Marcus Fedarko

Hi! I just graduated with a PhD in computer science from the University of California, San Diego, where I worked in the Pevzner Lab. In my research, I develop methods for the assembly and visualization of microbiome sequencing data.

Before grad school I was an undergraduate student at the University of Maryland, where I worked in the Pop Lab.

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

That's probably it for now.

Curriculum Vitae Google Scholar GitHub

Research projects

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

Other writings and talks

• "Visualization and assembly methods for microbiome sequencing data" PhD Thesis
  As is the current norm in many scientific fields, this is a "stapler thesis" -- the bulk of this document is just five existing / in-preparation papers smushed together.
• 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!
• Research Exam Report
  The research exam is a required step for PhD students in UCSD's computer science department. 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.
• Statement of Purpose PDF
  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.
• LaTeX guide for new users PDF
  Final project for ENGL 390H (Spring 2016, UMD).