Daniel MacArthur

Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'

📣 We are recruiting! Please share!!

Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺

We have two roles available 👇

🧵 1/4

Leena Peltonen School of Human Genetics in full-swing!

@gosiatrynka.bsky.social
@dgmacarthur.bsky.social
@bpasaniuc.bsky.social
@tuuliel.bsky.social
@hilarycmartin.bsky.social
@sashagusevposts.bsky.social
@zkutalik.bsky.social
@mashaals.bsky.social
@alemedinarivera.bsky.social

This implies there is a huge literature of small microbiome association studies that is JUST NOISE. (As observed for these other fields)

About a hundred reasons not to use Excel.

Yes, these are politely described as 'spreadsheet' horror stories, but we all know which bit of software we're really talking about.

(HT @pgmj.bsky.social)

Is peer-review dead? A scientist’s plea to fix a broken system - Healthy Debate Peer-review may not be over, but the era of exploitative, opaque and corporatized gatekeeping should be.

Peer review is not quite dead but it’s on life support and the current model of scientific publishing is a burning platform. healthydebate.ca/2025/06/topi...

UMAP of the 9 populations and 86 cell types identified after quality control and clustering

Preprint out today!

A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date

www.medrxiv.org/content/10.1...

OurDNA Symposium 2025: Partnering for impact The OurDNA Symposium brings stakeholders together for important conversations about building the foundation for equitable genomics in Australia.

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...

Two charts present survival rates for childhood leukemia over time, specifically focusing on Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML). In the top panel, for ALL, a series of curved lines represent overall survival rates plotted against years since diagnosis. The lines show a marked increase in survival rates from the late 1960s, when only 14% of children survived more than five years post-diagnosis, to around 94% in the 2010s. Key intervals are labeled, with different colors indicating different periods of diagnosis, ranging from 1972-1975 to 2010-2015. The bottom panel illustrates survival rates for AML, which are consistently lower overall compared to ALL. Like the top graph, it features several colored lines indicating specific periods. The highest point noted indicates a survival rate of 65%. The graph captures trends in survival as well, showing gradual improvement over time, from 1975-1977 up to 2011-2017. Data sources for these visualizations are cited at the bottom: Mignon Loh et al. (2023) for ALL and Todd M Cooper et al. (2023) for AML, both from the Children's Oncology Group. The chart is published by Our World in Data, and licensed under Creative Commons by the author, Saloni Dattani.

I wrote a new piece on how much progress has been made in treating childhood leukemia.

The answer is: quite a lot!

Before the 1970s, fewer than 10% of children diagnosed survived 5 years after diagnosis.

Now most are cured and around 85% survive that long.
ourworldindata.org/childhood-le...

I worry that not enough of a big deal is being made about how long-term the devastation of these budget cuts to our scientific and health agencies will be, beyond the absolute ruin they will cause in the acute period.

Drosophila Genetic Database The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

Colossal scientist now admits they haven’t really made dire wolves Despite a huge media fanfare in which Colossal Biosciences claimed to have resurrected the extinct dire wolf, the company's chief scientist now concedes that the animals are merely modified grey wolve...

Jesus. Excellent work by Michael Le Page, and utterly infuriating scenario. As Michael points out, the press release from Colossal called these dire wolves throughout. But now they want to argue that they never claimed that. Scandalous, really.
www.newscientist.com/article/2481...

Careers - Centre for Population Genomics

Excited to be in Milan for #eshg2025! If you’re interested in leading analysis of large, diverse cohorts with WGS and cellular genomic data in Australia, I’d be keen to chat - we’re looking to fill a variety of senior comp bio roles: populationgenomics.org.au/careers/ #eshg25

Scalable automated reanalysis of genomic data in research and clinical rare disease cohorts Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necess...

🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬

github.com/populationge...

A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!

The Cambridge Companion to Workday
The Routledge Handbook of Dual-Factor Authentication
The Oxford Handbook of Figuring Out How To Add A Signature To This PDF, Why The Hell Is This So Difficult

A graph showing the price per pound for different vehicles and types of cheese. There are a surprising number of cheeses in the top half, such as Roquefort.

This is the best graph I've seen in a while 📊

What happens to science under autocracy? The rise of the National Socialist Party in 1930s Germany provides an (admittedly extreme) example. Prior to the early 1930s, scientists at German institutions won a third of Nobels. 10 years later, that number was 5%, and has never recovered.

KJ Muldoon, a 9½-month-old boy with a rare condition, made medical history by receiving the first custom gene-editing treatment. The technique used has the potential to help people with thousands of other uncommon genetic diseases.

Read more: nyti.ms/44H77pg

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Release DeepVariant 1.9.0 · google/deepvariant DeepVariant: In this version we have updated our training scheme for the HG002 sample with the newly released HG002-T2T truth set which improves accuracy against that truth set. Our labeling metho...

Release of DeepVariant and DeepSomatic v1.9

DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).

DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.

github.com/google/deepv...

Author-Paid PublicationFees Corrupt Science and Should Be Abandoned Thomas J. H Morgan & Paul E. Smaldino

As grant money starts drying up, it's more important than ever not to waste it on paying publishers' open access "article processing fees" when we can host PDFs for free. Tom Morgan and I wrote a paper on this, forthcoming at Science and Public Policy. Accepted draft here: osf.io/preprints/os...

It's a 24 panel illustration, with a rotor (circle) with 24 open circles. For each increment from 1 to 24, an additional circle is filled with blue or pink, in ways that create a symmetrical axis of mass, allowing the rotor to be balanced when rotating at high speeds. The pinks generally show the odd numbers (divisible by 3) while the blues are the paired (divisible by 2) I think?

Weird intersection of math & centrifuge balancing:
Visual proof that it's possible to balance a 24-position centrifuge rotor for any number of equally-filled tubes EXCEPT 1 and 23.

Some of these are anxiety-inducing, though.

(🧑‍🎨: aliyoh, labrats subreddit)

These boxes are not moving. A mind-bending optical illusion by Japanese artist Jagarikin.

We've worked on eQTLs and CRISPR for 10+ years now, and 4 years ago I hypothesized about their orthogonal strengths and weaknesses, for a review paper with @dgmacarthur.bsky.social. It’s exciting to finally have enough empirical data for a systematic analysis.
www.science.org/doi/10.1126/...

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...

Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease...

New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology.
www.biorxiv.org/content/10.1...

Two things that are true at the same time:

1. The massive cuts to science funding in the US is a terrible blow that can't be patched by efforts elsewhere.

2. It's great that the EU and many individuals countries are stepping up; it helps science and many US scientists willing/able to relocate.

1/n 🚨Very excited to share our recent work!🚨
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...

"WE'VE ARRANGED A society based on science and technology, in which nobody understands anything about science technology. And this combustible mixture of ignorance and power, sooner or later, is going to blow up in our faces. Who is running the science and technology in a democracy if the people don't know anything about it?" "Science is more than a body of knowledge, it's a way of thinking. A way of skeptically interrogating the universe with a fine understanding of human fallibility. If we are not able to ask skeptical questions, to interrogate those who tell us that something is true, to be skeptical of those in authority, then we're up for grabs for the next charlatan, political or religious, who comes ambling along."

I think a lot about what Carl Sagan said in one of his final interviews.