Daniel MacArthur

Daniel MacArthur

@dgmacarthur.bsky.social

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.

5.6K followers1.2K following70 posts

Daniel MacArthur reposted

Angli Xue
@anglixue.bsky.social

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.comGenetic regulation of cell type-specific chromatin accessibility shapes immune function and disease riskUnderstanding 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 ...
Angli Xue@anglixue.bsky.social

New preprint alert: tinyurl.com/tenk10k-multiome. Excited to share our analysis on the impact of genetic variants on single-cell chromatin accessibility in blood, using scATAC-seq and WGS from over 1,000 donors and 3.5M nuclei as part of TenK10K phase 1 🧬 🧵👇 (1/n)

tinyurl.comGenetic regulation of cell type-specific chromatin accessibility shapes immune function and disease riskUnderstanding 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 multi-omics data have constrained our understanding of the regulatory pathways that link variants to cell type-specific gene expression. Here we present chromatin accessibility profiles from 3.5 million peripheral blood mononuclear cells (PBMCs) across 1,042 donors, generated using single-cell ATAC-seq and multiome (RNA+ATAC) sequencing, with matched whole-genome sequencing, generated as part of the TenK10K program. We characterized 440,996 chromatin peaks across 28 immune cell types and mapped 243,273 chromatin accessibility quantitative trait loci (caQTLs), 60% of which are cell type-specific. Integration with TenK10K scRNA-seq data (5.4 million PBMCs) identified 31,688 candidate cis-regulatory elements colocalized with eQTLs; over half (52.5%) show evidence of causal effects mediated via chromatin accessibility. Integrating caQTLs with GWAS summary statistics for 16 diseases and 44 blood traits uncovered 9.8% - 30.0% more colocalized signals compared with using eQTLs alone, many of which have not been reported in prior studies. We demonstrate cell type-specific mechanisms, such as a regulatory effect on IRGM acting through altered promoter chromatin accessibility in CD8 effector memory T cells but not in naive cells. Using a graph neural network, we inferred peak-to-gene relationships from unpaired multiome data by incorporating caQTL and eQTL signals, achieving up to 80% higher accuracy compared to using paired multiome data without QTL information. This improvement further enhanced gene regulatory network inference, leading to the identification of 128 additional transcription factor (TF)-target gene pairs (a 22% increase). These findings provide an unprecedented single-cell map of chromatin accessibility and genetic variation in human circulating immune cells, establishing a powerful resource for dissecting cell type-specific regulation and advancing our understanding of genetic risk for complex diseases. ### Competing Interest Statement L.C., E.B.D., and K.K.H.F. are employed at Illumina Inc. D.G.M. is a paid advisor to Insitro and GSK, and receives research funding from Google and Microsoft, unrelated to the work described in this manuscript. G.A.F reports grants from National Health and Medical Research Council (Australia), grants from Abbott Diagnostic, Sanofi, Janssen Pharmaceuticals, and NSW Health. G.A.F reports honorarium from CSL, CPC Clinical Research, Sanofi, Boehringer-Ingelheim, Heart Foundation, and Abbott. G.A.F serves as Board Director for the Australian Cardiovascular Alliance (past President), Executive Committee Member for CPC Clinical Research, Founding Director and CMO for Prokardia and Kardiomics, and Executive Committee member for the CAD Frontiers A2D2 Consortium. In addition, G.A.F serves as CMO for the non-profit, CAD Frontiers, with industry partners including, Novartis, Amgen, Siemens Healthineers, ELUCID, Foresite Labs LLC, HeartFlow, Canon, Cleerly, Caristo, Genentech, Artyra, and Bitterroot Bio, Novo Nordisk and Allelica. In addition, G.A.F has the following patents: "Patent Biomarkers and Oxidative Stress" awarded USA May 2017 (US9638699B2) issued to Northern Sydney Local Health District, "Use of P2X7R antagonists in cardiovascular disease" PCT/AU2018/050905 licensed to Prokardia, "Methods for treatment and prevention of vascular disease" PCT/AU2015/000548 issued to The University of Sydney/Northern Sydney Local Health District, "Methods for predicting coronary artery disease" AU202290266 issued to The University of Sydney, and the patent "Novel P2X7 Receptor Antagonists" PCT/AU2022/051400 (23.11.2022), International App No: WO/2023/092175 (01.06.2023), issued to The University of Sydney. ### Funding Statement A.X. is supported by NHMRC Investigator grant 2033018. J.E.P. is supported by NHMRC Investigator grant 2034556, and a Fok Family Fellowship; D.G.M. is supported by an NHMRC investigator grant (2009982). G.A.F. and the BioHEART Study have been supported by NHMRC Investigator Grant, NSW Health Office of Health and Medical Research, and the NSW Health Statewide Biobank scheme. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Human Research Ethics Committee of St Vincent's Hospital gave ethical approval for this work. The National Statement on Ethical Conduct in Human Research of the National Health and Medical Research Council gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Raw caQTL summary statistics will be available at Zenodo website prior to acceptance. [https://github.com/powellgenomicslab/tenk10k\_phase1\_multiome][1] [1]: https://github.com/powellgenomicslab/tenk10k_phase1_multiome

Daniel MacArthur reposted

Nicky Whiffin
@nickywhiffin.bsky.social

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.comSaturation editing of RNU4-2 reveals distinct dominant and recessive disorders - NatureSaturation 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.
Daniel MacArthur
@dgmacarthur.bsky.social

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!

Zornitza Stark@zornitza.bsky.social

🤗 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

Daniel MacArthur reposted

Molly Przeworski
@mollyprz.bsky.social

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.orgCollateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signatureMutations 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 ...
Daniel MacArthur
@dgmacarthur.bsky.social

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!

Angli Xue@anglixue.bsky.social

New preprint alert: tinyurl.com/tenk10k-multiome. Excited to share our analysis on the impact of genetic variants on single-cell chromatin accessibility in blood, using scATAC-seq and WGS from over 1,000 donors and 3.5M nuclei as part of TenK10K phase 1 🧬 🧵👇 (1/n)

tinyurl.comGenetic regulation of cell type-specific chromatin accessibility shapes immune function and disease riskUnderstanding 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 multi-omics data have constrained our understanding of the regulatory pathways that link variants to cell type-specific gene expression. Here we present chromatin accessibility profiles from 3.5 million peripheral blood mononuclear cells (PBMCs) across 1,042 donors, generated using single-cell ATAC-seq and multiome (RNA+ATAC) sequencing, with matched whole-genome sequencing, generated as part of the TenK10K program. We characterized 440,996 chromatin peaks across 28 immune cell types and mapped 243,273 chromatin accessibility quantitative trait loci (caQTLs), 60% of which are cell type-specific. Integration with TenK10K scRNA-seq data (5.4 million PBMCs) identified 31,688 candidate cis-regulatory elements colocalized with eQTLs; over half (52.5%) show evidence of causal effects mediated via chromatin accessibility. Integrating caQTLs with GWAS summary statistics for 16 diseases and 44 blood traits uncovered 9.8% - 30.0% more colocalized signals compared with using eQTLs alone, many of which have not been reported in prior studies. We demonstrate cell type-specific mechanisms, such as a regulatory effect on IRGM acting through altered promoter chromatin accessibility in CD8 effector memory T cells but not in naive cells. Using a graph neural network, we inferred peak-to-gene relationships from unpaired multiome data by incorporating caQTL and eQTL signals, achieving up to 80% higher accuracy compared to using paired multiome data without QTL information. This improvement further enhanced gene regulatory network inference, leading to the identification of 128 additional transcription factor (TF)-target gene pairs (a 22% increase). These findings provide an unprecedented single-cell map of chromatin accessibility and genetic variation in human circulating immune cells, establishing a powerful resource for dissecting cell type-specific regulation and advancing our understanding of genetic risk for complex diseases. ### Competing Interest Statement L.C., E.B.D., and K.K.H.F. are employed at Illumina Inc. D.G.M. is a paid advisor to Insitro and GSK, and receives research funding from Google and Microsoft, unrelated to the work described in this manuscript. G.A.F reports grants from National Health and Medical Research Council (Australia), grants from Abbott Diagnostic, Sanofi, Janssen Pharmaceuticals, and NSW Health. G.A.F reports honorarium from CSL, CPC Clinical Research, Sanofi, Boehringer-Ingelheim, Heart Foundation, and Abbott. G.A.F serves as Board Director for the Australian Cardiovascular Alliance (past President), Executive Committee Member for CPC Clinical Research, Founding Director and CMO for Prokardia and Kardiomics, and Executive Committee member for the CAD Frontiers A2D2 Consortium. In addition, G.A.F serves as CMO for the non-profit, CAD Frontiers, with industry partners including, Novartis, Amgen, Siemens Healthineers, ELUCID, Foresite Labs LLC, HeartFlow, Canon, Cleerly, Caristo, Genentech, Artyra, and Bitterroot Bio, Novo Nordisk and Allelica. In addition, G.A.F has the following patents: "Patent Biomarkers and Oxidative Stress" awarded USA May 2017 (US9638699B2) issued to Northern Sydney Local Health District, "Use of P2X7R antagonists in cardiovascular disease" PCT/AU2018/050905 licensed to Prokardia, "Methods for treatment and prevention of vascular disease" PCT/AU2015/000548 issued to The University of Sydney/Northern Sydney Local Health District, "Methods for predicting coronary artery disease" AU202290266 issued to The University of Sydney, and the patent "Novel P2X7 Receptor Antagonists" PCT/AU2022/051400 (23.11.2022), International App No: WO/2023/092175 (01.06.2023), issued to The University of Sydney. ### Funding Statement A.X. is supported by NHMRC Investigator grant 2033018. J.E.P. is supported by NHMRC Investigator grant 2034556, and a Fok Family Fellowship; D.G.M. is supported by an NHMRC investigator grant (2009982). G.A.F. and the BioHEART Study have been supported by NHMRC Investigator Grant, NSW Health Office of Health and Medical Research, and the NSW Health Statewide Biobank scheme. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Human Research Ethics Committee of St Vincent's Hospital gave ethical approval for this work. The National Statement on Ethical Conduct in Human Research of the National Health and Medical Research Council gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Raw caQTL summary statistics will be available at Zenodo website prior to acceptance. [https://github.com/powellgenomicslab/tenk10k\_phase1\_multiome][1] [1]: https://github.com/powellgenomicslab/tenk10k_phase1_multiome

Daniel MacArthur reposted

Ewan Birney
@ewanbirney.bsky.social

One for the reading pile and this scQTL x Disease in a MR framework feels a v powerful approach (more tissues / cell types please!) -

Albert Henry@alberthenry.bsky.social

1. 🚨New preprint: tinyurl.com/tenk10k-causal. We explored causal effects of gene expression in immune cell types on complex traits and diseases by combining single-cell expression quantitative trait loci (sc-eQTL) mapping in 5M+ cells from 1,925 donors in TenK10K study and GWAS. 🧵

tinyurl.comSingle-cell genetics identifies cell type-specific causal mechanisms in complex traits and diseasesGenome-wide association studies (GWAS) have been instrumental in uncovering the genetic basis of complex traits. When integrated with expression quantitative trait loci (eQTL) mapping, they can elucid...
Daniel MacArthur
@dgmacarthur.bsky.social

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:

Albert Henry@alberthenry.bsky.social

1. 🚨New preprint: tinyurl.com/tenk10k-causal. We explored causal effects of gene expression in immune cell types on complex traits and diseases by combining single-cell expression quantitative trait loci (sc-eQTL) mapping in 5M+ cells from 1,925 donors in TenK10K study and GWAS. 🧵

tinyurl.comSingle-cell genetics identifies cell type-specific causal mechanisms in complex traits and diseasesGenome-wide association studies (GWAS) have been instrumental in uncovering the genetic basis of complex traits. When integrated with expression quantitative trait loci (eQTL) mapping, they can elucid...

Daniel MacArthur reposted

Greg Findlay
@gregfindlay.bsky.social

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.orgSaturation genome editing of BRCA1 across cell types accurately resolves cancer riskGermline 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 (...

Daniel MacArthur reposted

Nicky Whiffin
@nickywhiffin.bsky.social

🚨 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 🧵👇

alexblakes.bsky.social@alexblakes.bsky.social

I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2! tinyurl.com/3j9r56s8 @rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social

medrxiv.orgBiallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changesGenetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
Daniel MacArthur
@dgmacarthur.bsky.social

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.

alexblakes.bsky.social@alexblakes.bsky.social

I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2! tinyurl.com/3j9r56s8 @rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social

medrxiv.orgBiallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changesGenetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...

Daniel MacArthur reposted

Hope Tanudisastro
@htanudisastro.bsky.social

#HGSA2025 week kicks off with the OurDNA symposium tomorrow (with a preview of the OurDNA browser!) Register to attend online here👇

Daniel MacArthur@dgmacarthur.bsky.social

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

Daniel MacArthur reposted

Nicky Whiffin
@nickywhiffin.bsky.social

📣 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

Daniel MacArthur
@dgmacarthur.bsky.social

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

Daniel MacArthur reposted

Edward Nirenberg
@enirenberg.bsky.social

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.

Daniel MacArthur reposted

Philip Ball
@philipcball.bsky.social

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.comColossal scientist now admits they haven’t really made dire wolvesDespite 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...

Daniel MacArthur reposted

Zornitza Stark
@zornitza.bsky.social

🤗 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.orgScalable automated reanalysis of genomic data in research and clinical rare disease cohortsReanalysis 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...

Daniel MacArthur reposted

Megan L. Cook
@meganlcook.bsky.social

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

Daniel MacArthur reposted

Marshall Burke
@marshallburke.bsky.social

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.

Daniel MacArthur reposted

The New York Times
@nytimes.com

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

Daniel MacArthur reposted

Michael Baym
@baym.lol

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

Daniel MacArthur reposted

Andrew Carroll
@acarroll.bsky.social

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.comRelease DeepVariant 1.9.0 · google/deepvariantDeepVariant: 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...

Daniel MacArthur reposted

Paul Smaldino
@psmaldino.bsky.social

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...

Daniel MacArthur reposted

c0nc0rdance
@c0nc0rdance.bsky.social

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)

Daniel MacArthur reposted

Tuuli Lappalainen
@tuuliel.bsky.social

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.orgSpatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traitsSpatially 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...

Daniel MacArthur reposted

Tuuli Lappalainen
@tuuliel.bsky.social

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.

This post is unavailable.

Daniel MacArthur reposted

Irene Gallego Romero
@ee-reh-neh.bsky.social

🎉 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.

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social

Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans https://www.biorxiv.org/content/10.1101/2025.05.04.652069v1