Ph.D. Student in Microbiology
Aquatic Microbiology Lab
Cornell University
Integrating environmental, genetic, and biochemical data
We can find microbes in every ecological niche on Earth; I find this fact delightful. I’m a microbiologist studying how bioinformatics and system biology approaches can help us understand the complex exchanges of nutrients within natural and constructed microbial communities. I'm also an R and Julia programmer with a weakness for cat-related coding. On this page you can access my publications and some of my personal projects as a bioinformatician. You can also view my CV here. Always happy to chat about bacteria, coding, or the Great British Bakeoff, so please feel free to reach out via Twitter or email.
As a researcher, I enjoy using diverse methods of data collection and analysis to answer exciting questions concerning complex systems
I've been lucky to work in diverse research areas, whether studying organisms from the deep ocean to pathogenic virulence. Feel free to peruse my published work on my Google Scholar page
As a current Ph.D. student in the Schmidt Lab, I study the formation, structure, and function of freshwater microbial communities in New York. Current projects include characterizating microbial communities of Lake Ontario and disturbance experiments in Cornell's experimental ponds. Excited to share more as these projects develop!
Staphylococcus aureus can be understood as Faye Dunaway in Mommy Dearest: sometimes it's a pleasant skin commensal, and other times it's eating you up like raw steak (sorry, that's a "niche" joke). That switch from nice to nasty is regulated by a complex mix of two-component systems and nutritional sensors. In this work, we showed that branched-chain fatty acids are required for Staph to become virulent, by modulating the two-component system SaeRS
Ireland is still debating the slippery question of how to regulate seaweed harvesting. Coastal communities have a long history of sustainably managing their seaweed harvest, but new laws increasingly centralize regulatory decisions. In this work, we talked to seaweed harvesters to get their perspective on how their industry should be regulated. I hope it “kelps” you to learn more about seaweed!
When you picture coral, you might imagine sun-drenched reefs populated by sassy little clownfish. But there's a whole world of coral most of us will never get to see. Balanophyllia is a solitary cup coral that looks like a cursed ice-cream cone and flourishes in some of the darkest, coldest waters on Earth. In this work, we characterized the reproduction of this deep-sea coral using histology and SEM.
S. oneidensis is sort of like a labrador retriever: it'll eat anything you drop on the floor. This freshwater bacterium is able to use an astonishing range of terminal electron acceptors during anaerobic respiration, so it can "breathe" crazy things like iron or uranium. Central to this versatility is the use of redox-active cofactors called flavins. In this work, we examined the synthesis and acquisition of flavins in the periplasm of this charismatic microbe.
I'm just beginning my journey as a graduate student and a data analyst, but I'm silly proud of these projects! Use links below to navigate my first R package and my first Shiny website
I wanted to learn Julia, and what better way to pick up a language than writing a package? CUBScout makes working with codons easy in Julia. You can calculate codon frequency, multiple codon usage bias measures (e.g. B, MILC, and SCUO), and multiple expressivity predictions (e.g. E, MELP, and GCB). Feel free to read the documentation or peruse the source code.
This is my first R package, and it allows you to interactively calculate doubling times from growth curve data in a Shiny app! This link will take you to the Github repo for the package, while you can click here to copy the code to install this package in R:
This website is probably the dumbest thing I've ever made and I'm so proud of it. I expanded my skills in machine learning and shiny applications to create a website that walks you through imaginary data science projects with my cats (they are the fat cats in question). I hope you enjoy!
I've had a great time teaching basic R programming and statistical analysis to the NUIG Geography Master's cohort. This class is a 4-hour fast-track to gain immediately applicable skills in R coding, data import, and hypothesis testing at a graduate level, without getting bogged down in statistical formulas or computer science jargon. Click here to access the course materials, which include practice data.
Thanks again for stopping by! I grew up fishing and camping in Wisconsin, received my B.S. in Microbiology from the University of Minnesota and then traveled to Ireland to complete my M.Sc. in Geography in Galway as a Fulbright Scholar. After spending two years in Washington, D.C. as a research assistant at Georgetown University, I have begun my Ph.D. in Microbiology at Cornell University. Outside the lab, you can find me backpacking with my boyfriend, cross-country skiing, and baking pies with my two cats.
Feel free to reach out via email at arp277@cornell.edu or on Twitter at @AugustusPendle1