Jonathan Frazer

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.

@m1quelag.bsky.social

A depiction of expression patterns of the FOXP1, FOXP2, and FOXP4 genes in the brain, based on the developmental human RNA sequencing dataset of BrainSpan (http://www.brainspan.org/). Data cover different prenatal timepoints starting at 8-to-10 weeks postconception (abbreviated as pcs), postnatal timepoints from 0-to-12 months (abbreviated as mos), and expression measured in adulthood. A dashed vertical line represents time of birth. Individual dots are shown each representing one brain sample, and lines show loess curves fitted through the datapoints. The analyzed brain regions are A1C, primary auditory cortex; CB, cerebellum; CBC, cerebellar cortex; DFC, dorsolateral prefrontal cortex; DTH, dorsal thalamic nucleus; HIP, hippocampus; IPC, inferior parietal cortex; ITC, inferior temporal cortex; M1C, primary motor cortex; MD, mediodorsal thalamic nucleus; MFC, medial frontal cortex; OFC, orbitofrontal; S1C, primary sensory cortex; STR, striatum; TC, superior temporal cortex; V1C, primary visual cortex; VFC, ventromedial prefrontal cortex. This image comes from Figure 1 of a paper entitled “Molecular networks of the FOXP2 transcription factor in the brain” written by den Hoed, Devaraju and Fisher, published in the journal EMBO Reports in August 2021 (Volume 22, article e58203).

More than two decades have passed since we discovered that rare disruptions of the FOXP2 gene disturb development of proficient speech/language skills. Today we know of multiple FOXP genes that are directly implicated in distinct brain-related conditions with differences in symptoms & severity.🧪 1/n

A phylogenetic approach to comparative genomics Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

Designing allosteric modulators to change GPCR G protein subtype selectivity - Nature Studies of the G-protein-coupled receptor NTSR1 show that the G protein selectivity of this receptor can be modified by small molecules, enabling the design of drugs that work by switching receptor su...

Now online @nature.com!

Want to change the consequences of receptor activation?

Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥

So many new possibilities! 🧪🧠🟦

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

🧵👇

@nstroustrup.bsky.social

Applications are open for the @crg_eu PhD Programme! 20 fully funded positions — including one in our group through the Evolutionary Medical Genomics ITN.

Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics.

www.crg.eu/en/content/t...

Announcing our new protein design server evedesign.bio:
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.

The second session (Thr 09/10, morning) was dedicated to the Genomic Basis & History of Disease.

Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.

I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...

The most beautiful data is on the horizon!

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/

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/

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)

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 👇

1/

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.

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 🧵