Jon Belyeu Computational Geneticist

jbelyeu jbelyeu jon-belyeu jbelyeu Curriculum Vitae

About me

I'm a Senior Bioinformatics Scientist at Illumina, specializing in variant calling within complex medically relevant regions of the genome.

I've worked at Illumina since June 2021, after earning my PhD in Genetics at the University of Utah. I also have a BS in Bioinformatics (with a minor in Computer Science) from Brigham Young University.

Illumina Bioinformatics Research

Complex medically relevant variant calling

Many genes with impacts on human health contain repetitive sequences (or are fully within genomic repeats) making variant calling much more challenging. I work on targeted variant calling software to recover and genotype variants with clinical impacts that occur inside these regions.

I'm working on several of these, but have recently presented a poster at ASHG 2022 on targeted copy number calling of the KIV-2 repeat within the LPA gene, with a manuscript in draft. Stay tuned for more.

Graduate Research

De novo structural variants in ASD

There is a known enrichment of SVs in Autism Spectrum Disorders (ASD). I analyzed the rates and patterns of spontaneous SVs in a very large ASD family cohort as well as a cohort of large, multigenerational Utah families (published in AJHG) to learn more about how often these variants occur, what effects they have in ASD risk, the impact of parental age on SV risk, and the molecular mechanisms responsible. My work was featured in a Spectrum News article after I presented a poster at ASHG 2020.


Visually reviewing the sequencing evidence for SVs is very important, because lots of false positives variant calls occur. Samplot (published in Genome Biology) facilitates making plots, filtering, and even curating via a deep learning classifier.


I developed a tool (published in GigaScience) for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis, with support for sequencing data from BAM or CRAM files from Illumina, or long-read technologies (ONT/PacBio).

Undergraduate research

Codon Bias

I worked with Justin Miller, under the supervision of Dr. Ridge, in a project targeted toward understanding evolutionary implications of non-random codon bias, leading to publication of Missing something? Codon aversion as a new character system in phylogenetics in Cladistics (2017).

Seismic Event Detector

In a project for a BYU CS Capstone in Big Data, my team (Artem Golotin, Darian Ramage, and I) developed a scalable system for monitoring streaming seismic signals in a developing aftershock sequence. This could be used to study earthquakes in more detail (as well as to identify illicit nuclear testing). Presented at LLNL and BYU.


Bioinformatics tools

  • Linux/Unix
  • Algorithm development
  • Computational tool development/distribution
  • Parallel processing
  • Supercomputing
  • AWS
  • Conda
  • Nextflow
  • Matplotlib
  • ggplot2
  • Git

Programming Languages

  • Python
  • Bash/Shell
  • R
  • C/C++ (some)
  • Java (some)


I'm a huge fan of the outdoors and spend as much time as I can hiking, canyoneering, or skiing. Check out my Instagram for more.