You may have heard of superEnhancer from this paper pmc.ncbi.nlm.nih.gov/articles/PM... but the computational tool to identify superEnhancers was written 12 years ago in python2. I then found a python3 re-written version. I will modernize it with claude code and upload it to pypi.

Learn Your Way learnyourway.withgoogle.com/

12 websites to learn computation and many others! 🧵 Bookmark 👇

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?

Winter morning. I made myself hot cocoa in a glass. It tasted perfect. I finished it, walked to the sink, and put the glass down. I'll wash it later.

Free deep learning book with ipython notebooks udlbook.github.io/udlbook/

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

1/ AI won't replace you. But a biologist using AI will. Especially in bioinformatics, where the questions never stop coming.

Winter break. 7 AM. My 7-year-old woke up early. Not to read. Not to play outside. He grabbed his iPad and started playing video games.

People go to the gym for physical training instead of doing farm work; soon, we'll visit thought training centers to exercise our brains because AI is making us dumb. :) or smarter?

having fun to modernize my ChIP-seq snakemake workflow using claude code github.com/crazyhottom... it was written 10 years ago for internal lab use and then I made it public on github. Many things are broken. - MACS now have python3 support

Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion www.nature.com/articles/s4...

8 links to BETTER understand principal component analysis (PCA) 🧵 👇

🧵 You’re not behind in bioinformatics. The truth? The field just evolves faster than any single human can follow.

My 3-year-old sat on the floor with her puzzle. Big pieces first. She flew through it. "Done, Daddy!" "Great! Want to try a harder one?"

Editing DNA methylation in vivo www.nature.com/articles/s4...

1/ Most bioinformaticians will hit 2026 with vague goals like "learn more deep learning." By February, they're back to old patterns. I spent last week with norovirus tearing through my family, thinking: what separates those who level up from those who stay stuck? A blueprint.

🧵 Bioinformatics Tip: Why Wet Biologists Should Involve Bioinformaticians Early 1/ Waiting until after the data is generated to call a bioinformatician is like asking for an autopsy. They’ll tell you what went wrong, but can’t revive your experiment.

Christmas morning, 7 AM. My kids bolted to the Christmas tree. "Quiet!" I whispered. "Mom's still sleeping. She was up late last night."

Merry Christmas! As the year-end approaches, be sure to take some time to reflect on 2025 and plan for 2026.

1/ Just when you think you’ve mastered scRNA-seq, spatial transcriptomics arrives. New tools. New puzzles. The cycle never ends.

1/You know the feeling. You open a CSV or log file in the terminal— and it’s chaos. Wrapped lines. Misaligned columns. Impossible to read. Here’s how to turn that mess into clarity:

Christmas Eve. My wife rushed out for last-minute gifts. Three hungry kids stared at me.

Generalizable and scalable protein stability prediction with rewired protein generative models www.nature.com/articles/s4...

Learn R and python in parallel www.anotherbookondatascience.com/

Stop losing your analysis files. The difference between chaos and clarity in computational biology is one habit: How you name your files/folders 🧵

Walking my kids to school this morning, my 3-year-old stopped. "The smoke smells good," she said.

CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease www.nature.com/articles/s4...

1/ Messy data feels like a locked door. You know the insights are inside, but every step is friction. Filtering. Plotting. Nothing works.

1/ Biology is no longer just about pipettes and Petri dishes. Your most powerful lab tool is hidden in plain sight: a keyboard. Learning to code can transform not just your research—but your career.

I picked up my kids from school and asked: "Library or home?" "Library!" they said. Our new local library is beautiful. Clean, quiet, filled with books and natural light. But there's a catch—computers everywhere. Games, videos, screens calling out to them.

Fundamental errors in RNA velocity arising from the omission of cell growth www.biorxiv.org/content/10....

1/ Ever see a stunning bioinformatics figure and think: “How on earth did they make that?” Let’s break it down so you can recreate it.

Bioinformatics data is messy. Here’s the nightmare that almost broke me 🧵👇

After dinner tonight, I did something different. Instead of rushing to my laptop, cleaning the kitchen, or scrolling my phone, I asked my three kids and my wife to play a game with me.

This trick saved me many times: copy a table from website or spreadsheet, paste to a dataframe in r github.com/MilesMcBain...

Computational prediction of human genetic variants in the mouse genome www.nature.com/articles/s4...

You can save millions $ for your organization if everyone follows best practices to fill in a spreadsheet. Do simple things to make bioinformatician's life easier. Read the full article here (happy to contribute to it a little) www.nature.com/articles/d4...

1/ Most bioinformatics errors don’t come from bad science. They come from work you can’t reproduce. And when that happens, you don’t just waste time. You risk patients’ lives.

A single-cell cytokine dictionary of human peripheral blood: 9.7M cells, 12 donors, 90 cytokines www.biorxiv.org/content/10....

Bioinformatics isn’t just running pipelines. The hardest part? Knowing when not to code. A thread on why context comes first 🧵

Want to master bioinformatics data visualization? I almost quit when I first tried ggplot2. But once I “got it,” it changed how I saw data forever. Here’s the hard-won path that makes ggplot2 click. 🧵

An open-source screening platform accelerates discovery of drug combinations www.nature.com/articles/s4...

Bioinformatics doesn’t break you with code. It breaks you with the invisible details in data. That’s where most people get lost. 🧵

Struggling to “get” bioinformatics? You’re not alone. The truth is: real understanding doesn’t happen the first time. It happens on the fifth. Or the tenth. Here’s my journey of relearning PCA, stats, and bioinformatics—and why repetition is the secret weapon. 🧵

Making a mistake is not the end of the world. Own it, admit it, learn the lesson, then move on. #lifelesson

CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model to generate segmentations with human-level performance across a range of bioimage data. www.nature.com/articles/s4...

LongVie 2, an end-to-end autoregressive video world model with: - Strong Controllability - Long-term Visual Fidelity - Temporal Consistency vchitect.github.io/LongVie2-pr...

If you’re waiting for perfect bioinformatics data, you’ll never publish. ChIP-seq taught me this the hard way

All three kids down. Norovirus swept through our house like wildfire. Belly aches. Vomiting. Fever.