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Jonathan Frazer

@jonnyfrazer.bsky.social
3.7K followers 942 following 121 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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Reposted by Jonathan Frazer
Ben de Bivort @debivort.bsky.social · 22/09/2026
Hello friends, the Harvard Life Science departments have banded together to hire a new colleague working at the intersection of Life Sciences and AI. Could be primarily an experimentalist, or could be primarily a compute/theorist. academicpositions.harvard.edu/postings/16773
academicpositions.harvard.edu
Tenure-Track Professor in Life Science and AI
The Life Sciences Departments in Harvard Faculty of Arts and Sciences seek to recruit a tenure-track professor whose research is at the interface of AI and life sciences, from methodological developme...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24/09/2026
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Ezequiel Galpern @eag91.bsky.social · 25/09/2026
🧬 What do deep-learning models for proteins actually learn? Our new review looks at how model predictions relate to fitness, folding stability and function. With @cwjpugh.bsky.social, Mafalda Dias & @jonnyfrazer.bsky.social 🔗 chemrxiv.org/doi/full/10....
chemrxiv.org
From sequences and structures to fitness, folding and function: challenges in the age of AI | ChemRxiv
Deep-learning models have transformed our ability to predict the phenotypic effects of sequence perturbations. Protein language models (pLMs) score the evolutionary propensity of any amino-acid substi...
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Centre de Regulació Genòmica (CRG) @crg.eu · 15/09/2026
We are at a critical moment for the future of European science. As @eu-life.bsky.social founder, and together with 100s of institutes and universities across the continent, we call for an ambitious funding pot for FP10. See Luis Serrano's comments in El Mundo. www.mundoamerica.com/entertainmen...
mundoamerica.com
European science calls for ambitious investment in research: "Current decisions determine Europe's future. We are falling behind China and the USA"
"To remain global leaders, a competitive economic power, and a sovereign actor, Europe needs strong science and innovation." Seven scientific organizations, representing...
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Reposted by Jonathan Frazer
Andres Bendesky @bendeskylab.com · 11/09/2026
We have a tenure-track faculty position in Evolutionary Biology in Columbia's E3B Department. Application deadline is October 15. Come be our colleague. Please RT! apply.interfolio.com/193016
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Jonathan Frazer @jonnyfrazer.bsky.social · 10/09/2026
Congratulations! Beautiful work. I know Mafalda and @m1quelag.bsky.social found it a pleasure to review.
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Nik Baya @nbaya.bsky.social · 19/08/2026
Introducing the BRaVa results browser v1! 🎉 1.2M+ individuals across 10 global biobanks 44 heritable, disease-relevant traits (and counting) 419M gene- & variant-level association tests ➡️ nikbaya.github.io/brava_browser/
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Arc Institute @arcinstitute.org · 20/08/2026
The 2026 Virtual Cell Challenge has begun! Submissions and the leaderboard are now open. This year's task: multi-context generalization and zero-shot prediction. Models will need to predict perturbation responses in cellular contexts with no training data. arcinstitute.org/news/virtual...
arcinstitute.org
The 2026 Virtual Cell Challenge: predicting perturbation responses in cell contexts a model has never seen | Arc Institute
Registration for the 2026 Virtual Cell Challenge is open at virtualcellchallenge.org. This year the task is zero-shot: we are not releasing a training set, and the evaluation dataset is far more expan...
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BIST-Barcelona Institute of Science and Technology @bist.eu · 16/06/2026
🦠 How did our cells originate? A study by @gabaldonlab.bsky.social at @irbbarcelona.org & @bsc-cns.bsky.social suggests cellular complexity emerged gradually over millions of years, rather than from a single evolutionary event. 📝 Published in @nature.com #BISTCommunity 👉 bist.eu/a-study-by-i...
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 10/08/2026
@eag91.bsky.social was recently the 100th speaker of our Variant Effects Seminar Series. The work he presented has just been published as a preprint. Learn more: tinyurl.com/mrxf5zxv @solersanchisx.bsky.social, @cwjpugh.bsky.social, @federicobilleci.bsky.social, @jonnyfrazer.bsky.social
lnkd.in
Blending physics-based models improves protein folding stability prediction | Ezequiel Galpern posted on the topic | LinkedIn
🎉 New preprint: “Blending physics-based and inverse folding models to disentangle variant effects on stability and function” ➡️ Read it on https://lnkd.in/dCDw-3nb Together with Xavier Soler Sanchis...
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Ben Lehner @benlehner.bsky.social · 09/08/2026
Conservation and divergence in the allosteric architectures of five human protein kinases. Excited to share our new preprint by @carlafolgado.bsky.social @tonibeltran.bsky.social @sangerinstitute.bsky.social @crg.eu @ibv-csic.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Conservation and divergence in the allosteric architectures of five human protein kinases
Protein kinases are central to biological regulation, dysregulated in many diseases, and the targets of a hundred clinically-approved drugs. Structural conservation of kinase active sites makes the de...
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Ezequiel Galpern @eag91.bsky.social · 08/08/2026
🚨 Paid MSc research opportunity at CRG Barcelona! With Mafalda Dias and @jonnyfrazer.bsky.social, we’re hosting a 4-month MSc project: 🧬 “Folding versus function: disentangling the molecular mechanisms of missense variants in gene-trait associations” More info 👇 www.crg.eu/en/content/t...
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Eli Weinstein @eliweinstein.bsky.social · 07/08/2026
Very excited about our new results, showing variational synthesis + large scale screens + co-designed training -> robust scaling laws for sequence-activity models.
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Jonathan Frazer @jonnyfrazer.bsky.social · 05/08/2026
Blend to disentangle! New preprint led by our talented postdoc @eag91.bsky.social
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Miquel Anglada-Girotto @m1quelag.bsky.social · 28/07/2026
1/ We’ve been working on making it easier to fine-tune AlphaGenome on new RNA-seq samples, with a focus on one of my favourite regulatory layers: splicing! Blog post: genomicsxai.github.io/blogs/2026-0...
genomicsxai.github.io
Beyond coverage tracks: fine-tuning AlphaGenome's splicing heads from scratch
Summary DeepMind has released AlphaGenome’s code and model weights, and the community has since developed alphagenome_ft and alphagenome-pytorch to enable seamless fine-tuning in both JAX and PyTorch....
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Peter Koo @pkoo562.bsky.social · 23/05/2025
Excited to share an update to D3 (DNA Discrete Diffusion) — an application of score-entropy discrete diffusion model for regulatory genomics! 🧬 Paper: biorxiv.org/content/10.110… (See thread below 👇) (1/n)
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Hannah Dickmänken @hannahdckmnkn.bsky.social · 29/01/2026
Paper alert! 💻 How many cells do you need to train reliable deep learning models in regulatory genomics? We asked how data quality, sequencing depth, and dataset size affect training of sequence-to-function models from scATAC-seq. Out now www.nature.com/articles/s41... (details below)
nature.com
Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling - Nature Communications
Generating high-quality training data for machine learning is costly. Here, authors include sequence-to-function modeling in benchmarking of custom and commercial droplet-based scATAC platforms, and r...
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Lars Velten @larsplus.bsky.social · 16/07/2026
@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity link.springer.com/article/10.1186/s13059-026-04186-9 Julia achieved three cool things with this work...🧵
link.springer.com
Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity - Genome Biology
Background Cell state-specific gene expression programs emerge from the interplay between cis-regulatory elements (CREs), such as enhancers, and transcription factors (TFs). Massively parallel reporte...
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Jonathan Frazer @jonnyfrazer.bsky.social · 09/07/2026
Absolutely awesome work!
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Elzo de Wit lab @ NKI @dewitlab.bsky.social · 06/07/2026
(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:
rdcu.be
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...
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Jonathan Frazer @jonnyfrazer.bsky.social · 28/06/2026
You can plant the name badges!!! #smbe2026
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Centre de Regulació Genòmica (CRG) @crg.eu · 15/06/2026
Mafalda Dias es finalista del premio Vanguardia de la Ciencia. Su línea de investigación está ayudando agilizar el diagnóstico de enfermedades raras, ofreciendo una evidencia adicional para médicos que ya tienen sospechas sobre ciertos genes implicados según los síntomas. ¡Vota ahora!
lavanguardia.com
“Diagnosticamos enfermedades raras analizando millones de años de evolución”
Vota a las finalistas del premio Vanguardia de la Ciencia
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Jonathan Frazer @jonnyfrazer.bsky.social · 01/06/2026
Mafalda has been shortlisted for the 2026 Premio Vanguardia de la Ciencia, one of the more visible science prizes in Spain. Her interview: www.lavanguardia.com/vanguardia-d... ...and we would be very grateful if you could vote here: www.lavanguardia.com/vanguardia-d...
lavanguardia.com
La IA mejora el estudio de las enfermedades raras
Vota a las finalistas del premio Vanguardia de la Ciencia
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Andrew Gordon Wilson @andrewgwils.bsky.social · 27/05/2026
How much does a language model forget when finetuned on new tasks? We show both model size and optimization matter and forgetting can be nearly eliminated with self-generated replay! arxiv.org/abs/2605.26097 w/Martin Marek, Dongkyu Cho, Shikai Qiu, Rumi Chunara, and Pavel Izmailov. 1/8
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ALLOX @alloxbio.bsky.social · 27/05/2026
AI drug discovery has a data problem. We're fixing it. At ALLOX, we've spent the last few years building something that didn't exist before: a platform that systematically maps functional hotspots at scale, measuring the effects of mutations on protein-protein interactions across the proteome.
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Kipoi @kipoizoo.bsky.social · 28/04/2026
Join us for our next Kipoi Seminar with Noor Youssef, Harvard Medical School @harvardmed.bsky.social @deboramarks.bsky.social 👉 Predicting Viral Evolution to Accelerate Vaccine and Therapeutic Design 🧬 Wed May 6, 5:30pm CET 🍃http://kipoi.org/seminar 🦋 @kipoizoo.bsky.social
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Jonathan Frazer @jonnyfrazer.bsky.social · 10/04/2026
Very nice paper from Regeneron www.nature.com/articles/s41...
nature.com
Population-scale repeat expansions elucidate disease risk and brain atrophy - Nature
Decreased brain volumes and increased NfL levels can be observed earlier than disease diagnosis in short-tandem-repeat-associated neurological diseases.
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IRB Barcelona @irbbarcelona.org · 08/04/2026
🧬 What if reading a tumor's mutations could tell us exactly how to fight it? Dr. @nlbigas.bsky.social is doing exactly that — decoding the genomic fingerprints of #cancer to guide personalized treatments. This is #CancerResearch, reimagined.
youtube.com
Biomedical genomics - Dr. Núria López-Bigas
Dr. Núria López-Bigas, Group Leader, Biomedical Genomics Laboratory, IRB Barcelona.
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Debora Marks @deboramarks.bsky.social · 23/03/2026
Meet evedesign: open-source AI, accessible protein design ✅Combine models for multiobjective optimization ✅Integrate experimental data ✅ Run on your own infrastructure 📄Paper: www.biorxiv.org/content/10.6... 💻Code: github.com/evedesignbio 🌐Webserver: evedesign.bio Collaborate: hello@evedesign.bio
deboramarkslab.substack.com
evedesign: accessible biosequence design with a unified framework
Unified protein design for computational researchers and experimentalists
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Claus Wilke @clauswilke.com · 11/03/2026
New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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Julia Rühle @juruehle.bsky.social · 04/03/2026
The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...
doi.org
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Alejo Rodriguez-Fraticelli @alejofraticelli.bsky.social · 26/02/2026
🚨 NEW @FraticelliLab PREPRINT JUST WENT LIVE biorxiv.org/content/10.6... Here, we describe PLSTCs, Soluplus-based expansion cultures of primary mouse *Acute Myeloid Leukemia* Stem Cells. And then we use LARRY barcoding to identify drivers of leukemogenicity and drug resistance!
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Fabian Theis @fabiantheis.bsky.social · 24/02/2026
Join us at Cell Symposia: Single-Cell Biology in the Era of AI (Dec 2–4, 2026, Munich) 🇩🇪 From multi-omics to AI-driven models of cellular dynamics — an exciting lineup across experimental & computational biology. Hope to see you there! 🔗 www.cell-symposia.com/single-cell-...
cell-symposia.com
Home – Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI
Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI
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Fabian Theis @fabiantheis.bsky.social · 23/02/2026
🚀 From modality-specific to compositional foundation models for cell biology Happy to share our new Perspective in Cell Systems. We describe an emerging shift toward compositional multimodal architectures 🧩 authors.elsevier.com/c/1mdzg8YyDf...
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Lars Velten @larsplus.bsky.social · 17/02/2026
Early bird registration is closing Feb 28! We will have an AMAZING party!
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Phillip Isola @phillipisola.bsky.social · 11/02/2026
Our grad-level "Deep Learning" course (MIT's 6.7960) is now freely available online through OpenCourseWare: ocw.mit.edu/courses/6-79... Lecture videos, psets, and readings are all provided. Had a lot of fun teaching this with @sarameghanbeery.bsky.social and @jeremybernste.in!
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Jonathan Frazer @jonnyfrazer.bsky.social · 09/02/2026
Post 3 of attempting to share more ML/Bio papers on Bluesky: Accelerating Scientific Research with Gemini: Case Studies and Common Techniques arxiv.org/abs/2602.03837
arxiv.org
Accelerating Scientific Research with Gemini: Case Studies and Common Techniques
Recent advances in large language models (LLMs) have opened new avenues for accelerating scientific research. While models are increasingly capable of assisting with routine tasks, their ability to co...
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Jonas Hübotter @jonhue.bsky.social · 29/01/2026
Training LLMs with verifiable rewards uses 1bit signal per generated response. This hides why the model failed. Today, we introduce a simple algorithm that enables the model to learn from any rich feedback! And then turns it into dense supervision. (1/n)
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Jonathan Frazer @jonnyfrazer.bsky.social · 06/02/2026
Post 2 of sharing interesting ML/bio papers that don’t seem to be getting much attention on Bluesky. Three papers on self-distillation, all from the same week! arxiv.org/abs/2601.18734 arxiv.org/abs/2601.19897 arxiv.org/abs/2601.20802
arxiv.org
Self-Distilled Reasoner: On-Policy Self-Distillation for Large Language Models
Knowledge distillation improves large language model (LLM) reasoning by compressing the knowledge of a teacher LLM to train smaller LLMs. On-policy distillation advances this approach by having the st...
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Andrew Saxe @saxelab.bsky.social · 03/02/2026
Why don’t neural networks learn all at once, but instead progress from simple to complex solutions? And what does “simple” even mean across different neural network architectures? Sharing our new paper @iclr_conf led by Yedi Zhang with Peter Latham arxiv.org/abs/2512.20607
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Jonathan Frazer @jonnyfrazer.bsky.social · 03/02/2026
Bluesky doesn’t really shine yet as a place to discover papers, especially at the intersection of biology and ML. To help a little, I’m going to start sharing papers I find interesting. To kick things off, here’s one from @petar-v.bsky.social and colleagues at DeepMind arxiv.org/abs/2601.22950
arxiv.org
Perplexity Cannot Always Tell Right from Wrong
Perplexity -- a function measuring a model's overall level of "surprise" when encountering a particular output -- has gained significant traction in recent years, both as a loss function and as a simp...
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Ezequiel Galpern @eag91.bsky.social · 22/01/2026
"Probing the Dark Energy in the Functional Protein Universe" is now published in @pnas.org 🎉 www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 16/01/2026
For no reason, I remembered today that I too once got to take a picture holding Nobel Prize that I didn't earn
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Stein Aerts @steinaerts.bsky.social · 15/01/2026
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
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Sarah Gurev @sarahgurev.bsky.social · 13/01/2026
We’ve updated the EVEREST benchmark to include real-world viral evolution! www.biorxiv.org/content/10.1... Co-led by Noor Youssef and me, along with co-authors Navami Jain, Aarushi Mehrotra, Sarrah Leung, Abigail Jackson, @deboramarks.bsky.social, and with @cepi.net @futurehousesf.bsky.social!
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Manuel Irimia @mirimiam.bsky.social · 23/12/2025
🚨🚨🚨 We're looking for a research tech to work on alt splicing, pancreatic islets and diabetes. The goal is to set a high-throughput platform to investigate the role of alternative exons in beta cell biology! Interested in joining our lab at @melisupf.bsky.social? 👇 www.upf.edu/documents/d/...
upf.edu
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Lino Ferreira @linoafferreira.bsky.social · 24/11/2025
Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank! A thread... 🧵 www.medrxiv.org/content/10.1...
medrxiv.org
Interactions with polygenic background impact quantitative traits in the UK Biobank
Association studies have linked many genetic variants to a variety of phenotypes but under-standing the biological mechanisms underlying these signals remains a major challenge. Since genes operate wi...
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Jonathan Frazer @jonnyfrazer.bsky.social · 25/11/2025
LFB is NeurIPS-bound! 🎉 Mafalda, @cwjpugh.bsky.social and I will be in San Diego next week for NeurIPS -- happy to chat variant effect prediction (or just say hi). “From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models” openreview.net/pdf/a151f62e...
openreview.net
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Debora Marks @deboramarks.bsky.social · 24/11/2025
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
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Jonathan Frazer @jonnyfrazer.bsky.social · 24/11/2025
popEVE is out in Nature Genetics! 🎉 We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders. rdcu.be/eRu7K
rdcu.be
Proteome-wide model for human disease genetics
Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.
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