We are hosting the 2026 @abacbs.bsky.social conference at RMIT University City Campus Melbourne on 16-20 Nov 2026. Hope to see you there.
Davis McCarthy
@davisjmcc.bsky.social
Head, Bioinformatics and Cellular Genomics Lab, St Vincent's Institute of Medical Research, Melbourne. Stats, AI/ML, bioinformatics, genomics, single-cell. https://www.svi.edu.au/researchers/dr-davis-mccarthy/
Despite a long history of world-leading discoveries, Australia's science system is going backwards – at the very moment the rest of the world is moving forward, fast. That's why we've launched BACK AUSTRALIA'S ABILITY, a call to every Australian to do exactly that.
Dr Kate Firipis once wanted to be a teacher, inspired by a childhood curiosity about the world around her. Today, she’s part of a team working on lab-grown skin that could transform recovery from severe wounds. Donate today to support researchers like Kate: www.svi.edu.au/support-us/d...
Every discovery begins with a bright spark✨ Donate now to support the next generation of scientists at SVI and help make future discoveries possible: www.svi.edu.au/support-us/d...
I have registered! If I can, so can you. And you should. We'll learn interesting things.
Irene Gallego Romero@ee-reh-neh.bsky.social · 5mo agoRegistration for MSS26 in Melbourne will close next Monday - we still have a few tickets available, and an amazing line-up of speakers across all areas of variant effects work, so if you were on the fence, check out our program and then smash that "Register now" button! www.mss2026.org
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
biorxiv.org
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
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
Bioinformatician/Staff Scientist in Medical Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
🎓 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
ARC Postgraduate Research Scholarship
A $40,109 per annum stipend scholarship for research students within the Faculty of Science.
sydney.edu.au
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.
It's time... theconversation.com/how-the-war-...
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...
theconversation.com
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.
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...
nature.com
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
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
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
@wcrismani.bsky.social · 9mo ago🧵 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...
🧵 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...
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...
medrxiv.org
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.
Melissa Sweet@melissasweetdr.bsky.social · 9mo agoMonique Ryan urges Australia to fast track medical innovation funding as Trump guts research www.theguardian.com/australia-ne...
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
Have physicists finally solved the ‘golfer’s curse’?
Team says it has hit on an explanation for heartbreaking “lip outs”
science.org
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...
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....
biorxiv.org
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
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.
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!
Jeffrey Pullin@jeffreypullin.bsky.social · last yr.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...
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.
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!
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
abacbs.org
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
embl.wd103.myworkdayjobs.com