If anyone regrets not being able to attend my recent regression modeling course you can still access the slides, exercises, and recordings with a late donation. For donation instructions see betanalpha.github.io/courses/.

#mathshy #statistics

As a (to me very enjoyable) part of this paper, we worked out what mutation-selection balance looks like in finite populations with varying degrees of inbreeding.

Preprint by Gravel et al addressing an interesting question. Given carriers of a mutation and a population-scale pedigree, can we identify the most recent common ancestor of all carriers? "20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"

A whole Advent Calendar of Nigel Farage repeating Vladimir Putin's talking points. Brilliant. bylinetimes.com/2025/12/10/n...

An interesting rabbit hole that I have yet dug into is that population structure alone cannot drive genetic variance inflation in the estimates. We did a spatial simulation exhibiting a very strong isolation-by-distance pattern. The estimated variance components are consistent.

Very very happy that this work is out. Led by the brilliant @epigenci.bsky.social and other fab collaborators! I have been thinking about this for years, but couldn’t do it without the team;) Enjoy the reading!

Am I the only person to read teaspoon as teasposons 😂😂

In deeper pedigrees, the estimand pertains to the founders of the population. In SNP LMMs, do you know who these are?

Genetic variance of a population is a random variable and not a parameter. It becomes one only if you condition on a particular population in space and time. Given this choice, the variance of other populations is still left as a random variable.

@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...

Wonderful story from a young scientist about his experience with @official-smbe.bsky.social and competing in GHIST. I'm so glad to see the next generation thriving. Jaison is an author on the GHIST paper, and the 2025 competition ends in 14 days. Now's your chance to dive in and join! ghist.bio

Haseman-Elston regression is bit of an irony for massive biobanks because it throws away the statistical precision that was gained by accounting for more samples. You might be able to analyze more data, but you don't get more information out of it.

I still give this advice routinely for students looking for career advice. Write and learn in public. One thing I missed in this post is CONSISTENCY. As with athletic pursuits, people overestimate what you can accomplish in a week and underestimate what you can do in a year. Writing is the same.

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

This tells us that population structure itself, which does not contribute to "directional" allele frequency stratification, can't create fixed effects. What happens there is selection? well that I think is still an open question. (8/8).

This makes PCs obsolete as a means to handle fixed genetic contributors. Of course, there are non-genetic contributors aligning with genetic factors so PCs might have role, but it has nothing to do with genetics. (7/n)

I greatly appreciate Ochoa group's long-lasting effort to define the quantity first and trying to estimate it. They've been stressing that PCs are unnecessary in LMMs are in fact harmful in certain cases. I have some thoughts. (1/n) academic.oup.com/genetics/adv...

Every time one anti-vaxxer is quoted in the media, one million scientists and healthcare workers should also be quoted in support of vaccines. False equivalence in the media is killing us.

I think what you are calling stochastic developmental variation is the outcome of unmeasured environmental perturbations and genetic-environmental interactions on a highly complex and possibly chaotic system, and definitely contributes to the observed non-genetic variance. :)

Is it possible to download the whole tree from the math genealogy project?

Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG

Our work (by Drew DeHaas) on an extremely simple yet efficient binary genotype format - designed to facilitate scalable bioinformatics tool development. www.biorxiv.org/content/10.1...

Very proud of this manuscript with two talented undergraduate students, Aditya Syam and Chris Adonizio. We are continuing to push towards more scalable statistical genetics with Genotype Representation Graphs, and this is the start. www.biorxiv.org/content/10.1...

Method works from simple and complex scenarios in jointly estimating epoch time, population size, migration rate (symmetric or asymmetric), growth rate, and admixture proportion. Software integrated with msprime, demes, tsinfer/tsdate, relate, and singer. github.com/aprilweilab/...

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

I want to try something again at #ASHG25 this year: I'll block some time on Thursday and Friday afternoons to meet with trainees who would be interested to chat on any topic. I did this last year and it was great to meet a whole bunch of new people, at all career stages!

Our paper (Brieuc Lehmann is the first author) is now online in Genetics. academic.oup.com/genetics/adv...

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

Truly impressive number of birds migrating tonight. More than 800 MILLION birds up in the air right now❗ #BirdMigration

English is only my second language so I had no idea about many of the gendered animal names. Peahen is so obvious but I never had heard of it before. What’s news to you? HT @Iearnenglishtip

Despite this being true, I feel that a lot of gems from the old days are lost in the present literature. People just do things as if those early findings don't exist.

Within-family heritability estimates for behavioural and disease phenotypes from 500,000 sibling pairs of diverse ancestries https://www.medrxiv.org/content/10.1101/2025.09.17.25336022v1

SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution https://www.biorxiv.org/content/10.1101/2025.09.01.673541v1

PCA for visualising large #pedigrees? Check out this brief and accessible blog post wp.me/pbTxyW-1ve @roslininstitute.bsky.social @highlanderlab.bsky.social Thanks to co-authors @epigenci.bsky.social @gregorgorjanc.bsky.social and Ros Craddock!

Save the date! #PEQG26 June 9-12 2026 in Asilomar, CA. Happens only every 2yrs, but is my favorite conference. Full website coming soon, and registration and abstract submission opens November 14, but I'm allowed to tease that keynotes will be @jnovembre.bsky.social @jennytung.bsky.social and me!

Announcing SimHumanity, a baseline SLiM 5.0 model of the full human genome, replete with demographic history, autosomes, X/Y, and mtDNA. A shared starting point for reproducible evolutionary simulations. We’d love your feedback! #SLiM #evolution #genomics www.biorxiv.org/content/10.1...

Our pedigree PCA article is now online on GSE: doi.org/10.1186/s127... Thanks @epigenci.bsky.social , @gregorgorjanc.bsky.social , Rosalind Craddock!

This always blows my mind. Dude mapped qtl for a quantitative trait to a chromosome in 1923!

Assessment of segregation variance estimates from derivation, simulations, and empirical data in autotetraploid species exemplified in potato https://www.biorxiv.org/content/10.1101/2025.08.13.670171v1

AlphaSimR course edin.ac/3wfGSEj Week 3 opens with a discussion on genetic variation between relatives, with a focus on siblings. While mutation is the ultimate source of genetic variation (by introducing new alleles), recombination shuffles the existing genetic variation through meiosis.

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats code github.com/const-ae/lin...

You can save #tidyplots in multiple formats by piping through multiple rounds of `save_plot()` 🤩 #rstats #dataviz #phd

Looks like a great resource for teaching popgen inference.

Thanks! This is amazing! So the term 'Manhattan Plot' is not originally a GWAS term at all. Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:

This is how you can visualize time course data in #tidyplots ⏱️ #rstats #dataviz #phd

Does anyone know who first used the term "Manhattan Plot"? Wikipedia links to a 2010 paper by Greg Gibson. I haven't yet found an earlier use, but Greg's phrasing suggests that he did not invent the term. doi.org/10.1038/ng07...