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Omar Cornejo

Omar E Cornejo

Field of Study: Population and Evolutionary Genomics
Title: Assistant Professor
Degrees: PhD. Biological and Biomedical, Emory University
Homepage: Homepage/Lab Web Site Link
Google Scholar:  Google Scholar
Office: 429B Heald Hall
Phone: 509-335-0179
Fax: nan
Mailing Address: School of Biological Sciences
Washington State University
PO Box 644236
Pullman,WA 99164-4236


Our ability to understand how pathogens and hosts have adapted to each other, requires a deep understanding of how basic evolutionary processes that have shaped the genetic architecture of these organisms. In my research, we use a multidisciplinary approach that combines computational biology, population genetic/genomic analyses, phylogenetics, simple mathematical modeling, and wet lab experiments to address these issues. Developing a better understanding of the forces shaping the genetic architecture of organisms will have enormous implications on the design of strategies for the management of populations and species of interest.

We are interested in the inference of the evolutionary history of populations and how genomic data can be used to learn. We apply these methods to answer questions in different systems: i) Humans; ii) Bacteria; iii) Malarial parasites; and iv) Plants. Yet the questions addressed in these systems are similar in nature. Some of the questions we address in our research are:

I. How important is homologous recombination for the evolution of traits involved in host shifts or adaptation to new environments?

ii. During which stages of the complex life cycle of organisms do we expect to find hotspots of adaptation?

iii. How has the demographics impacts the accumulation of deleterious mutations, impacting the fitness of individuals

iv. What is the demographic (population decline/growth) and selection scenario (selection coefficient, mode of selection and initial frequency) that explains the evolution of adaptive variants in populations. This question is especially important while trying to understand the evolution of disease resistance mechanisms and the evolution of virulence factors

We are experts in the generation and analysis of next generation sequencing data and we provide a great learning environment for students and postdocs with a quantitative inclination.

If interested in any of these topics, do not hesitate in contacting me at to discuss possibilities to join the lab.

Representative Publications:

  • Osorio J, Quackenbush CR, Cornejo O.E. (2018) Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLOS One 13(10): e0203973.
  • Cornejo OE, Yee M-C, Mockaitis K, Adams A, Strandberg R, Livingston D, Stack C, Umaharan P, Royaert S, Tawari NR, Ng P, Schnell R, Phillips W, Bustamante CD, Motamayor JC. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into the domestication process. Communications Biology 1. Article number: 167(2018)
  • Xia, C., Wang, M., Cornejo, O.E., Jiwan, D.A., See, D.R., Chen, X. (2017). Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Frontiers in Microbiology 2017;00-12. doi: 10.3389/fmicb.2017.02394.
  • Livingstone III, D., Stack, C., Mustiga, G., Rodezno, D., Suarez, C., Amores, F., Feltus, A., Mockaitis, K., Cornejo, O.E., Motamayor, JC. (2017). A large chocolate chip – development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps. Frontiers in Plant Science 8:2008.
  • Cornejo OE*, Hickey RJ, Suzuki H, Forney LJ*. (2017). Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes. Evolutionary Applications 2017;00:1–13.
  • McManus KF, Tavarella A, Henn B, Bustamante CD, Sikora M*, Cornejo OE*. (2017) Population genetic analysis of the DARC locus (Duffy) reveals complex evolutionary history of a malaria resistance locus. PLOS Genetics 13(3): e1006560. doi:10.1371/journal.pgen.1006560. (Highlighted in Science, Mar 2017: Dramatic evolution within human genome may have been caused by malaria parasite)
  • Cornejo OE, Fisher D, Escalante AA. (2015) Genome-wide patterns of genetic polymorphism and signatures of selection in Plasmodium vivax. Genome Biology and Evolution. 7(1): 106-119. (Highlighted in Nature Reviews Microbiology in the News and Analysis – Genome Watch section, March 2015)
  • Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T Jr, Grimes V, Renouf MA, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TV, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O’Rourke DH, Jakobsson M, Gilbert MT, Nielsen R, Willerslev E. (2014) The genetic prehistory of the New World Arctic. Science. 345 (6200) DOI: 10.1126/science.1255832
  • Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506 (7487): 225 – 229 doi:10.1038/nature13025
  • Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. (2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution. 30(4): 881-893. [Highlighted in Science: “How Sweet it is: genes show how bacteria colonized human teeth” by Ann Gibbons]