About Me

Designed, wrote, tested, and documented high performance tooling to call haplotypes in error-corrected high throughput sequencing data and estimate sample proportions in mixed samples.

Helped rewrite and validate legacy pipelines in Nextflow and worked to improve performance by over 20%. Wrote a multi-threaded python service which monitors for new sequencing runs, demultiplexes them, and uploads results to DnaNexus and/or AWS S3. This service included logging to a Slack bot and was deployed and managed using Ansible. Wrote high performance bioinformatics tools in Rust to generate VCF files from raw variant call data and to annotate variant calls according to specific requirements

Quickly learned Scala and contributed to new features and bug fixes in high performance tools used for processing high throughout sequencing data

I was the programmer/Analyst for the Hall Lab at Penn State. I lead development of open-source software for cleaning, analyzing, and integrating multi-omic data including CLARITE and pandas-genomics. I also designed and managed the lab website.

Promoted to senior manager position, requiring management of multiple programmers in the design and development of commercial software used for the analysis of high throughput sequencing data for forensic analysis As part of a small team, designed and developed high performance server-based commercial software for probabilistic mixture analysis of forensic samples using Markov Chain Monte Carlo strategies and Bayesian statistics

Research and design new algorithms such as copy number variation (CNV) and mutation scoring for implementation in NextGENe software which is used by over 100 research labs. Write and maintain scripts to generate gigabytes of test data and analyze results from the software in order to ensure it is working as expected. Interact with customers everyday to explain results and guide them through using the software. Develop over a dozen application notes, webinars, and scientific posters used to demonstrate and market the software.