Chatomics! — The Bioinformatics Newsletter
Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 150K+ 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
4 tests before you trust vibe-coded results
Hello Bioinformatics lovers, Tommy here. With less than 100 days left in 2026, what's one thing you want to achieve by then? Fall is here. One falling leaf tells you autumn has come. （一叶知秋） Let's get into today's newsletter. Claude Code once handed me a script to highlight Ensembl gene IDs in my volcano plot that looked perfect, ran without a single error, but the Ensembl ID does not match my intended gene. I caught it only because I cross-checked the mapping and I do not see my expected gene...
What 1 year of Claude Code taught me
Hello Bioinformatics lovers, Tommy here. It is the Chinese Mid-autum festival today during which the families get together and eat the moon cakes. Travel safely if you are in the areas that the huge Nor'easter storm hits. I am staying home because of the heavy rain and strong wind. Be safe. Now, let's get into today's newsletter. We over-expressed a wild-type protein that belongs to a multi-subunit complex, expecting it to restore the complex's function. As a control, we also over-expressed a...
Why your gene signature won't replicate
Hello Bioinformatics lovers Tommy here. Today's newslettere is Sponsored by Bright Data. Bright Data turns any public website into a hosted data API from a single prompt. ========= I typed one line into Claude Code: install the Bright Data CLI, my API key is in .zshrc, connect the MCP. It handled the install, the config, all of it. I restarted Claude Code and the bright-data server showed up with its tools loaded. Then I asked in plain English: find the top 5 most discussed AI papers today on...
Why I walk to the wet lab before I write code
Hello Bioinformatics lovers, Tommy here. Today's newsletter is Sponsored by Apodex =============================== Four years ago I spent an afternoon hand-pulling metadata out of a GEO scRNA-seq dataset. I wrote a whole blog post about how annoying it was. Last week I gave Apodex 1.1 the same job. One prompt: read this paper, find the supplementary file and the GEO dataset, give me a metadata CSV with responder status. Supplementary Table S1 has no R/NR column. It derived the labels from the...
When does a foundation model actually help
Hello Bioinformatics lovers, Tommy here. Kids school starts this week. Ready to learn something new? Twenty RNA-seq samples. Responders and non-responders to a drug. Two ways to find what separates them, and one of them will fool you if you're not careful. Option A: run the samples through an RNA foundation model, pull sample embeddings, feed those into logistic regression or lasso, validate with leave-one-out cross-validation. You might see an AUC of 0.9. Everyone gets excited. Too good to...
What's the real efficiency gain of AI in your workflow
Hello Bioinformatics lovers, Tommy here. Another issue of the chatomics newsletter. Honest question: What's the real efficiency gain of AI in your workflow? Even for coding, it is more likely 2x (or less) my efficiency rather than 10x.For data analysis, now I can do much faster experiments, but need more time to verify the logic and results. Verify the AI results Biology domain knowledge is your edge.For software engineering, I can quickly vibe code an application but probably need a real...
12,000 cells in, 12,000 cells out
Hello Bioiinformatics lovers, Tommy here. Summer is almost over. I hope you take the time to relax and learn new things. I am using it daily for my bioinformatics analysis, and it can trip you over if you are not careful. Claude Code built me a metacell analysis last week. I started with 12,000 cells. When it finished, the matrix still had 12,000 cells. That number told me everything. (You still need to read the code and output carefully to find things off) The number does not seem to be...
The batch effect that flipped a landmark study
Hello Bioinformatics lovers, Tommy here. Today's newsletter is a little late :) In 2014, the Mouse ENCODE Consortium reported something that should not have been possible. They sequenced tissues from mice and humans, then compared the gene expression profiles. The samples clustered by species, not by tissue. A mouse liver looked more like a mouse skin than a human liver. That contradicted decades of comparative biology. It is a surprise if you know biology A year later, Yoav Gilad and Orna...
I called it noise. It was stress.
Hello Bioinformatics lovers, Tommy here. We will talk about why biological background is important for Bioinformatics analysis. A single-cell dataset came back looking wrong to me. I put it down to noise and moved on. The wet lab biologist who ran the experiment looked at the same plot and said the cells were under stress at that point. The pattern stopped being noise and became a result. No parameter sweep would have gotten me there. The information was not in the count matrix. It was in the...
The plotting skill no package gives you
Hello Bioinformatics lovers, Tommy here. Today, we will talk about data visualization, a critical skill for bioinformatics. Type kuva box samples.tsv --group-col group --value-col expression --terminal and a box plot appears inside your shell. No file, no image viewer, the plot renders in the terminal itself. kuva is a new scientific plotting library written in Rust. It covers 60 plot types, outputs SVG by default, and adds PNG and PDF through optional backends. The terminal rendering is the...
Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 150K+ 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