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...

Cell-type-resolved genetic variation shapes inflammatory bowel disease risk - Nature

Single-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-loc...

nature.com

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!

Jeffrey Pullin@jeffreypullin.bsky.social · 3mo ago

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:

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:

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

journals.plos.org

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

Exome sequencing directly implicates 68 genes in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic immune-mediated disorder of the gastrointestinal tract whose genetic basis is only partly resolved because most risk variants identified by genome-wide as...

bit.ly

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:

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

journals.plos.org

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...

🧬 New preprint: "The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications" Why do some genetically supported drug targets succeed in the clinic while others fail? Across 100,526 GWAS, the same evidence flags constrained gene functions rarely safe to modulate.

The Open Targets Platform spring 🌼 release is out — and this one marks the beginning of something we've been building towards for a while.

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...

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...

Irene Gallego Romero@ee-reh-neh.bsky.social · 5mo ago

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!

Irene Gallego Romero@ee-reh-neh.bsky.social · 5mo ago

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.

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

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 ago

Ancestral and environmental diversity shape the immune landscape in Indonesia https://www.biorxiv.org/content/10.64898/2026.02.15.704933v1

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

bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo ago

Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1

Share insights on using multimodal biological frameworks at #BiologyAtScale26 🧬 Contribute towards multidisciplinary knowledge exchange, and bridge gaps across genetics, cell biology, and human health. 📅 29 June -1 July 2026 Submit an abstract by 20 April ➡️ bit.ly/4mYud02 #ComplexTraits 🧪

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 👇

Nikhil Milind@nikhilmilind.dev · 7mo ago

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

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

High false sign rates in transcriptome-wide association studies

Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...

doi.org

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

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...

tinyurl.com

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

High false sign rates in transcriptome-wide association studies https://www.biorxiv.org/content/10.64898/2025.12.19.695550v1

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...

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

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...

Denoising image-based spatial transcriptomics data with DenoIST

Image-based spatial transcriptomics (IST) technologies provide unprecedented resolution of gene expression in tissue sections, but suffer from contamination of cells' gene expression profiles due to i...

biorxiv.org

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....

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...

nature.com

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!

Systematic comparison of colocalization methods using protein quantitative trait loci

Colocalization is frequently performed as a step to triage findings from genetic investigations linking molecular and disease data. However, the reliability and consistency of the various colocalizati...

biorxiv.org

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...

Large-scale GWAS meta-analysis of serum antibody levels reveals distinct genetic architectures

Antibodies are the principal effector proteins of humoral immunity. Dysregulated antibody production is a feature of a number of heritable immune-mediated diseases, such as the antibody deficiencies a...

medrxiv.org

I'm very excited to be attending my first #ASHG25 this week! Come find me at poster board 1090F to talk about flexible and efficient eQTL mapping with quasar!

I'm very excited to be attending my first #ASHG25 this week! Come find me at poster board 1090F to talk about flexible and efficient eQTL mapping with quasar!

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...

Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus - Nature Communications | Open Targets

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 Kaur Alasoo analysed 3,734 lymphoblastoid cell line samples across...

linkedin.com

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...

Clinical and genetic spectrum of Fanconi anemia in Australia and New Zealand

Fanconi anemia (FA) is a rare genetic condition that predisposes to progressive bone marrow failure, a specific spectrum of malignancies, including he…

sciencedirect.com