Publications, Dissertations, Job Hunts, and a Pandemic

I started this github site as a place to expand my professional reach by posting my random musings on bioinformatics, Linux, data science, and etc. I made a few reasonably cogent posts, but then life got in the way! It's been a really busy time, a very eventful year. I'm now in a very different position than I was last summer. It's exciting progress, but hanging over all of it is the COVID-19 pandemic. I'm going to write another post specifically dealing with job hunting as a Ph.D. student, but here I thought I'd kick off my blog again with a general update since it's been a while.

Wrappig up Grad School During the COVID-19 Pandemic

My lack of posts began mostly as a consequence of the need to grind harder than I ever had before on my dissertation research. However, I was succcessful and finished my third publication during my Ph.D. program. It's since been accepted in PNAS, but I'm not sure when the final version will be available. Until then, you can read the bioRxiv version:

Abundant expression of maternal siRNAs is a conserved feature of seed development

As with many things in grad school, progress on this paper wasn't consistent. It happened in a series of spurts, with a large portion of the work really only happening once we got the final sequencing samples we had been waiting on last summer.

Along with that comes the need to write a dissertation. Since I had thee papers my committee was happy for me to do what's called a "staple dissertation." The name here is a bit incorrect, I did have to write more besides putting together my papers. However, this also took a significant amount of time.

While this was all going on, I attempted a short-lived bioinformatics/data science student group. Though, in the end wrangling grad students is a bit like herding cats. Still, I think it probably helped other grad students, which was the point.

Back in January I really started to look at job postings more seriously because I had known from the very beginning that my goal was to go back to industry. Mostly I was looking at bioinformatics scientist-type positions. I really threw myself into this, and I think all-in-all I probably put out 150 applications.

Then, as we all know, the pandemic hit in a big way for all of us. Labs were shut down, jobs were lost, colleges went online. I was in the phase of my Ph.D. where I needed to write my dissertation and apply for jobs, so I wasn't disrupted as much as most. However, it was definitely disheartening to have my job interviews dry up. Luckily, it seems that people with bioinformatics experience are still in high demand though and I was able to land a good job regardless. Not without becoming more and more concerned on a daily basis and the rejection emails started to roll in. Overall though, I think that the prospects for biology and bioinformatics in particular are still strong. We might not be "essential" workers, but it's hard to justify to employing people like us at a time when we could actually discover something vitally important to help with the current situation. Or, at the very least, the pandemic underscores that biology is important, and needs to be taken seriously, funded, and considered more by society in general. The pandemic will be temporary, but perhaps society will continue to think about biologists more frequently.

Just last week, I defended my Ph.D. It was a fantastic moment, even if it had to happen over a Zoom meeting. Following this, and wrapping up everything, I'll be moving to Boston to be closer to my new employer, Seven Bridges Genomics. There, I will be working as a "Genomics Scientist" to aid bioinformatics workflow development and coordination of data and metadata availability for their public programs. It's a great way to move on from grad school.

Moving forward, I'm going to try to keep up with posting things. Lots of exciting things happening! Hopefully I can keep my skills sharp, and I think this blog will be essential for that.