Paul Geeleher
@PGeeleher
@StJude. Hiring postdocs and staff scientists: http://geeleherlab.org/open-positions/
Creative use of UK Biobank WGS data: fishing out non-human DNA reads from WGS data to measure latent Epstein-Barr viral infection. The plot below shows phenome-wide associations of "EBV DNAemia" in half a million individuals. Nyeo et al. bioRxiv 2025 biorxiv.org/content/10.110…
It’s finally out! 🥳 We are super happy to see our biomarkers for predicting resistance to chemotherapy! More info 👇🏻 & in the “behind the paper” post communities.springernature.com/posts/towards-…
🚨Chemo treatment upgrade!🚨 Check out our approach to modernise chemotherapy treatment published today in @NatureGenet. From @CNIOStopCancer @TailorBio @CR_UK nature.com/articles/s4158… More details 👇
Cancer chemotherapy does a number (as in mutations) to blood cells 2 new reports using single-cell sequencing show the deleterious effects of these drugs, yet another reason for better therapeutic approaches nature.com/articles/s4158… nature.com/articles/s4158… nature.com/articles/s4158…
Data diversity, quality & relevance rules over model size any day of the week. Very clever approach of generating synthetic protein sequences from backbone structures to give big boosts to pLMs.
Learning on GigaRef yielded a small increase in the fraction of expressed proteins. Increasing model and dataset scale further improved the expression rate. Augmenting training with structure-based synthetic data from BackboneRef produced the highest expression success rate.
In a joint paper with @OwainEvans_UK as part of the Anthropic Fellows Program, we study a surprising phenomenon: subliminal learning. Language models can transmit their traits to other models, even in what appears to be meaningless data. x.com/OwainEvans_UK/…
New paper & surprising result. LLMs transmit traits to other models via hidden signals in data. Datasets consisting only of 3-digit numbers can transmit a love for owls, or evil tendencies. 🧵
There are much more structural variants within our genomes than previously conceived, >26,000 per person nature.com/articles/s4158… nature.com/articles/s4158…
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07/0…
🧬Indels drive the separation into m-SBS3a & SBS3b HRd signatures Only SBS3b strongly predicts survival in ovarian cancer patients, exceeding other genetic markers ➕utility of MMRd signatures also improved with indel+SNV joint inference Read more: 👇 genomemedicine.biomedcentral.com/articles/10.11…
Read ‘The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability across multiple tumor types.’ from @sangerinstitute and collaborators in @NatureGenet, here ⤵️ nature.com/articles/s4158…
Cisplatin and temozolomide combinatorial treatment triggers hypermutability and immune surveillance in experimental cancer models dlvr.it/TM0Npb
Our paper is now in @NatureBiotech! Topological velocity inference from spatial transcriptomic data. TopoVelo infers the direction of differentiation/migration; quantifies spatial cell influence; and identifies morphology changes during differentiation. 🧵rdcu.be/ewqMB
🤯 in @CellCellPress An alternate receptor for adeno-associated viruses cell.com/cell/fulltext/… carboxypeptidase D [CPD] is an alternate AAV receptor- totally explains why AAV8 vectors are SO efficient at pancreatic exocrine cell transduction for CRISPR engineering.
The effects of oncofusions and other protein variants on chromatin remodeling are identified by PROD-ATAC go.nature.com/3Wib3qr rdcu.be/euaAl
Defining and benchmarking open problems in single-cell analysis bit.ly/4l8dsiF
The first cancer vaccines matched to a person’s unique tumor neoantigens are forging ahead, with expectations running high as the field awaits results from the first pivotal trial nature.com/articles/s4158… rdcu.be/euaoK
Did you know that cancer cells can 'eat' each other to survive? This is called 'entosis' The weaker cell invades the stronger one, which breaks it down and takes its nutrients
GW: ultra-fast chromosome-scale visualization of genomics data. #GenomeVisualization #Bioinformatics #Genomics @naturemethods nature.com/articles/s4159…
📣 Cell developmental state matters in B-ALL. Our study out today in @NatureCancer: Multipotent lineage potential in B cell acute lymphoblastic leukemia is associated with distinct cellular origins and clinical features | Nature Cancer nature.com/articles/s4301…
Genome-Wide (GW): an interactive browser for ultrafast chromosome-scale genomics data visualization. nature.com/articles/s4159…
One thing that really bothers me with the new "virtual cell" terminology is that is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/