I am interested in understanding the evolutionary history of organisms (specially, but not limited to, microorganisms) and how selection, mutation and recombination shape genomic variation. Some of the questions addressed in my lab are: ii) Can we understand from retrospective genomic analysis the demographic history of (micro)organisms and identify candidate genes that might have been involved in their adaptation to their current niche (either host or environment)? In the case of pathogenic microorganisms, these questions are interesting not only from a pure population genetic perspective but also have a strong link with health-related problems. ii) What ecological and evolutionary scenarios can explain the maintenance of toxic agents that kill organisms that produce them? It is a fascinating question that can be addressed with a combination of mathematical modeling, experimentation and molecular techniques and could lead to the discovery and perhaps better understanding of anti-bacterial agents. iii) What are the genetic basis of phenotypic variation in complex traits like disease susceptibility in organisms with very distinct genomic architectures like Theobroma cacao or humans.
Motamayor, J.C., Mockaitis, K., Schmutz, j., Haiminen, N.,
Livingstone, D., Cornejo O.E., Findley, S., Zheng, P., Utro, F.,
Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M.,
Scheffer, B., Feltus, A., Gutierrez, O., Amores, F., Phillips, W.,
Marelli, J.P., May, G.D., Bretting, P., Shapiro, H., Ma, J.,
Bustamante, C.D., Schnell, R.J., Main, D., Gilbert, D., Parida, L.,
and Kuhn, D.N. (2013) The genome sequence of the most cultivated
cacao type and its use in the mapping of oligogenic traits: pod
color as an example. Genome Biology (June 3rd)
Cornejo, O.E., Lefébure, T., Pavinski-Bitar, P.D., Lang, P., Richards, V.P., Eilertson, Do, T., K., Beighton, D., Zeng,L., Ahn, S-J, Burne, R.A., Siepel, A.C., Bustamante, C.D., and M. Stanhope. (2013). Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution 30 (4): 881-893 (Highlighted in Science vol 339 no. 6122 pp. 896-897: "How Sweet It Is: Genes Show How Bacteria Colonized Human Teeth", Ann Gibbons)
Utro, F., Cornejo, O.E., Livingstone, D., Motamayor, J.C., and Parida, L. (2012). ARG-Based genome-wide analysis of cacao cultivars. BMC Bioinformatics 13 (Supp19): S17.
Dewey F., Chen, R., Cordero, S., Ormond, K., Caleshu, C., Karczewski, K., Carrillo, M., Wheeler, M., Dudley, J., Byrnes, J., Cornejo, O.E., Knowles, J., Woon, M., Sungkuhl, K., Gong, L., Thorn, C., Hebert, J., Capriotti, E., David, S., Pavlovic, A., West, A., West, J., Thakuria, J., Ball, M., Zaranek, A., Rehm, H., Church, G., Bustamante, C.D., Snyder, M., Altman, R., Klein, T., Butte, A., and E. Ashley. (2011). Phased whole genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics 7(9): e1002280. doi:10.1371/journal.pgen.1002280
Cornejo, O.E., McGee, L., and Rozen, D.E. 2010. Polymorphism in the competence peptide does not limit recombination in Streptococcus pneumoniae. Molecular Biology and Evolution 27: 694-702.
Levin BR, Cornejo, O.E. (2009). The Population and Evolutionary Dynamics of Homologous Gene Recombination in Bacteria. PLoS Genetics 5(8): e1000601. doi:10.1371/journal.pgen.1000601.
Cornejo, O.E., Rozen, D.E., May, R.M., and Levin, B.R. (2009). Oscillations in Continuous Culture Populations of Streptococcus pneumoniae: Population Dynamics and the Evolution of Clonal Suicide. Proceedings of the Royal Society, London. B series, 276(1659):999-1008.
Cornejo, O.E., and Escalante, AA. (2006). The origin and age of Plasmodium vivax. Trends in Parasitology, 22(12): 558-563.