I’m an Assistant Researcher associated with the lab for data-intensive biology at UC Davis run by Titus Brown. My research is focused around developing methods to improve large-scale sequence comparisons. As part of this work, I help maintain and develop sourmash, branchwater, and associated workflows.
From 2017-2020 (with NCE to 2021), I was funded by an NSF Postdoctoral Research Fellowship in Biology, also advised by Titus Brown at UC Davis.
Facilitating de novo transcriptomics
Building off a project from my PhD work and a previously-existing workflow at the dib-lab, I constructed an automated de novo transcriptome assemblies, elvers. Elvers leverages the snakemake workflow management system to run popular quality control, assembly, annotation, and expression tools to produce high-quality de novo reference assemblies with minimal user input. The framework operates as a “black box” for those unfamilar with python and coding, but offers complete flexibility and customization for advanced users. Quick-Start here.
The California opalescent (market) squid is a primary forage species for fish, sharks, mammals, and seabirds in the California Current and also is one of California’s largest fishery species. These squid lay eggs that are attached to the seafloor for the duration of development (~1 month at 11˚C), where they are exposed to variations in temperature, pH, and oxygen as a result of upwelling and longer-term events such as El Nino/La Nina events (ENSO). Investigating the transcriptional and signaling mechanisms that allow these squid to thrive and develop at lower oxygen and pH conditions may provide insight to understand and predict future acclimation or adaptation to climate change in the ocean. In collaboration with Mike Navarro and the Levin lab, we exposed squid embryos to constant low-pH, low-oxygen conditions during development. We are currently investigating the gene expression response of these squid, with particular attention to pathways that regulate development. For a cartoon depiction of the “super” market squid life cycle and fishery, check out this squidtoons comic, created by collaborator Garfield Kwan.
The adult and developmental transcriptomes are nearing completion and data will be available soon. Contact me for more details.
If you don’t know anything about mantis shrimp, check out this Oatmeal comic for a fun introduction.
In collaboration with Maya deVries and Jennifer Taylor, I am investigating the transcriptome response of Neogonodactylus bredini to high temperature and low pH conditions. Their larger project is focused on impacts of warming and ocean acidification on the carapace and smashing appendage. Contact me for more details.
I was fortunate to be funded by an NSF IGERT to SIO for Global Change, Ecosystems and Society, an NSF GRFP, and the San Diego Diversity Fellowship for six years during my PhD, including a small research grant of $12k from a network of local donors. Many thanks to all who have made it possible for me to work on such interesting questions.