@mathiesoniain

Population genetics, ancient DNA, statistics.

 Philadelphia, PA
med.upenn.edu/mathieson-lab/
Joined April 2012
  • Tweets2.3K
  • Following672
  • Followers3.6K
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Iain Mathieson retweeted
Shai Carmi@ShaiCarmi21 Jul 2024
The Silicon Valley people interviewed seem almost apathetic to the realities of life of anyone outside their bubble. Their "social engineering" efforts destroyed the world's democracies. Should we let them into reproductive medicine?
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"...and what did that produce? The cuckoo clock.”
Prof Francois Balloux
@BallouxFrancois8 Jul 2024
Many seem to believe that governments without a clear political majority lead to instability, chaos and economic doom ... Switzerland ...
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The market can stay irrational longer than you can stay solvent.
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Two incredible papers. Forget about ML. Coalescent HMMs are and always will be king. biorxiv.org/content/10.1101/… biorxiv.org/content/10.1101/…
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Very annoying that people are taking seriously the genetically inferred bottleneck that is almost certainly wrong. pnas.org/doi/10.1073/pnas.23…

Hominin population bottleneck coincided with migration from Africa during the Early Pleistocene ice...

Two recently published analyses make cases for severe bottlenecking of human populations occurring in the late Early Pleistocene, one case at about...

pnas.org
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Our paper "Interpreting GANs to infer natural selection from genetic data" is out in Genetics! Thank you @petrelharp as editor. academic.oup.com/genetics/ad… I will be talking about this work at #TAGC24 tomorrow (Friday) at 2pm. "Methodological Advances in Population Genomics" session.
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Completely agree - I always find claims in papers about the number of "novel" variants to be silly. Every position in the genome is variable somewhere. Patterns of LD *are* population specific but of more limited interest.
Graham Coop@Graham_Coop28 Feb 2024
The use of the phrase “ancestry-specific variant” is increasing, particularly to describe rare Single-nucleotide variants (SNVs). But these alleles are not ancestry-specific. They have not yet been found elsewhere, but they will be. 1/n
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Couldn't agree more! Nothing wrong with PCA.
Jonathan Pritchard@jkpritch20 Feb 2024
It's a pity that All of Us used UMAP to visualize ancestry variation in their new marker paper, out today in Nature. The UMAP algorithm, by design, exaggerates the distinctiveness of the most frequent ancestries, a message that can be misinterpreted by the public.
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Uh... missing genotypes "might appear" as 0 instead of .
Kieran Samuk@ksamuk6 Feb 2024
PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.
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"Disease Evolution in the Human Past" - Join us March 21st 2024 @TheCrick for a half-day symposium in the Medicine at the Crick series. 🦠 Johannes Krause | “The genetic history and origin of the Black Death” @MPI_EVA_Leipzig 🦟 Lucy van Dorp | “Tracking zoonotic pathogens in space and time" @LucyvanDorp 📈 Iain Mathieson | “Natural selection in Britain from the Stone Age to the present day” @mathiesoniain 🌍 Carina Schlebusch | “Past Lives, Present Insights: Biomolecular Stories from Ancient Africa” @cschlebu 👥 Matthew Hurles | “Population demography and the genetic architecture of developmental disorders" @mehurles Everyone in the clinical and scientific community is welcome! Register 👉 crick.ac.uk/whats-on/medicin…
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Perhaps not only psychological traits!
Kevin Mitchell@WiringTheBrain13 Nov 2023
Developmental noise is an overlooked contributor to innate variation in psychological traits pubmed.ncbi.nlm.nih.gov/3609…
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Iain Mathieson retweeted
Yun S. Song@yun_s_song13 Sep 2023
After lengthy anticipation, we finally got to compare PrimateAI-3D with our Cross-Protein Transfer (CPT) model doi.org/10.1186/s13059-023-0… Below is a summary of our findings, including a comparison of ESM-1b and ESM-1v protein language models. 1/8

Cross-protein transfer learning substantially improves disease variant prediction

Genome Biology - Genetic variation in the human genome is a major determinant of individual disease risk, but the vast majority of missense variants have unknown etiological effects. Here, we...

link.springer.com
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Trying to access some data from EGA, but the access policy is blank and the link to the data access committee brings up a page saying "Oops..the server made a poo poo".
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This is a good explanation. In my opinion this is the major limitation of the paper.
Vince Buffalo@vsbuffalo27 Jun 2023
On the Clark paper: correlation functions often decay over various distances (genetic, environmental, spatial, etc). Observing a correlation that varies over genetic relatedness is not evidence that the cause is genetic, since many other processes create correlations that decay.
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more replies
Anything that changes randomly every generation would decay exponentially. Imagine with probability p you adopt one of your parents' religions and w.p. 1-p the predominant religion. Then correlation of religion decays as genetic relatedness (+same assortative mating fudge factor)
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Also does not have to be a single factor. Since most things will decay in the same way, the explanation can be a combination of many environmental (and, yes, maybe genetic) factors, but I don't think it's really possible to distinguish them.
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"0.07-0.01% of variance" nature.com/articles/s41467-0…
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I was under the impression we should use chr:pos_ref_alt to identify SNPs and not rsids, and assumed I should also no t rely one rsids when converting across builds, but UCSC disagrees: genome.ucsc.edu/FAQ/FAQrelea…. Am I wrong?
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Finally! Here the TRIAL VERSION 2023.1 of THE MAP. Pls do comment, using either mail or reply function. We have tried to include all of the many comments that have reached us, but there is certainly room for more. @leizarchaeology @oeai_oeaw @BarbaraHorejs
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