# Alexander Swafford

> Bioinformatics Software Engineer

Location: San Mateo, California, United States
Profile: https://flows.cv/alexanderswafford

I am a Bioinformatics Software Engineer with a breadth of cross-disciplinary experience in genomics, primarily focusing on developing custom tools, APIs, and pipelines to support scientific research. I am passionate about bridging the divide between engineering and science, translating the needs of researchers into projects and code, as well as clearly communicating between the domains.

## Work Experience
### Software Engineer, Bioinformatics @ Joint Genome Institute
Jan 2021 – Present
- Maintain and update 20yr legacy codebase of the Fungal and Algal Genomics team
- Rewrite, optimize, and merge annotator scripts into production code
- Build analytics pipelines for large scale genomic analysis in HPC environment
- Test and integrate third party tools and software to improve existing functionality

### Software Engineer, Bioinformatics @ Synthego Corporation
Jan 2018 – Jan 2020
- Developed and managed a scalable suite of gene editing design tools
- Adopted and maintained a legacy LIMS through end of life
- Scaled computational biology scripts for whole-genome designs
- Refactored and developed algorithms from bioinformaticists into production code

### Software Engineer 2 @ Illumina
Jan 2015 – Jan 2018 | Santa Clara, California
- Developed clinical research APIs to leverage next generation sequencing data
- Created parsers for large scale ETL of clinical data
- Built an R package with researchers to integrate genomic APIs for analysis

### Software Engineer @ Dart Neuroscience
Jan 2014 – Jan 2015 | Claremont, CA
Worked with a group of neuroscientists and a hardware team to design and implement a software/hardware testing suite for pharmaceutical research. We designed and implemented a context-free domain-specific language that would be readable by research scientists with no prior CS experience, as well as editable by those with a brief introduction to it. Additionally, we integrated with a hardware system that was custom built from scratch.

### Software Development Engineer Intern @ Amazon
Jan 2014 – Jan 2014 | Seattle

### Engineering Intern @ BlackRidge Technology
Jan 2012 – Jan 2012 | Santa Clara
Ran tests on Linux boxes using the command line, Wireshark, and Ostinato, and Bugzilla
  - Verified that reported bugs did not reappear in new builds.
  - Searched for any undetected bugs
Set up and executed the protocol for wiping boxes and setting up the BIOS and keys for FCS

### Research Intern @ Cornell University
Jan 2010 – Jan 2010 | Appledore Island, ME
One week research continuation of Ecology of Animal Behavior
     - Field work on spider population dynamics and behavior, data gathering and interpretation


## Education
### Bachelor of Science in Computer Science
Harvey Mudd College

### Marine Biology
Cornell University


## Contact & Social
- LinkedIn: https://linkedin.com/in/aswafford

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Source: https://flows.cv/alexanderswafford
JSON Resume: https://flows.cv/alexanderswafford/resume.json
Last updated: 2026-03-31