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

• 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.
• 2019– pyfastg
  Library for parsing FASTG-format assembly graph files.
• 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).