A Few Things I am Learning as I am Building
Specifically tied to my current research project regarding the gene conservation of the BBB in human, mouse, and macaque.
Almost a year ago, when I had my first research experience, which resulted in a published paper, I began to understand one thing:
I genuinely have no clue about anything.
And I am not declaring this to make myself smaller in any way — but rather as a result of having done research once. The overwhelming amount of information you can find nowadays on any given topic is astounding. And the paper I worked on was a systematic review with little bioinformatical ground (which I am now focusing on).
So when I got the chance to do a more bioinformatically centered research project, I didn’t hesitate, because I knew that no matter how much I’d prepare, it would prove to be quite useless in the face of the ever-growing number of bioinformatics pipelines for every imaginable biological problem you can think of. And so far, it has been one of the hardest things I have done.
Get Yara Comments’s stories in your inbox
Join Medium for free to get updates from this writer.
The project aims at comparing the conservation of genes in the blood-brain barrier (BBB) of human, mouse, and macaque. As a secondary question, I thought it might be useful to analyse the RNA datasets of these species in order to get expression levels of conserved genes.
Now, why might this project be useful as a learning opportunity? I think the answer is tied to the importance of the actual question one might answer: Are the models we currently use for drug development for neurodegenerative diseases sufficient in their accuracy, since they start in mouse, progress to macaque and then start their clinical trials in humans? With a staggering 86–92% failure rate, it seems like these models might be outdated. Or, maybe the models are not outdated — maybe we are not understanding the underlying functions of the BBB itself.
Now, I am not saying that my particular project will offer new insight into this issue. Rather, it remains a guided project for me to understand why I am doing this particular research, how this could affect research topics, and what skills I can hone by sticking to a hard research question — even if my computational knowledge might not be enough.
When I started this project, I had little academic guidance from systematic research. I had not developed the skills to look into a research paper and decide which information is important to what I am building. Now I can say that the skill has improved and might be adequate for someone at my stage of research. The past year taught me that skipping over the research already done in your field leads you nowhere. My first bioinformatics pipeline did not work as I supposed it would, mainly because of my inability to check what other research teams had done in the BBB gene comparison space.
After a review of what I had built so far, I returned to reading multiple papers and understanding different methods for gene conservation. So far, I have an understanding, but no new pipeline yet.
Nevertheless, sharing these updates helps me keep track of what I am working on and the progress I have made (since these projects take a while to come to fruition). For now, I am building a rough pipeline sketch (again) for the gene conservation of the BBB across human, mouse, and macaque.
PS: If you have read the other articles, you will notice that this project is also my case study for Theioptera. Currently, under these conditions, it performed best for guiding me through papers — it does not work well for bioinformatics (yet).
