Sign in

Daniel MacArthur

@dgmacarthur.bsky.social
5.7K followers 1.3K following 70 posts

Genomics, big data, open science, diversity. Director of the Centre for Population Genomics, focused on building a more equitable future for genomic medicine. Opinions my own.

PostsRepliesMedia
Reposted by Daniel MacArthur
Zornitza Stark @zornitza.bsky.social · 25/06/2026
📣 Out now @naturemedicine.bsky.social 🧬🤖 👉 rdcu.be/fqasl Our automated reanalysis tool Talos enables broad adoption and delivers timely + equitable #raredisease #diagnosis at scale! ♻️ Runs monthly on >10K datasets 🎯High specificity 💰Low running costs 🤗Open source @dgmacarthur.bsky.social
02211
Reposted by Daniel MacArthur
Angli Xue @anglixue.bsky.social · 11/05/2026
I am happy to share the updated preprint of our TenK10K multiome project. tinyurl.com/tenk10k-mult.... The full caQTL summary from 922 donors and 3.5M nuclei is now available for download, plus many key summary results! Lots of new analyses since v1. Quick tour of what's changed 👇
tinyurl.com
Genetic regulation of cell type-specific chromatin accessibility shapes immune function and disease risk
Understanding how genetic variation influences gene regulation at the single-cell level is crucial for elucidating the mechanisms underlying complex diseases. However, limited large-scale single-cell ...
3103
Reposted by Daniel MacArthur
Steven R. Shaw, PhD @shawpsych.bsky.social · 29/04/2026
This mug should be awarded to every academic who served as department chair.
A coffee mug that says—I  accidentally became important at work and it’s ruining my life.
28713
Reposted by Daniel MacArthur
Nicky Whiffin @nickywhiffin.bsky.social · 09/04/2026
Super excited that our two companion papers on saturation genome editing (SGE) of RNU4-2 and discovery of a novel recessive neurodevelopmental disorder (NDD) were published yesterday 🥳 SGE experiment: www.nature.com/articles/s41... Recessive NDD characterisation: www.nature.com/articles/s41... 🧵
nature.com
Saturation editing of RNU4-2 reveals distinct dominant and recessive disorders - Nature
Saturation genome editing of RNU4-2 identifies the functional and clinical impact of variants across the entire gene and delineates variants that cause a new recessive neurodevelopmental disorder distinct from ReNU syndrome.
45016
Reposted by Daniel MacArthur
Jeffrey Barrett @jeffbarrett.eu · 25/02/2026
My day is summed up by this exchange with @dgmacarthur.bsky.social
Snippet of a chat expressing that Claude Code is a big deal
292
Reposted by Daniel MacArthur
Eric Topol @erictopol.bsky.social · 21/10/2025
What did the largest trial of an early detection of cancer blood test show? erictopol.substack.com/p/the-larges...
erictopol.substack.com
The Largest Study of a Multi-Cancer Early Detection Blood Test
Reviewing the new data and the "liquid biopsy" field
310437
Reposted by Daniel MacArthur
Nicky Whiffin @nickywhiffin.bsky.social · 16/10/2025
Planning your afternoon poster session at #ashg25? Come say hello! This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬
073
Daniel MacArthur @dgmacarthur.bsky.social · 14/10/2025
Awesome work by @zornitza.bsky.social and collaborators showing the immediate value of WGS for newborn screening in a cohort of 1,000 Australian babies. Now we need larger, more diverse cohorts to show this approach can achieve population scale!
0136
Reposted by Daniel MacArthur
Zornitza Stark @zornitza.bsky.social · 09/10/2025
🤗 Out now @naturemedicine.bsky.social results of our genomic NBS study BabyScreen+ 👶🧬 👉 www.nature.com/articles/s41... 1,000 babies WGS using existing cards 600+ conditions 13 day TAT 16 diagnoses (vs 1 in std NBS) High clinical impact High parental acceptability
02515
Reposted by Daniel MacArthur
Molly Przeworski @mollyprz.bsky.social · 02/09/2025
In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...
biorxiv.org
Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature
Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...
510946
Daniel MacArthur @dgmacarthur.bsky.social · 02/09/2025
And now the fourth preprint from the TenK10K phase 1 dataset, led by @anglixue.bsky.social from @drjosephpowell.bsky.social's team - looking at genetic impacts on cell type-specific chromatin accessibility in 1,000 individuals who also have WGS and scRNA-seq!
0140
Reposted by Daniel MacArthur
Scissors @scissors.myatproto.social · 01/09/2025
I think 182 year old research articles should be free I want to read about the man
RESEARCH ARTICLE • Volume 39, Issue 1001, P221-
222, November 05, 1842
A MAN WITH THREE TESTICLES.
F. Macann
1062846374
Reposted by Daniel MacArthur
Ewan Birney @ewanbirney.bsky.social · 01/09/2025
One for the reading pile and this scQTL x Disease in a MR framework feels a v powerful approach (more tissues / cell types please!) -
0112
Daniel MacArthur @dgmacarthur.bsky.social · 01/09/2025
Another preprint from the TenK10K program! This work, led by @alberthenry.bsky.social and Anne Senabouth, leverages the unprecedented power of this WGS/single cell RNA-seq cohort to explore causal influences of blood gene expression on immune diseases and traits. Thread:
0122
Reposted by Daniel MacArthur
Greg Findlay @gregfindlay.bsky.social · 18/08/2025
Our latest research is out today on ‪@medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
medrxiv.org
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk
Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence for variants in BRCA1 , over half of reported single-nucleotide variants (...
16921
Reposted by Daniel MacArthur
Nicky Whiffin @nickywhiffin.bsky.social · 18/08/2025
🚨 New preprint led by amazing duo @rociorius.bsky.social and @alexblakes.bsky.social in collaboration with @cassimons.bsky.social, @dgmacarthur.bsky.social and many other amazing folks! ❤️ We describe the clinical phenotype of a recessive NDD associated with biallelic variants in RNU4-2 🧬 See 🧵👇
0268
Daniel MacArthur @dgmacarthur.bsky.social · 18/08/2025
New preprint! The outcome of a wonderful collaboration with @nickywhiffin.bsky.social’s team to define a new recessive syndrome associated with inherited variants in RNU4-2, the non-protein-coding gene that keeps on giving.
0194
Reposted by Daniel MacArthur
Hope Tanudisastro @htanudisastro.bsky.social · 13/08/2025
#HGSA2025 week kicks off with the OurDNA symposium tomorrow (with a preview of the OurDNA browser!) Register to attend online here👇
051
Reposted by Daniel MacArthur
Nicky Whiffin @nickywhiffin.bsky.social · 31/07/2025
📣 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
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'
14443
Reposted by Daniel MacArthur
Andrea Ganna @andganna.bsky.social · 30/07/2025
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
0569
Reposted by Daniel MacArthur
Kevin Mitchell @wiringthebrain.bsky.social · 27/07/2025
This implies there is a huge literature of small microbiome association studies that is JUST NOISE. (As observed for these other fields)
1257
Reposted by Daniel MacArthur
Will Lowe @conjugateprior.org · 17/07/2025
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)
eusprig.org
Horror Stories | European Spreadsheet Risk Interest Group
3446
Reposted by Daniel MacArthur
Jim Woodgett @jwoodgett.bsky.social · 26/06/2025
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...
healthydebate.ca
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.
1378
Reposted by Daniel MacArthur
Open Targets @opentargets.org · 26/06/2025
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...
UMAP of the 9 populations and 86 cell types identified after quality control and clustering
1197
Daniel MacArthur @dgmacarthur.bsky.social · 23/06/2025
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...
events.humanitix.com
OurDNA Symposium 2025: Partnering for impact
The OurDNA Symposium brings stakeholders together for important conversations about building the foundation for equitable genomics in Australia.
0109
Reposted by Daniel MacArthur
Saloni @scientificdiscovery.dev · 09/06/2025
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...
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.
524870
Reposted by Daniel MacArthur
Edward Nirenberg @enirenberg.bsky.social · 03/06/2025
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.
472273495
Reposted by Daniel MacArthur
Dmitri Petrov @petrovadmitri.bsky.social · 03/06/2025
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...
philanthropy.cam.ac.uk
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 ...
4144147
Reposted by Daniel MacArthur
Philip Ball @philipcball.bsky.social · 22/05/2025
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...
newscientist.com
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...
16568173
Daniel MacArthur @dgmacarthur.bsky.social · 24/05/2025
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
populationgenomics.org.au
Careers - Centre for Population Genomics
0147
Reposted by Daniel MacArthur
Zornitza Stark @zornitza.bsky.social · 23/05/2025
🤗 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!
medrxiv.org
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...
12413
Reposted by Daniel MacArthur
Megan L. Cook @meganlcook.bsky.social · 19/05/2025
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
310621
Reposted by Daniel MacArthur
Emily Rae @ecrmaths.bsky.social · 17/05/2025
This is the best graph I've seen in a while 📊
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.
21350120
Reposted by Daniel MacArthur
Marshall Burke @marshallburke.bsky.social · 16/05/2025
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.
13513257
Reposted by Daniel MacArthur
The New York Times @nytimes.com · 16/05/2025
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
2234545
Reposted by Daniel MacArthur
Michael Baym @baym.lol · 14/05/2025
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
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
145875575
Reposted by Daniel MacArthur
Andrew Carroll @acarroll.bsky.social · 13/05/2025
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...
github.com
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...
1209
Reposted by Daniel MacArthur
Paul Smaldino @psmaldino.bsky.social · 09/05/2025
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...
Author-Paid PublicationFees Corrupt Science and Should Be Abandoned 
Thomas J. H Morgan & Paul E. Smaldino
10408140
Reposted by Daniel MacArthur
c0nc0rdance @c0nc0rdance.bsky.social · 08/05/2025
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)
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?
1316036
Reposted by Daniel MacArthur
Wonder of Science @wonderofscience.bsky.social · 07/05/2025
These boxes are not moving. A mind-bending optical illusion by Japanese artist Jagarikin.
26293172353
Reposted by Daniel MacArthur
Tuuli Lappalainen @tuuliel.bsky.social · 06/05/2025
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/...
193
Reposted by Daniel MacArthur
Tuuli Lappalainen @tuuliel.bsky.social · 06/05/2025
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...
19842
Reposted by Daniel MacArthur
Tuuli Lappalainen @tuuliel.bsky.social · 05/05/2025
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...
biorxiv.org
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...
47428
Reposted by Daniel MacArthur
Tuuli Lappalainen @tuuliel.bsky.social · 06/05/2025
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.
1399
Reposted by Daniel MacArthur
Mingyuan "Merlin" Li @supmerlin.bsky.social · 05/05/2025
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...
33615
Reposted by Daniel MacArthur
David Ho @davidho.bsky.social · 04/05/2025
I think a lot about what Carl Sagan said in one of his final interviews.
"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."
246188266426
Reposted by Daniel MacArthur
Irene Gallego Romero @ee-reh-neh.bsky.social · 05/05/2025
🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.
58329
Reposted by Daniel MacArthur
Paul Gardner @ppgardne.bsky.social · 30/04/2025
Talk about impactful: ReNu syndrome linked to the RNU4-2 variation was discovered this time last year & now a global community has grown around those affected by the disease: www.renusyndrome.org/map
1146