paul Jay, Daniel Jeffries, Fanny Hartmann, A.V. and Tatiana Giraud (2024). Trends in Genetics, 40(7): 564-579.
The impact of environmental fluctuations, sexual dimorphism, dominance reversal and plasticity on the pigmentation-related genetic and phenotypic variation in D. melanogaster populations – A modelling study. Laurent Freoa, Jean-Michel Gibert and A.V. (2024). Preprint, hal-04597232.
Deleterious mutations can contribute to the evolution of recombination suppression between sex chromosomes. Paul Jay, A.V. and Tatiana Giraud (2024). Preprint, bioRxiv 2024.11.18.624013.
Stepwise expansion of recombination suppression on sex chromosomes and other supergenes through lower load advantage and deleterious mutation sheltering. Paul Jay, A.V. and Tatiana Giraud (2025). Preprint, bioRxiv 2025.06.27.661902.
The fate of mutations on Y chromosomes and autosomes: a unified Wright-Fisher framework accounting for segregation time. Ariel Offenstadt, Sylvain Billiard, Tatiana Giraud, A.V. and Paul Jay (2026). Preprint, hal-05576108.

Statistical inference for population and population genetics models:

Inference in two dimensions: allele frequencies versus lengths of shared sequence blocks. Nick Barton, Alison Etheridge, Jerome Kelleher and A.V. (2013). Theor. Popul. Biol., 87: 105-119.

Finding the best resolution for the Kingman-Tajima coalescent: theory and applications. Raazesh Sainudiin, Tanja Stadler and A.V. (2015). J. Math. Biol., 70: 1207-1247.

Full likelihood inference from the site frequency spectrum based on the optimal tree resolution (and Supplementary material). Raazesh Sainudiin and A.V. (2018). Theor. Popul. Biol., 124: 1-15.

Bayesian estimation of population size changes by sampling Tajima's trees. Julia Palacios, A.V., Lorenzo Cappello, Zhangyuan Wang, John Wakeley and Sohini Ramachandran (2019). Genetics, 213: 967-986.

An efficient coalescent model for heterochronously sampled molecular data. Lorenzo Cappello, A.V. and Julia Palacios (2024). Journal of the American Statistical Association, 119(548): 2437-2449.
Quantifying the impact of different forms of stress on fungal growth: an inference method based on high-resolution pictures of the mycelial network. Lena Kuwata, Thibault Chassereau, Florence Chapeland-Leclerc, Pascal David, Eric Herbert, Gwenaël Ruprich-Robert, Milica Tomasevic and A.V. (2025). Preprint, hal-05149818. GitHub repository.

Branching processes and other population models:

Quenched convergence of a sequence of superprocesses in Rd among Poissonian obstacles. A.V. (2009). Stochastic Process. Appl., 119: 2598-2624.

Escape probabilities for branching Brownian motion among mild obstacles. Jean-François Le Gall and A.V. (2012). J. Theor. Probab., 25: 505-535.

Graph-Theoretic Algorithms for the Isomorphism of Polynomials Problem. Charles Bouillaguet, Pierre-Alain Fouque and A.V. (2013). Eurocrypt.

Hyphal network whole field imaging allows for accurate estimation of anastomosis rates and branching dynamics of the filamentous fungus Podospora anserina. Jonathan Dikec, Adélaïde Olivier, Cécilia Bobée, Yves D'Angelo, Rémi Catellier, Pascal David, Frédéric Filaine, Sébastien Herbert, Christophe Lalanne, Hervé Lalucque, Laurent Monasse, Matthieu Rieu, Gwenaël Ruprich-Robert, A.V., Florence Chapeland-Leclerc and Eric Herbert (2020). Scientific Reports, 10: 3131.

The role of mode switching in a population of actin polymers with constraints. François Robin, Anne Van Gorp and A.V. (2021). J. Math. Biol., 82(3): 1-43.

Ergodic behaviour of a multi-type growth-fragmentation process modelling the mycelial network of a filamentous fungus. Milica Tomasevic, Vincent Bansaye and A.V. (2022). ESAIM: P & S, 26: 397-435.
A spatial measure-valued model for chemical reaction networks in heterogeneous systems. Lea Popovic and A.V. (2023). Ann. Applied Probab., 33(5): 3706-3754.

Communication networks:

A stochastic analysis of resource sharing with logarithmic weights. Philippe Robert and A.V. (2015). Ann. Applied Probab., 25: 2626-2670.

A scaling analysis of a star network with logarithmic weights. Philippe Robert and A.V. (2019). Stochastic Process. Appl., 129: 1749-1781.

Popularisation papers (maths):

Théorèmes limites pour des processus de branchement et de coalescence spatiaux. A.V. (2010). Thesis summary, MATAPLI, 92: 53-60.

Les différentes échelles de temps de l'évolution. Vincent Bansaye, Sylvie Méléard and A.V. (2013). MATAPLI, 100: 101-116.
Decision-making tools for healthcare structures in times of pandemic. Thierry Garaix, Stéphane Gaubert, Julie Josse, Nicolas Vayatis and A.V. (2022). Anaesth. Crit. Care Pain Med, 41: 101052.
Promouvoir les interactions entre mathématiques et sciences du vivant, de la Terre et de l'Homme. Arnaud Guillin, Laure Saint-Raymond and A.V. (2024). La lettre de CNRS Sciences humaines & sociales, 89: 24-26 (juillet 2024).