Aaron Ho

I’m an experienced computational researcher with over 4 years of expertise in developing software and analyzing genomic data. My work spans diverse areas, including next-generation sequencing (NGS), single-cell data, and genetic variation analysis. At the Salk Institute, I contributed to advancing computational tools and techniques to support cutting-edge genomic research.

I specialize in leveraging computational methods to uncover meaningful insights from complex datasets, aiming to bridge the gap between biological research and data-driven solutions. With a strong foundation in bioinformatics, I’m passionate about applying innovative approaches to solve challenging problems in genomics and beyond.

I’m always excited to explore new opportunities to contribute to impactful research and push the boundaries of what’s possible in computational biology.

Areas of Expertise

• Bioinformatics and Functional Genomics
• Programming and Software Development
• Data Analytics and Visualization
• High Performance Computing
• Data Structures and Algorithms
• Brazillian Jiu-Jitsu Purple Belt

Highlights

Publications

1. Zhou, J. L., de Guglielmo, G., Ho, A. J., Kallupi, M., Pokhrel, N., Li, H.-R., Chitre, A. S., Munro, D., Mohammadi, P., Carrette, L. L. G., George, O., Palmer, A. A., McVicker, G., & Telese, F. (2023). Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. Nature Neuroscience, 1–12. https://doi.org/10.1038/s41593-023-01452-y


2. Chen, H. V., Lorenzini, M. H., Lavalle, S. N., Sajeev, K., Fonseca, A., Fiaux, P. C., Sen, A., Luthra, I., Ho, A. J., Chen, A. R., Guruvayurappan, K., O’Connor, C., & McVicker, G. (2023). Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases. American Journal of Human Genetics, 110(4), 703–714. https://doi.org/10.1016/j.ajhg.2023.03.008

Preprints

1. Lorenzini, M. H., Balderson, B., Sajeev, K., Ho, A. J., McVicker, G. (2025). Joint single-cell profiling of CRISPR-Cas9 edits and transcriptomes reveals widespread off-target events and their effects on gene expression. https://doi.org/10.1101/2025.02.07.636966


2. Laub, D., Ho, A. J., Jaureguy, J., Klie, A., Salem, R., McVicker, G., Carter, H. (2025). GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics. https://doi.org/10.1101/2025.01.15.633240

Software Projects

WASP2

WASP2 is an optimized software tool designed for allele-unbiased read filtering and high-throughput allele-specific analysis. Built for efficiency and scalability, it enables streamlined detection of allelic imbalance in gene expression and chromatin accessibility , including support for single-cell datasets.

GenVarLoader

GenVarLoader is an advanced data-loading tool designed to enhance deep learning applications in personalized genomics.  By storing genomic data in optimized memory-mapped formats, it achieves approximately 1,000x faster data throughput and 2,000x better compression compared to existing methods.

MMA Math Dashboard

If Fighter A beats Fighter B, and Fighter B beats Fighter C...then Fighter A can beat Fighter C. This is the law commonly referred to as MMA Math

Pulling from a database of thousands of fighters, this interactive dashboard calculates if Fighter A can beat Fighter B using MMA Math. The dashboard also visualizes statistics and records for fighters alongside the path to victory.

Research on Intermediary SARS-CoV-2 Hosts

A research report highlighting the critical role of bioinformatics when looking into the origins of SARS-CoV-2.

Through the use of comparative genomics and phylogenetic analysis, I build upon current research and show why COVID-19 may have come from pangolins.

Bioinformatics Scripts and Algorithms

A collection of python scripts for manipulating and analyzing sequence data. Designed to increase productivity by providing computational solutions for key research problems.

Modularly written with ease of use in mind, all scripts require no additional downloads and feature command line functionality to ensure compatibility with existing pipelines.

...And More On the Way

I'm always looking to improve my skills. Check out my current progress and other projects on GitHub!