Bioinformatics Algorithms Online Course

I was in charge of rewriting problem statements, test cases, and the code base for the interactive online version of the quintessential bioinformatics textbook, Bioinformatics Algorithms: An Interactive Approach by Pavel Pevzner and Philip Compeau.

Abterra Biosciences Valens Pipeline

I worked to improve a pipeline for de novo antibody sequencing. I was in charge of thinking of clever algorithms to interpret mass spectrometer data to return amino acid sequences of the analyzed antibody, implementing them within the broader Valens pipeline, benchmarking the performance of each solution, presenting on the results, and making iterative improvements on the best solutions.

Analysis of Single Cell Transcriptomic Atlas of Hematopoiesis Over the Human Lifespan

I was given raw scRNA-seq data of over 58,000 cells across 26 samples from human donors from 10wks gestational age to 77 years old. I was in charge of first performing quality control, alignment, and quantification of the raw sequencing data to generate a count matrix before using this count matrix to investigate various questions we had about how hematopoiesis in humans changes over time. Lastly, I was heavily involved in the writing of the paper and the revision process.