Jon Belyeu Computational Geneticist

jbelyeu jon-belyeu jbelyeu Curriculum Vitae

About me

I'm a graduate research student pursuing a PhD in Human Genetics at the University of Utah. My current work is in identifying, curating, and understanding genomic structural variants (SVs).

I earned my Bachelor's of Science Degree in Bioinformatics with a minor in Computer Science from Brigham Young University in 2016.

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 (preprint on BioRxiv) 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.

Samplot

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

SV-plaudit

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.

jrbelyeu@gmail.com

Skills

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)

Pastimes

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: