Hi! I'm Tommy Tang
I am a bioinformatician/computational biologist with six years of wet lab experience and over 12 years of computation experience. I will help you to learn computational skills to tame astronomical data and derive insights. Check out the resources I offer below and sign up for my newsletter!
New post from chatomics! Exploring Spatial Transcriptomics A Dive into Visium Data Analysis in Python
Hello Bioinformatics lovers, I enabled my blog https://divingintogeneticsandgenomics.com/#posts RSS feed. So whenever I have a new blog post, it will be sent to your email. This is different from my weekly Saturday newsletter. My blog posts are mostly technical tutorials. This is new update from my blog: Exploring Spatial Transcriptomics A Dive into Visium Data Analysis in Python Published on May 3, 2025 Why guest posting? I want to write more hands-on tutorials, but I realized: I am not an...
Matrix Factorization: The Secret Language of Gene Expression
Hello Bioinformatics lovers, Tommy here. Summer is finally here in Boston! I look forward to more outdoor activities with the kids. Okay, let's get into today's topic: Matrix Factorization Matrix algebra used to feel abstract. Something from a dusty textbook. All symbols, no meaning. Then I applied it to biology. And suddenly, it was everywhere—in my RNA-seq pipelines, my proteomics scripts, even single-cell analysis. Let me show you what changed. The Matrix Is the Foundation of -Omics...
Seven Books for you to learn bioinformatics
Hello Bioinformatics lovers, It was my birthday on April 24th. I gave a PCA and CCA for a single-cell annotation workshop on the same day. It is pretty meaningful for me to distribute knowledge on a special day. You should go and follow the step-by-step tutorial here https://divingintogeneticsandgenomics.com/talk/2025-pythia-cell-anno/ Today's newsletter is simple: seven books to learn bioinformatics. 1. Data Analysis for the Life Sciences https://leanpub.com/dataanalysisforthelifesciences...
Heatmaps Are Lying to You (Unless You Understand These 2 Things)
Hello Bioinformatics lovers,How is your learning going? Are you learning a bit more than yesterday? The past week was challenging for me. Two sick kids and a sick wife. Three extracted wisdom teeth did not stop bleeding I had them fixed, going back to the dental office, and then I became sick. (If you have kids, you know how it works when one of them is sick...) However, I still got quite a bit done. I made this video for the ChIP-seq analysis tutorial in the playlist. Okay, let's talk about...
From Wet Lab to Code: Why Biologists Should Embrace Data and AI (But Carefully)
Hi Bioinformatics lovers, How are you doing? It is April, but it still feels like winter here in Boston. It makes us warm that we hosted Josh Starmer (you should go and check out his Statquest YouTube video on statistics and machine learning) at our home. I even got his "The StatQuest Illustrated Guide to Neural Networks and AI" book signed by him! Our kids had a lot of fun playing UNO with him. Tripple BAM Okay, let's dive into our topic today: Learn coding and AI. I used to be just like...
This Bioinformatics Mistake Costs Labs Thousands (But You Can Avoid It)
Hello Bioinformatics lovers, Tommy here. Welcome, all the new subscribers! Today's newsletter is a little late. I usually write it the day before and send it out early Saturday morning. The previous week and coming weeks are super busy, and I have a presentation every week.I still get nervous when I give a presentationEven after 17 years in the US. And it is NORMAL. Okay, let's dive into today's topic. The communication between Bioinformatician and wet lab scientists. Avoid This Costly Lab...
GSEA Demystified: How to Make Sense of Gene Set Enrichment Analysis
Hello Bioinformatics lovers, I post a long post on Linkedin every day. I then pick the one with the most views and expand it to this newsletter. It is surprising to me that the GSEA post gets the most impressions, although the method was published over 10 years ago. I am a data scientist, and I use data to guide my decisions:) So, let's learn more about it! If you've ever worked with RNA-seq data, you've probably been asked to perform Gene Set Enrichment Analysis (GSEA). It is one of the most...
The Secret to Recreating Any Bioinformatics Figure (It’s easier than You Think)
Hello Bioinformatics lovers, Tommy here. I want to teach you the fundamentals so you understand how to solve a problem from the ground up! The other day, I was on Reddit and saw someone ask how to generate the figure below. Let me give you some general principles for approaching this type of problem. How to Recreate Bioinformatics Figures Have you ever seen a great figure in a paper and wondered how to make something similar? The key is to break it down step by step before you start coding....
Learn to Fish: Mastering Matrices for Bioinformatics
Hello Bioinformatics lovers, Tommy here. The purpose of this newsletter is simple: teach you how to fish, not just hand you fish. There are so many concepts I wish I had learned differently. Let’s break them down in a way that makes sense. 1. Common statistical tests are just linear models Many statistical tests—like t-tests and ANOVA—are just special cases of linear models. Understanding this will change how you see statistics. Check out this great resource:Tests as Linear Models 2. Matrix...
How I Would Learn Bioinformatics From Scratch 12 Years Later: A Roadmap
Hello Bioinformatics lovers, First of all, thanks to all the subscribers and I hope you get value from this newsletter. I want to shout out to Krittiyabhorn (Namthip), a PhD student in Thailand. Her journey should be an inspiration for all of you. Just get started! read her post here. And make sure you check out her blog posts too. They are all well-written and attending to details. The best way to learn is to "just play around". Unfortunately, many of the students just do not get started....
I am a bioinformatician/computational biologist with six years of wet lab experience and over 12 years of computation experience. I will help you to learn computational skills to tame astronomical data and derive insights. Check out the resources I offer below and sign up for my newsletter!