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Very excited to share new work from my PhD on a new software package for eQTL mapping: quasar. The quasar software package is a C++ program designed to provide a flexible and efficient eQTL mapping. www.medrxiv.org/content/10.1...
Jeffrey Pullin
@jeffreypullin.bsky.social
PhD Student, MRC Biostatistics Unit University of Cambridge Gates Cambridge Scholar Bioinformatics, genetics, single-cell, statistics Australian 🇦🇺
201 followers323 following52 posts
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Very excited to share new work from my PhD on a new software package for eQTL mapping: quasar. The quasar software package is a C++ program designed to provide a flexible and efficient eQTL mapping. www.medrxiv.org/content/10.1...
Jeffrey Pullin reposted
Excited about our new preprint: we asked whether genomic foundation models (GFMs) can boost common variant discovery in GWAS beyond standard functional annotations. Across 27 UK Biobank traits: not yet. Paper below! doi.org/10.64898/202...
Jeffrey Pullin reposted
I'll be at #ASHG2026 this year! I'm presenting some recent work (with @huishengzhu.bsky.social) on extracting all the information we can out of rare-variant burden test statistics for downstream meta-analysis. Catch me at poster 8357F to talk about the project or stat gen / pop gen.
Jeffrey Pullin reposted
Jeffrey Pullin reposted
Out now in Nature! Genetic analysis of the largest single-cell dataset of Inflammatory Bowel Disease (IBD)-relevant tissues nominates effector genes and cell types at over half of known IBD loci, including 74 for which this is the first candidate effector gene 🖥️🧬 www.nature.com/articles/s41...
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
This work was led by @greales7.bsky.social and supervised by @chr1sw.bsky.social and Elena Vigorito!
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
Jeffrey Pullin reposted
My last piece of work at the Wallace group. Please check it out and let us know what you think! 😀Thanks @jeffreypullin.bsky.social for summarising it!
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
Jeffrey Pullin reposted
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
Jeffrey Pullin reposted
Excited to share this new preprint from a large collaborative effort using #exome + #genome sequencing, moving beyond GWAS to implicate 68 genes in #IBD through rare protein-coding variation. bit.ly/43h72GA @broadinstitute.org @mgbresearch.bsky.social
Jeffrey Pullin reposted
Super excited to see this out! Fantastic collaboration with Luke O'Connor and trainees Amber Shen and Xinran Wang. Thread with details will come soon, but linear ARG provide a HIGHLY efficient representation of genotype data that can be treated as a linear operator www.biorxiv.org/content/10.6...
Jeffrey Pullin reposted
Jeffrey Pullin reposted
Jeffrey Pullin reposted
It's out! I hope this work encourages folks to move beyond a standard "one variant, one gene" QTL paradigm and consider proxitropic variant effects. Big thanks to the reviewers and editors at @ajhgnews.bsky.social for their help! @sbmontgom.bsky.social www.sciencedirect.com/science/arti...
Jeffrey Pullin reposted
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...
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
Very excited to see this work be the first to use the quasar method for eQTL mapping!
First, a couple of weeks ago: www.biorxiv.org/content/10.6... Single cell RNAseq on blood from 200 donors across 4 sites in Indonesia spanning regional axes of genetic and environmental diversity. This is one of very few scRNA data sets from the Global South, including urban and rural settings.
Jeffrey Pullin reposted
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
Jeffrey Pullin reposted
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
Ancestral and environmental diversity shape the immune landscape in Indonesia https://www.biorxiv.org/content/10.64898/2026.02.15.704933v1
Jeffrey Pullin reposted
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1
Jeffrey Pullin reposted
New preprint alert: we use sign errors as a test of how well TWAS works. Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
Jeffrey Pullin reposted
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
Jeffrey Pullin reposted
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Jeffrey Pullin reposted
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits https://www.biorxiv.org/content/10.64898/2025.12.23.696273v1
Jeffrey Pullin reposted
High false sign rates in transcriptome-wide association studies https://www.biorxiv.org/content/10.64898/2025.12.19.695550v1
Jeffrey Pullin reposted
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...
Jeffrey Pullin reposted
Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation https://www.medrxiv.org/content/10.1101/2025.11.20.25340664v1
Jeffrey Pullin reposted
Great new work led by Aaron Kwok from @davisjmcc.bsky.social’s group. A tool to “denoise” contaminating transcripts from image based spatial data. www.biorxiv.org/content/10.1...
Jeffrey Pullin reposted
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....
Jeffrey Pullin reposted
New pre-print: "Systematic comparison of colocalization methods using protein quantitative trait loci" led by @hwang_seongwon at www.biorxiv.org/content/10.1.... Which method does best? Find out!
Jeffrey Pullin reposted
New: GWAS of serurm antibody levels. Interesting findings include genetically correlated traits with hard-to-find shared causal variants, and apparently genetically uncorrelated traits sharing causal variants that operate in inconsistent directions www.medrxiv.org/content/10.1...
Jeffrey Pullin reposted
Jeffrey Pullin reposted
Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type! An Open Targets team led by Krista Freimann and @kauralasoo.bsky.social analysed 3,734 lymphoblastoid cell line samples across nine cohorts, identifying four robust loci www.nature.com/articles/s41...
Jeffrey Pullin reposted
I feel incredibly privileged to share this study on Fanconi anaemia, based on a small but important cohort. This work describes the genetics and clinical outcomes of patients in Australia and New Zealand with a diagnosis of FA. www.sciencedirect.com/science/arti...
Jeffrey Pullin reposted
Multi-ancestry GWAS can increase power and precision, but how should we analyze them? Pooled or stratified? We answer that question in a paper out today in AJHG, led by Julie Dias and Haoyu Zhang. 1/7 www.cell.com/ajhg/fulltex...
Jeffrey Pullin reposted
New preprint alert: tinyurl.com/tenk10k-multiome. Excited to share our analysis on the impact of genetic variants on single-cell chromatin accessibility in blood, using scATAC-seq and WGS from over 1,000 donors and 3.5M nuclei as part of TenK10K phase 1 🧬 🧵👇 (1/n)
Jeffrey Pullin reposted
After 1.5 years of work in @kauralasoo.bsky.social’s lab, we finally published my preprint! We introduce gpu-coloc, a GPU-accelerated implementation of coloc, show comparability to CLPP and aim to provide practical guidelines. Now accessible on BioRxiv: www.biorxiv.org/content/10.1...
Jeffrey Pullin reposted
Excited to see our (w/ @chr1sw.bsky.social) work published in @natcomputsci.nature.com! We developed a new framework, surrogate functional false discovery rate (sffdr), that integrates summary statistics of related traits to improve power in GWASs. Paper: www.nature.com/articles/s43...
Jeffrey Pullin reposted
Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...
Jeffrey Pullin reposted
I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2! tinyurl.com/3j9r56s8 @rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social
Really enjoying reading this paper describing the new GWAS method LDAK-KVIK - I'm particularly struck by the results describing the "difficulty of constructing accurate PGS for binary phenotypes." 1/2 www.nature.com/articles/s41...
Jeffrey Pullin reposted
Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS. www.biorxiv.org/content/10.1...
Jeffrey Pullin reposted
Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome now on medRXiv www.medrxiv.org/content/10.1...
Jeffrey Pullin reposted
🔔Paper alert! Extremely excited to share a preprint from our lab! Spearheaded by @axel-schmidt.bsky.social, a super talented medical & computational geneticist, we studied latent Epstein-Barr virus (EBV) infection at population-scale. Interested in how this works & what we found? Read along! 👇
Host control of latent Epstein-Barr virus infection https://www.medrxiv.org/content/10.1101/2025.07.19.25331823v1
Jeffrey Pullin reposted
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025. These things can take time and patience is key!
📢OUT TODAY @natgenet.nature.com 📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk. By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...