Matthew Davis

PhD Candidate, Plant Biology

I'm a PhD candidate interested in plant genomics, mutation biology, and somatic variation. Feel free to explore some of my recent work and interests here! If you'd like to talk more, we can get in touch at the bottom of the page.

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About

Hi, I'm Matt, a PhD candidate at the University of California, Davis. I study plant biology, with a focus on somatic mutation. I'm very interested in how we can use mutation to better understand plant development and anatomy.

When I'm not thinking about science, I love photography, going to the zoo, exploring the great variety of California's natural environments, or tinkering with new hobbies and side projects.

Me at Linda Falls in Napa County, California

Recent Publications

You can check out all of my current publications on my Google Scholar profile.

My five most recent publications can be seen here:

Projects

Packages

ggenomics

An R package for visualizing genomic features using ggplot2 syntax. Provides functions to dynamically plot genomes for exploratory data analysis of genomic datasets.

  • R

Analysis

Walnut Mutation Accumulation

Scripts and analyses investigating somatic mutation accumulation in clonally propagated walnut plants, supporting research into how plants acquire mutations over vegetative generations. The manuscript this data supports is currently available as a preprint on bioRxiv and in review.

  • R

Teaching

R Club for Graduates

Graduate-level R club materials focused on applied data analysis using R and R Markdown.

  • R
  • R Markdown
  • Teaching

R Club for Undergraduates

A summer R course for undergraduate students with weekly R Markdown lessons and hands-on exercises introducing and basic data workflows.

  • R
  • R Markdown
  • Teaching

RMarkdown and Tidyverse Introduction

A teaching resource introducing R Markdown and the tidyverse for students getting started with reproducible analysis, data wrangling, and basic visualization in R. Originally created for lectures in PLS 206 at UC Davis.

  • R
  • R Markdown
  • tidyverse

SACNAS Workshop

Workshop materials for an introductory bioinformatics activity using sequence identification, BLAST, k-mer counting, principal components, and dendrograms to explore biological relationships.

  • Python
  • BLAST
  • Bioinformatics

Get In Touch

I'm expecting to graduate soon, and I'm excited for the next step. Whether you have a question about my work, want to discuss project ideas, or want to talk science, please feel free to reach out with professional inquiries. Send me an email below, or click the icons to check out other ways to connect!

Send me an email