Pavel Dimens

Hi, I'm

Pavel

I study population ecology in marine systems using genomics

My focus has typically been highly migratory marine fishes, but sometimes crabs and other fun things get mixed in! I also emphasize lowering the barrier of entry to learn new tools/methods and try to develop user-friendly tools within my discipline.

About Me

I’m an marine fish ecologist masquerading as a bioinformatician/geneticist. I studied a coastal shark species for my Masters degree and all the tuna species for my PhD.

Over the years I developed an affinity for the technical and analytical parts of research, along with a [some would argue] pedantic attention to detail in presentation aesthetics. As a result, I design 99% of all of my graphics, templates, gifs from scratch.

I also adhere to modern approaches to research reproducibility, so I lean heavily on integrating GitHub, Jupyter Notebooks, conda environments, and Snakemake workflows for ~100% transparency.

Besides work, I enjoy playing guitar, cooking, hiking, swimming, rock climbing, scuba diving, relaxing and doing nothing, coding in Julia, carpentry, and the occasional metroidvania or RPG video game.

Here are a few technologies I've been working with recently:

Julia
R
Python
Bash
Jupyter
Snakemake
SLURM
ddRAD-seq
Haplotag linked-reads
Oxford Nanopore
GitHub Actions

Experience

Postdoctoral Fellow - Cornell University

Sept 2023 - present

Using haplotag linked-read technology, I’m investigating the population-level climate change induce range shifts in the American Shad (Alosa sapidissima).

STEM Technical Developer - eCornell

Aug 2021 - Sept 2023

I worked as a Technical Developer for STEM (Science Technology Engineering Math) courses. The courses included:

Big data management
Machine learning
Natural language processing
SQL database management
Building interactive devices with circuitry and microcontrollers

PhD Student/Research Assistant - Univ Southern Mississippi

Jan 2016 - Mar 2022

Dissertation

I was a PhD student under the advisement of Dr. Eric Saillant at the Gulf Coast Research Laboratory in Ocean Springs, MS. My committee included Dr. Leila Hamdan, Dr. Kenneth Jones, Dr. Frank Hernandez, and the legendary James “Jim” Franks.

Assembled 5 tuna genomes (long reads, short reads, hybrid)
Created linkage maps from F1 crosses
ddRAD-seq
Whole-genome evolutionary comparisons
Population structure and demography of Blackfin and Yellowfin tunas

Masters Student/Research Assistant - TAMU-Corpus Christi

Aug 2012 - Dec 2015

Thesis

I was a Masters student under the advisement of Dr. David Portnoy at Texas A&M Univeristy - Corpus Christi. My committee included Drs. Derek Hogan and Jose Guardiola. I was also mentored under the watchful eye of Dr. Stuart Willis. [link]

ddRAD-seq
Coastal shark longlining
Teaching Assistant: Anatomy and Physiology, Biology

Fellow - Eurasia Foundation

Mar 2014 - May 2014

I was part of a team consisting of experts from Russia and the United States to review best practices of the maintenance and stewardship of national parks and refuges between the two nations.

Intern - Dauphin Island Sea Lab

Aug 2012 - Aug 2014

I was an intern in the Carmichael lab (oyster ecology/restoration, manatee ecology, sediment microchemistry) and the Powers lab (reef fish, shark, and oyster ecology).

GS-05 Wildlife Technician - USDA

June 2011 - Dec 2011

I was a member of a team stationed at John F. Kennedy International Airport (New York City) to prevent wildlife-aviation conflicts. This included monitoring the taxiways and airport perimeter, and wildlife removal.

Education

2017 - 2022

Doctor of Philosophy - Coastal Sciences

University of Southern Mississippi

Advisor: Eric Saillant

Chapter 1: Genomic resources for the Yellowfin tuna - link
Chapter 2: Population structure and demography of the Yellowfin tuna in the Atlantic Ocean
Chapter 3: Population structure and demography of the Blackfin tuna in the Atlantic Ocean - link
Chapter 4: Evolutionary history of the Thunnus genus using whole genome comparisons

Dissertation

2014 - 2016