Off-pore Nucleoporin sPOM121 Transcriptionally Propels β-Catenin–driven Tumor Progression and Immune Escape in Prostate Cancer aacrjournals.org/cancerdisco...

1/ Everyone’s chasing AI. But in bioinformatics, solid foundations still win. Here’s why mastering the basics matters more than ever. 🧵

1/ R vs Python for bioinformatics? Which one should you learn first? I’ve used both. I started with one. Here’s what I learned the hard way:

He asked if the moon was fake My wife called after parent-teacher night. Second grade report: math is decent, English needs work. Especially writing and reading.

Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer aacrjournals.org/cancerdisco...

I gave a talk on good enough practices for reproducible Bioinformatics at the DataDrivenPharma event organized by Ilya a while ago. Thanks, Eric Ma, for hosting us. Please find the slide deck at this link divingintogeneticsandgenomics.com/talk/2025-m...

1/ You can't bolt AI onto chaos. In biotech, if your data is a mess, your AI won't save you. Build the data strategy first. Here's how.

When "better" means less My colleague saw me eyeing the ping pong table in our office building.

Subclonal immune evasion in non-small cell lung cancer www.cell.com/cancer-cell...

Efficient Genomic Data Analysis with tile(). 1/ Working with large genomic datasets? The tile and slidingWindows functions from GenomicRanges can help you split and analyze your data efficiently. Here’s how they work and why they’re useful. 🧵👇

1/ Your genomics analysis just failed. Not because your pipeline broke or your statistics were wrong. But because you were not clear when the sample was taken. Here's why treatment timing changes everything in cancer genomics:

"Is Molly here?" This morning, I dropped my 3-year-old at daycare—usually my wife's routine, but today was different.

The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression www.cell.com/cancer-cell...

1/ Three months ago, you made a figure. Today, someone wants you to change it. You have no idea which script created it. This moment—right here—is where reproducibility dies in bioinformatics.

1/ You tested 10,000 genes. 500 are significant (p < 0.05). Exciting? Maybe. But if you used raw p-values, you just got played by randomness. Let’s talk FDR.

300 Seats. One Empty Space. My first Moth StorySlam in Boston. The room packed. Laughter rolling through the crowd like waves.

A pan-KRAS inhibitor and its derived degrader elicit multifaceted anti-tumor efficacy in KRAS-driven cancers www.cell.com/cancer-cell...

1/ You think clinical trial genomics is simple: compare pre‑ vs post‑treatment RNA‑seq. But even getting clean metadata? That’s a war.

How cancer drugs work 👇 1/ Suna was 28. Melanoma. Chemo scorched her. Then a new treatment didn’t kill the tumor—it woke up her immune system. Her own T-cells hunted it down. She lived.

Kids asleep. Screen glowing. Another post to write. 620+ days of daily bioinformatics content. Every single day

A good proteomics resource: www.proteinatlas.org/humanproteo...

Democratizing protein language model training, sharing and collaboration www.nature.com/articles/s4...

1/ You probably do not understand p-values.

Writing online has taught me more than I ever expected. Here’s why I do it and what I’ve learned along the way. 🧵

"Frankenstein's patchwork"

You also want to use RRIDs for your research materials, including cell lines. Links a persistent identifier to the physical resources you use so that others know the exact antibody/cell line/etc that you used. Database contains info about contamination RRIDs.org

The Dishes Were Still There 2-hour commute. Back aching. Kids picked up. Dinner cooked.

"Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting." www.nature.com/articles/s4...

On-target off-tumor toxicity of claudin18.2-directed CAR-T cells in preclinical models www.nature.com/articles/s4...

I regret not learning this well in college, and it changed how I approach bioinformatics today. Here’s my story and why you should avoid my mistake.

12:00 AM. The Choice. Kids asleep. Body exhausted. Brain foggy. I still hadn't recorded my bioinformatics tutorial video. "I'll do it tomorrow."

Benchmarking large-scale single-cell RNA-seq analysis www.biorxiv.org/content/10....

1/ Want to master bioinformatics (or any skill)? Here's the hard truth: There’s no shortcut to success. Like building a skyscraper, it takes careful planning, consistent effort, and patience. Let me share how to get there—step by step. 🧵

chatomics! new blog post: Understanding prcomp() center and scale Arguments for Single-Cell RNA-seq PCA divingintogeneticsandgenomics.com/post/unders...

you have to be an intentional observer and listener, and you will find stories in your life everywhere.

The Question I Almost Missed 👇 It was a perfect fall Saturday in Boston—trees with beautiful color, crisp air and golden light. I saw none of it. "Dad, is it harder to jump sideways or forward?" "What? Say that again."

Big pharma seduced by transcription factors again. What has changed? www.nature.com/articles/s4...

I used to spend a week curating single-cell studies by hand. Now AI does it in 5 minutes. But this isn’t about job loss—it’s about leverage. Let me show you why every bioinformatician should embrace AI:

How is your p-value histogram look like? chatomics blog post: Downstream of bulk RNAseq: read in salmon output using tximport and then DESeq2 divingintogeneticsandgenomics.com/post/downst...

Tonight, I was that parent. Sweating in the cold. Pushing a stroller. Chasing kids through the dark.

Nature Biotech: Ad hoc, post hoc and intrinsic-hoc in bioinformatics www.nature.com/articles/s4...

I am reposting this challenge for AI companies: create an agent to tidy this spreadsheet. If your AI agent can do it, I will subscribe and use it.

1/8 Your groundbreaking research might be built on a lie. That cell line you've been studying for months? There's a real chance it's not what the label says. And you're far from alone in this nightmare.

Hey, all the AI x Bio companies. I have an idea. if your agent can read this paper www.nature.com/articles/s4... download the data, and replicate the figures, I am going to subscribe.

You'll be a completely different person in a year if you 👇 Spend 30 minutes to 1 hour each day reflecting on your day. Ask yourself: - What new thing did I learn? - What interesting thing did I read? - Am I 0.1% better than yesterday? I guarantee it. #lifelesson

AutoSpectral improves spectral flow cytometry accuracy through optimised spectral unmixing and autofluorescence-matching at the cellular level www.biorxiv.org/content/10....

You think two genes are correlated. But what if there's a third gene pulling the strings? Let’s talk about partial correlation in bioinformatics.

"Analysis of 744 patients with resected PDAC revealed that patients with initial isolated liver-metastatic recurrence (n = 100) had significantly worse overall survival than those with initial isolated lung-metastatic recurrence (n = 31)." www.nature.com/articles/s4...

After 13 years of analyzing sequencing data, I am an "expert" in doing it. I gained those experiences not because I am smarter, but simply because I made more mistakes, and encountered more problems.

Sample swaps are the silent killer in bioinformatics. Your results look clean—but are you sure you're analyzing the right samples?