Statistical and Population Genomics

Group Structure

Group Leader: Miguel Pérez Enciso (ICREA Research Professor)
Researchers: Sebastián Ramos Onsins
Postdoctoral Researchers: Luca Ferretti (until Nov 2012), Bruno Nevado
PhD Students: William Orlando Burgos, Erica Bianco, Elizabete Da Silva (since April 2013), Anna Esteve (until October 2012)
Undergrad or Master Students: Eduard Casas (2013)

Summary

Our interests are to combine the development of methods and software with analyzing real data, both from a population genetics point of view and in experimental crosses, to identify the loci responsible for complex variation in domestic animals and plants. We focus on the pig as a model of domestic species, and we participated in the international consortium leading to pig genome sequence (Nature, 2012). We have developed statistical methodologies to take advantage of the high throughput technologies for classical problems in genetics, like understanding of the main mechanisms that shape the variability among the individuals, and which are the effects of domestication and modern selection on this variability.

Research Projects

  • Development of algorithms and statistical methods for population genomics
  • Development of software for the genome analysis of natural and domesticated populations using NGS data.
  • Analysis of the genome variability on Domesticated Populations.
  • Study the advantages of using complete sequence for genetic improvement.
  • Population genetics of village pigs in the Americas.
  • Genomewide, worldwide characterization of variation in the pig.

Selected Publications

Ferretti L., Raineri E., Ramos-Onsins S.
Neutrality tests for sequences with missing data.
(2012) Genetics, vol. 191 (4), pp. 1397-1401

Groenen M.A.M., Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., Rothschild M.F., Rogel-Gaillard C., Park C., Milan D., Megens H.-J., Li S., Larkin D.M., Kim H., Frantz L.A.F., Caccamo M., Ahn H., Aken B.L., Anselmo A., Anthon C., Auvil L., Badaoui B., Beattie C.W., Bendixen C., Berman D., Blecha F., Blomberg J., Bolund L., Bosse M., Botti S., Bujie Z., Bystrom M., Capitanu B., Carvalho-Silva D., Chardon P., Chen C., Cheng R., Choi S.-H., Chow W., Clark R.C., Clee C., Crooijmans R.P.M.A., Dawson H.D., Dehais P., De Sapio F., Dibbits B., Drou N., Du Z.-Q., Eversole K., Fadista J., Fairley S., Faraut T., Faulkner G.J., Fowler K.E., Fredholm M., Fritz E., Gilbert J.G.R., Giuffra E., Gorodkin J., Griffin D.K., Harrow J.L., Hayward A., Howe K., Hu Z.-L., Humphray S.J., Hunt T., Hornshooj H., Jeon J.-T., Jern P., Jones M., Jurka J., Kanamori H., Kapetanovic R., Kim J., Kim J.-H., Kim K.-W., Kim T.-H., Larson G., Lee K., Lee K.-T., Leggett R., Lewin H.A., Li Y., Liu W., Loveland J.E., Lu Y., Lunney J.K., Ma J., Madsen O., Mann K., Matthews L., McLaren S., Morozumi T., Murtaugh M.P., Narayan J., Nguyen D.T., Ni P., Oh S.-J., Onteru S., Panitz F., Park E.-W., Park H.-S., Pascal G., Paudel Y., Perez-Enciso M., Ramirez-Gonzalez R., Reecy J.M., Rodriguez-Zas S., Rohrer G.A., Rund L., Sang Y., Schachtschneider K., Schraiber J.G., Schwartz J., Scobie L., Scott C., Searle S., Servin B., Southey B.R., Sperber G., Stadler P., Sweedler J.V., Tafer H., Thomsen B., Wali R., Wang J., Wang J., White S., Xu X., Yerle M., Zhang G., Zhang J., Zhang J., Zhao S., Rogers J., Churcher C., Schook L.B.
Analyses of pig genomes provide insight into porcine demography and evolution.
(2012) Nature, vol. 491 (7424), pp. 393-398

Quevedo J.R., Bahamonde A., Perez-Enciso M., Luaces O.
Disease liability prediction from large scale genotyping data using classifiers with a reject option.
(2012) IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9 (1), pp. 88-97.

Raineri E., Ferretti L., Esteve-Codina A., Nevado B., Heath S., Perez-Enciso M.
SNP calling by sequencing pooled samples.
(2012) BMC Bioinformatics, vol. 13 (1), number 239

Burgos-Paz W., Souza C.A., Castello A., Mercade A., Okumura N., Sheremet’Eva I.N., Huang L.S., Cho I.C., Paiva S.R., Ramos-Onsins S., Perez-Enciso M.
Worldwide genetic relationships of pigs as inferred from X chromosome SNPs
(2013) Animal Genetics, vol. 44 (2), pp. 130-138

Burgos-Paz W., Souza C.A., Megens H.J., Ramayo-Caldas Y., Melo M., Lemus-Flores C., Caal E., Soto H.W., Martinez R., Alvarez L.A., Aguirre L., Iniguez V., Revidatti M.A., Martinez-Lopez O.R., Llambi S., Esteve-Codina A., Rodriguez M.C., Crooijmans R.P.M.A., Paiva S.R., Schook L.B., Groenen M.A.M., Perez-Enciso M.
Porcine colonization of the Americas: A 60k SNP story.
(2013) Heredity, vol. 110 (4), pp. 321-330

Esteve-Codina A., Paudel Y., Ferretti L., Raineri E., Megens H.-J., Silio L., Rodriguez M.C., Groenen M.A.M., Ramos-Onsins S.E., Perez-Enciso M.
Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.
(2013) BMC Genomics, vol. 14, Art. number 148
Ferretti L., Ramos-Onsins S.E., Perez-Enciso M.
Population genomics from pool sequencing.
(2013) Molecular Ecology, vol 22 (22), pp. 5561-5576

Perez-Enciso M.
Future implications of full-scale genomics for animal breeding: Personalized indices?
(2013) Journal of Animal Breeding and Genetics, vol. 130 (1), pp. 2-3

Segura J., Ferretti L., Ramos-Onsins S., Capilla L., Farre M., Reis F., Oliver-Bonet M., Fernandez-Bellon H., Garcia F., Garcia-Caldes M., Robinson T.J., Ruiz-Herrera A.
Evolution of recombination in eutherian mammals: Insights into mechanisms that affect recombination rates and crossover interference.
(2013) Proceedings of the Royal Society B: Biological Sciences, vol. 280 (1771), Art. number 20131945