About me
Hello! I’m Aaron, a PhD student at the University of California, San Diego in the Center for Marine Biotechnology and Biomedicine at Scripps Institution of Oceanography. I have worked in the lab of Prof. Eric Allen since 2018. I leverage my background in computer science to explore communities of marine microorganisms in silico for potential applications in bioenergy and biotechnology.
Before starting my PhD, I got my bachelor’s degree in Bioinformatics at UC San Diego. I worked as an instructional assistant for two years in UC San Diego’s Jacobs School of Engineering during undergrad. My specialty was the theoretical bases of computer science, with a focus on discrete mathematics, computational complexity, and algorithm design. I became interested in genome assembly and sequence alignment during a course on advanced algorithms, and eventually moved away from teaching computer science theory in favor of computational biology research.
Research Aims
My current and future dissertation work is centered around algal polysaccharides and the microbes that degrade them, which have implications in energy production, aquaculture, and marine ecosystem dynamics. Parallel to my disseration, I partner with corporate R&D teams, government labs, and academic research groups as both a generalist bioinformatician and a microbial genomics specialist.
Enzymatic degradation of macroalgal polysaccharides
My dissertation work focuses on the sugars inside seaweeds, which are notoriously difficult to break down using physical or chemical treatments. I use the gut of the herbivorous Hawaiian chub as a model system for studying the bacteria that degrade seaweeds in nature. This work is in parternship with the mariculture firm Ocean Era, who are excited by the potential discovery of novel enzymes that can degrade macroalgae. If successful, this work would enable the integration of partially digested seaweed compounds into commercial fish feed and improve the sustainability of aquaculture. Likewise, an more efficient method for algal decomposition improves the viability of seaweed-based biofuel production.
Improving algae farm productivity
In one research project, I have collaborated with the Hawaiian algaculture company Global Algae to develop an system that monitors the microbiome of commercially grown algae. In the first stage of the project, I assembled the genome of a commercial Nitzschia inconspicua strain and revealed the genetic factors that made this strain suitable for biofuel production. These genomic resources are publicly available at the Joint Genome Institute’s PhycoCosm portal to power future algal research. In the second stage of this project, I am also using metatranscriptomic data to quantify how the diatom microbiome responds to different nutrient levels and other stresses.
Characterizing extremophile algae
In ongoing collaborations with molecular biologists at the California Center for Algal Biotechnology, I leverage my experience with algal ‘omics to catalogue the resillience of novel Chlamydomonas strains. Some strains display promising tolerance to temperature, pH, salt, and light conditions that limit the growth of similar algae used by algaculture farms. As a bioinformatician in one branch of this project, I am harnessing information encoded in their assembled genomes to identify genes that power this tolerance. In another branch, I am helping develop a computational tool to identify promoters related to starch and lipid production in green algae, in preparation for genetic engineering and growth trials.
Bioinformatics support
Outside of my primary research projects, I also collaborate with wet lab biologists to integrate computational approaches into their studies. These contributions often extend beyond my primary niches of algal and bacterial genomics. These projects include investigating the metabolic capacity of sponge microbiomes, the infection strategies of deep sea viruses, and the responses of a keystone crustacean to stresses associated with climate change.