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S. Evan Staton

Botanist, Genome Biologist, Data Scientist

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About Me

Professionally, I am a computational biologist and application developer that is passionate about writing quality software to improve science and facilitate discovery. My background is in biology with a focus on plants. I am trained as a plant geneticist and most of my work centers around developing novel computational methods for understanding patterns of genome evolution.

I am currently employed with a private agricultural genomics company in Saskatoon, SK, Canada where I work on delivering insights for a wide variety of projects. Formerly, I was a Research Associate at the Beaty Biodiversity Research Centre and Department of Botany at UBC. If you would like to discuss one of my projects or a collaboration, please send me message.

When I am not working I enjoy staying active (cycling, hiking, running, rock climbing) and above all I things I enjoy reading to learn new things.

Latest Software Development Projects

Tephra

A tool for discovering transposable elements and describing patterns of genome evolution

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Tephra is a command line tool for the annotation of all transposable element types in a genome.

The structure of intact transposable elements is used by Tephra to determine patterns of genome evolution such as transposon diversity and abundance, transposon insertion times, and patterns of recombination and DNA removal. There is also a highly efficient utility for genome masking provide a custom repeat library, which may be derived from Tephra or any other source.

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Transposome - A toolkit for annotation of transposable element families from unassembled sequence reads

Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data. This tool allows you to infer the abundance of repeat types in the genome without a reference genome sequence. The output files make it easy to quickly summarize genomic abundance by transposable element class, superfamily, family, or any other level of the repeat taxonomy.

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HMMER2GO - Annotate DNA sequences for Gene Ontology terms

This is a tool for identify coding regions in a transcriptome or genome assembly, finding Gene Ontology (GO) terms associated with those regions based on Pfam domain matches, and creating associations for statistical analysis of GO term mappings.

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Web Development Portfolio

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SGD - Sunflower Genome Database website

The website contains a number of interactive tools for genome analyses such as a BLAST tool that links to a genome browser, an interactive gene expression browser, and provides access to many genomic data sets. The site is written with the Express.js framework, and I use Gulp for automation of linting, templating, image compression, and other routine tasks.

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DivSeek Canada website

This is a pilot project for DivSeek International that I have contributed to that aims to bring genomic and breeding resources to lentil, flax, and sunflower.

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Other Projects

transposons.org - A novel transposon database

The goal of this project is to develop a database of transposable elements that has a modern and interactive website, an API, and web-based analysis tools. Annotations will be derived from Tephra and user submitted data. This is an unfunded project that is currently in the design phase, but the site will be available at the URL transposons.org (which I own).

App::Droplets Open Source

This is a command-line tool for DigitalOcean's REST API called droplets. After setting up an API key on the DigitalOcean website, you can check on all your existing droplets, query the available droplet sizes and prices by region, create new droplets, or log on to droplets (either existing droplets or ones you just created) without leaving the command line. You can also destroy one or all your droplets in one command. I find this very useful for testing software on different systems.

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App::Archive2iTunes Open Source

This is a small application I developed to fetch live shows from archive.org and add them to your iTunes library from the command line. This saves you a few manual steps when you find a show that you would like to add to your library.

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Work Experience

Research Associate - University of British Columbia (2019 - 2020)

Computational biologist, web developer and Linux system administrator of local and cloud compute infrastructure. This work is done in collaboration with Loren Rieseberg.

Postdoctoral Fellow - University of British Columbia (2014 - 2019)

Developing computational solutions for analyzing patterns of genome evolution from large-scale DNA sequencing and genotyping projects. Linux system administration of local compute cluster; database and website development. This work is done in collaboration with Loren Rieseberg.

Graduate Research Assistant - University of Georgia (2008 - 2014)

Develop computational methods for the analysis of genome evolution from emerging DNA sequencing technologies. This work was carried out in the lab of John Burke.

Graduate Research Assistant - Miami University (2006 - 2008)

Develop in situ hybridization protocols for non-model system in plants for the study of transposable element genome localization. This work was carried out in the lab of Richard Moore.

Graduate Research Assistant - Miami University Center for Bioinformatics and Functional Genomics (2006 - 2008)

Perform daily maintenance of Sanger sequencers (ABI 3130, 3130xl, 3730xl), Beckman-Coulter pipetting robot, microarray scanners, fragment analyzers, PCR machines, centrifuges, and other standard molecular biology equipment.

My GitHub