Targeting TROP2 in drug-tolerant persister cells delays EGFR tyrosine kinase inhibitor resistance in non-small-cell lung cancer www.cell.com/cancer-cell...

1/ Bioinformatics is more about biology + informatics. It’s about formats. And pain.

1/ I asked a senior labmate for help when I started bioinformatics. They refused to share their script. Like it was gold. That stung.

Sixteen years of driving. Not one accident. Until this week, at a red light, when I rolled into the car in front of me. Slow enough that the damage was small — their bike rack punched a neat hole in my bumper. I called Geico, filed everything, nobody hurt.

PPARα activation overcomes fibroinflammatory liver microenvironment-associated anti-PD-1 resistance in hepatocellular carcinoma by mediating GSDME-dependent pyroptosis www.nature.com/articles/s4...

MIT FREE course! The Missing Semester of Your CS Education 2026. It now has an agentic coding session! missing.csail.mit.edu/2026/agenti...

1/ My friend spent two years on a project that was broken before he ever touched a pipette. The transgenic mice arrived. The gene knock-in was supposedly already validated. He just started running experiments on top of it.

A chromatin-informed transcriptional regulatory framework to stratify patients and guide therapy selection in triple-negative breast cancer www.nature.com/articles/s4...

resources to bookmark: 237 Cohorts, 2256 Datasets. Xena UCSC gives you prepared datasets for genomics data analysis xenabrowser.net/datapages/

1/ You don’t become a bioinformatician by solving problems. You become one by surviving the tools.

protip: use web archive (waybackmachine) to find the content of the broken web link web.archive.org/

I was teaching my four-year-old to play Guess Who. The rules are simple: you take turns asking questions, narrow it down, first to guess the other person's character wins.

Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis www.nature.com/articles/s4...

Understand NGS sequencing files bioinf.comav.upv.es/courses/seq...

If I told you the answer to “How many ER binding sites are in MCF7 cells?” is anywhere between 1,000 and 20,000—would you believe me?

Genome Biology: DeMixNB: deconvolution of sparse-count RNA sequencing data for tumor cells using embedded negative binomial distributions link.springer.com/article/10....

DeMixNB: deconvolution of sparse-count RNA sequencing data for tumor cells using embedded negative binomial distributions

Genome Biology - Estimating tumor-specific transcript proportions from mixed bulk samples has potential to inform novel biology. However, estimation accuracy using existing methods in sparse-count...

link.springer.com

Plasticity of extrachromosomal DNA segregation during drug adaptation www.nature.com/articles/s4...

Data is the bottleneck. Not your foundation models. 1/ This diagram is one pathway. PI3K/AKT. Seven different receptor types feeding in, three classes of PI3K, two mTOR complexes branching out downstream. And it is still a simplification.

The pitfalls of class prediction in omics 🧵 1/ You think you’ve built the perfect omics predictor. The accuracy is high. The p-value is low. But is it real—or just a story your data whispered back?

Artificial integlligence in drug discovery www.nature.com/articles/s4...

🧵 1/ In high-dimensional bio data—transcriptomics, proteomics, metabolomics—you're almost guaranteed to find something “significant.” Even when there’s nothing there.

1/ Bioinformaticians, I’ll say it loud: Never blindly trust the data you're given. Not from collaborators. Not from vendors. Not even from “reliable” sources. Here’s why:

My next newsletter "I called it noise. It was stress." arrived today. Subscribe to get it and stay in the loop on everything I'm creating. divingintogeneticsandgenomics.kit.com/profile

Data visualization is a critical step in data analysis. 8 links to bookmark for better data visualization:🧵

want to up-level your bioinformatics skills? End-to-end tutorial on RNAseq analysis 👇 Chatomics! new blog post: Do not repeat yourself: List column to do RNAseq differential expression analysis divingintogeneticsandgenomics.com/post/list-c...

1/"I have a presentation tomorrow." If you've ever collaborated with wet lab scientists as a bioinformatician… you’ve heard this. And died inside a little.

If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/

AI is a tool. Same as every other tool. Most people get this backwards. Something from a panel stuck with me last month.

1/ Bioinformatics moves fast. If you rely only on recipes from books, you’ll soon find they’re obsolete. Let me show you why. 🧵

Toward generalizable and interpretable AI in regulatory genomics www.nature.com/articles/s4...