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jonnyfrazer.bsky.social
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.
99 posts 3,486 followers 721 following
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It's great to see some new notices of funding opportunities from NIH, but here's a reminder that Harvard researchers remain ineligible to apply for any federal grants. "Harvard should no longer seek GRANTS from the federal government, since none will be provided." www.harvard.edu/research-fun...

submitted 2 days ago • 16 comments

“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.” www.lunduniversity.lu.se/article/lund...

submitted 4 days ago • 0 comments

🚨 Internship Alert! 🚨 Exciting opportunity @Genentech for a Computational Biology intern in Aging Research! 🧬 Work on #single-cell transcriptomics & imaging data to advance #aging biology insights with @mkoutrouli.bsky.social & me. Applications due June 26: lnkd.in/dBE28Wtk

submitted 4 days ago • 1 comment

✈️ 𝐓𝐫𝐚𝐯𝐞𝐥 𝐆𝐫𝐚𝐧𝐭𝐬: 𝐁𝐫𝐢𝐧𝐠𝐢𝐧𝐠 𝐆𝐥𝐨𝐛𝐚𝐥 𝐕𝐨𝐢𝐜𝐞𝐬 𝐭𝐨 #ESEB2025 🌍 At #ESEB2025, we believe great science should be accessible to all, regardless of geography or background. 📅 𝐄𝐱𝐩𝐥𝐨𝐫𝐞 𝐚𝐯𝐚𝐢𝐥𝐚𝐛𝐥𝐞 𝐠𝐫𝐚𝐧𝐭𝐬:  🔗 https://lnkd.in/dXRzeUks

submitted 4 days ago • 0 comments

End-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...

submitted 5 days ago • 0 comments

Average zero-shot mutation effect predictions across related sequences to reduce noise and improve accuracy. @cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias www.biorxiv.org/content/10.1...

submitted 7 days ago • 0 comments

Also, Charlie's #VariantEffect25 talk is available here www.youtube.com/watch?v=johJ...

submitted 9 days ago • 0 comments

Reminder that the MSCA postdoctoral program exists. If you have a PhD and want to work in a European lab, you have until September to apply. Just contact them now. ec.europa.eu/info/funding...

submitted 10 days ago • 0 comments

📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41... Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.

submitted 11 days ago • 4 comments

We have updated our preprint about 850,000 person UK-Danish haplotype sharing - sheding light on the rich history each person carries with them in their DNA and comparing this to historical records. Xiaolei Zhang postdoc in my group led this work. www.biorxiv.org/content/10.1...

submitted 12 days ago • 1 comment

Do protein language models store different structural elements in factorizable subnetworks? To find out, we masked out PLM weights to suppress performance on CATH subcategories or secondary structure elements while maintaining performance on other sequences or residues.

submitted 14 days ago • 1 comment

1 plant hormone receptor ☘️ 3,500 mutants, to single-site saturation 🧬 >45,000 binding and abundance measurements 📶 Very happy to present our latest work – where deep mutational scanning meets the world of small molecules.

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

 With @benlehner.bsky.social [1/7]

submitted 14 days ago • 3 comments

I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.

submitted 15 days ago • 3 comments

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

submitted 18 days ago • 1 comment

If I was applying for PhD positions, Eli’s group would be at the top of my list.

submitted 18 days ago • 0 comments

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

submitted 25 days ago • 35 comments

Both translational and fundamental curiosity-driven research are needed to fuel the incredible progress we're seeing in genomic medicine; an important message in this article and and some lovely quotes from @sarahlwynn.bsky.social www.ft.com/content/25dd...

submitted 18 days ago • 0 comments

Thank you so much!

submitted 21 days ago • 0 comments

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

submitted 21 days ago • 0 comments

Recasting the perils of phylodynamic non-identifiability as a feature not a bug, we show that a unique forward-equivalent process enables exact and efficient simulation from arbitrarily large populations. With M Celentano, S Prillo, @yun-s-song.bsky.social www.pnas.org/doi/10.1073/pnas.2412978122

submitted 27 days ago • 0 comments

🚨With some delay, we're excited to announce that our proposal for a MSCA Doctoral Network on Evolutionary Medical Genomics (EvoMG-DN) got funded! 🎉 🧬 14 labs and 2 companies across 7 European countries will be coordinated by the EvoMG Joint Program at @crg.eu & @upf.edu. europa.eu/!NNq63m

submitted 24 days ago • 1 comment

Rose Orenbuch at #VariantEffect25

submitted 24 days ago • 0 comments

And now, the final talk of #VariantEffect25. @roseorenbuch-art.bsky.social from Harvard Medical School presents work from our long-standing collaboration, and one that’s very close to my heart: Proteome-wide model for human disease genetics

submitted 24 days ago • 1 comment

High-content meets high-throughput at #VariantEffect25: Katie Partington from @dougfowler.bsky.social lab presents: Variant in situ sequencing (VIS-seq) enables the measurement of visual phenotypes thousands of PTEN variants

submitted 24 days ago • 0 comments

Another local hero! Up next at #VariantEffect25: @taylor-mighell.bsky.social from @benlehner.bsky.social lab presents: Two wrongs make a right: can GPCR antagonists rescue mutant receptors? 🧬🧪🔁

submitted 24 days ago • 0 comments

Next up at #VariantEffect25: Nobuhiko Tokuriki from @ubcmedicine.bsky.social presents: Exploring evolutionary and fitness landscapes of β-lactamases

submitted 24 days ago • 0 comments

Another speaker I’ve been looking forward to seeing present in person for years! Next up at #VariantEffect25: @lindorfflarsen.bsky.social presents: Understanding the effects of missense variants using analyses of protein stability and conservation

submitted 24 days ago • 0 comments

Solving the many mysteries of amyloids 🧩🧬, next up at #VariantEffect25: @marianomartin.bsky.social from @bennibolo.bsky.social Lab presents: Deep mutagenesis reveals the interplay between RIPKs amyloid nucleation and protein activity

submitted 24 days ago • 0 comments

Day 3 of #VariantEffect25 and what a beautiful morning! 🌞🌊🧬 First up: Tim Whitehead presents An experimental platform for learning antibody molecular recognition

submitted 24 days ago • 0 comments

Last talk of the day at #VariantEffect25! Joseph Rosenbluh sends us off to dinner with: Systematic functional characterization of CDH1 variants

submitted 25 days ago • 0 comments

Next at #VariantEffect25 we have Jason Moffat from from SickKids @sickkidsto.bsky.social presenting: A comprehensive variant effect map for TAFAZZIN with saturation prime editing

submitted 25 days ago • 0 comments

Charting the path from mutation to medicine, next we have #VariantEffect25 Sven Diederichs from @uniklinik-fr.bsky.social presents: Saturation mutational scanning uncovers druggability of all FGFR kinase point mutations 💊

submitted 25 days ago • 1 comment

From short linear motifs to big biological insights, next up at #VariantEffect25 @ivarssonlab.bsky.social presents: Towards a map of the motif-based interactome in health and disease

submitted 25 days ago • 0 comments

Next up at #VariantEffect25 we have Arvind Kumar, aka the Sherlock Holmes of the human genome 🕵️‍♂️🧬, presents: Non-coding variant interpretation using deep learning and evolutionary conservation.

submitted 25 days ago • 0 comments

Mapping the bigger picture! Next up at #VariantEffect25: Ulrich Stelzl presents: Functional characterization of protein networks through deep mutational protein–interaction perturbation scanning

submitted 25 days ago • 0 comments

Next up at #VariantEffect25: @pollyfordyce.bsky.social presents: Microfluidics for quantitative and high-throughput biophysics and biochemistry 💧

submitted 25 days ago • 0 comments

Welcome back from lunch. Now for a quick overview of the AVE workstreams before we start the next session at #VariantEffect25.

submitted 25 days ago • 0 comments

@cwjpugh.bsky.social at #VariantEffect25

submitted 25 days ago • 0 comments

Bringing that GP probabilistic magic, next up at #VariantEffect25: Carlos Martí-Gomez presents: Learning sequence–function relationships with scalable and biologically interpretable Gaussian process models

submitted 25 days ago • 0 comments

Proud supervisor moment! Next up at #VariantEffect25: Charles Pugh @cwjpugh.bsky.social, PhD student in Mafalda’s and my group, presents: From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models #AI #ProteinML

submitted 25 days ago • 0 comments

Welcome back from the break! Next up @juliadiumenge.bsky.social from @alloxbio.bsky.social Mapping allosteric sites at scale to develop better drugs

submitted 25 days ago • 0 comments

Next up at #VariantEffect25 all the way from BGI, Ju Zheng presents: Innovative high-throughput DNA synthesis: Enhancing Systematic Exploration of Protein Sequence-Function Relationships

submitted 25 days ago • 0 comments

Next up at #VariantEffect25: Translating computational genomics into clinical clarity we have @shawnfayer.bsky.social from @uwgenome.bsky.social presenting "A cluster-based method for guiding the use of variant effect predictors in clinical variant classification clinical clarity"

submitted 25 days ago • 0 comments

Good morning from #VariantEffect25 – Kicking off Day 2 we have @mattcoelho.bsky.social from @sangerinstitute.bsky.social presenting "Prospective mapping of DNA variants modulating therapy response in cancer using gene editing" 🧪🧬💥

submitted 25 days ago • 0 comments

#VariantEffect25 — so up-to-date you can see the talk the day of the publication!

submitted 25 days ago • 0 comments

Good views, food and even better company at #VariantEffect25

submitted 26 days ago • 1 comment

And now for the last talk of day 1 of #VariantEffect25 we have Steven Brenner @stevenbrenner.bsky.social: From Computer to Clinic: Calibrating variant impact predictors yields a ClinGen clinical recommendation up to strong evidence in genome variation interpretation

submitted 26 days ago • 0 comments

Next up at #VariantEffect25 we have @filippostocco.bsky.social Guiding Generative Protein Language Models with Reinforcement Learning with Feature Extraction 🧬🤖 #AI #SynBio

submitted 26 days ago • 0 comments