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BCM - Computational and Mathematical Biology

Publications
Teaching
TESS / POPS
sNMF
LFMM
LEA
Software

Olivier François, PhD, Publications in Scholar Google

  

Publications (2000-2016)


  • Martins, H., Caye, K., Luu, K., Blum, M. G., François, O. Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Molecular Ecology, bioRxiv 054585, 2016.
  • Seigneurin, A., Labarère, J., François, O., Exbrayat, C., Dupouy, M., Filippi, M., Colonna, M. Overdiagnosis and overtreatment associated with breast cancer mammography screening: A simulation study with calibration to population-based data. Breast (28), 60, 2016.
  • O. François. Running Structure-like population genetic analysis with R. R tutorials in population genetics, PDF, U. Grenoble-Alpes, 1-8, 2016.
  • P. Trémeaux, A. Caporossi, C. Ramière, E. Santoni, et al. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains. Clinical Microbiology and Infection, 22 (5), 460, e1-460 e10, 2016.
  • O. François, L.P Waits. Clustering and Assignment Methods in Landscape Genetics. In: Landscape Genetics: Concepts, Methods, Applications (eds N. Balkenhol, S. A. Cushman, A. T. Storfer and L. P. Waits), John Wiley and Sons, Ltd, Chichester, UK. doi: 10.1002/9781118525258.ch07, 2016.
  • O. François, H. Martins, K. Caye, S.D. Schoville. Controlling false discoveries in genome scans for selection. PDF, Molecular Ecology 25 (2), 454-469, 2016. Tutorials and examples.
  • K. Caye, T.M. Deist, H. Martins, O. Michel, O. François. TESS3: Fast inference of spatial population structure and genome scans for selection. PDF, Molecular ecology resources 16 (2), 540-548, 2016.
  • F. Jay, O. François, E.Y. Durand, M.G.B Blum. POPS: A software for prediction of population genetic structure using latent regression models. Journal of Statistical Software 68 (9), doi: 10.18637/jss.v068.i09, 2015. Download PDF.
  • E. Frichot, O. François LEA: An R package for lanscape and ecological association studies. Methods in ecology an evolution 6 (8), 925-929, 2015. Link to MEE. Download PDF.
  • E. Frichot, O. François LEA : Un package R pour la génomique du paysage. Quatrièmes rencontres R, Grenoble 26-28 juin, 2015. Download PDF.
  • E. Frichot, S.D. Schoville, P. de Villemereuil, OE Gaggiotti, O. François Detecting adaptive evolution based on association with ecological gradients: Orientation matters! Heredity 115, 22-28 2015. Link to Heredity.
  • S. Larrat, O. Kulkarni, J-B. Claude, R. Beugnot, MGB Blum, K. Fusillier, J. Lupo, P. Tremeaux, A. Plages, A. Marlu, H. Duborjal, A. Signori-Schmuck, O. François, J-P. Zarski, P. Morand, V. Leroy Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic Hepatitis C patients. Journal of clinical microbiology 53, 389-397, 2015.
  • P. de Villemereuil, E. Frichot, E. Bazin, O. François, OE Gaggiotti Genome scan methods against more complex models: when and how much should we trust them? Molecular ecology 23 (8), 2006-2019, 2014.
  • N. Coquery, O. François, B. Lemasson, C. Debacker, R. Farion, C. Rémy, E. Barbier Microvascular MRI and unsupervised clustering yield histology-resembling images in two rat models of glioma Journal of Cerebral Blood Flow and Metabolism 34, 1354-1362, 2014.
  • E. Frichot, F. Mathieu, T. Trouillon, G. Bouchard, O. François Fast and efficient estimation of individual ancestry coefficients Genetics 196 (4), 973-983, 2014. Link to Genetics.
  • E. Frichot, S.D. Schoville, G. Bouchard, O. François Testing for associations between loci and environmental gradients using latent factor mixed models Molecular Biology and Evolution, 30 (7), 1687-1699, 2013. Link to MBE.
  • M. Arenas, O. François, M. Currat, N. Ray, L. Excoffier Influence of admixture and Paleolithic range contractions on current European diversity gradients Molecular Biology and Evolution, 30 (1), pp. 57-61, 2013. Link to MBE.
  • E. Frichot, S.D. Schoville, G. Bouchard, O. François Correcting principal component maps for effects of spatial autocorrelation in population genetic data, Frontiers in Genetics 3, 254, 2012. Link to Frontiers in Genetics. Download PDF.
  • S.D. Schoville, A. Bonin, O. François, S. Lobreaux, C. Melodelima, S. Manel Adaptive genetic variation on the landscape: Methods and cases, Annual Review of Ecology, Evolution and Systematics, 43 (1), pp. 23-43, 2012. Link to AREES.
  • K. Csilléry, O. François, MGB. Blum. abc: an R package for Approximate Bayesian Computation (ABC). Methods in Ecology and Evolution, 3 (3), pp. 475-479, 2012. Link to MEE. Download PDF.
  • F. Jay, S. Manel, N. Alvarez, EY Durand, W. Thuiller, R. Holderegger, P. Taberlet, O. François. Forecasting changes in population genetic structure of Alpine plants in response to global warming. Molecular Ecology 21 (10), pp. 2354-2368, 2012. Link to Molecular Ecology. Download PDF.
  • A. Seigneurin, O. François, J. Labarère, P. Oudeville, J. Monlong, M. Colonna. Overdiagnosis for non-progressive cancer detected by screening mammography: stochastic simulation study with calibration to population based registry data. British Medical Journal BMJ, 343:d7017, 2011. Link to BMJ.
  • F. Jay, M. Blum, E. Frichot, O. François. Modèles à variables latentes en génétique des populations. Journal de la Société Française de Statistique, 152 (3), pp. 3-20, Novembre 2011. Link to J-SFdS.
  • O. François, G. Laval Deviance Information Criteria for Model Selection in Approximate Bayesian Computation. Statistical Applications in Genetics and Molecular Biology, 10(1), 33, 2011. Link to SAGMB .Link to an Arxiv preprint.
  • P. Sjödin, O. François. Wave-of-advance models of the diffusion of the Y chromosome haplogroup R1b1b2 in Europe. PLoS ONE 6(6), e21592, 2011. Link to the paper.
  • R. Leblois, K. Kuhls, O. François, G. Schonian, T. Wirth. Guns, germs and dogs: On the origin of Leishmania chagasi. Infection, Genetics and Evolution, 11, pp. 1091-1095, 2011. PDF
  • F. Jay, O. François, M. Blum. Predictions of Native American Population Structure Using Linguistic Covariates in a Hidden Regression Framework. PLoS ONE 6(1): e16227, 2011. Link to the paper.
  • K. Csilléry, M. Blum, O. Gaggiotti, O. François. Approximate Bayesian Computation (ABC) in practice. Trends in Ecology and Evolution, 25, pp. 410-418, 2010. PDF
  • K. Csilléry, M. Blum, O. Gaggiotti, O. François. Invalid arguments against ABC: A reply to AR Templeton. Trends in Ecology and Evolution, 25, pp. 490-491, 2010. PDF
  • O. François, E. Durand. Spatially explicit Bayesian clustering models in population genetics. Molecular Ecology Resources (Special Issue on Spatial Genetics), 10, pp. 773-784, 2010. PDF
  • O. François, M. Currat, N. Ray, E. Han, L. Excoffier, J. Novembre. Principal component analysis under population genetic models of range expansion and admixture. Molecular Biology and Evolution, 27, pp. 1257-1268, 2010.PDF.
  • G Segelbacher, SA Cushman, BK Epperson, MJ Fortin, O François et al. Applications of landscape genetics in conservation biology: Concepts and challenges. Conservation Genetics, 11, pp. 375-385, 2010.
  • MGB Blum, O. François Non-linear regression models for Approximate Bayesian Computation. arXiv:0809.4178 Statistics and Computing, 20, pp. 63-73, 2010. PDF
  • E. Durand, O. François. Probabilistic analysis of a genealogical model of animal group patterns. Journal of Mathematical Biology, 60, pp. 451-468, 2010 PDF, link to JMB.
  • E. Durand, F. Jay, O.E. Gaggiotti, O. François. Spatial inference of admixture proportions and secondary contact zones. Molecular Biology and Evolution, PDF, 26, pp. 1963-1973, 2009.
  • E. Durand, C. Chen, O. François. Comment on 'On the inference of spatial structure from population genetics data' . Bioinformatics, PDF, 25, pp. 1802-1804, 2009. Example data set used in our response Rep05_Fst04
  • M R Garcia-Gil, O. François, S Kamruzzahan and P Waldmann Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine. Heredity, 103, pp. 90-96, 2009 link
  • Y. Bouchenak-Kelladi, GA Verboom, TR Hodkinson, N Salamin, O. François, G Ni Chonghaile, V Savolainen. The origins and diversification of C4 grasses and savanna-adapted ungulates Global Change Biology, 15, 2397-2417, 2009 link .
  • M. Emily, P. Casez, O. François Risk assessment for hospital-acquired infections: a risk-theory approach Risk Analysis, Apr;29(4):565-75, 2009. link .
  • O. François, MGB Blum, M. Jakobsson, NA Rosenberg Demographic history of European populations of Arabidopsis thaliana PLoS Genetics, 4(5): e1000075, 2008, link .
  • O. François Convergence Analysis of Evolution Strategies with Random Numbers of Offspring. PDF, Parallel Problems Solving from Nature PPSN 2008, Lecture Notes in Computer Science 5199 Springer, pp 21-30, 2008.
  • C. Chen, E. Durand, F. Forbes, O. François. Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study. PDF, Molecular Ecology Notes, Volume 7, Issue 5, pp. 747-756, 2007.
  • E. Durand, M.G.B Blum, O. François. Prediction of group patterns in social mammals based on a coalescent model. Journal of Theoretical Biology, PDF, Vol. 249(2), pp. 262-270,2007.
  • O.Francois, C. Mioland, Gaussian approximation for phylogenetic branch length statistics under stochastic models of biodiversity, PDF, Mathematical Biosciences, Volume 209, Issue 1, pages 108-123, 2007.
  • A.Cercueil, O.Francois, S.Manel The Genetical Bandwidth Mapping: a Wombling-based approach to assess the spatial genetic structure of populations, PDF, Theoretical Population Biology, 71(3), 332-341, 2007.
  • S. Ancelet, G. Guillot, O.Francois Hidden Markov random fields and the genetic structure of the Scandinavian brown bear population. Journal de la Societe Francaise de Statistique, tome 148, vol 1, 2007.
  • M. Emily and O.François. A statistical approach to estimating the strength of cell-cell interactions under the differential adhesion hypothesis, PDF, Theoretical Biology and Medical Modelling, Vol. 4:37, Septembre 2007.
  • O.Francois, S. Ancelet, G. Guillot. Bayesian clustering using Hidden Markov Random Fields in spatial population genetics, Genetics version, PDF, 174, 805-816, 2006.
  • C. Chen, F. Forbes, O.Francois Fastruct: Model-based clustering made faster. PDF, Molecular Ecology Notes, 6, 980-983, 2006. Download the FASTRUCT program (Windows).
  • M.G.B. Blum, O.Francois, S. Janson The mean, variance and joint distribution of two statistics sensitive to phylogenetic tree balance, PDF, The Annals of Applied Probability, Vol. 16, No. 4, 2195-2214, 2006.
  • M.G.B. Blum, E. Heyer, O.Francois, F. Austerlitz Matrilineal fertility inheritance detected in Hunter-Gatherer populations using the imbalance of gene genealogies, PLoS Genetics Aug. 4, 2(8) 2006.
  • M.G.B. Blum, O.Francois Which random processes describe the Tree of Life? A large-scale study of phylogenetic databases. PDF and Supplementary material,  Systematic Biology, 2006, 55(4): 685-691.
  • M.Emily, O.Francois Conditional coalescent trees with two mutation rates and their application to genomic instability, Genetics, 172(3): 1809-2180, 2006.
  • N. Bortolussi, E. Durand, M. Blum, O.Francois. APTreeshape: Statistical analysis of phylogenetic tree shape, PDF,  Bioinformatics. Available Online , 22(3): 363-364, 2006.
  • M. Blum and O. Francois On statistical tests of phylogenetic imbalance: the Sackin and other indices revisited, PDF, Mathematical Biosciences, 195 (2), 141-153, June 2005.
  • M. Blum and O. Francois External branch length and minimal clade size under the neutral coalescent, PS, Advances in Applied Probability, 37 3, pp. 647-662, 2005.
  • M. Emily, D. Morel, R. Marcelpoil and O.Francois. Spatial correlation of gene expression measures in Tissue Microarray core analysis, Journal of Theoretical Medicine, Vol 6, 1, pp. 33-39, March 2005.
  • M. Blum, C. Damerval, S. Manel and O. Francois Brownian models and coalescent structures, PDF, Theoretical Population Biology, 65 3, pp. 249-261, May 2004.
  • S. Manel, E. Bellemain, J. Swenson and O. Francois Assumed and inferred genetic structure of populations: The Scandinavian brown bears revisited, Molecular Ecology, 13 5, pp. 1327-1331, May 2004.
  • E. Fontenas and O. Francois Improved bounds for the finite-time behavior of the simulated annealing algorithm  PS, Journal of Applied Probability, Vol 40, 4, pp.961-969, 2003.
  • A. Bienvenue and O. Francois Global Convergence for Evolution Strategies in Spherical Problems: Some Simple Proofs and Difficulties, PDF, Theoretical Computer Science A, Vol 306/1-3, pp. 269-289, 2003.
  • A. Cercueil and O. Francois Sharp asymptotics for fixation times in stochastic population genetics models at low mutation probabilities PDF, Journal of Statistical Physics, 110, 1-2, pp. 311-332, January 2003.
  • L.M. Mohamed Abdallahi, C. La Rota, M. Béguin and O. Francois Parameter estimation in an interacting point processes model for multidimensional neuronal data: a Gibbsian approximation approach, PDF, Biological Cybernetics,Volume 89, Number 3, pp. 170-178, September 2003.
  • O. Francois Global optimization with exploration/selection algorithms and simulated annealing, PDF, The Annals of Applied Probability, vol 12, pp. 248-271, 2002.
  • A. Bienvenue, M. Joannides, J. Berard, E. Fontenas, O. Francois Niching in Monte Carlo Filtering Algorithms Electronic preprint available  In P. Collet, JK Hao, E. Lutton, M. Schoenauer eds, Artificial Evolution Selected Papers, 5th International Conference, EA 2001, Le Creusot, France, Lecture Notes in Computer Science 2310, Springer-Verlag, pp. 11--22, 2002.
  • A. Cercueil, O. Francois Monte Carlo simulation and population-based optimization, Electronic preprint available Congress on Evolutionary Computation 2001, pp. 191-198, COEX center, Seoul, IEEE Press, 2001.
  • O. Francois, C. Lavergne Design of evolutionary algorithms: a statistical perspective, PDF, IEEE Transactions on Evolutionary Computation, vol5,N°2,april, pp. 129-148, 2001.
  • O. Francois Large deviations, evolutionary computation and comparisons of algorithms, in Parallel Problem Solving from Nature VI, Schoenauer et al. eds, pp. 79-88, Lecture Notes in Computer Science 1917, Springer-Verlag, 2000.
  • O. Francois Geometric inequalities for concentrated Markov chains, PDF, Journal of Applied Probability, 37, 1, pp. 15-28, 2000.
  • O. Francois, C. La Rota, J. Horikawa, T. Hervé Diffusion and innovation rates for multidimensional neuronal data with large covariances, Network: Computation in Neural Systems, 11, 211-220, 2000.
  • O. Francois, L.M. Mohamed Abdallahi, J. Horikawa, T. Taniguchi, T. Hervé Statistical procedures for spatio-temporal neuronal data with application to optical recording of the auditory cortex, Neural Computation, 12, pp. 1821-1838, 2000.
  • O. Francois An evolutionary strategy for global minimization and its Markov chain analysis, PDF, IEEE Transactions on Evolutionary Computation, vol. 2, 3, pp. 77-91, 1998.