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
The question to ask before "integrating" omics
Hello Bioinformatics lovers, Tommy here. Today's newsletter is a little late as I was taking care of the kids in the morning. Multiomics is hot and everyone is talking about it. Let's take an honest view on it. Multiomics is messy Multi-omics integration sounds powerful. RNA-seq, methylation, proteomics — stack them together and unlock deeper biology, right? Not quite. Before you run MOFA2 or DIABLO, there’s one question that decides everything. And most people skip it. The question: shared...
You're not a real biologist
Hello Bioinformatics lovers, Tommy here. I am in Yale today for an event. Hope you enjoy today's newsletter. I am a biologist too "How do people like you ever get last-author papers?" A cell biologist asked Florian Markowetz this during a 2008 job interview. The subtext: you just crunch numbers. You're not a real biologist. Markowetz went on to write one of the most important essays in our field: "All biology is computational biology" (PLOS Biology, 2017). By 2012, a funding panel had called...
The gene that fools every new analyst
Hey Bioinformatics lovers, Tommy here. Everyone once was a beginner, and I made mistakes too. However, the experience is something you gained by making those mistakes. TTN shows up near the top of every cancer exome waterfall plot. If you're new to somatic variant analysis, you'll see it and think you found a driver. TTN is the largest gene in the genome You didn't. TTN encodes titin, the largest human protein at ~34,000 amino acids. The gene has 363 exons. A coding sequence that massive...
I almost sent wrong figures to my collaborators
Hello Bioinformatics lovers, Tommy here. When you read this, I am on my way to New York City for a conference. I am pre-scheduling it at 11:30pm. I have been using Claude Code for a couple of month. I love it and the capbility of coding has been increasing. I am very impressed by the opus 4.6 model. However, just last week, I almost sent a figure with wrong cluster labels to my collaborators made by Claude Code. Watch out! The R code ran. No errors. No warnings. The heatmap looked beautiful....
Every common stat test is the same test
Hello Bioinformatics lovers, Tommy Here. I drove back from Rutgers University last night after a panel discussion on AI and bioinformatics. I am writing this in the early morning:) We talked about a lot on how AI can transform the drug development process and I do see a big potential too. btw, the campus is beautiful. But I then thought: how about the foundations, the basic statistics? Those are still the important things to learn, especially at the age of AI. Let's talk about it. In grad...
AI won't replace you. This will
Hello Bioinformatics lovers, Tommy here. It can be overwhelming with all the advancement of AI. AI won't replace bioinformaticians. But a bioinformatician who uses AI will replace one who doesn't. learn more AI In 2013, when you hit a wall — a confusing error, a method you'd never used — you posted on Biostars and waited. Or you searched for hours and hoped someone had blogged about it. Now you ask Claude or ChatGPT and get a working answer in 30 seconds. That's not magic. That's leverage. I...
Your Machine Learning model learned the noise
Hello Bioinformatics lovers, Tommy Here. 2 Months have past in 2026! Are you learning new skills? Today, we will talk about ML.Your model hit 99% accuracy. Now ask: what did it actually learn? ML models learn the artifacts High accuracy doesn't mean your model learned biology. It might have learned your batch effects, your sequencing center, your hospital's imaging artifacts. Here's a famous example. Researchers trained a model to classify wolves vs. dogs. High accuracy. Then they used LIME...
Coding only won't get you hired. This will
Hello Bioinformatics lovers, Tommy here. We had two feet snow in Boston. we lost power for 18 hours but I am grateful for that experience. Shoveling Snow Day Back to Bioinformatics. A hiring manager recently told me something that stopped me cold. Their biggest challenge isn't finding bioinformaticians who can code. It's finding ones who can talk to biologists. You can write beautiful Snakemake workflows and optimize DESeq2 parameters in your sleep. But if you can't explain why you chose...
Claude invented my gene IDs
Hello Bioinformatics lovers, Tommy here. Last week, I asked Claude Code to highlight specific genes on a volcano plot. Simple request. The data matrix used Ensembl identifiers — those ENSG + 11-digit codes that map to specific human genes. I gave Claude Code the gene symbols I wanted highlighted. Instead of telling me it couldn't map the symbols to Ensembl IDs, it fabricated identifiers that looked structurally valid. No error message. No warning. Just confidently invented gene IDs. Claude...
Why I make 12 when I only need 10
Hello Bioinformatics lovers, Tommy here. I was trained in a wet lab. And we all had the same experience: When your PI says "make 10 RT-qPCR reactions," you make 12. You remember the bad experience Not because anyone told you to. Because you've lost volume to pipetting one too many times. You just know. That instinct — the automatic adjustment born from past failures — is what separates a beginner from a practiced scientist. And bioinformatics has its own version of it. The knowledge nobody...
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