Jonathan Frazer

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...

🚨 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!

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

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-...

🚀 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...

Early bird registration is closing Feb 28! We will have an AMAZING party!

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!

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...

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

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)

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...

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

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

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...

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

"Probing the Dark Energy in the Functional Protein Universe" is now published in @pnas.org 🎉

www.pnas.org/doi/10.1073/...

For no reason, I remembered today that I too once got to take a picture holding Nobel Prize that I didn't earn

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

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!

🚨🚨🚨

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/...

My guess is main conference (bridge) workshops (panda)

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...

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...

...and if you are interested in doing a PhD with Mafalda and I, we currently have one opening, with deadline this Sunday! www.crg.eu/en/content/t...

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...

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:

...and if you are interested in doing a PhD with Mafalda and I, we currently have one opening, with deadline this Sunday! www.crg.eu/en/content/t...

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.

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

New AI model enhances diagnosis of rare diseases PopEVE system outperformed rivals such as Google DeepMind’s AlphaMissense

PopEVE covered by @financialtimes.com today! www.ft.com/content/bc49...

Today we introduce Mafalda Dias and @jonnyfrazer.bsky.social from CentreGenomic Regulation @crg.eu ,with one PhD position open in their lab.

Learn more about the PhD programme and how to apply → www.evomg-dn.eu

#PhD #DoctoralTraining #ResearchCareers #LifeSciences #Genomics #EvolutionaryBiology

🚨 Two weeks left to apply!

🚨 15 days left to apply!
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu

#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions

scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction Recent large-scale single-cell foundation models have shown promise for exploring cellular states, yet they often underperform compared to simpler, domain-specific methods, raising concerns about…

🚀 Excited to share our preprint scConcept: a contrastive pretraining framework for technology-agnostic single-cell representations.
We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics.
📘 www.biorxiv.org/content/10.1...

Estimation and mapping of the missing heritability of human phenotypes - Nature WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...

First time on Bsky and first big announcement!

I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.

Our manuscript is here: www.nature.com/articles/s41....

(1/N) Thrilled to share that our paper HiPoNet (High dimensional Point cloud Network) to be presented at NeurIPS 2025! HiPoNet treats an entire high-dimensional point cloud as a datapoint! It captures multi-scale geometry and topology of the cloud perform classification and regression tasks.