Ran Blekhman

9.6K posts

Ran Blekhman

@blekhman

Professor of Medicine at @UChicago. Decoding the human microbiome. https://t.co/v7TIGaAfYu

Chicago Katılım Kasım 2012

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Ran Blekhman@blekhman·20 Şub

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👉cell.com/cell/current 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

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Ran Blekhman@blekhman·4d

The Global Microbiome Conservancy is doing something incredibly important: creating a “seed bank” of human microbiomes from around the world, preserving diversity before it vanishes. Enjoyed discussing it with the NYT for this wonderful story: nytimes.com/2026/07/08/mag…

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Ran Blekhman@blekhman·5d

Good night from Chicago

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Ran Blekhman@blekhman·3 Tem

Claude Science is incredible. I gave it some sequencing data, and in 8 hours it did a full analysis, generated figures, wrote a paper, submitted it for publication, got rejected, revised and resubmitted, got rejected again, it is now applying for positions in industry

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Ran Blekhman@blekhman·28 Haz

@mbeisen I agree that this is legal and fair use. What I am worried about is that this will make scientists less likely to publicly share their work. Already starting to see this sentiment. As a fan of open science, it's s concerning

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Michael 英泉 Eisen@mbeisen·28 Haz

@blekhman I agree with most of this, except for (3) about it being done without consent. When you share a work of science you do not - AND SHOULD NOT - control how or by whom it is used. You head down that path you quickly end up in a bad place.

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Ran Blekhman@blekhman·28 Haz

I wanted to like QED's new 1% preprint ranking. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review: open.substack.com/pub/blekhman/p…

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Ran Blekhman@blekhman·26 Haz

It's pretty wild that AI is still so hard when there's only two bits (1 and 0)

Zach Ocean@zachocean_

it's pretty wild that biology is still so hard when there's only like 25k protein coding genes

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Ran Blekhman@blekhman·16 Haz

Just start writing. My new post: substack.com/home/post/p-20…

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Ran Blekhman@blekhman·13 Haz

Chicago in the summer is unbeatable

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Ran Blekhman@blekhman·11 Haz

Excellent thread. We always use CLR transformation in metagenomics, so I was confused why it wasn't used in single-cell genomics Apparently the "CLR" function in the most common single-cell analysis tool failed all the benchmarks because it was implemented incorrectly 😶

Lior Pachter@lpachter

Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale + log. Move on. Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/

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Ran Blekhman retweetledi

Arjun Raj@arjunrajlab·29 May

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

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Ran Blekhman@blekhman·30 May

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.

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Ran Blekhman@blekhman·25 May

Wabash Avenue bridge, Chicago, today

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Ran Blekhman@blekhman·23 May

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

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Ran Blekhman@blekhman·21 May

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. huggingface.co/spaces/Hugging…

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Ran Blekhman@blekhman·17 May

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 open.substack.com/pub/blekhman/p…

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Ran Blekhman@blekhman·17 May

Also, the idea that peer-review provides some kind of protection against bad AI-generated content is absurd arstechnica.com/science/2024/0…

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Ran Blekhman@blekhman·17 May

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/

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Ran Blekhman@blekhman·8 May

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

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Sambhawa Priya@sambhawa_priya·7 May

🔬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

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Ran Blekhman@blekhman·1 May

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!

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