Marcus Fedarko

Hi! I'm a postdoc at the University of Maryland. I work in the Pop Lab, where I develop methods for the assembly and visualization of microbiome sequencing data.

Previously, I was a PhD student at the University of California, San Diego in the Pevzner Lab.

I can be reached via email at mfedarko (at) umd (dot) edu.

That's probably it for now.

Curriculum Vitae Google Scholar GitHub

Research projects

(This is not an exhaustive list; there are a few other things in the oven.)

2023– wotplot
Library for creating and visualizing dot plot matrices.
2020–2022 strainFlye
Pipeline for the analysis of rare mutations in metagenomes.
2019–2021 EMPress
Visualization tool for phylogenetic trees and associated data.
2018–2020 Qurro
Visualization tool for log-ratios of compositional data.
2016– MetagenomeScope Undergrad Thesis
Visualization tool for (meta)genome assembly graphs.

Other writings and talks

2018–2025 PhD Thesis PhD Thesis Defense Slides
It's mostly just five papers (3 published + 2 in-preparation) smushed together.
2024 Guest lecture: "Metagenome assembly"
In January 2024, I gave a guest lecture for ESE 184 ("Computational Tools for Decoding Microbial Ecosystems") at Caltech. Here are the slides for that!
2018–2021 Research Exam Report
The research exam is a required milestone for PhD students in UCSD's CSE department, sort of analogous to a qualifying exam. Note that I completed my research exam in 2021 (when the department required that students write a survey paper); their requirements have since been relaxed to allow students to reuse existing papers for the research exam.
2017 Statement of Purpose Statement
When I was applying to grad schools, I wished I had more examples of what these statements looked like. Here's the one I used when I applied to UCSD.
2016 LaTeX guide for new users Guide
Final project for ENGL 390H (Spring 2016, UMD).