.jpg?sfvrsn=f434ac55_1 "Zhu, Justin10 (1)")
Hi y’all, my name is Justin Zhu. I’m a graduate student in Dr. Rovshan Sadygov Lab. In general, I’m a bioinformatician, but specifically in this lab we do proteomics. Very generally, the identification and quantification of protein on a systems level. Throughout my time in the lab, I’ve been on different projects.
The first project was focused on the behavior of the False Discovery Rate (FDR) during peptide identification. The FDR is used to control for family-wise error rate without being overly stringent like Bonferroni Correction. This is crucial in modern proteomics as bottom-up approaches depend on proper peptide identification for subsequent processes. I was involved in running simulations and deriving approximations for the Variance of the False Discovery Proportion (FDP).
The second project I worked on was determining if immonium ions could help determine amino acid sequence and composition in mass spec data. Immonium ions can be considered as the single ionized amino acid resulting from fragmentation. The peptide identification process is a computational expensive process as it must contend with the combinatorial nature of sequences. If one could determine which amino acid existed and in what proportion. This would greatly enhance the speed and specificity of the current process.
The current project I am working on is to benchmark algorithms to infer Protein-Protein Interaction (PPI) networks from protein abundance data. PPI networks in a sense represent how proteins regulate each other. Being able to infer this network in-silico would decrease time to determining key protein targets/pathways. One can imagine, especially in diseased or cancerous tissue, how determining the PPI is regulated (or for that matter dysregulated) could be helpful.
I got involved in research because I wanted to work in bioinformatics. In undergrad I got hooked onto programming and wanted to apply it to my biology major, so in the summers I went around working for different labs. Those experiences cemented my desire to work where these fields intersect, where bioinformatics lies. Outside of the lab I play chess, and I like to volunteer at the local farmer’s market. I’m a fountain of random facts. People are surprised that I’m from Canada and that I’m a certified polar bear mechanic. I’m allergic to bananas, I have my Scuba license and sometimes I cosplay. As for aspirations, I don’t have any grandiose ones.
Currently, I’d like to graduate and do at least one post-Doc position. Unlike more traditionally sciences, I don’t have a pet model system or disease to study. The allure of bioinformatics is in the process. In the more abstract sense, I’ve always found the marriage between computer science (calculated, discrete, formal) and biology (messy, continuous, full of exceptions) to be gratifying. It’s not about reducing biology to a rigid set of rules; it is about discovering the intricacies that lie underneath all the chaos.