Low Coverage Thoughts

     Whether you’re on board with them or not, LLMs are taking over our education system, workplaces, and everyday lives. I consider myself fortunate that I’ve gone through the majority of education without the presence of LLMs. I can only imagine how many corners I might’ve cut during my intro CS and software engineering classes back in undergrad if I could’ve just asked Claude to fix my code. But today’s students face that constant neon glow in the back of their minds urging them to take the easy way out, and I suspect the same dynamic is creeping into the workplace as well. That’s exactly why it feels worth talking about how bioinformaticians can use LLMs not to sidestep the learning process, but to actually deepen our understanding of concepts and accelerate our workflows.       In my experience, learning with LLMs is actually much easier than working with them. Being able to quickly acquire specific and generally accurate information while studyin...

Imagine a world where you could pay to find out what your DNA says about the likelihood that you drive for leisure, or how fast you tend to walk. Well, that world already exists. For around $300, you can discover your genetic probability for everything from your addiction likelihood, to your “probability for older age of first sexual intercourse.” As strange as it sounds, this is a real service that I paid for, backed by real data and real studies—like the Mills et al. paper that identified 371 genetic variants linked to age at first sex and birth, many associated with externalizing behavior.   Last summer I sent in a cheek swab to Nebula Genomics, and 4 months later, I received a full mutation analysis of my genome along with some other information about ancestry and microbiome. I was ecstatic about getting the results, and in all honesty didn’t care if I found out anything negative. I’ve since made changes to my vitamins, supplements, and lifestyle choices. The SNP rs1172362...

Aside from my bioinformatics journey, I work as a “brand ambassador”, which is a glamorous way of saying that I set up corporate networking events. Last night I had an event in downtown Boston for a bunch of board members, and got to listen to them all talk about what their companies were up to (sadly there were no biotech companies). At a certain point in the night, I got bored of hearing about “smart, scalable data-driven solutions to next-gen problems backed by AI blockchain models,” and decided to play buzzword bingo with myself to pass the time. I’m sure you can probably guess what word that I checked off over and over and over again. The AI craze is absolutely real, but I wonder how many of the executives dumping money into it actually understand what they are implementing it for?  It seems like since covid, the surge of AI has created a corporate hysteria, driven by grossly exaggerated headlines, and overall lack of understanding. Articles warn of AI revolutionizing every in...

I’m starting this blog to share my thoughts and experiences as an MS student trying to find my footing in the field of bioinformatics. As the name — which I’m actually quite proud of — suggests, these are my unfiltered and potentially unmapped thoughts on whatever topic happens to excite me any given week. The reason I'm blogging publicly is to motivate myself to explore topics I enjoy, build a professional presence in bioinformatics, and keep a personal log of experiments and ideas to reflect on and share. Hopefully, the name Low Coverage Thoughts will one day feel like an ironic nod to these early steps in the field. This past week, I had the pleasure of attending the 3rd Spatial Biology for Drug Development Summit. It was my first conference in Boston, and overall it was a great experience — not only free to attend, but also with free food (which means a lot for a grad student). I came in with only my own research and no hands-on experience in spatial transcriptomics, proteomic...