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Population Genomics of microorganisms and their hosts in health and disease

Population Genomics of microorganisms and their hosts in health and disease

Welcome to the Cornejo Lab

Disparities in health and risk to disease can be explained by the evolutionary history of the host and the historical exposure to pathogens. It is the result of their interaction in time and space that result in the striking differences in outcomes between the interaction of hosts and microbes

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 our 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.


Although our focus is in the analysis of pathogens relevant to human health and disease we have examined and continue to examine this problem in other systems


We use genomic data to infer the demographic history of populations and use these demographics to better understand how selection has shaped specific regions of the genome to contribute to species adaptations. We investigate these questions in different systems: i) Humans; ii) Microbiomes; iii) Malarial parasites; and iv) Plants. Some of the questions we address in our research are:

  1. How are microbiomes structured by host genetics and the physiological niche created by the host?
  2. How do differences in microbiome composition modulate phenotypes in hosts?
  3. How important is homologous recombination for the evolution of traits involved in host shifts or adaptation to new environments in microbes and hosts?
  4. During which stages of the complex life cycle of organisms do we expect to find hotspots of adaptation?
  5. How has the demographics impacts the accumulation of deleterious mutations, impacting the fitness of individuals?

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. You can learn more about what we do in our lab in the Research section.

Some of the questions currently addressed in our lab can be more thoroughly explored in our Research Areas. If you are interested in any of these research topics do not hesitate to contact us. For more information on the opportunities in for Undergraduate, Graduate and Postodoctoral positions visit our Opportunities section.

News of interest

The Cornejo Lab is 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).


We are happy to announce our partnership with LunaDNA to identify key priorities in women’s health related research. We part from the principle that we need to listen to women to help define what these priorities should be. As our colleague Erica Ramos rightly points out: “Researchers often assume or guess about what’s important to women. It’s high time we centered the women’s health agenda on what women say matters most to them.” It is time we change that. In our lab we are committed to listen and help reshape research agendas that listen to these needs.


We are joining the Human Pangenome Reference Consortium (HPRC), a large effort to generate a human reference that is representative of human diversity. The effort is coordinated from Washington University and it involves a large number of researchers from multiple institutions across the US. Our involvement will focus on the genetic analysis of variants of the human leukocyte antigen (HLA) system.