Lightnews — Scholar-powered news

Davis McCarthy @davisjmcc.bsky.social · 22d

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

Reposted by Davis McCarthy

Yupei You @youyupei.bsky.social · 23d

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....

www.biorxiv.org

1 5 12

Reposted by Davis McCarthy

wcrismani.bsky.social @wcrismani.bsky.social · 27d

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…

www.sciencedirect.com

1 5 7

Davis McCarthy @davisjmcc.bsky.social · 28d

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

3

Reposted by Davis McCarthy

wcrismani.bsky.social @wcrismani.bsky.social · Sep 5

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.

2 10 16

Reposted by Davis McCarthy

Irene Gallego Romero @ee-reh-neh.bsky.social · Aug 14

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:

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

1 4

Reposted by Davis McCarthy

arxiv stat.ML @arxiv-stat-ml.bsky.social · Aug 7

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

2 6

Davis McCarthy @davisjmcc.bsky.social · Jul 23

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 · Jul 22

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...

Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar

Identifying genetic variants that affect gene expression, expression quantitative trait loci (eQTLs), is a major focus of modern genomics. Today, various methods exist for eQTL mapping, each using dif...

www.medrxiv.org

1 2 13

Davis McCarthy @davisjmcc.bsky.social · Jul 23

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 🫠)

6

Reposted by Davis McCarthy

Chelsea Parlett @chelseaparlett.bsky.social · Jul 23

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.

4 4 27

Reposted by Davis McCarthy

Stegle Lab @steglelab.bsky.social · Jul 4

📢 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.

1 8 16

Reposted by Davis McCarthy

abacbs.bsky.social @abacbs.bsky.social · Jul 4

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-

www.abacbs.org

6 8

Reposted by Davis McCarthy

Oliver Stegle @oliverstegle.bsky.social · Jun 26

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

17 14

Davis McCarthy @davisjmcc.bsky.social · Jun 25

Increasingly, I think one of the most important questions people need to ask (and answer) themselves is "How much is enough?"

1

Davis McCarthy @davisjmcc.bsky.social · Jun 25

Applications for this position will close on Friday 30 June

So if you or anyone you know might be interested in applying, time to get your skates on!

Davis McCarthy @davisjmcc.bsky.social · Jun 16

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬

You’d join a welcoming, supportive, and brilliant team.

Why not spend a few years in Melbourne and be part of something exciting?

Apply here: www.seek.com.au/job/84737876

#ScienceCareers #PostDoc #Bioinformatics

Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK

Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics

www.seek.com.au

1 4

Davis McCarthy @davisjmcc.bsky.social · Jun 25

Nice work :D

Reposted by Davis McCarthy

Michael Totty @mictott.bsky.social · Jun 6

🚨 New paper published in @natmethods.nature.com!

We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.

📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/

🧵👇

SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods

SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...

nature.com

1 13 31

Reposted by Davis McCarthy

Daniel MacArthur @dgmacarthur.bsky.social · Jun 23

Hey Australian genetics/genomics friends: the OurDNA Symposium will be in Sydney on 14 August, just before the HGSA meeting. Learn more about inclusive recruitment for genomics and get a preview of the OurDNA variant browser! events.humanitix.com/ourdna-sympo...

OurDNA Symposium 2025: Partnering for impact

The OurDNA Symposium brings stakeholders together for important conversations about building the foundation for equitable genomics in Australia.

events.humanitix.com

9 10

Davis McCarthy @davisjmcc.bsky.social · Jun 20

I would also very much like a mixed model in edgeR 😉

afaik (given I haven't been an active developer for years), it hasn't been possible to implement a mixed model in a way that's compatible with the empirical Bayes information sharing...and for edgeR eBayes is more important if there's a tradeoff

1 1

Reposted by Davis McCarthy

Sonika Tyagi @tsonika.bsky.social · Jun 18

New preprint from the lab

@tyagilab.bsky.social

medRxivpreprint @medrxivpreprint.bsky.social · Jun 18

Semantic Encoding in Medical LLMs for Vocabulary Standardisation https://www.medrxiv.org/content/10.1101/2025.06.16.25329716v1

1 3 4

Davis McCarthy @davisjmcc.bsky.social · Jun 18

Yes, also open for PhD applicants too. We accept students who apply and are enrolled through the Faculty of Medicine, Dentistry and Health Sciences. Email me if you'd like to discuss further

1

Reposted by Davis McCarthy

Patrick Gibbs @patrickgibbs.bsky.social · Jun 16

I cannot recommend Davis’s group more highly! In addition to excellent research, he has been a great mentor!

Davis McCarthy @davisjmcc.bsky.social · Jun 16

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬

You’d join a welcoming, supportive, and brilliant team.

Why not spend a few years in Melbourne and be part of something exciting?

Apply here: www.seek.com.au/job/84737876

#ScienceCareers #PostDoc #Bioinformatics

Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK

Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics

www.seek.com.au

1 3

Davis McCarthy @davisjmcc.bsky.social · Jun 17

Come for the science, stay for the March Mammal Madness!

1

Davis McCarthy @davisjmcc.bsky.social · Jun 16

🔍 We're looking for:
- PhD in computational field
- Strong programming skills (R/Python/Julia)
- Genomics/bioinformatics experience
- HPC expertise

💼 What we offer:
• 3-year contract
• $98-106K + generous super
• Supportive research environment

#bioinformatics #computationalbiology #postdoc

🧵3/3

1 1

Davis McCarthy @davisjmcc.bsky.social · Jun 16

We're do cool stuff: single-cell genetics, spatial transcriptomics, biomedical imaging, and (dare I say it) AI (ahem, deep learning).

EG:

Developing an AI reader to detect breast cancer: www.nature.com/articles/s41...

Spatial transcriptomics in pulmonary fibrosis: www.nature.com/articles/s41...

Comparison of AI-integrated pathways with human-AI interaction in population mammographic screening for breast cancer - Nature Communications

Successful human-AI collaboration could greatly contribute to breast cancer mammographic screening. Here, the authors use a large-scale retrospective mammography dataset to simulate and compare five p...

www.nature.com

1 2