At last, my work with Andrew Kern on a quantitative genetics model of background selection in humans is live at PLoS Genetics! journals.plos.org/plosgenetics/a…

Hyperiax: Tree traversals using JAX github.com/ComputationalE…
Developed by the team at Centre for Computational Evolutionary Morphometry, initially for applications in phylogenetic analysis of morphological data, but Hyperiax has evolved into a general tree traversal, message passing and edge/node computation framework.…

This is exciting work. Faster and better sampling of ancestral recombination graphs (the fundamental structure of genetic ancestry) is a game changer for many questions in population genetics.

Here is a detailed thread about SINGER (thanks Yun S. Song for putting it together!). I will keep improving SINGER and developing new ARG inference/applications methods. Feedbacks/critiques are welcome, and they can be incorporated into our future works!

Super excited about this new method by Yun Deng 邓赟.

Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples dlvr.it/T4B7pX

#TAGC24 I will be presenting at the “Deleterious Mutations” session tomorrow (PgmNr 168) at 11:45am. This is a new example of application of ARG inference, with Vince Buffalo teaching me a lot in this topic. Come and enjoy if you are interested in yet another way to use ARGs!

I'm pleased to share an alpha version of GRanges, a Rust library for working with genomic ranges and their associated data.

I wondered if it was possible to write a library that:

1. Has tidyverse-like syntax for genomic data manipulation.
2. Is extremely performant.

It is.🚀

Join Korneliussen-group as a PhD-student in computational biology! You will part of an exciting and dynamic research environment. The position is fully funded for 3 years🧬
candidate.hr-manager.net/ApplicationIni…

Reposting this criticism of All of Us and their use of ancestry labels
twitter.com/Graham_Coop/st…

Hopefully, this will be the last time we'll see UMAP for human population genetic variation. When Jonathan Pritchard takes a stand - who usually is reluctant to engage on these issues - you know that somebody screwed up.

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.

I’m excited to share our work on the somatic evolution of the mitochondrial genome: nature.com/articles/s4155… . Mt-genomes are a dynamic subcellular population. But, how does the interaction between nuclear and mitochondrial ancestry impact mutation within individuals’ lifespans?

Very cool thread on diffeomorphisms that should be of interest to anybody interested in geometric morphometrics.

California newts are everywhere in Tilden tonight.

After four years of hard work, via a PhD and a pandemic, it feels surreal to write that my research is being published today in four articles in the journal nature (all open access). I am a joint first author on three of them, and we're on the cover!

nature.com/articles/s4158…

Word

youtu.be/MJqUeJOjc0c?si…

🧬 New study uses simulations to investigate genetic rescue (GR) & trait evolution
The authors delve into factors shaping the success of GR, like trait complexity and dominance effects. See the paper here: doi.org/10.1093/jhered…
1/2

Elon Musk picked a fight with Nordic workers. We’re gonna make him lose. Help us get the message out: Dear Elon Musk - Get unionized or get out!

Happy to share a new preprint from the lab on ARGs, selection, and ancient DNA. biorxiv.org/content/10.110… We present CLUES2, a full-likelihood method that extends the work of Stern et al. 2019. Improvements include (1) the ability to use ARGs on ancient samples, allowing for 1/n