Hello Bioinformatics lovers,

How are you doing this week? Are you better than last week in terms of mastering bioinformatics?

Curiosity is the best teacher. Always stay curious and learn the new things out there.

If you do not know NotebookLM yet, try it out. It turned my blog post on AI and drug discovery into a podcast! Listen to it here https://notebooklm.google.com/notebook/6357db4d-2088-453e-bff2-56cb1c09f15a/audio.

You can use NotebookLM to research bioinformatics topics.

Now let's dive into today's topic. My regret is not learning linear algebra well during college.

I barely passed the exam for it (and calculus, it was a nightmare :) .

To be fair..

It was not taught well and it sounded too boring. I did not know what the application of matrix multiplication was, not until...

Many years later, I started to learn bioinformatics. I find many data are just data matrices:

1. an RNAseq expression matrix is a gene-by-sample matrix, with entries to be read counts for each gene
2. a single-cell expression matrix is a gene-by-cell matrix, with entries to be read counts for each gene
3. a ChIP-seq count matrix is a peak-by-sample matrix, with entries to be the number of reads in each peak
4. a drug response matrix is a drug-by-sample matrix, with entries to be IC50 for example

and many more... in other words,

Matrix is EVERYWHERE for bioinformatics (and many other data science topics)!

Read this blog post on Matrix factorization on single-cell RNAseq data to see how useful it is! I am writing a blog post on how Seurat PCA projection and label transfer work for single-cell RNAseq data in low-level details.

Man, it is hard. I have already spent 6 hours for the last 3 nights on it. But I enjoyed it as I also learned the topic deeper. I will publish it tomorrow and will share it with all of you.

During the writing of the post, I really wished I learned linear algebra better during college:) but it is never too late to learn. You can take MIT1806, which is a great course for linear algebra.

What's your regret?

Let me know by replying to this email.

Happy Learning!

Tommy aka crazyhottommy

PS:

If you want to learn Bioinformatics, there are four ways that I can help:

1. My free YouTube Chatomics channel, make sure you subscribe to it.
2. I have many resources collected on my github here.
3. I have been writing blog posts for over 10 years https://divingintogeneticsandgenomics.com/​
4. Lastly, I have a book called "From Cell Line to Command Line" to teach you bioinformatics.

Stay awesome!