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Jonathan Frazer

@jonnyfrazer.bsky.social

3.6K followers 790 following 100 posts

Probabilistic machine learning to address questions in evolution and health #EvolutionaryMedicine. PI at the Centre for Genomic Regulation, co-leading a group with Mafalda Dias. Previously Harvard.

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Jonathan Frazer @jonnyfrazer.bsky.social · May 26

Want to improve your protein or genomic language model’s performance at zero-shot variant effect prediction? We propose a simple adjustment to likelihood-based predicton

Charlie Pugh @cwjpugh.bsky.social · May 26

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n

www.biorxiv.org/content/10.1...

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...

www.biorxiv.org

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Jonathan Frazer @jonnyfrazer.bsky.social · 14d

The most beautiful data is on the horizon!

Arnau Sebé-Pedrós @arnausebe.bsky.social · 14d

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...

Reposted by Jonathan Frazer

Anshul Kundaje @anshulkundaje.bsky.social · 16d

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Yun S. Song @yun-s-song.bsky.social · 16d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Reposted by Jonathan Frazer

EurIPS Conference @euripsconf.bsky.social · 15d

Most of the #EurIPS workshops now have their websites online 🙌

A lot of them have active call for participation and/or papers, so if you see something relevant to your field of research please consider submitting!

Links for most workshops are available at: eurips.cc/workshops/

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Reposted by Jonathan Frazer

Yun S. Song @yun-s-song.bsky.social · 16d

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Jesse Engreitz @jengreitz.bsky.social · 20d

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:

The E2G Portal! e2g.stanford.edu

This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.

Uses cases 👇

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Reposted by Jonathan Frazer

NeurIPS Conference @neuripsconf.bsky.social · 20d

NeurIPS 2025 financial assistance and volunteer applications are now open for both San Diego and Mexico City! The deadline for both applications is 1 Oct AoE. See neurips.cc/Conferences/... for more details.

NeurIPS 2025 Financial Assistance

Main Navigation

neurips.cc

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Reposted by Jonathan Frazer

Samuel King @samuelhking.bsky.social · 21d

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

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Reposted by Jonathan Frazer

Martin Pacesa @martinpacesa.bsky.social · Aug 27

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

www.nature.com/articles/s41...

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Dr. Davey F. Wright ⛏️🦕🧬 @daveyfwright.bsky.social · Sep 2

I'm hoping to take 1 MSc & 1 PhD student next year in the areas of Phylogenetic, Computational, and/or Evolutionary Paleobiology. Please reach out if you are interested in joining the @oupaleobiology.bsky.social, especially if interested in working on fossil echinoderms. Link for more info below. 🧪

News

PhD and MSc positions in Phylogenetic, Computational, and/or Evolutionary Paleobiology [Posted September 2025. Deadline is January 15, 2026. See below for information about the lab, student opportu…

daveyfwright.wordpress.com

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Reposted by Jonathan Frazer

Timothy Fuqua 🏳‍🌈 @timothyfuqua.bsky.social · Aug 28

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab!

"De-novo promoters emerge more readily from random DNA than from genomic DNA"

This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

De-novo promoters emerge more readily from random DNA than from genomic DNA

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

www.biorxiv.org

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Reposted by Jonathan Frazer

Anshul Kundaje @anshulkundaje.bsky.social · Aug 19

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.

Details below
careersearch.stanford.edu/jobs/computa...

Plz RT

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Reposted by Jonathan Frazer

Joe Marsh @jmarshlab.bsky.social · Aug 19

New paper out today in PLOS Comp Biol:
journals.plos.org/ploscompbiol...

Intrinsically disordered regions make variant prediction deceptively easy for benign changes but very hard for pathogenic ones. Our work shows why current tools struggle here, and why disorder-aware approaches are needed.

Assessing variant effect predictors and disease mechanisms in intrinsically disordered proteins

Author summary Some parts of proteins, known as intrinsically disordered regions, do not fold into fixed shapes. Instead, they stay flexible and play key roles in controlling how cells work, often by ...

journals.plos.org

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Reposted by Jonathan Frazer

alexblakes.bsky.social @alexblakes.bsky.social · Aug 18

I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2!

tinyurl.com/3j9r56s8
@rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social

Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes

Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...

www.medrxiv.org

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Reposted by Jonathan Frazer

Scott McGrath @smcgrath.phd · Aug 14

🧪 A generative AI framework designed new antibiotics by exploring uncharted chemical space.

The approach yielded two lead compounds effective against multidrug-resistant N.gonorrhoeae and S.aureus in mouse models of infection. 🧬💻 #MLSky

A generative deep learning approach to de novo antibiotic design

A generative AI platform is developed for de novo antibiotic design, yielding lead compounds with selective antibacterial activity, distinct mechanisms of action, and in vivo efficacy against multidru...

www.cell.com

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Reposted by Jonathan Frazer

Ezequiel Galpern @eag91.bsky.social · Aug 12

❗New Preprint w/ C Bueno (‪@cabb99.bsky.social‬), IE Sánchez (@nachoquique.bsky.social‬), PG Wolynes & DU Ferreiro (@diegulise.bsky.social‬)

We define the Protein Dark Energy and use it to localize and quantify the functional evolutionary constraints on natural proteins

arxiv.org/abs/2508.08109

Probing the Dark Energy in the Functional Protein Universe

We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the prote...

arxiv.org

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Reposted by Jonathan Frazer

Andrew Gordon Wilson @andrewgwils.bsky.social · Aug 8

A common takeaway from "the bitter lesson" is we don't need to put effort into encoding inductive biases, we just need compute. Nothing could be further from the truth! Better inductive biases mean better scaling exponents, which means exponential improvements with computation.

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Reposted by Jonathan Frazer

Ran Blekhman @blekhman.bsky.social · Aug 9

This is not just HHMI. All Chan Zuckerberg Initiative funding calls are CLOSED. The Gates Foundation has no Grand Challenges funding opportunities. I've never seen anything like this. Private foundations have just decided to stop supporting biomedical research.

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Reposted by Jonathan Frazer

Manuel Irimia @mirimiam.bsky.social · Aug 6

🧬🧬🧬 New review from the lab:

Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks

authors.elsevier.com/sd/article/S...

By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.

Three major trends in comparative transcriptomics

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Yun S. Song @yun-s-song.bsky.social · Jun 6

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io

Please help spread the news.

Home - ProbGen 2026

Your Site Description

probgen2026.github.io

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Reposted by Jonathan Frazer

David Kelley @drkbio.bsky.social · Jul 21

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...

Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS

Genome-wide association studies (GWAS) have identified thousands of trait-associated loci. Prioritizing causal variants within these loci is critical for characterizing trait biology. Statistical fine...

www.biorxiv.org

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Reposted by Jonathan Frazer

Peter Koo @pkoo562.bsky.social · Jul 16

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

Peter Koo @pkoo562.bsky.social · Jul 16

Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!

genomebiology.biomedcentral.com/articles/10....

Evaluating the representational power of pre-trained DNA language models for regulatory genomics - Genome Biology

Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of ...

genomebiology.biomedcentral.com

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Reposted by Jonathan Frazer

Andrew Gordon Wilson @andrewgwils.bsky.social · Jul 17

Excited to be presenting my paper "Deep Learning is Not So Mysterious or Different" tomorrow at ICML, 11 am - 1:30 pm, East Exhibition Hall A-B, E-500. I made a little video overview as part of the ICML process (viewable from Chrome): recorder-v3.slideslive.com#/share?share...

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EurIPS Conference @euripsconf.bsky.social · Jul 16

EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅

EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu

eurips.cc

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Francis Bach @bachfrancis.bsky.social · Jul 13

What if AI isn’t about building solo geniuses, but designing social systems?
Michael Jordan advocates blending ML, economics, and uncertainty management to prioritize social welfare over mere prediction.
A must-read rethink.
arxiv.org/abs/2507.062...

A Collectivist, Economic Perspective on AI

Information technology is in the midst of a revolution in which omnipresent data collection and machine learning are impacting the human world as never before. The word "intelligence" is being used as...

arxiv.org

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Arnau Sebé-Pedrós @arnausebe.bsky.social · May 7

Check out our latest work on the evolution of animal genome regulation out today in @nature.com. Nicely summarized below by @ianakim.bsky.social.
www.nature.com/articles/s41...

This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu

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