Jon Deaton

Hello, my name is Jon Deaton. This is my personal website where you can find information about me and some of the work, school, and projects that I have been a part of.

I am originally from Longmeadow, MA, and I was a competitive gymnast for 15 years. I did my undergraduate studies at Stanford University in Bioengineering. At Stanford I also completed premedical requirements with the intent of attending medical school and practicing medicine as a physician. Through my study of bioengineering, I came to understand that through that through engineering I could create larger impact on the fields of medicine and biology than I could as a physician. I now aspire to use the combination of bioengineering and computer science to advance biomedical engineering research.


Stanford, CA


(413) 531-1568

Honors Thesis in Bioengineering

Links Elsewhere



Python, C/C++, MATLAB, Java, Molecular Biology, NGS DNA Sequencing, Circuit Design, Linux/UNIX, Statistics, 3D Printing, OnShape CAD, Microfluidics Fabrication, Cell Culture, Bioinformatics, DNA quantification


Lisp Interpreter in C
August 2017 - August 2018

As a personal project I implemented an interpreter for the Lisp programming language in pure C. The interpreter can be used to run Lisp programs saved in files, or from an interactive shell. This Lisp interpreter showcases many features including variable and function declaration, arithmetic operations, first class/lambda functions, closures, curying, recursive functions, a mutable global interpreter environment, dynamic scoping, memory allocation and automatic/deterministic memory management without garbage collection.

You can get the source code for this repository on GitHub.
GitHub Source
Heat Stroke Prediction
October 2016 - March 2017

Heat stroke kills thousands of people annually across the globe. The 2015 Indian heat wave, for example, resulted in over 2,300 deaths over a two-month period. To address the need for personalized heat stroke prevention in India, we created an inexpensive wearable device that measures physiological and environmental parameters and uses machine learning to determine and inform the user of heat stroke risk via text message or cell phone application in real time. Our approach is novel because we are using heat stroke patient data from literature to inform our algorithms and are determining the parameters most indicative of heat stroke. We have developed a prediction algorithm and are assembling relevant sensors and transmitting data. We implemented and tested our system in high-risk environments to assess accuracy by obtaining sensitivity, specificity, accuracy, and positive predictive value for our algorithm. We crated proof-of-concept prototypes to demonstrate viability of a heat stroke prediction device. Future versions would leverage decreasing costs for wearable sensors with bluetooth capability.

You can view more information about this project here:
One page description
Final Poster
GitHub Source
PhaMers – K-mer based Phage Identification Algorithm
September 2015 - March 2017

Discovering novel phage sequences from metagenomic data is often challenging. This study presents PhaMers (Phage k-Mers), a phage identification tool that uses supervised learning to identify metagenomic sequences (contigs) as phage or non-phage on the basis of tetranucleotide frequencies. PhaMers compares the tetranucleotide frequencies of metagenomic contigs to those of phage and bacteria reference genomes from online databases. Using PhaMers, we identified 103 novel phage sequences in hot spring samples from Yellowstone National Park. We applied a microfluidic-based mini-metagenomic approach to sequence environmental samples and produce metagenomic sequence datasets. We analyzed assembled contigs using PhaMers and VirSorter, a publicly available phage identification and annotation pipeline. We present the performance of PhaMers in identifying genomic fragments of phages and its ability to predict phage taxonomic classification. We also present putative hosts and taxa for some novel phage sequences.

You can learn more about this project here:
Honors Thesis
GitHub Source

Remote Access E.Coli Fermentor
January 2016 - March 2016

In BIOE 123, teams of 2-3 students design and build an E. Coli fermentor. The fermentor must hold a culture of 200 mL, maintain a temperature of 37 ̊C ± 1 ̊C, provide adequate aeration and agitation, and display live plots of optical density for red and green light. In addition, each team conceives of an original requirement, that their fermentor must also meet. My team used a Raspberry Pi to allow remote monitoring and control of our fermentor via Wi-Fi. This project was presented at the 2016 Tau Beta Pi Engineering Showcase at Stanford University.

Heap Allocator, CS 107 "Computer Organization and Systems", Final Project
March 2017

In the final project of CS 107, we designed and implemented our own heap manager for handing out and organizing dynamically allocated memory. The main goal was to create and test our own version of the malloc/realloc/free functions typically available through stdlib for requesting dynamically allocated memory in the C/C++ programing environment. Our implementation of malloc/realloc/free had to meet benchmarks of 65% memory utilization (calcualted as the percentage of allocated space of that handed out by the page manager) and 80% throughput (as compared to the time efficiency of the standard glibc versions of these utilities)

The heap allocator that me and my partner implemented made use of a linear-log spaced explicit free list (inspired by this blog) to store blocks of memory handed back by the client with the free/realloc functions. Our implementation surpassed both benchmarks earning 76% utilization of the heap and 97% throughput. Though code for this project cannot be shared publicly since this project is repeated for each offering of the course, you may contact me to see the code for this project.

Biologic Glutathione Sensor
October 2014 - December 2014

In Bioe 44: "Fundamentals for Engineering Biology Lab", my team developed a biologic sensor of glutathione. Our sensor was a DNA plasmid encoding a protein that would sense glutathione and actuate by triggering the synthesis of GFP. Our sensor was engineered to function in HeLa cells. Final paper

Work Experience

Bioinformatics Software Test Engineer, Illumina, San Diego CA
June 2017 - Current

I supported continuous integration pipelines through automated test development and security testing. I used C# to develop automated tests for software that controls the DNA sequencer. Tests involved monitoring communication with DNA sequencer firmware, verifying successful interaction with cloud platforms, and analyzing software logs. I also developed continuous integration tools including an internal web service for storing and viewing performance test results, using AngularJS and MongoDB.

Bioengineering Lab Researcher / Quake Lab, Stanford University
June 2014 - June 2017

In the Quake Lab I worked on molecular biology and bioinformatics projects related to DNA sequencing and characterization. In my largest project I analyzed the frequencies of short DNA "words" with machine learning algorithms to identify novel viral DNA sequences in metagenomic sequencing data. I created a software tool in Python to accomplish this (github.com/jondeaton/PhaMers) and discovered over 100 novel viral DNA sequences.

My molecular biology research in the Quake Lab has involved the design and debugging of novel molecular biology protocols to analyze DNA. My experiments primarily involve extraction, purification, amplification, and sequencing of RNA and DNA with and without microfluidic platforms.

Research Associate Intern, Illumina, San Diego CA
Mar 2012 - Dec 2014

During my summer internship at Illumina I worked on bioengineering problems in a protein engineering group. I designed and performed experiments with the goal of optimizing library preparation protocols in human exome sequencing. I also used Python to automate data analyses of DNA sequencing. These analysis tools are used to assess DNA sequencing run performance and inform researchers about how changes to sequencing reaction conditions affect outcome data quality.

Tutor, Peninsula Tutoring, San Francisco Bay Area, CA
November 2015 - June 2015

While working with Peninsula Tutoring I tutored high school and middle school students in math and science.

Gymnastics Camp Coach, Stanford Boy's Gymnastics, Stanford, CA
June 2013

I coached intermediate level gymnasts at a week long gymnastics summer camp.

Camp Counselor, Springfield Boy’s and Girl’s Club, Springfield MA
June 2009 - September 2010

I taught underprivileged elementary school students in summer educational program. This program was designed to help students struggling with challenges outside of school keep up academically with their peers.


MS in Computer Science - Stanford University, Stanford, CA
September 2017 - Current

I study computer science as a master's student at Stanford, focusing on Artificial Intelligence. My coursework has included the study of probabalistic graphical modeling, algorithmis analysis, operating systems and systems programming, deep learning, machine learning, and cryptography.

BSH in Bioengineering - Stanford University, Stanford, CA
September 2012 - December 2017

As an undergraduate I studied bioengineering and also completed premedical requirements. I took 5 years to gradaute as an undergraduate due to the large number of classes required for bioengineering and premedicine that conflicted with practice times for gymnatics. In my study of bioengineering I focused on the intersection of computer science and the biological sciences. Not only did I take several computer science classes, but also my honors thesis and senior capstone projects focused on the application of machine learning to solve biological and medical problems.

Williston Logo Williston Northampton School, Easthampton MA
September 2008 - May 2012

I went to high school at the Williston Northampton School in Easthampton Massachusetts. The majority of my free time in hich school was spent training gymnastics intensively.


PhaMers identifies novel bacteriophage sequences from thermophilic hot springs Jonathan Deaton, Feiqiao Yu, Stephen Quake bioRxiv 169672; doi: https://doi.org/10.1101/169672

Awards / Recognition

Tau Beta Pi National Engineering Honors Society Member
Tau Beta Pi: March 2017
Engineering students are invited to join Tau Beta Pi if they rank among the top 20% of engineering students in their graduating class or have demonstrated exemplary integrity in engineering.
NCAA First Team Academic All American
NCAA Men's Gymnastics: April 2015
The Academic All American awards are given to the athletes participating in the NCAA championships earning a sufficiently high cumulative GPA. First Team Academic All Americans must have GPA > 3.85.
NCAA First Team Academic All American
NCAA Men's Gymnastics: April 2014

NCAA First Team Academic All American
NCAA Men's Gymnastics: April 2013

Lincoln D. Granniss Yale University Scholarship
Williston Northampton School: May 2013

The Lincoln D. Granniss Yale University Scholarship is awarded a student of Williston Northampton’s upcoming senior class who is qualified academically and extracurricularly to be a strong candidate for admission to Yale University.

Dwight Church Award for the Outstanding Senior
National Gymnastics Judges Association: March 2013

This award is given each year to the outstanding senior gymnast competing at the Region 6 championships.


2017 Tau Beta Pi Engineering Showcase – Stanford University, CA
April 17, 2017
Topic: Heat Stroke Risk Monitor and Prediction Algorithm
Physical Biology of the Cell Conference 2017 – Kona, Hawaii
April 5, 2017
Topic: PhaMers Phage Identification Algorithm and Novel Phage Characterization
Rice 360 Global Health Engineering Competition – Rice University, TX
March 24, 2017
Topic: Heat Stroke Risk Monitor and Prediction Algorithm (presented by other group members)
Quake Group Presentation – Quake Lab, Stanford University CA
March 7, 2017
Topic: PhaMers Phage Identification Algorithm and Novel Phage Characterization
Boundaries of Life Meeting – California Institute of Technology, CA
January 18, 2017
Topic: PhaMers Phage Identification Algorithm and Novel Phage Characterization
Stanford Undergraduate Research Symposium – Stanford University, CA
October 5, 2016
Topic: PhaMers Phage Identification Algorithm and Novel Phage Characterization
iAspire Presentation – Illumina Headquarters, San Diego, CA
April 7, 2016
Topic: Human exome sequencing optimization and sequencing run quality assessment algorithm
2016 Tau Beta Pi Engineering Showcase – Stanford University, CA
April 7, 2016
Topic: Remote Access Fermentor
Bioengineering REU Presentation – Stanford University, CA
August 2015
Tpoic: Single Cell Distribution of Mitochondrial Genome Copy Count in K562 Cells
Bioengineering REU Presentation – Stanford University, CA
August 2014
Topic: Cyanobacteria Genome Copy Count & Microfluidic Multiple Displace Amplification Reaction

Volunteer Work

Clinical Volunteer
November 2015 - June 2015

I volunteered in a neurology unit at the Stanford Hospital and Clinics where I helped nurses and secretaries accomplish tasks throughout the unit. I also interacted with patients and their friends and family to improve their overall experience at the hospital.


USA Junior National Team Member, Men's Gymnastics
2008 - 2013

I was a member of the USA Junior National team for 5 years. To become a member of the national team I placed within the top seven gymnastics of my age group at national championships. Being on the national team earned me the opportunity to train at week-long training camps at the USA Olympic Training Center in Colorado Springs, CO several times a year. This opportunity also allowed me to represent the United States in three international competitions in Lilleshall in the UK, Bejjing, China (left), and Medellín, Colombia.

Stanford Men's Gymnastics
September 2012 - April 2015

During my undergraduate career at Stanford, I was a member of the Stanford Men's Gymnastics Team for four years. For Stanford's team I competed all events but rings, and helped the team to win two second place and one third place titles at the NCAA championships. Being a gymnast on the Stanford Men's Gymnastics team required 20 hours of intensive training each week in addition to weekly competitions across the country during the winter season. I was a NCAA First Team Academic All-American at the 2013, 2014, and 2015 NCAA championships, and an Elite 89 Scholar Athlete in 2014.

Unfortunately, during my senior year at Stanford, chronic injuries to my shoulders and ankles from 15 years of intensive gymnastics prevented me from competing. Despite this, I remained a contributing member of the team through a role as team manager.

Of all the things I learned in gymnastics, my favorite by far was bouncing on the trampoline. I have a compilation of clips on YouTube of me doing trampoline and some other things.