Ran Blekhman

Professor of Medicine at @UChicago. Decoding the human microbiome.

[Ran Blekhman @blekhman]

These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today!

We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe

[Cell @CellCellPress]

The new issue is out👉https://t.co/DWf0VlDvUt

Featuring an engineered Newcastle disease virus that selectively and safely lysed tumors in refractory cancer patients, the identification of rhodoquinone as a mammal mitochondrial electron carrier, and a metagenome-informed metaproteomics approach unravelling the interplay between the host, gut microbiome, and diet to identify disease biomarkers.

📷credit: SciStories⁠

[Arjun Raj @arjunrajlab]

Can someone start a journal called “Cell Atlases” so that the rest of the journals can go back to publishing interesting things?

[Ran Blekhman @blekhman]

Reminder: giving an AI the prompt "You are a world expert in X" doesn't make it a world expert.

It doesn't give the model additional knowledge or improve its reasoning.

All it does is change the *style* of the output, so it sounds like an expert, even when it's wrong.

[Ran Blekhman @blekhman]

Wabash Avenue bridge, Chicago, today

[Ran Blekhman @blekhman]

1. An embryo can't have an IQ score. This is like saying the embryo has an 800 credit score or a 2000 chess Elo. It's nonsense

2. These polygenic scores have negligible predictive value for an individual's IQ - they explain a small proportion of variance at the population level

[Gene Smith @GeneSmi96946389]

A friend of mine had her embryos screened by Herasight and they found one with an IQ score in the 99.99th percentile

[Ran Blekhman @blekhman]

I've said it before: the bottleneck is not speed.

This DNA model is 275x faster, but it creates a tree of life that groups drosophila with plants. How is AI going to solve cancer if it can't get the most basic biology right?

[Leandro von Werra @lvwerra]

We are releasing Carbon: a crazy fast DNA model

Carbon is 275x faster than the next best model. So fast you can process the whole human genome on a single GPU in <2 days.

Here are the tricks we used:

When modelling DNA sequences a lot of the performance comes down to tokenizing the sequences in a smart way. BPE tokenizer struggle because there are no whitespaces and character (called base in DNA) level tokenizers waste a lot of compute on too many tokens.

Carbon is built with a unique tokenizer: we split sequences in chunks of 6 bases, but during both training and inference we can work with single base resolution. That's similar to having word tokens but resolving them at the character level. All possible thanks to the DNA tokens unique structure.

The architecture combined with the tokenizer makes the model 275x faster than the previous SoTA (Evo2) at this size.

We built an interactive demo so you can explore how the model can generate DNA sequences, investigate the structure of genes, predict the effect of mutations, generate and fold proteins and even reconstruct parts of the tree of life.

https://t.co/OWEUoxAFjG

[Ran Blekhman @blekhman]

Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted.

Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia

https://t.co/rMQZxP5S4o

[Ran Blekhman @blekhman]

Also, the idea that peer-review provides some kind of protection against bad AI-generated content is absurd

https://t.co/EdZRdEAafn

[Ran Blekhman @blekhman]

This is genuinely funny. ArXiv exists because peer-review is slow, arbitrary, and not trustworthy.

Now arXiv is making peer-review its judge, treating it as the only real trust signal.

[Thomas G. Dietterich @tdietterich]

The penalty is a 1-year ban from arXiv followed by the requirement that subsequent arXiv submissions must first be accepted at a reputable peer-reviewed venue. 4/

[Ran Blekhman @blekhman]

Happening today!!

[Ran Blekhman @blekhman]

🧬 AI in Genomics Symposium next week!

We're bringing together leading scientists from across academia and industry pushing the boundaries of AI in genomics research

Join us May 8 at the University of Chicago - KCBD Auditorium, 9:30–5:00, reception to follow

[Sambhawa Priya @sambhawa_priya]

🔬How do clinical exposures shape the gut microbiome, and how do longitudinal clinical–microbiome signatures predict patient outcomes?

Come find out at my poster #194 today at 7:30 pm at @cshlmeetings Biology of Genomes 2026! #bog26 @blekhman

[Ran Blekhman @blekhman]

Looking forward to #DDW2026!

I will be presenting new work on host–microbiome interactions at single-cell resolution, led by Liz Gibbons in my lab

Sunday, 8-9:30, W190a, session "AI-based approaches to unraveling gut microbiome complexity"

Come find me - happy to talk!

[Ran Blekhman @blekhman]

@PracheeAC No, sorry - this is in-person only

[Ran Blekhman @blekhman]

🧬 AI in Genomics Symposium next week!

We're bringing together leading scientists from across academia and industry pushing the boundaries of AI in genomics research

Join us May 8 at the University of Chicago - KCBD Auditorium, 9:30–5:00, reception to follow

[Ran Blekhman @blekhman]

@ClementYChow

[Ran Blekhman @blekhman]

Visited Zion National Park for the first time - impossible to convey how beautiful it is

[Ran Blekhman @blekhman]

I wrote about why every lab should have AI use guidelines, and how to do it.

https://t.co/q6qSntHO7p

[Ran Blekhman @blekhman]

source: https://t.co/7rbzPkQWVM

[Ran Blekhman @blekhman]

When we looked at this a few years ago, Nature Genetics had the longest time from preprint to publication

[Sasha Gusev @SashaGusevPosts]

Monthly median Received to Accepted time (days) at Nature Genetics

[Ran Blekhman @blekhman]

Southern Utah countryside. The Google Pixel 10 has an amazing camera

[Ran Blekhman @blekhman]

Layers. Today in Chicago