, ou algorithme en ligne, est un algorithme qui reçoit son entrée non pas d'un seul coup, mais comme un flux de données
, Regression-based latent factor models, Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining, KDD '09, p.53, 2009.
DOI : 10.1145/1557019.1557029
, Enhancements to the ADMIXTURE algorithm for individual ancestry estimation, BMC Bioinformatics, vol.12, issue.1, p.30, 2011.
DOI : 10.1007/BF01441146
, Fast model-based estimation of ancestry in unrelated individuals, Genome Research, vol.19, issue.9, pp.1655-1664, 2009.
DOI : 10.1101/gr.094052.109
, A tutorial on statistical methods for population association studies, Nature Reviews Genetics, vol.5, issue.10, pp.781-791, 2006.
DOI : 10.1038/nrg1155
, Enhanced Localization of Genetic Samples through Linkage-Disequilibrium Correction, The American Journal of Human Genetics, vol.92, issue.6, pp.882-894, 2013.
DOI : 10.1016/j.ajhg.2013.04.023
, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the royal statistical society. Series B (Methodological), pp.289-300, 1995.
, Nonlinear Programming, In : Journal of the Operational Research Society, vol.483, issue.26, pp.334-334, 1997.
, Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies, Bioinformatics, vol.3
DOI : 10.1038/ng.2285
, Inferring Continuous and Discrete Population Genetic Structure Across Space, p.189688, 2017.
DOI : 10.1101/189688
URL : https://www.biorxiv.org/content/early/2017/09/15/189688.full.pdf
, Cross-validation of component models: A critical look at current methods, Analytical and Bioanalytical Chemistry, vol.55, issue.5, pp.1241-1251, 2008.
DOI : 10.1007/s00216-007-1790-1
, Genotype Imputation with Millions of Reference Samples, The American Journal of Human Genetics, vol.98, issue.1, pp.116-126, 2016.
DOI : 10.1016/j.ajhg.2015.11.020
, Graph Regularized Nonnegative Matrix Factorization for Data Representation IEEE Transactions on Pattern Analysis and Machine Intelligence 33, 2011.
, A Singular Value Thresholding Algorithm for Matrix Completion, SIAM Journal on Optimization, vol.20, issue.4, 2010.
DOI : 10.1137/080738970
, AmiGO: online access to ontology and annotation data, Bioinformatics, vol.25, issue.2, pp.288-289, 2008.
DOI : 10.1038/75556
URL : https://academic.oup.com/bioinformatics/article-pdf/25/2/288/16889779/btn615.pdf
, High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics, Journal of the American Statistical Association, vol.103, issue.484, 2008.
DOI : 10.1198/016214508000000869
, The History and Geography of Human Genes, 1994.
, Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study, Molecular Ecology Notes, vol.101, issue.41, pp.747-756, 2007.
DOI : 10.2307/2408641
URL : https://hal.archives-ouvertes.fr/hal-00370267
, Selecting the number of principal components: Estimation of the true rank of a noisy matrix, The Annals of Statistics, vol.45, issue.6, p.64, 2014.
DOI : 10.1214/16-AOS1536SUPP
, Nonnegative Matrix and Tensor Factorizations: Applications to Exploratory Multi-Way Data Analysis and Blind Source Separation, pp.1-477, 2009.
DOI : 10.1002/9780470747278
, Bayesian spatial modeling of genetic population structure, Computational Statistics, vol.52, issue.1, pp.111-129, 2008.
DOI : 10.1111/j.1469-1809.1949.tb02451.x
, (sept. 1993) Statistics for Spatial Data Wiley Series in Probability and Statistics
, On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life, 1859.
, Genomic Control for Association Studies, Biometrics, vol.280, issue.4, pp.31-73, 1999.
DOI : 10.1126/science.280.5366.1077
URL : http://www.stat.cmu.edu/%7Eroeder/publications/dev-roeder1999.pdf
, Multiple common variants for celiac disease influencing immune gene expression, Nature Genetics, vol.573, issue.4, pp.295-302, 2010.
DOI : 10.4049/jimmunol.170.8.3986
, Spatial Inference of Admixture Proportions and Secondary Contact Zones, Molecular Biology and Evolution, vol.38, issue.2, pp.1963-1973, 2009.
DOI : 10.1038/ng1702
, Cross-Validatory Choice of the Number of Components From a Principal Component Analysis, Technometrics, vol.80, issue.1, 1982.
DOI : 10.1016/S0021-9673(01)85348-6
, The approximation of one matrix by another of lower rank, Psychometrika, vol.1, issue.3
DOI : 10.1007/BF02288367
, Large-Scale Simultaneous Hypothesis Testing, Journal of the American Statistical Association, vol.99, issue.465, pp.96-104
DOI : 10.1198/016214504000000089
, Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis, PLoS Genetics, vol.81, issue.9
DOI : 10.1371/journal.pgen.1001117.s003
, Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics., Proceedings of the National Academy of Sciences 93, p.43, 1996.
DOI : 10.1073/pnas.93.19.10528
, Inference of Population Structure Using Multilocus Genotype Dat a: Linked Loci and Correlated Allele Frequencies, Genetics, vol.1644, pp.1567-1587, 2003.
, WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas, International Journal of Climatology, vol.23, issue.2, 2017.
DOI : 10.1007/s11442-013-1033-7
, Design of Experiments, BMJ, vol.1, issue.3923, 1937.
DOI : 10.1136/bmj.1.3923.554-a
, A Map of Local Adaptation in Arabidopsis thaliana, Science, vol.140, issue.5, 2011.
DOI : 10.1016/S0176-1617(11)81027-8
, Spatially explicit Bayesian clustering models in population genetics, In : Molecular Ecology Resources, vol.10, issue.32, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00655070
, Controlling false discoveries in genome scans for selection, Molecular Ecology, vol.38, issue.2, pp.454-469, 2016.
DOI : 10.1038/ng1702
, Waits (sept. 2015) Clustering and Assignment Methods in Landscape Genetics, Landscape Genetics, pp.114-128
, LEA: AnRpackage for landscape and ecological association studies In : Methods in Ecology and Evolution 6.8. Sous la dir, pp.925-929, 2015.
, Fast and Efficient Estimation of Individual Ancestry Coefficients, Genetics, vol.196, issue.4, pp.973-983
DOI : 10.1534/genetics.113.160572
URL : https://hal.archives-ouvertes.fr/hal-01119670
, Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models, Molecular Biology and Evolution, vol.44, issue.Database issue, p.52
DOI : 10.1038/ng.2310
URL : https://hal.archives-ouvertes.fr/hal-00861179
, Pathwise coordinate optimization, The Annals of Applied Statistics, vol.1, issue.2, pp.302-332, 2007.
DOI : 10.1214/07-AOAS131
URL : http://doi.org/10.1214/07-aoas131
, Regularization Paths for Generalized Linear Models via Coordinate Descent, Journal of Statistical Software, vol.33, issue.1, 2010.
DOI : 10.18637/jss.v033.i01
URL : https://doi.org/10.18637/jss.v033.i01
, A Factor Model Approach to Multiple Testing Under Dependence, Journal of the American Statistical Association, vol.104, issue.488, pp.1406-1415, 2009.
DOI : 10.1198/jasa.2009.tm08332
URL : https://hal.archives-ouvertes.fr/hal-00458049
, Empirical Bayes Shrinkage and False Discovery Rate Estimation, Allowing For Unwanted Variation, p.12, 2017.
, On the convergence of the block nonlinear Gauss???Seidel method under convex constraints, Operations Research Letters, vol.26, issue.3, pp.127-136, 2000.
DOI : 10.1016/S0167-6377(99)00074-7
, Estimating the location and shape of hybrid zones, Molecular Ecology Resources 11.6, pp.1119-1123, 2011.
DOI : 10.3390/ijms12020865
, Celiac disease: Prevalence, diagnosis, pathogenesis and treatment, World Journal of Gastroenterology, vol.18, issue.42, 2012.
DOI : 10.3748/wjg.v18.i42.6036
URL : http://doi.org/10.3748/wjg.v18.i42.6036
, Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions, SIAM Review, vol.53, issue.2, 2011.
DOI : 10.1137/090771806
, Adaptation to Climate Across the Arabidopsis thaliana Genome, Science, vol.11, issue.7, 2011.
DOI : 10.1105/tpc.11.7.1337
, Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models, Heredity, vol.31, issue.2, 1999.
DOI : 10.1038/hdy.1996.173
, The Elements of Statistical Learning Series in Statistics. issn : 2197-568X, 2009.
, Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel, Nature Genetics, vol.164, issue.2, pp.212-216, 2012.
DOI : 10.2307/2408641
, Fast and accurate genotype imputation in genomewide association studies through pre-phasing, Nature Genetics, vol.448, pp.955-959, 2012.
, Generating samples under a Wright-Fisher neutral model of genetic variation, Bioinformatics, vol.18, issue.2, 2002.
DOI : 10.1093/bioinformatics/18.2.337
, Principal Component Analysis " . In : Principal component analysis, pp.115-128, 1986.
, Gestion des données manquantes en analyse en composantes principales, Journal de la Société Française de Statistique 150, pp.28-51, 2009.
, Efficient Control of Population Structure in Model Organism Association Mapping, Genetics, vol.178, issue.3, 2008.
DOI : 10.1534/genetics.107.080101
, Learning the parts of objects by non-negative matrix factorization, 1999.
, Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis, PLoS Genetics, vol.3, issue.13, pp.53-69, 2007.
, DISTRIBUTION, Genetics, vol.741, pp.175-195, 1973.
, Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation, Science, vol.4, issue.7151, 2008.
DOI : 10.1038/nature05951
, Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis, Nature Biotechnology, vol.32, issue.2, pp.142-147, 2013.
DOI : 10.1186/gm301
, Mixed model association for biobank-scale data sets " . In : bioRxiv. doi : 10 eprint : https://www.biorxiv.org/content/ early, p.12, 1101.
DOI : 10.1101/194944
, The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog), Nucleic Acids Research, vol.26, issue.D1, 2016.
DOI : 10.1093/nar/gku1061
, Les mathématiques de l'hérédité, p.43, 1948.
, The detection of disease clustering and a generalized regression approach, Cancer research 27.2 Part 1, pp.209-220, 1967.
, The effects of human population structure on large genetic association studies, Nature Genetics, vol.4, issue.Suppl 1, 2004.
DOI : 10.1038/nrg1229
, Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics, Molecular Ecology, vol.2520, pp.5029-5042, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01432547
, Spectral Regularization Algorithms for Learning Large Incomplete Matrices, Journal of machine learning research 11, pp.2287-2322, 2010.
, The Ensembl Variant Effect Predictor
, Low-Rank Optimization with Trace Norm Penalty, SIAM Journal on Optimization, vol.23, issue.4, pp.2124-2149, 2013.
DOI : 10.1137/110859646
URL : https://hal.archives-ouvertes.fr/hal-00924110
, Genes mirror geography within Europe, Nature, vol.81, issue.7218, pp.274-274, 2008.
DOI : 10.1038/nature07331
URL : http://europepmc.org/articles/pmc2735096?pdf=render
, A Novel and Fast Approach for Population Structure Inference Using Kernel-PCA and Optimization, Genetics, vol.198, issue.4, pp.1421-1431
DOI : 10.1534/genetics.114.171314
, Principal components analysis corrects for stratification in genome-wide association studies, Nature Genetics, vol.15, issue.8, pp.904-909, 2006.
DOI : 10.1111/j.1469-1809.1949.tb02451.x
, Inference of population structure using multilocus genotype data, Genetics, vol.1552, pp.945-959, 2000.
, PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, The American Journal of Human Genetics, vol.81, issue.3, 2007.
DOI : 10.1086/519795
, Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies, Nature Methods, vol.13, issue.5, pp.443-445
DOI : 10.1093/bioinformatics/btu049
, fastSTRUC- TURE: Variational Inference of Population Structure in Large SNP Data Sets, Genetics, vol.1972, issue.21, pp.573-589
, Epigenome-wide association studies for common human diseases, Nature Reviews Genetics, vol.14, issue.8, pp.529-541, 2011.
DOI : 10.1038/sj.ejhg.5201538
URL : http://europepmc.org/articles/pmc3508712?pdf=render
, Fast spatial ancestry via flexible allele frequency surfaces, Bioinformatics, vol.3020, pp.2915-2922
, A practical guide to environmental association analysis in landscape genomics, Molecular Ecology, vol.22, issue.17, pp.4348-4370, 2015.
DOI : 10.1111/mec.12199
, The Bayesian Bootstrap, The annals of statistics 9.1, pp.130-134, 1981.
DOI : 10.1214/aos/1176345338
, The interpretation of interaction in contingency tables, Journal of the Royal Statistical Society. Series B, issue.1, pp.238-241, 1951.
, From patterns to pathways: gene expression data analysis comes of age, Nature Genetics, vol.32, issue.Supp, 2002.
DOI : 10.1038/ng1033
, Testing for genetic associations in arbitrarily structured populations, Nature Genetics, vol.475, pp.550-554
, False Discovery Rates: a New Deal, 2016.
, False Discovery Rate, In : International Encyclopedia of Statistical Science, pp.504-508978, 2011.
DOI : 10.1007/978-3-642-04898-2_248
, Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data, The Annals of Applied Statistics, vol.6, issue.4
DOI : 10.1214/12-AOAS561
, Estimation of individual admixture: Analytical and study design considerations In : Genetic Epidemiology 28, pp.289-301, 2005.
, Regression shrinkage and selection via the lasso, Journal of the Royal Statistical Society. Series B, vol.59, pp.267-288, 1996.
, The Genetic Structure and History of Africans and African Americans, Science, vol.105, issue.3, pp.1035-1044, 2009.
DOI : 10.1073/pnas.0510792103
, Convergence of a Block Coordinate Descent Method for Nondifferentiable Minimization, Journal of Optimization Theory and Applications, vol.109, issue.3, pp.475-494, 2001.
DOI : 10.1023/A:1017501703105
, Confounder adjustment in multiple hypothesis testing, The Annals of Statistics, vol.45, issue.5, pp.1863-1894, 2017.
DOI : 10.1214/16-AOS1511SUPP
, Genetic Data Analysis II., Biometrics, vol.53, issue.1, pp.445-0878939024, 1996.
DOI : 10.2307/2533134
, Cross-Validatory Estimation of the Number of Components in Factor and Principal Components Models, Technometrics, vol.35, issue.4, pp.397-405, 1978.
DOI : 10.1016/S0021-9673(01)85348-6
, Detecting individual ancestry in the human genome, Investigative Genetics, vol.156, issue.1, 2015.
DOI : 10.1534/genetics.112.139808
, No free lunch theorems for optimization, IEEE Transactions on Evolutionary Computation, vol.1, issue.1, 1997.
DOI : 10.1109/4235.585893
URL : http://www.cs.ubc.ca/~hutter/earg/papers07/00585893.pdf
, Pitfalls of predicting complex traits from SNPs, Nature Reviews Genetics, vol.43, issue.7, pp.507-515, 2013.
DOI : 10.1038/ng.823
, A model-based approach for analysis of spatial structure in genetic data, Nature Genetics, vol.74, issue.6, pp.725-731, 2012.
DOI : 10.1006/geno.2000.6331
, Efficient multivariate linear mixed model algorithms for genome-wide association studies, Nature Methods, vol.54, issue.4, pp.407-409
DOI : 10.1017/S0016672309000111
URL : http://europepmc.org/articles/pmc4211878?pdf=render
, Sparse multivariate factor analysis regression models and its applications to integrative genomics analysis, Genetic Epidemiology, vol.67, issue.1, 2016.
DOI : 10.1111/j.1467-9868.2005.00503.x
, Epigenome-wide association studies without the need for cell-type composition, Nature Methods, vol.3, issue.3, pp.79-82, 2014.
DOI : 10.1038/nprot.2008.211
, TESS3 : fast inference of spatial population structure and genome scans for selection, Molecular Ecology Resources, vol.16, issue.2, pp.540-548, 2016.
, Fast Inference of Individual Admixture Coefficients Using Geographic Data. Accepted to The Annals of Applied Statistics, 2017.
, Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics, Molecular Ecology, vol.49, issue.20, pp.5029-5042, 2016.
DOI : 10.1111/j.1365-313X.2006.02994.x
, Algorithmes Pour l'Estimation des Coefficients de Métissage dans des Populations Continues Spatialement, 48èmes Journées de Statistique de la SFdS, pp.30-33, 2016.
, tess3r : étude du jeu de données Arabidopsis thaliana RegMap, Cinquièmes Rencontres R, pp.22-24, 2016.
, tess3r : un package R pour l'estimation de la structure génétique des populations spatialisées, 2016.