Nathan Johnson Email & Phone Number

Versatile bioinformatics scientist and engineer with extensive experience in pipeline development, algorithm design, NGS data analysis, and genomic data science. I have a proven track record of building reliable bioinformatics software and delivering critical insights from next-generation sequencing (NGS) data to drive innovation in gene therapy and beyond.My career spans biotech and healthcare, with roles at Spark Therapeutics, Children’s Hospital of Philadelphia, and Illumina, Inc., where I’ve consistently delivered innovative bioinformatics solutions.In my most recent role at Spark Therapeutics, I developed fully automated Nextflow pipelines for vector and plasmid characterization. These cloud-based workflows, built on Seqera Platform with AWS, are user-friendly and generate interactive reports accessible via browser. This system has significantly scaled Spark's operations in this area, playing a key role in the team's success.Additionally, I led scientific deep dives into complex and low-abundance contaminant sequences and tricky variant calls, and helped troubleshoot sequencing issues arising in the lab to ensure data integrity and quality.During my time at Illumina, I applied machine learning and statistical models to advance NGS analysis. I led development of a genome segmentation model that led to a patent application and publication. Additionally, I created a Python package for efficiently analyzing data quality across hundred of human whole genomes. Other projects included developing truth sets for complex variant types, improving genotyping algorithms, and identifying highly conserved genes to help a CAP/CLIA lab prioritize variants for diagnosis of rare genetic disease.I also like to teach! I recently led a successful workshop series for non-programmers, helping colleagues build foundational skills in programming, data science, and bioinformatics in a fun and approachable way.I’m also fascinated by the application of neural networks to automated recognition and translation, especially in the study of ancient Mesopotamian cuneiform documents. My diverse background includes a Ph.D. in physics, where I worked on a lunar laser-ranging experiment, before pivoting my passion for problem-solving and coding towards bioinformatics and genomics.If you'd like to discuss working together, send me a message!

Listed skills include Instrumentation, Python, Bioinformatics, Statistics, and 11 others.