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Population Genomics of microorganisms and their hosts in health and disease

Population Genomics of Microorganisms and their Hosts


I am glad you are interested in our lab! If you have landed here, please visit our new website. We have moved to the Ecology and Evolutionary Biology Department at UC Santa Cruz!

Thank you!


Understanding how adaptation impacts organismal health and disease requires understanding how evolutionary processes have shaped host and microbe genomes. In our lab we study how natural selection allows microbes to adapt to their hosts and how hosts develop disease resistance. We focus on the evolutionary context under which selection drives the gain or loss of important genetic variants using study systems in humans, microbiomes, malarial parasites, and plants.

Some of the questions we address in our research are:
  • How have historical changes in host populations impacted the evolution of their dependent species?
  • How do differences in microbiome composition modulate phenotypes in hosts?
  • How important is homologous recombination for the evolution of traits which allow for species to change hosts or environments?
  • How do demographics impact the accumulation of deleterious mutations in a population, and ultimately the fitness of individuals?


Our work requires a multidisciplinary approach that combines computational biology, population genetic/genomic analyses, phylogenetic reconstructions, functional genomics, mathematical modeling, and wet lab experiments to address these issues.  Some of the questions currently addressed in our lab can be more thoroughly explored in our Current Research. If you are interested in any of these research topics do not hesitate to contact me.

Lab mission:

To address complex biological questions in an inclusive and supportive environment that cultivates curious, productive, and collaborative scientists

Diversity & Inclusion Statement

In the Cornejo lab we are committed to maintaining and promoting an inclusive environment that motivates and supports all people. We understand that diversity goes beyond a collection of labels and we provide a flexible, supportive, and safe environment by focusing on the whole person as an individual and responding to their needs. As a Latino academic, I believe in the inherent fluidity of the labels that are imposed to us – as Latinos, we are many things and yet labeled under the same 6 letters. ‘Latino’, like all labels, is a convenient category but fails to capture the underlying richness of our lives which our lab actively embraces and enjoys. Our lab values the individual first, without regards to gender, sex, ethnicity, socioeconomic background, immigration status, religion, mental or physical disabilities, and educational backgrounds. We know that diversity is a contributing factor to the success of any human intellectual endeavor. Our lab thrives when there are multiple perspectives, voices, and diverse approaches to drive innovation and facilitate scientific discovery.

News of interest


Are host genetics involved in the evolution of their microbiomes? This is a controversial question at the moment. We are collaborating with Tomas Marques-Bonet at Universitat Pompeu Fabra to investigate the changes in the vaginal microbial composition of primates.




We are excited to announce a collaboration with Dr. Jennifer Frankovich and the Stanford PANS Program. We have been working for a year to develop a research program focused on the identification the microbial triggers that lead to the development of Pediatric Acute-onset Neuropsychiatric Syndrome (PANS).