Mathematical Oncology

Breaking Barriers: Introducing The Week in Bioinformatics to the Mathematical Oncology Community

Written by Harsha Meghadri - February 28, 2023

Dear members of the Mathematical Oncology family,

There is a simple way to package information that, under the right circumstances, can make it irresistible. All you have to do is find it.

Greetings from week in Bioinformatics substack, I would like to introduce you to the world of Bioinformatics before introducing myself. In one of many ways, Bioinformatics has started to make its way from its use in the sacrosanct halls of academic research to becoming a field of prevalence in everyday life.

If you have heard of 23&Me or MyHeritage or ancestry and used one of their services, you have indeed ventured into the field of bioinformatics. If not, did you have a recent COVID-19 jab; especially the mRNA vaccines from BioNTech? Then you have had an encounter with bioinformatics or the product of decades-long research that had Bioinformatics as a core component. Without us noticing, Bioinformatics has become a pivotal part of most healthcare applications, especially in hospitals where advancements in sequencing technologies are bringing a shift in diagnostics by implementing Machine learning models for the detection of breast cancer or as an assistant for radiologists and in clinical microbiology; where metagenomic sequencing is being applied to diagnose infections.

So, as you can assume that with such an impact on our modern lives, bioinformatics is a field that also suffers from a key pitfall like most advanced fields of biology, it is often not accessible for interpretation by the common public. The substack is an attempt to remedy that pitfall, as Malcolm Gladwell's quote above states. I am basically trying to package the information to make it irresistible for all. It is a lofty goal of sorts, but I believe that an attempt should be made to bridge the accessibility gaps.

The catalyst:

I have been writing on and off on different platforms for a while, most of it had something to do with science and a lot of it did not have a coherent thread or an overarching story to tell. Several of them still lie in dormant google cloud files collecting the proverbial dust, But the catalyst for me to start this substack was a video by Ali Abdaal. It got me thinking, of all the things I am partially good at; Writing is one of the core skills I need to hone and what better way to start than start a newsletter? But that’s not how weeklybioinfo substack started, I opened the substack put down “The generalist musings” as a stack title and hit a roadblock. After three months of hitting a wall on what to write, I decided to pick up something I do every day and write about it. As a PhD student at The German lung research centre in Hannover; I read a lot of bioinformatics papers especially the ones that have to do with exploring new computational methods for application in transcriptomics and drug repurposing.

So, I decided it would be a good practice to write about what I learned and share it with the world. This is how the newsletter started, it is still in its infancy as I weave across the new and current research every week and try to comprehend it myself, so I am able to explain and summarise it to the community. So, I am basically learning cool stuff that's happening along with you. I want to thank you for that.

The Sagas:

When Jeffrey asked how I pick my articles? I had to pause for a second, as random as it might seem at first even for me, I realized there is a small story that is building. The story of our subject, the cell; It is just such a finely tuned machine that had to be studied for almost a few centuries to get to a point where we are starting to understand the complexities that it packages. The first few posts were about spatial transcriptomics, an emerging field that merges histology, bioinformatics and microscopy into a convergent technology. It is providing us insights into the behaviour of cells within the context of tissue. With remarkable advancements in each field, the convergent nature of this technology piqued my interest. So, I wrote some explainers on that.

The same goes for the current topics that I am picking, I like the convergent nature of technology; Each complementing the other to solve a challenge that was deemed too hard to crack over a decade ago (say machine learning in the form of Alpha Fold, cracking the protein structure problem). It is my humble, possibly ignorant and näive opinion that the field of biology and bioinformatics has become much more multidisciplinary and will likely stay that way in the years to come. So, the sagas in the blog would be an attempt to document them and break it down to the general public (still challenging them to search and ask questions, i.e., It will likely take time to fully understand what I write) so they are informed and can seek to satiate their curiosity. I will also start recording podcasts with colleagues across the field to give insights into their daily research, how they got here, and their journeys towards becoming stewards of the field.

If you are curious about how I identify papers, It's a relatively simple system. I have a TweetDeck of selected topics I follow, I believe that scientists have an inherent interest to communicate their results, so Twitter is a good source. Similarly, I have set up an RSS feed in my personal slack channel from biorxiv that keeps me updated on topics of interest. Based on these, and the previous post I have written, I pick the five most relevant articles and give them a glance through and start writing about two of them. As much as I would like to write about them all, I realize my limitation of being human and would avoid anything that would lead me to burnout.

The Hominid

So, if you made it here, I would now introduce myself in a few bullet points.

  • Sri Harsha Meghadri, call me Harsha. I am from India and am currently a PhD student in Germany.
  • My background is in molecular virology followed by bioinformatics.
  • Apart from research, I enjoy reading, taking walks if the sun is shining, pretending to be a photographer, talking philosophy, and cooking Indian food to feed my friends to their necks.
  • So, I think you can classify me as a nerd, I am pretty sure that all my social media recommender algos do it already.

If you like the idea of exploring bioinformatics and would like to know further about the blog and maybe join our tiny community, join the subscribers chat for updates and please check out the post below and drop in a Hello:

The who, why and how of this.

Image Credits

The cover image was created by Harsha Meghadri using Midjourney. It shows an Imagined image of a community in the style of Georges-Pierre Seurat.
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