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BCM - Computational and Mathematical Biology  

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Luu K, E Bazin, MGB Blum. pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources 1:67-77 (2017)

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Lotterhos KE, O François, MGB Blum. Not just methods: User expertise explains the variability of outcomes of genome-wide studies. biorXiv:10.1101/055046 (2016) The website to increase your expertise in genome scans for selection

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Martins H, K Caye, K Luu, MGB Blum, O François. Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Molecular Ecology 25:5029–5042 (2016)

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Lemaire L, F Jay, I-Hung Lee, K Csilléry, MGB Blum. Goodness-of-fit statistics for approximate Bayesian computation. ArXiv:1601.04096 (2016)

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Bertl J, MGB Blum. Can secondary contact following range expansion be distinguished from barriers to gene flow? biorXiv:10.1101/043398 (2016)

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Trémeaux P, A Caporossi, MA Thélu, M Blum, V Leroy, P Morand, S Larrat. Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges. Critical reviews in clinical laboratory sciences 53:1-11 (2016)

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Duforet-Frebourg N, K Luu, G Laval, E Bazin, MGB Blum. Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular Biology and Evolution, 33:1082-1093 (2016)

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Besleaga T, M Blum,  R. Briot, V Vovc, I Moldovanu, P Calabrese. Individuality of breathing during volitional moderate hyperventilation. Eur J Appl Physiol, 116:217-225 (2016)

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Jay F, O François, EY Durand, MGB Blum. POPS: A Software for Prediction of Population Genetic Structure Using Latent Regression Models. J Stat Softw, 68 (2015) POPS webpage

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Duforet-Frebourg N,  LM Gattepaille, MGB Blum,  M Jakobsson. HaploPOP: a software that improves population assignment by combining markers into haplotypes. BMC Bioinformatics, 16:242 (2015)

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Merker M, C Blin, S Mona , N Duforet-Frebourg , S Lecher, E Willery, M Blum, S Rüsch-Gerdes et al., T Wirth. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nature Genetics, 47: 242-249 (2015)

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Larrat S, O Kulkarni, JB Claud, R Beugnot, MGB Blum, K Fusillier, J Lupo, P Tremeaux, A Plages, A Marlu, H Duborjal, A Signori-Schmuck, O François, JP Zarski, P Morand, V Leroy (2014). Ultra-deep pyro-sequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients. J Clin Microbiol, 53: 389-397 (2015)

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Karakachoff M, N Duforet-Frebourg, F Simonet, S Le Scouarnec, N Pellen, S Lecointe, E Charpentier, F Gros, SCauchi, P Froguel, N Copin, the D.E.S.I.R. Study Group, T Le Tourneau, V Probst, H Le Marec, S Molinaro, B Balkau, R Redon, J-J Schott, MGB Blum, C Dina.  Fine-scale human genetic structure in Western France. European Journal of Human Genetics, 23:831-836 (2014)

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Duforet-Frebourg N, E Bazin, MGB Blum. Genome scans for detecting footprints of local adaptation using a Bayesian factor model. Molecular Biology and Evolution, 31:2483-2495 (2014) PCAdapt software

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Prangle D, MGB Blum, G Popovic, SA Sisson. Diagnostic tools of approximate Bayesian computation using the coverage property. Australia and New Zealand Journal of Statistics, 56: 309-329 (2014)

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Duforet-Frebourg N, MGB Blum. Non-stationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging. Evolution, 68: 1110-1123 (2014)

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Gattepaille LM, M Jakobsson, MGB Blum. Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity 110: 409-419 (2013)

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Jay F, P Sjödin, M Jakobsson, MGB Blum. Anisotropic isolation by distance: the main orientations of human genetic differentiation. Molecular Biology and Evolution 30: 513-525 (2013)
Front cover of mbe

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Blum MGB, MA Nunes, D Prangle, SA Sisson. A comparative review of dimension reduction methods in approximate Bayesian computation. Statistical Science, 28: 189-208 (2013)

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Schlebusch CM, P Skoglund, P Sjödin, LM Gattepaille, D Hernandez, F Jay, S Li, M De Jongh, A Singleton, MGB Blum, H Soodyall, M Jakobsson. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338: 374-379 (2012)

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Ben Khelifa M, C Coutton, MGB Blum, 25 co-authors, PF Ray. Identification of a new recurrent Aurora kinase C mutation in both European and African men with macrozoospermia. Human reproduction, 27: 3337-3346 (2012)

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Blum MGB, O François. Discussion on "Constructing summary statistics for ABC: semi-automatic ABC" written by P Fearnhead and D Prangle. Journal of the Royal Statistical Society : Series B 74:454 (2012)

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Sjödin P, AE Sjöstrand, M Jakobsson, MGB Blum. Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period. Molecular Biology and Evolution 29:1851-1860 (2012) Supp Mat

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Csilléry K, O François, MGB Blum. abc: an R package for Approximate Bayesian Computation (ABC). Methods in Ecology and Evolution 3: 475-479 (2012)

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Jay F, MGB Blum, E Frichot, O François. Modèles à variables latentes en génétique des populations. Journal de la société française de statistique 152:3-20 (2011)

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Jay F, O François, MGB Blum. Predictions of Native American Population Structure Using Linguistic Covariates in a Hidden Regression Framework. PLoS ONE 6: e16227 (2011)
 
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Blum MGB, M Jakobsson. Deep divergences of human gene trees and models of human origins. Molecular Biology and Evolution, 28: 889-898 (2011)
Featured by Faculty of 1000.
There is also a press release from the CNRS,
and a Web article in the French journal Pour La Science.
 
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Blum MGB Approximate Bayesian Computation: a nonparametric perspective. Journal  of the American Statistical Association, 105: 1178-1187, Supp Mat 1, Supp Mat 2 (2010)
 
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Blum MGB, V-C Tran.  HIV with contact tracing: a case study in Approximate Bayesian Computation. Biostatistics, 11: 644-660 (2010)

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Blum MGB Choosing the Summary Statistics and the Acceptance Rate in Approximate Bayesian Computation. In COMPSTAT 2010-Proceedings in Computational Statistics, ed. G. Saporta, Y. Lechevallier.  Springer, Physica Verlag pp 47-56 (2010)
 
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Csilléry K, MGB Blum,  OE Gaggiotti, O François. Approximate Bayesian Computation in practice. Trends in Ecology & Evolution, 25: 410-418 (2010)
 
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Csilléry K., MGB Blum,  OE Gaggiotti, O François. Invalid arguments against ABC: A reply to AR Templeton. Trends in Ecology & Evolution, 25: 490-491 (2010)
 
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Blum MGB, O François. Non-linear regression models for Approximate Bayesian Computation.
Statistics and Computing, 20: 63-73  (2010).
Supporting Information.
R code
2 Examples in R: Parameter estimation; Model selection
Now implemented in the abc R package
 

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Naderi S, H-R Rezaei, F Pompanon, MGB Blum, R Negrini, H-R Naghash, O Balkız, M Mashkour, O Gaggiotti, P Ajmone-Marsan, A Kence, J-D Vigne, P Taberlet. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proceedings of the National Academy of Sciences, 105: 17659-64 (2008)
A digest of the paper can be found in the CNRS website
 
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Forhan G, J-L Martiel, MGB Blum. A deterministic model of admixture and genetic introgression: The case of Neanderthal and Cro-Magnon. Mathematical Biosciences, 216:71-76 (2008)
 
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François O, MGB Blum, M Jakobsson, NA Rosenberg. Demographic history of European populations of Arabidopsis Thaliana. PLoS Genetics 4(5)(2008)
A report in the CNRS website about this work
 

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Durand E, MGB. Blum and O François. Prediction of group patterns in social mammals based on a coalescent model. Journal of Theoretical Biology 249: 262-270 (2007)
 
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Blum MGB and NA Rosenberg. Estimating the number of ancestral lineages using a maximum likelihood method based on rejection sampling. Genetics 176: 1741-1747 (2007).
 
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Rosenberg NA and MGB Blum. Sampling properties of homozygosity-based statistics for linkage disequilibrium. Mathematical Biosciences 208: 33-47 (2007).
 
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Mooers A.O., L. J. Harmon, M. G. B. Blum, D. H. J. Wong and S.B. Heard. Some models of phylogenetic tree shape in Reconstructing Evolution: new mathematical and computational advances (O. Gascuel and M. Steel, eds.), Oxford University Press, Oxford (2007).
 
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Rosenberg N. A., S. Mahajan, C. Gonzalez-Quevedo, M. G. B. Blum, L. Nino-Rosales, V. Ninis, P. Das, M. Hegde, L. Molinari, G. Zapata, J. L. Weber, J. W. Belmont and P. I. Patel. Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India. PLoS Genetics 2: 2052-2061 (2006).
 
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Blum MGB , O.François and S. Janson. The mean, variance and joint distribution of two statistics sensitive to phylogenetic tree balance. Annals of Applied Probability 16: 2195-2214 (2006).
 
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Blum MGB, E Heyer, O François and F Austerlitz. Matrilineal fertility inheritance detected in hunter-gatherer populations using the imbalance of gene genealogies. PLoS Genetics, 2:1138-1146 (2006).
 
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Blum MGB and O François. Which random processes describe the Tree of Life? A large-scale study of phylogenetic tree imbalance. Systematic Biology 55: 685-691 (2006). Supplementary Material
 
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Blum MGB and O François. On statistical tests of phylogenetic imbalance: the Sackin and other indices revisited. Mathematical Biosciences, 195: 141-153 (2005).
 
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Blum MGB and O Francois. External branch length and minimal clade size under the neutral coalescent. Advances in Applied Probability, 37: 647-662 (2005).
 
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Bortolussi N , E Durand, M Blum, O Francois. APTreeshape: Statistical analysis of phylogenetic tree shape. Bioinformatics, 22: 363-364 (2005).
 
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Blum MGB, C Damerval , S Manel and O François. Brownian models and coalescent structures. Theoretical Population Biology 65: 249-261, 2004.
 
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HDR/PhD

Statistique bayésienne et applications en génétique des populations. Manuscrit d'HDR, 2012
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De la forme des généalogies en phylogénie et génétique des populations. Manuscrit de thèse, 2005.
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