Chatomics! — The Bioinformatics Newsletter

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...

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...

Hello Bioinformatics lovers, Tommy here. AI is taking over the world. It is the same with Bioinformatics. I watched Claude Code parse my VCF files, run comparisons, generate plots, and spit out insights — all faster than I could type the commands myself. Commands I learned through years of hard experience. Typed in seconds. It was exciting. And honestly? A little unsettling. After two months of using Claude Code for bioinformatics work, here's what I've learned: AI is remarkably good at the...

Hey Bioinformatics lovers, Tommy here. Today's newsletter will be short. I am in Singapore for the 40th AAAI conference. I visited the Genome Institute of Singapore (GIS) and gave a talk about reproducible bioinformatics. Read the slides here I added a couple of tips using AI tools such as Claude Code to write documentation and revamp R/Pthon packages. I hope you find it helpful. I met Tim Stuart (author of Signac. if you work on single-cell ATAC, check it out!). He is a faculty member now in...

Hello Bioinformatics lovers, How is your first week of 2026? We are all busy with setting goals, but the real power is in executing them daily (e.g., I have been posting on LinkedIn for 693 consecutive days). The math is simple: you hit your daily goal --> you will hit your weekly goal --> you will hit your monthly goal --> you will hit your yearly goal --> you will hit your 5-year goal --> you will hit your 10-year goal. Life has to be intentional. If you have an idea where you want to be in...