Patrick Gibbs
@patrickgibbs.bsky.social
PhD Student at Cambridge University. Interested in Quantitative Genetics.
Roughly half of common disease heritability is pleiotropic across diseases, with shared variance 1.51x enriched in the genetic component. Work led by Yujie Zhao (co-supervised by Alkes and me) is now out in @natgenet.nature.com www.nature.com/articles/s41...
Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs
The phenotypic effects of germline variants are often mediated through gene regulation. Expression quantitative trait loci (eQTLs) are genetic variants associated with changes in gene expression. Understanding how eQTLs vary across populations is essential for characterising the genetic and regulatory drivers of trait diversity. Meta-analysing eQTL studies from multiple populations enables more robust detection of eQTLs and can reveal regulatory mechanisms shaped by population-specific environmental or ancestry-related factors. However, across the multi-ancestry eQTL literature, a wide range of methods have been used to quantify eQTL portability across ancestry groups. Because different studies employ different portability metrics, it is challenging to form a coherent view of the regulatory landscape across populations. In this work, we analyse eQTL summary statistics from ten datasets matched on tissue type and sequencing technology. We compare portability metrics used previously and show that they can yield markedly different patterns of apparent regulatory conservation or divergence. We then examine the statistical determinants of portability across metrics and demonstrate that sample size, minor allele frequency, and linkage disequilibrium are major drivers of the observed differences in eQTL portability across studies. These findings highlight that differences in statistical power stemming from factors such as population size and allele frequency must be accounted for when evaluating eQTL portability. To address this issue, we introduce a new approach designed to correct for these factors when calling eQTL portability. Finally, we show that empirical Bayes multivariate adaptive shrinkage provides a powerful framework for meta-analysing multiple eQTL studies, with the ability to pool signals across populations to produce more robust effect-size estimates within each population. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council, https://ror.org/011kf5r70, Ideas Grant 2020501, Investigator Grant 1195595
doi.org
Irene Gallego Romero@ee-reh-neh.bsky.social · 5mo agoFinally, today's offering! www.biorxiv.org/content/10.6... This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social
Finally, today's offering! www.biorxiv.org/content/10.6... This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social
biorxiv.org
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs https://www.biorxiv.org/content/10.64898/2026.02.26.708346v1
Hi yes I will have more to say about this in a few hours but please enjoy this paper. It's been a huge labour of love and effort for the last four years, and a significant part of our research efforts, and I'm so so so thrilled it's finally ready to share. Tldr: scRNA-seq in Indonesia hard but fun
bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo agoAncestral and environmental diversity shape the immune landscape in Indonesia https://www.biorxiv.org/content/10.64898/2026.02.15.704933v1
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
I cannot recommend Davis’s group more highly! In addition to excellent research, he has been a great mentor!
Davis McCarthy@davisjmcc.bsky.social · last yr.📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
seek.com.au
Very happy to share that I will soon start a PhD at Cambridge University funded by the Harding Distinguished Scholar Fellowship, supervised by @mikeinouye.bsky.social and Angela Wood. I’ll work on prediction methodologies for health trajectories, using molecular data, and Electronic Health Records.
The FT reports OpenAI suspects DeepSeek of "a potential breach of intellectual property." As a columnist for NYT, which is suing OpenAI for copyright infringement, and the author of nine books OpenAI apparently used to train its model, I couldn't possibly comment. www.ft.com/content/a0df...
OpenAI says it has evidence China’s DeepSeek used its model to train competitor
White House AI tsar David Sacks raises possibility of alleged intellectual property theft
ft.com
Very happy to share my first paper! Here we take a look at different models for producing genomic prediction across a wide range of traits. We find that very specific conditions of where ML approaches can out preform linear regression.
Adaptive Evolution Lab@adaevo.bsky.social · 2y ago📣 New Paper out!!! 📣 When is ML outperforming good old parametric regression for genomic predictions? Go check 👇 doi.org/10.1093/gene...
Earlier this year, I was nominated and funded by unimelb to attend the Heidelberg Laureate forum in Germany. The conference connects 200 developing researchers from maths and compsci to award winning scientists inc. winners of the Fields Medal and Turing award. It was an absolute blast!
Over 30 prominent scientists call for a ban on the creation of a "mirror cell"--a microbe made of molecules that are mirror images of their natural forms. It could cause a mind-boggling global disaster. Here's my story [gift link] 🧪https://nyti.ms/3OUCXp6
A ‘Second Tree of Life’ Could Wreak Havoc, Scientists Warn (Gift Article)
Research on so-called mirror cells, which defy fundamental properties of living organisms, should be prohibited as too dangerous, biologists said.
nyti.ms