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Statistical and Population Genomics

Our interests are to combine the development of methods / software with analyzing real data, both from a population genetics point of view and QTL / association analysis. The research goals are the following:

Development of statisitcal methods and software. We study statistical methodologies to take advantage of the high throughput technologies, focusing on the search of the genetic causes of traits of interest (e.g., domestication traits). We develop statistical tests to detect extreme patterns of variation and software focus in the analysis of variability and in QTL /association analysis.

Analysis of genomic data in Sus scrofa We have been interested in the study of empirical data, starting from single-locus strategies based on candidate genes to the analysis of genome-wide data using different sequencing and sampling strategies, in order to understand the patterns of the observed variability in Sus scrofa. We explore methods to combine external information (e.g., metabolic pathways, interactome) with nucleotide diversity statistics to explore potential selective sweeps using a holistic rather than gene by gene approach.

Selected Publications

Pérez-Enciso, M. 2003

Fine mapping of complex trait genes combining pedigree and linkage disequilibrium information: A Bayesian unified framework

Genetics. 163: 1497-1510

 

Pérez-Enciso, M._, Misztal, I. 2004

Qxpak: A versatile mixed model application for genetical genomics and QTL analyses

Bioinformatics 20:2792-2798

 

Esteve-Codina A, R. Kofler, H. Himmelbauer L. Ferretti, A.P. Vivancos, M.A.M. Groenen, J.M. Folch, M.C. Rodríguez, M. Pérez-Enciso. 2011

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

Heredity, 107: 256-64

 

Amaral AJ, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MAM. 2011

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA

Plos One, 2011 Apr 4:e14782

 

Groenen, M. A., A. L. Archibald, H. Uenishi, C. K. Tuggle, Y. Takeuchi, M. F. Rothschild, C. Rogel-Gaillard, C. Park, D. Milan, H. J. Megens, S. Li, D. M. Larkin, H. Kim, L. A. Frantz, M. Caccamo, H. Ahn, B. L. Aken, A. Anselmo, C. Anthon, L. Auvil, B. Badaoui, C. W. Beattie, C. Bendixen, D. Berman, F. Blecha, J. Blomberg, L. Bolund, M. Bosse, S. Botti, Z. Bujie, M. Bystrom, B. Capitanu, D. Carvalho-Silva, P. Chardon, C. Chen, R. Cheng, S. H. Choi, W. Chow, R. C. Clark, C. Clee, R. P. Crooijmans, H. D. Dawson, P. Dehais, F. De Sapio, B. Dibbits, N. Drou, Z. Q. Du, K. Eversole, J. Fadista, S. Fairley, T. Faraut, G. J. Faulkner, K. E. Fowler, M. Fredholm, E. Fritz, J. G. Gilbert, E. Giuffra, J. Gorodkin, D. K. Griffin, J. L. Harrow, A. Hayward, K. Howe, Z. L. Hu, S. J. Humphray, T. Hunt, H. Hornshoj, J. T. Jeon, P. Jern, M. Jones, J. Jurka, H. Kanamori, R. Kapetanovic, J. Kim, J. H. Kim, K. W. Kim, T. H. Kim, G. Larson, K. Lee, K. T. Lee, R. Leggett, H. A. Lewin, Y. Li, W. Liu, J. E. Loveland, Y. Lu, J. K. Lunney, J. Ma, O. Madsen, K. Mann, L. Matthews, S. McLaren, T. Morozumi, M. P. Murtaugh, J. Narayan, D. T. Nguyen, P. Ni, S. J. Oh, S. Onteru, F. Panitz, E. W. Park, H. S. Park, G. Pascal, Y. Paudel, M. Perez-Enciso, R. Ramirez-Gonzalez, J. M. Reecy, S. Rodriguez-Zas, G. A. Rohrer, L. Rund, Y. Sang, K. Schachtschneider, J. G. Schraiber, J. Schwartz, L. Scobie, C. Scott, S. Searle, B. Servin, B. R. Southey, G. Sperber, P. Stadler, J. V. Sweedler, H. Tafer, B. Thomsen, R. Wali, J. Wang, S. White, X. Xu, M. Yerle, G. Zhang, J. Zhang, S. Zhao, J. Rogers, C. Churcher and L. B. Schook (2012)

"Analyses of pig genomes provide insight into porcine demography and evolution."

Nature 491:393-8

 

Ferrettii, L, Ramos-Onsins, S.E., Pérez-Enciso, M. 2013

Population genomics from pool sequencing

Mol. Ecol. In press

 

Ferretti L, Raineri E, Ramos-Onsins S.

Neutrality tests for sequences with missing data

Genetics. 2012 Aug;191(4):1397-401. doi:

 

Heidel AJ, Ramos-Onsins SE, Wang WK, Chiang TY, Mitchell-Olds T.

Population history in Arabidopsis halleri using multilocus analysis

Mol Ecol. 2010

 

Ferretti L, Perez-Enciso M, Ramos-Onsins S.

Optimal neutrality tests based on the frequency spectrum

Genetics. 2010 Sep;186(1):353-65. doi: