Davis McCarthy

An international team, including Associate Professor Davis McCarthy and colleagues, has developed a breast screening artificial intelligence (AI) tool that estimates a woman’s risk of developing breast cancer more accurately than current methods.

Find out more: www.svi.edu.au/news-events/...

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

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...

I have an opening for a staff scientist or bioinformatician in my group at the Sanger Institute (closing date 24 March). Our current projects focus on disentangling rare and common variant contributions to rare neurodevelopmental conditions and to neurodevelopmental and perinatal traits. 1/2

ARC Postgraduate Research Scholarship A $40,109 per annum stipend scholarship for research students within the Faculty of Science.

🎓 PhD scholarship

We are recruiting a PhD student to develop new methods for analysing spatial omics data at the University of Sydney, cosupervised by @shazanfar.bsky.social and me. Ideal for students with backgrounds in statistics, data science, computer science or bioinformatics

Apply by 18 Jan

Australia’s medical and scientific research sectors save lives and are vital to our economy. The government has to step up and lean in to their potential.

It’s small-minded and short-sighted to force them to wither on the vine, when we have money put aside for this purpose in the Future Fund.

oh good lord no

Oddly, I'm also 1208 off a nice number 🤨

Sorry, Tim, I don't think I'm going to be able to write that many papers by then

Ryan Bingham: Let's just say that I have a number in mind and I haven't hit it yet.

[Up in the Air, 2009]

Frikkin amazing stuff.

How the war was won: the campaign to stop medical research cuts One day in April, Walter and Eliza Hall Institute of Medical Research director Douglas Hilton called his communications manager, Penny Fannin, into his office. “He said he’d heard significant cuts wer...

It's time... theconversation.com/how-the-war-...

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

Our cornetto work is now published at www.nature.com/articles/s41...

It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva

Just presented at #abacbs2025 yesterday.

No, I'm still here! Hanging out at St Vincent's Institute as ever. Would love to catch you if possible when you're here!

Good to see you enjoying the sunshine! (and hopefully enjoying some exciting bioinformatics too)

The McCarthy lab @davisjmcc.bsky.social is very excited to be in beautiful Adelaide for the 10th ABACBS conference. Look at our happy faces @aaronkwc.bsky.social @ameliadunstone #ABACBS2025

Very cool that you're in Adelaide for ABACBS, Zam! Sorry not to be there this year. Are you dropping by Melbourne on your trip?

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...

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...

This is an amazing story

Recommended reading for anyone with even a passing interest in genetics, rare diseases, gene therapy, development...humans, biology, anything really!

It's been cool to watch as the picture has come together over the last year or so

Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...

🧵 Our latest preprint is available.

It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.

Read more here 👉 www.medrxiv.org/content/10.1...

This is absolutely the most obvious thing to do. The govt should be shoveling all the funding it can at getting all the researches in the US who have been cut by Trump.

Have physicists finally solved the ‘golfer’s curse’? Team says it has hit on an explanation for heartbreaking “lip outs”

Known as a “lip out” or the “golfer’s curse,” the sometimes strange behavior of golf balls has bedeviled players for centuries. Now, physicists have figured out how they happen. Just don't expect the discovery to improve your game... Fun story by @annademming.bsky.social for @science.org

i can only imagine the licensing agreement needed to get that name over the line

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches Long-read RNA sequencing enables full-length transcript profiling and improved isoform resolution, but variable platforms and evolving chemistries demand careful benchmarking for reliable application....

Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches.
www.biorxiv.org/content/10.1...

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…

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...

expertise, maybe...energy, ah that's a different issue...

Thrilled to share our latest work on meiotic recombination, where we mapped rates and distributions by sequencing thousands of individual sperm. This study was led by Stevan Novakovic and @caitlinharris.bsky.social , in collaboration with @davisjmcc.bsky.social and Cynthia Liu.

A comparison of 10x reagent costs between Australia and Indonesia. The overall cost of these (and everything else) is twice as high in Indonesia.

Now that I've given my talk at today's excellent #ourdna symposium I can share this slide I put together for it. I knew these numbers, because I was the one paying for things, but still:

Valentine Svensson
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111

When Jeffrey "graduated" from our lab to go to do a PhD at Cambridge I knew big things would come - and boy was I vindicated!

Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects.

Awesome 🌟, well done!