Mark James Adams

"Years and years ago, there was a production of The Tempest, out of doors, at an Oxford college on a lawn, which was the stage, and the lawn went back towards the lake in the grounds of the college, and the play began in natural light. But as it developed, and as it became time for Ariel to say his farewell to the world of The Tempest, the evening had started to close in and there was some artificial lighting coming on. And as Ariel uttered his last speech, he turned and he ran across the grass, and he got to the edge of the lake and he just kept running across the top of the water — the producer having thoughtfully provided a kind of walkway an inch beneath the water. And you could see and you could hear the plish, plash as he ran away from you across the top of the lake, until the gloom enveloped him and he disappeared from your view. And as he did so, from the further shore, a firework rocket was ignited, and it went whoosh into the air, and high up there it burst into lots of sparks, and all the sparks went out, and he had gone. "When you look up the stage directions, it says, 'Exit Ariel.”

Eleven years ago, I wrote to Tom Stoppard to ask about this coup de théâtre from 1949. It took me down an unexpected rabbit hole - in memory of Stoppard, here's what I found.

Genetic prediction with ARG-powered linear algebra Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...

www.biorxiv.org/content/10.1...

We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.

Noisily and angrily finding fault with heritability estimates, rather than putting energy into developing the methodological advances that address previous limitations.

We are all mosaics: vast genetic diversity found between cells in a single person Technical advances allow researchers to trace the genetic changes that occur over time.

One for the heredity scolds: construct a multi-tissue GRM where people
are differentially related to themselves.

www.nature.com/articles/d41...

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

🚨 SynthNet is out 🚨
Researchers propose new constructs and measures faster than anyone can track. We (@anniria.bsky.social @ruben.the100.ci) built a search engine to check what already exists and help identify redundancies; indexing 74,000 scales from ~31,500 instruments in APA PsycTests. 🧵1/3

The dispersal of domestic cats from North Africa to Europe around 2000 years ago The domestic cat (Felis catus) descends from the African wildcat Felis lybica lybica. Its global distribution alongside humans testifies to its successful adaptation to anthropogenic environments. Unc...

The dispersal of domestic cats from North Africa to Europe around 2000 years ago | Science www.science.org/doi/10.1126/...

Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors Ancestral Recombination Graphs (ARGs) are fundamental population genetic structures that encode the genealogical history of a sample of haplotypes along the genome. They have recently received substan...

We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1....
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
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Out now in @natgenet.nature.com, our Comment analyzing uses of the Human Genome Diversity Project (HGDP), a controversial dataset in human genomics research. A 🧵

rdcu.be/eRu65

1/

Yes, that's a good instance of when genetic variance can be a poor estimator of heritability.

Heritability is the regression of offspring on parent phenotypes.

Everything else is an estimator of that.

The causal viewpoint is of course important, but the underlying population genetic setting has to be addressed in advance as it accounts for the ideal setting without causal complications.
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The missing heritability question is now (mostly) answered Not with a bang but with a whimper

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

Is Matrix Multiplication Ugly? A few weeks ago I was minding my own business, peacefully reading a well-written and informative article about artificial intelligence, when I was ambushed by a passage in the article that aroused …

A trace only a mother could love.

mathenchant.wordpress.com/2025/11/21/i...

"Open the pod bay doors, please, HAL."

"I'm sorry, Dave. I'm afraid I can't do that."

"Roses are red / space is chilly / open the pod bay doors / and stop being silly."

Precision medicine for depression: identifying multi-Omic, immunological markers for treatment-resistant depression | Precision Medicine Doctoral Training Programme | Usher Institute Precision Medicine Project - Precision medicine for depression: identifying multi-Omic, immunological markers for treatment-resistant depression

Fully-funded PhD opportunity in psychiatric genetics in Edinburgh. Come work with to understand antidepressant response profiles.

usher.ed.ac.uk/precision-me...

The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute ...

70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.

pmc.ncbi.nlm.nih.gov/articles/PMC...

BICCN: A cell census of the developing human brain Expanding cell-type atlases to include developing human, mouse and non-human primate brains using multimodal genomics.

Huge new collection of papers on cell-type atlases of the developing brain in primates and mice. www.nature.com/immersive/d4...

How do genetic association studies rank genes? Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.

@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪

www.nature.com/articles/d41...

Starting to scope out a TRE/SDE/RAP* for our research cohort.

It won't be hosted by a global cloud provider. I want to make it feel more like using the on-prem infrastructure you're used to.

* = Trusted Research Environment / Safe Data Environment / Research Analysis Platform

The Passing of the Tree of Life Web Project The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…

The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...

We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT

It's not every day that you get a new imputation reference panel.

allofus-anvil-imputation.terra.bio

Cameron Patrick - Some Quarto PDF formatting tips, with particular reference to thesis writing I’ve just spent most of a day faffing around trying to get Quarto to produce a nice PDF file that I like the look of and which meets my university’s formatting requirements for a PhD thesis. Maybe my ...

This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...

🚨 Position Alert! 🚨
I am looking for a full-time Research Scientist 1 to join my lab in Albuquerque, NM at the Center on Alcohol, Substance Use, and Addiction (CASAA). We will be studying how stress and trauma influence cannabis and substance use. 🧠🌿 (1/5)

Non-paywalled link to my commentary on @vw1234.bsky.social and colleagues new paper in @nature.com rdcu.be/eI2NG

University of Colorado Boulder Department of Psychology & Neuroscience is searching for TWO tenure track assistant professors. This is open to all department areas, including Behavioral, Psychiatric, and Statistical Genetics🧬 jobs.colorado.edu/jobs/JobDeta...

'Is artificial intelligence a scientific study?'
'Not really…'

— Muriel Spark, Symposium, 1990

Direct effect of genetic ancestry on complex traits in a Mexican population Human populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...

Brilliant paper by Visscher et al.

Populations differ in traits/disease burden. Are these differences due to genetics?

Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.

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

Photograph of a presenter at a wooden podium in front of a slide with the question "Why Scotland" and bullet points "Top quality health research " and "Long standing, high quality health, social, and demographic data"

Photograph of a speaker at a podium in front of a slide showing the Generation Scotland Executive Committee ("Gang of Four")

At a symposium celebrating the 20th year of the @genscot.bsky.social cohort. David Porteous giving an overview of the origins of the cohort, answering the question "Why Scotland"