About

Learn more about me

Mark Pampuch

Biotechnology Researcher and Technology Specialist

  • Birthday: 17 August 1998
  • City: Toronto, ON, Canada
  • Age: 23
  • Degrees: •︎ HBSc in Biology
    ⤴︎ Spec. in Genetics
    •︎ MSc in Biochemistry
  • Email: markpampuch@gmail.com

Biography

I am a biotech researcher specializing in the fields of biochemistry and genetics. My fascination with biology has led to pursue research in the field of synthetic biology, a field which offers a unique opportunity to engineer living systems in a way that can solve some of the world's most pressing problems, such as disease, climate change, and food insecurity. I have gained a deep appreciation for the complexity and beauty of biological systems, as well as the power of genetic engineering to manipulate these systems for our benefit. It is a challenging field that requires a strong foundation in biology, chemistry, and mathematics, as well as the ability to think creatively and critically about complex problems. Throughout my research, I have worked towards increasing nutrient uptake in crops, developing novel antibiotic technologies, and improving DNA delivery methods. A big component of my research has also been in the field of bioinformatics, which lies at the intersection of biology, statistics, and computer science. I have developed numerous applications to answer specific research questions and analyze large amounts of genetic data. In my free time I like to exercise and volunteer in my local community. I am always interested in learning new skills and meeting new people, so feel free to reach out!

Work History

2023 - Present

In my most recent role, I had the privilege of working at the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. I was invited to work there as a visiting researcher by Dr. Kyle J. Lauersen who I met at a science conference. When I arrived I was immediately captivated by the institution's profound commitment to scientific research and possession of state-of-the-art equipment. I worked in the Sustainable & Synthetic Biotechnology Group, where my work consisted primarily of optimizing high-molecular weight DNA isolation protocols and next generation sequencing analyses of bioprospected organisms with high industrial potential. The funding for the biosciences and the level of computational and automation infrustracture found at KAUST allowed me to perform research at much higher levels than I had previously experienced. This environment did not just facilitate my research; it also equipped me with invaluable skills and dramatically accelerated my growth as a scientist.

Mark Pampuch
Mark Pampuch

2021 - 2023

In a significant chapter of my career, I had the opportunity to pursue synthetic biology research at Western University, within a lab spearheaded by Dr. Bogumil Karas. Initially joining as a research assistant, my love for the pioneering and cutting-edge research ultimately led me to pursue a Master of Science in Biochemistry in the same lab. Working in Dr. Karas's lab allowed me to learn a lot about synthetic biology. I even took upon the challenge of performing are very large-scale data analysis project in addition to my laboratory projects, which was not the domain of expertise within this lab however Dr. Karas was kind enough to let me pursue it and despite not having much experience doing that kind of work beforehand. My expereince in this lab has been extemely beneficial. It honed my critical thinking and problem solving skills and I feel fortified having conquered many challenging problems. It led me to grow tremendously as a researcher, having the ability to blend both wet-lab and dry-lab work together in a way that is very beneficial to the research process and a unique skill.

2019 - 2020

My first exposure to laboratory research came in the form of working at the Agriculture and Agri-Food Canada London Research and Development Centre under the supervision of Dr. Krzysztof Szczyglowski. My research pertained to improving natural interactions with soil microbes and legume crops in an effort to reduce the amount of artificial fertizilers used in modern agriculture and reduce environmental impacts caused by nitrogen found in agricultural runoffs. This work was instrumental in my career because I found a passion for research and would stay into the late hours of the day trying to collect more data to answer the scientific questions I had burning inside of me. I also learned a lot about the importance of collaboration and communication in the scientific community. I was fortunate to have worked in such a great lab with such a great team of scientists. This experience was a turning point in my career as it set me down the path of research and I am grateful for the opportunity to have taken part in it.

Mark Pampuch
Mark Pampuch

2018

My first professional experience came in the form of working at the medical technology company MolecuLight Inc., which was based out of the MaRS Discovery District innovation hub in Toronto. I worked as an intern and was fortunate to have worked with a great team aiming to deliver a product that could make a great impact in the medical field. When I joined the team, the company was in the middle of obtaining FDA approval for their wound-care device. My primary roles were to help process the data from the clinical trial studies and help conduct research on potential customers and competitors. I learned a lot of what it takes it bring new technology out to the market and the trials and tribulations startups face. I left this experience with a lot of insight and perspective of what science looks like in the industrial space.

Achievements

Academic Awards

Publications

In Scholarships

GPA

IT and Programming Knowledge

General

Python (Most familiar)
R (Great at data analysis and data viz)
Unix/bash (Very familiar. I do a lot of CLI work)
Git/Github (Performed solo and collaborative work)
AWK (Very useful for processing large datasets)
Groovy (For writing data analysis pipelines)
Java (Learned to understand other languages)
Javascript(Comfortable interacting with the web)
CSS/Sass (Made a few web projects)
HTML (Know how to webscrape too)
SQL (Familiar with relational databases)
Julia (Working on this right now)
C(Know the basics)
Verilog(Familiar with hardware logic)

Data anaylsis

Tidyverse(For general data analysis)
Bioconductor(For genomics data analysis)
ggplot2/matplotlib (For visualizing data)
numpy/pandas (For certain data analyses)

Dataflow Programming

Nextflow(Current System I use)
Snakemake (First System I used)

Containerization

Docker(For creating reproducible software)
Seqera Wave (Working on this right now)

Supercomputing/HPC's

Slurm(I work on Scientific Computing Clusters)

Web Development

React (Comfortable with key libraries too)
Django(Used for a few projects)
Node.js/Express (Familiar with)
MongoDB/Mongoose(Familiar with)

Machine Learning

PyTorch(Know how to build AI models)

Skills

DNA Work

an RNA molecule

RNA Work

a protein molecule

Protein Work

Microscopy

Software Development

Data Analysis

Scientific Writing

Automation

Web Design

Video Editing

Photo Editing

Graphic Design

Work Showcase

Below I've highlighted some of my biggest projects and achievements. I hope to demonstrate that I have a very versatile skillset and have a natural curiosity which drives me to learn new skills and improve my competancies in a variety of fields.

I truly believe it is important to be to be a interdisciplinary person, in order to both help bridge knowledge gaps on teams and expand your own understanding of how the world works. I am confident that I can bring value to any organization I'd like to work with and I hope that you will agree after reading about my experiences below. Click on the fields to learn more.

Entries in this section take a long time to put together. I am slowly working on it in my free time. Check back periodically to read each section as it is completed. To view a completed post, click here.

Wet Lab Showcase

Science Showcase

Science/Software Showcase

Science Showcase

Science/AI Showcase

Web Software Showcase

Business Showcase

Publications

My Research Publications

2024

Walker, E.J.L., Pampuch, M., Tran, G., and Karas, B. J. (2024) Spheroplasted cells: a game changer for DNA delivery to diatoms. bioRxiv. (Preprint) https://doi.org/10.1101/2024.10.10.617634

 

2023

Walker, E.J.L., Pampuch, M., Chang, N., Cochrane, R.R., and Karas, B.J. (2023) Design and assembly of the 117-kb Phaeodactylum tricornutum chloroplast genome. Plant Physiology. https://doi.org/10.1093/plphys/kiad670

 

2022

Pampuch, M., Walker, E.J.L., and Karas, B.J. (2022) Towards synthetic diatoms: The Phaeodactylum tricornutum Pt-syn 1.0 project. Current Opinion in Green and Sustainable Chemistry. https://doi.org/10.1016/j.cogsc.2022.100611

Blog

A collection of thoughts and things I've learned throughout the years

coming soon

Contact

Contact Me

If you'd like to work with me, I'd be happy to add value to your organization.

The easiest way to contact me is through my gmail. You can send an email to me directly from this site using the embedded form below if you wish. Otherwise, feel free to check me out and connect with me on social media.

Email Me

markpampuch@gmail.com

Social Profiles

Loading
Your message has been sent. Thank you!