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Pfeifer, Susanne P.; Laurent, Stefan; Martins Conde e Sousa, Vitor; Linnen, Catherine R.; Foll, Matthieu; Excoffier, Laurent; Hoekstra, Hopi E.; Jensen, Jeffrey D. (2018). The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Molecular Biology and Evolution, 35(4), pp. 792-806. Oxford University Press 10.1093/molbev/msy004
Amorim, Carlos Eduardo G.; Daub, Joséphine; Salzano, Francisco M.; Foll, Matthieu; Excoffier, Laurent (2015). Detection of convergent genome-wide signals of adaptation to tropical forests in humans. PLoS ONE, 10(4), pp. 1-19. Public Library of Science 10.1371/journal.pone.0121557
Fischer, Martin; Foll, Matthieu; Heckel, Gerald; Excoffier, Laurent (2014). Continental-Scale Footprint of Balancing and Positive Selection in a Small Rodent (Microtus arvalis). PLoS ONE, 9(11), e112332. Public Library of Science
Foll, Matthieu; Gaggiotti, Oscar; Daub, Joséphine; Vatsiou, Alexandra; Excoffier, Laurent (2014). Widespread Signals of Convergent Adaptation to High Altitude in Asia and America. American journal of human genetics, 95(4), pp. 394-407. Cell Press 10.1016/j.ajhg.2014.09.002
Perry, George H.; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L.; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J.; Barreiro, Luis B. (2014). Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 111(35), E3596-E3603. National Academy of Sciences NAS 10.1073/pnas.1402875111
Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu (2013). Robust demographic inference from genomic and SNP data. PLoS genetics, 9(10), e1003905. Public Library of Science 10.1371/journal.pgen.1003905
Sunnaker, Mikael; Busetto, Alberto Giovanni; Numminen, Elina; Corander, Jukka; Foll, Matthieu; Dessimoz, Christophe (2013). Approximate Bayesian Computation. PLoS computational biology, 9(1), e1002803. Public Library of Science 10.1371/journal.pcbi.1002803
Alves, Isabel; Srámková Hanulová, A.; Foll, Matthieu; Excoffier, Laurent (2012). Genomic Data Reveal a Complex Making of Humans. PLoS genetics, 8(7), e1002837. San Francisco, Calif.: Public Library of Science 10.1371/journal.pgen.1002837
Hofer, Tamara; Foll, Matthieu; Excoffier, Laurent (2012). Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics, 13(1), p. 107. London: BioMed Central 10.1186/1471-2164-13-107
Excoffier, Laurent; Foll, Matthieu (2011). fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics, 27(9), pp. 1332-1334. Oxford: Oxford University Press 10.1093/bioinformatics/btr124
Fischer, Martin C.; Foll, Matthieu; Excoffier, Laurent; Heckel, Gerald (2011). Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Molecular Ecology, 20(7), pp. 1450-1462. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2011.05015.x
Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisso, Scott A.; Fagundes, Nelson; Chikhi, Lounes; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Fraçois; ... (2010). In defence of model-based inference in phylogeography. Molecular Ecology, 19(3), pp. 436-446. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2009.04515.x
Foll, Matthieu; Fischer, Martin C.; Heckel, Gerald; Excoffier, Laurent (2010). Estimating population structure from AFLP amplification intensity. Molecular Ecology, 19(21), pp. 4638-4647. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2010.04820.x
Gaggiotti, Oscar E.; Foll, Matthieu (2010). Quantifying population structure using the F-model. Molecular ecology resources, 10(5), pp. 821-830. Oxford: Blackwell Science 10.1111/j.1755-0998.2010.02873.x
Ray, Nicolas; Currat, Mathias; Foll, Matthieu; Excoffier, Laurent (2010). SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics, 26(23), pp. 2993-2994. Oxford: Oxford University Press 10.1093/bioinformatics/btq579
Excoffier, Laurent; Foll, Matthieu; Petit, Rémy J. (2009). Genetic Consequences of Range Expansions. Annual review of ecology, evolution, and systematics, 40(1), pp. 481-501. Palo Alto, Calif.: Annual Reviews Inc. 10.1146/annurev.ecolsys.39.110707.173414
Excoffier, Laurent; Hofer, Tamara; Foll, Matthieu (2009). Detecting loci under selection in a hierarchically structured population. Heredity, 103(4), pp. 285-298. London: Oliver and Boyd 10.1038/hdy.2009.74
Gaggiotti, Oscar E.; Bekkevold, Dorte; Jorgensen, Hanne B.H.; Foll, Matthieu; Carvalho, Gary R.; Andre, Carl; Ruzzante, Daniel E. (2009). Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: atlantic herring as a case study. Evolution, 63(11), 2939 - 2951. Hoboken, N.J.: Wiley 10.1111/j.1558-5646.2009.00779.x
Guillot, Gilles; Foll, Matthieu (2009). Correcting for ascertainment bias in the inference of population structure. Bioinformatics, 25(4), pp. 552-554. Oxford: Oxford University Press 10.1093/bioinformatics/btn665
