For my Master's Thesis at UCSD, I spent over a year contributing in Nathan Lewis's Lab at UCSD, where I worked on experimental techniques for removing batch effects prior to sequencing. As a part of my thesis I validated current methods for batch effect removal, improved lab based techniques through algorithm design, and performed RNA-Seq based analyses for downstream validation. For the downstream analyses I have used network analysis, DEA, GSEA, PVCA, and sample distances. For data I have used private, public, and simulated RNA-Seq data to validate our results. My thesis in its entirety can be viewed here
Analysis of Rural and Urban Networks
As part of a project me and one other colleague investigated differences in rural and urban networks. We measured the differences in rural and urban networks with two source probes one set up in a rural location and the other in an urban location. Using these two probes we collected data over a 2 week period consisting of traceroutes and pings to various locations around the world. We compiled these results into a dataset using Python and measured route similarity, route consistency, and latency. Further we compared these results on a regional, national, and international level to illustrate the diminishing effect that source destination has over long distances. Other notable analyses include network redundancy and observations of the diurnal pattern.
As part of a project for my graduate Algorithms Design class, me and a team of four others created a greedy solution to optimize the game of Catan for a single player. As a part of this project we wrote vigorous definitions of the problem, proofs and complexity statements. Additionally we implemented our algorithm to verify and test our work. As a team member I was responsible for proofs about algorithmic complexity, write the code for the turn algorithm, and creating the turn algorithm. You can view our final paper here.
Understanding the maintenance of extrachromosomal DNA (ecDNA) in cancer
Computational Genomics Lab, UCSC
For six months in 2019 I worked as a research assistant in Benedict Paten's Lab at UCSC. As a research assistant I compared error rates of variant calling pipelines for long read and short read sequencing technologies using bash. Additionally I performed error analysis on variant pipelines primarily looking at false negatives and locations within chromosomes where these errors occur.
Human Computer Interaction Lab, UCSC
For six months in during 2018 I worked as a research assistant in an HCI lab at UCSC. The project we worked on involved determining the language of leaders within certain groups of members and my role involved modeling that language. To do this I used python and psychological theory to build textual analysis models. These models were applied to text pulled from an enormous set of graphlets from a database of forum conversations. To discern what language separates leaders from non-leaders I created a model to determine the linguistic progressiveness of a group compared to a community as a whole. I also used linguistic inquiry word count to perform other statistical analyses. As part of this role I also formulated figures and made several presentations to demonstrate my progress.