Davis McCarthy

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!

Gosh the number of times I see people testing differentially expressed genes and then applying a post-hoc fold-change threshold and I have to scream into the void WE WROTE A METHOD TO TEST THE INTERVAL NULL (...15+ years ago 🫠)

people don't actually want to test point-nulls in NHST, they want to test interval nulls and they rely on the structure of the test to define the "interval null" (*waves hands vaguely*) for them, rather than explicitly defining an interval null and testing it.

📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.

ABACBS 2025 Conference Adelaide, South Australia. Nov. 24-

The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025

Registrations and abstract submissions open next week, with abstracts due in August!