Pursuing Biomedical Informatics as a Potential Research Topic in Medical School

[teerock]

Hello, I am a pre-med student that is thinking about what research topics to pursue in medical school (regular MD, not MD/PhD). I have been programming for quite some time (I'm a career changer with training in engineering). I've come across Biomedical Informatics as a potential research area and I'd like to know more about the type of work that someone doing research in this field does.

For any medical students that are pursuing Bioinformatics research or research that uses Bioinformatics currently:
- What is your research topic and why did you choose this? What does a day in your life look like?
- What statistics/mathematics/computer science foundational concepts do you think are absolutely essential for your work?
- If you didn't have a bioinformatics/data science background, how did you go about learning what you needed to know for your work?

I've looked online a bit already to get an idea of what Bioinformatics sort of entails but I would like to hear from an actual person in the field. If there is a better place to ask this question, please let me know! Any help would be appreciated! Thanks!! =)

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[deleted849476]

Did bioinformatics research in undergrad so not entirely what you’re looking for but I feel it set me up for taking on similar research soon maybe during second year next year. SE bachelors, used BLAST+ with shell scripting, python, i think 1 Perl script, Excel, etc. Wasn’t doing anything statistically heavy so no R or even any special python libraries. The CS background was enormous, without it I wouldn’t have had time to learn programming, the command line, even just how to get data from an FTP host programmatically, etc. Someone would really have to be driven and have ample time without any background in CS to do anything meaningful as a complete newbie.

But that research was super nice because my average day was spent writing a script for an hour then executing it on loads of DNA sequence data which took upwards of 2 weeks in some cases. My mentor had little clue what I was doing behind the scenes so I had a lot of responsibility and had to communicate a lot for transparency...Would love to do something similar In med school. My topic was microbiome and I used data from the human microbiome project although my research question wasnt strictly clinical per se.. I’d want to do something more clinical in the future.

if you’ve got programming chops any micro dept could put you to work that’s for sure.

 

[Tangerine123]

I'm not a bioinformatician so I can't answer all the questions, but this is my experience in doing a PhD after medical school:

Finished med school, then I decided that I wanted to go into research so I applied and got accepted in a combined PhD/Residency.

I chose Neuroimaging and Neurogenetics as my topics because I went into Psychiatry.

With no previous background in Bioinformatics I just had to sit and learn everything from scratch. Joined some workshops in my University and learned the basics of R/Python/Matlab. Also took more specific courses like how to run a GWAS. Online courses (Coursera) also helped a lot.

At the beggining of the PhD I shadowed the last year students and they showed me how to use specific packages related to our field of work (Neuroimaging mostly).


Most things are user friendly, so it wasn't that overwhelming. At the end it also boils down to trial and error. You have little to no supervision at the PhD level, everything is up to you and you get limited time with the experts to solve questions.

As for my day to day life

I have 2 current projects. The first involves data analysis of a recently concluded 5 year clinical trial. However this project is stalled due to having issues with getting access to NIH databases, hopefully it gets resolved soon.

So right now I'm focusing on my 2nd project. Currently on the experimental phase.

I reclute my patients or healthy participants in the morning. Explaining the study and the informed consent lasts around an hour. Then I extract a blood sample and schedule them for 2 MRI sessions

In the afternoons I run my fMRIs. I don't have access to any radiology technician of any sort. Learned how to use an MRI and now I run my sequences together with a masters student.

I can check the data quality using a Matlab toolbox. But it will take me around 8 more months to finish the experimental phase and get to data analysis.

There are other PhD students (MDs and from other fields) and we get together with our PI once a week to discuss how our projects are going. Sometimes somebody else needs help with their project, so I help them out and learn new techniques and procedures in the process.

We do have a bioinformatician in our lab that helps us with pipelines and whatnot, but after a certain point we become more autonomous and don't rely so heavily on him.

I'm lucky to be in a really friendly and relaxed research group. When I don't have to reclute participants or run fMRIs I can just do Home Office or use the time to do other academic or personal activities.

If you haven't started anything yet then I suggest that you do look for a combined MD/PhD or a Residency/PhD program in the future.

I have the ability to switch back and forth between the PhD and the Residency components of my program on demand. If you do clinical and then 3-5 years of pure research then you might lose certain skills and will probably burn out faster.

 

[numbersloth]

Finished med school, then I decided that I wanted to go into research so I applied and got accepted in a combined PhD/Residency.

Are you in the US? Are residency programs like this common?

 

[Tangerine123]

Are you in the US? Are residency programs like this common?

I'm a US IMG in Germany. At some point I was torn between Europe and the US. The time it took me to speak German fluently from scratch was around the same time needed to study for the USMLE as an IMG ahahaha.

I do know that there are residency programs in the US that offer a combined research/PhD track.

Here's one of the programs in the US I considered.

Psychiatry Residency Research Program | NYU Langone Health

NYU Langone’s Department of Psychiatry offers a comprehensive Psychiatry Residency Research Program with two research tracks.

med.nyu.edu

 

[teerock]

Wow hey thanks yall for the replies! this is really helpful =)

I'm not the greatest programmer in the world or anything but I do enjoy it a lot and it's also just a really valuable tool to have in your pocket for solving problems and increasing work productivity/efficiency. I have a good amount of experience with python/excel macro programming/command-line but haven't touched matlab for years lol so maybe i'll revisit that a little. R has been on my list of things to learn for a while now haha... But anyway, good to know there are a few options for applying those skills in different fields of research.

I'm actually applying this cycle haha. I do have research experience but not the amount that I think is required to be seriously considered for an MD/PhD program. But wow I didn't even know there were Residency/PhD programs! that's great and something I will look into more. I know that I want to do research in general (during medical school and hopefully later on in my career as well). Congrats @Tangerine123 on the Residency/PhD btw! seems like it's pretty fun work, i like the flexibility in moving between research and residency stuff