Isaiah Paolo A. Lee, PhD

Associate Professor


PhD Evolutionary Biology, University of New Hampshire, NH USA

BS Molecular Biology and Biotechnology, University of the Philippines, Diliman, Philippines




Evolutionary Genomics and Systems Biology Laboratory

The Evolutionary Genomics and Systems Biology Laboratory makes use of next-generation sequencing data and computational methods to understand complex, population-level phenomena. We use a variety of approaches, including pan-genomics, phylogenomics, and evolutionary dynamics. Our current focus is on bacterial systems, but we are open to working on other organisms.

Research Area

  1. The current antimicrobial resistance crisis is fueled by rampant horizontal gene transfer. However, the distribution of gene transfer varies among bacteria, even within the same species. By taking a multi-pronged approach involving experimental evolution, genomics surveys, and agent-based modeling we hope to better understand the evolutionary forces that influence resistance gene mobility.
  2. Mycobacterium tuberculosis has infected most Filipinos at some point, including the lab principal investigator. While the success of an organism is often attributed to its ability to rapidly adapt to new environments, tuberculosis evolution is mostly clonal. We aim to use Mycobacterium pan-genomes from previously sequenced isolates to study how gene transfer (or its absence) plays a role in the pathogenicity of M tuberculosis.
  3. The Philippines is home to many species of pitcher plants. The adaptive radiation of Nepenthes is hypothesized to be driven by differences in nutrient acquisition through their pitchers. While new species of Nepenthes are still being discovered in the country, the microbiota responsible for the digestion in these pitchers remain understudied. Comparing the community compositions of these pitcher microbiomes should give us a better picture of the ecological diversity of these plants.


Selected Publications

Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience. 2023 Jul 13;26(8):107344. doi: 10.1016/j.isci.2023.107344. PMID: 37554437; PMCID: PMC10405257.

Lee IPA, Andam CP. Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis. Sci Rep. 2022 Jan 27;12(1):1515. doi: 10.1038/s41598-022-04995-5. PMID: 35087075; PMCID: PMC8795270.

Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Bacterial cooperation through horizontal gene transfer. Trends Ecol Evol. 2022 Mar;37(3):223-232. doi: 10.1016/j.tree.2021.11.006. Epub 2021 Nov 20. PMID: 34815098.

Lee IPA, Andam CP. Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle. BMC Microbiol. 2019 Dec 27;19(1):306. doi: 10.1186/s12866-019-1664-7. PMID: 31881843; PMCID: PMC6935241.