A Summer of Internship: Week 1 at Adebali Labs

Diving into the Deep End: Week 1 at Adebali Labs

Hey everyone! So, as some of you might know, this summer I've taken a leap from my computer science haven to the world of microbiology, diving into a sea I knew little about. Your friendly neighborhood coder (yours truly) landed an internship at Adebali Labs, working as a machine learning research assistant. And boy, what a ride the first week has been! Buckle up, I’m about to take you on a journey of mutant genes, wild types, and... well, some very long paper titles. 😅

Day 1-3: Lit Review Like No Other

So, on the very first day, I was handed a few papers and was told, “Read, absorb, and understand.” Easy, right? Wrong! I started off with this paper called “NGS read simulator to eliminate read nucleotide bias in sequence analysis” - or, for short, Boquila. To be honest, it took me a good minute to figure out the abbreviation! The paper was from our own lab, talking about a simulation tool for sequencing reads. Even though it wasn’t exactly what our project was about, it showed how important it is to get rid of nucleotide bias in sequences. It was kinda like debugging a code but in the DNA world!

Day 4-5: The XR-seq Chronicles

The next part of my lit journey introduced me to the XR-seq saga. Well, I call it a saga because there were two papers to dive into. The titles? Brace yourself - “Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution” and its sequel “Genome-wide mapping of nucleotide excision repair with XR-seq.” Phew! That was a mouthful. But trust me, these papers were the real deal. They introduced me to the role of CSB and XPC mutants - kind of like the superheroes of our project. While CSB mutants help in getting the Global Repair data for both transcribed and non-transcribed strands, the XPC mutants are the stars for Transcription-Coupled Repair.

Wrapping Up Week 1

After all the reading and decoding of these highly scientific papers, the first week came to a close. In a nutshell, it was all about understanding the tools and methodologies we'd be using. I've learned that while I may be out of my comfort zone, there's a lot of common ground between computer science and biology, especially when diving deep into research. This week was a solid stepping stone for what's to come in the following weeks.

until my next blog post – keep exploring