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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

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. 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

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.


MalariaGen Ag1000 project finalizes phase 3. The new release includes single nucleotide polymorphism (SNP) calls from Illumina deep whole-genome sequencing of 2,784 wild-caught mosquitoes from 19 countries, & 297 individuals from 15 lab crosses. 3 mosquito species are represented: An. gambiae, An. coluzzii & An. arabiensis.

Our work on the recombination maps of phase 1 of Ag1000 and the implications of the recombination architecture for the patterns of variation on linked sites is out. We find no evidence of differences in the patterns of Dxy and Fst variation in regions of the genome with disproportionally higher recombination rates. Check the preprint in the bioRxiv.