Chatomics! — The Bioinformatics Newsletter
Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free
Why KNN Isn’t as “Simple” as Everyone Says (Especially in Single-Cell RNA-seq)
Hello Bioinformatics lovers, Tommy here. KNN looks simple. But in single-cell RNA-seq, it’s an art disguised as an algorithm. Everyone talks about k-nearest neighbors (KNN) like it’s the easiest algorithm in machine learning. In theory, it is: You classify a point based on the majority of its k closest neighbors. Just one hyperparameter—k. What could go wrong? A lot, actually. The Hidden Complexity Choosing k is a balancing act: Small k → low bias, high variance. Large k → high bias, low...
The One Terminal Hack That Saved Me 10 Hours a Week (And Why You’re Still Wasting Yours)
Hey Bioinformatics lovers, Tommy here. Quick question: How many times have you stared at a blank terminal after a crash, wondering, “What the hell did I just type?” If you’re like most bioinformaticians I talk to, the answer is too damn many. Last week, I was knee-deep in a bulk RNA-seq analysis. Hours invested. curl to download the data, STAR to align the fastqs. Then—bam. yeah, pun intended :) Something went wrong. Everything gone. No history. No notes. Just me, rebuilding from scratch like...
Why 90% of your figure time isn’t plotting (it’s polishing)
Hello Bioinformatics lovers, Tommy here. It is the end of Fall in Boston. I am going to go apple-picking with the family today. So when you see this newsletter (pre-scheduled), we are on our way. (I am writing this newsletter at 1:15 am) We will discuss creating figures today! This is the ultimate skill you need to have as a bioinformatician. The hidden work of every figure When you think about making a figure as a bioinformatician, you probably imagine writing code, choosing colors, and...
The Truth About Bioinformatics No One Told You
Hi Bioinformatics lovers, Tommy here. Please forward this newsletter to someone if you think it will help them. I've just written a hands-on tutorial on up-leveling your skills in analyzing RNA-Seq data. I will show you how to use purrr::map() and list column to avoid repetition in your R code. Read it here. Today, we will talk about doing bioinformatics like doing an experiment: Bioinformatics is running experiments too Bioinformatics isn’t just crunching numbers. It’s not staring at a...
You’re wrong about protein abundance—and it’s costing you discoveries
Hello Bioinformatics lovers, Tommy here, I gave a talk at Boston University sharing my experience in learning bioinformatics. You can find the recording here. There is a Q&A section at the end that you may find helpful as well. Due to my background in a wet lab, I focus primarily on the biological side when I do bioinformatics analysis. (That's your strength if you are from a biology background) Most bioinformaticians fall into the same trap:They assume protein abundance equals protein...
The Lie That’s Keeping You From Mastering Bioinformatics
Hello Bioinformatics lovers, Tommy here. Everyone wants to master bioinformatics fast. There is no shortcut But here’s the cold truth: speed is a lie. Time is your ally. After 13 years in the field, here’s what I’ve learned. Bioinformatics is not a crash course It’s not “learn Python and call it a day.” It’s a craft. Like a language, you grow into it. I wrote my first “Hello, world” script 13 years ago. It was slow. Messy. Frustrating. But it was real learning. What time gives you With...
The One Skill That Separates Bioinformatics Pros from Frustrated Analysts
Hello Bioinformatics lovers, I just crossed 50K followers on LinkedIn! Hooray! I hadn't realized that so many people are interested in Bioinformatics. To celebrate this, today, I am going to talk about: Regular Expression! Regex: The hidden Superpower in Bioinformatics Messy data is the rule, not the exception, in bioinformatics. And yet, most wet lab scientists—and even many computational ones—don’t realize that the difference between chaos and clarity often comes down to one tool: regular...
What skills to learn to succeed in the coming 5-10 years
Hello Bioinformatics lovers, The other day, I saw Josh Starmer's post: Josh had a great answer: Do something that nobody/fewer people are doing. What comes to my mind is: a strong foundation in statistics. Yeah, everybody is talking about AI, but for Bioinformatics, conventional statistics is still more widely used in our daily work. For example, in addition to learning the most recent advancement of AI, I am re-reading this stats book: Data Analysis for the Life Sciences. I get to refresh my...
Why Deep Learning Isn’t Always the Answer in Bioinformatics
Hello Bioinformatics lovers, Tommy here. Summer is over in Boston. I love the chilly wind, and I can already smell the Fall. What's your current challenge in learning bioinformatics? Are you overwhelmed by the LLM and deep learning papers? Think you need deep learning for every bioinformatics problem? Think again. Most of the time, simpler models not only hold their ground—they win. Deep Learning is not always the solution, not even machine learning Structured biological data like gene...
Why being a “bioinformatics expert” is both true and false
Hello Bioinformatics lovers, People complain about my chatomics YouTube audio quality. I take the feedback! I just spent $100 on a wireless microphone, and I hope the audio quality will be much better. The fact is that when I started my channel 2 years ago, I did not think too much about the quality. I just opened loom, and started recording. over 120 videos later, I think I need to pay a little more attention to the quality now :) Thanks for your support as always! Today, we will talk about:...
Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free