Pai Kusuma

Gene expression changes aren’t just about mean shifts — variability shifts matter too, especially for aging. We're thrilled to introduce QRscore, a flexible non-parametric framework for detecting shifts in mean and variance across conditions. doi.org/10.1016/j.cr...

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

Invasion preferences suggest a possible role for Plasmodium falciparum parasites in the expansion of Duffy negativity in West and Central Africa https://www.biorxiv.org/content/10.1101/2025.07.09.663497v1

An image of Sulawesi Island that consist of four connecting peninsula shaping the island into something that looks like a letter "K" with adjacent small islands, annotated with colored circles and triangles marking the location of anoa (circle) and babirusa (triangle) from three types of region across the islands. Each region is accompanied by an art piece of the head of anoa and babirusa to mark the presence of one or both taxa in the region. There are both in the northern and southeastern peninsula of Sulawesi, only anoa in Buton south of the southeastern peninsula, and only babirusa in the Togean south of northern peninsula. In the right side of the head art, there are DNA icon with breakage illustrating "deleterious mutations" and a forest icon illustrating "habitat quality". An arrow going down, up, and left accompanying each icon to mark whether the abundance of each icon are high or low relative to the focal populations, which is marked with arrow pointing right to illustrate stability in magnitude. For both Buton and Togean, the amount of deleterious mutations are low relative to the larger island's peninsula, while it has better habitat quality relative to the larger island. This graphical abstract is an oversimplification of the work, I hope you read the paper for more elaboration.

My first PhD paper on the importance of populations in small islands for the survival of megafaunas is out!

In sum, the ~100 whole genome sequences of anoa & babirusa, forest cover & climate model of their habitat, all agree that small-island pops are dope.

#consgen

www.pnas.org/doi/10.1073/...

When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1

A hot take.
#ethics #DireWolf #CRISPR

but in both cases, "science" won.

Thrilled with the release of this Terra Australis volume about the West New Guinea, exploring the rich human past of this fascinating region. Honored to have contributed chapters to this volume.

A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...

Do mutations that drive evolution improve many traits or few?

Does this change over the course of evolution?

Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵

doi.org/10.1371/jour...

Excited to share a new preprint with @jnovembre.bsky.social ! We use a combination of population genetic theory, simulation, and data analysis to ask: how does study design in genetic studies (including biobanks) impact the discovery of rare, deleterious variants?

The genetics of inbreeding depression - Nature Reviews Genetics The genetic basis of inbreeding depression and of the related phenomenon, heterosis, has been a puzzle for many decades. Based on recent studies in many species, the authors argue that both phenomena ...

Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...

GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics. A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics

🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.

It's a common knowledge that EPAS1 is enriched, and pos selected, in Himalayan highlanders. But i keep being astonished by the peaked frequency in the Himalayan highlander population given relatively recent split with the Han.

Do we know the selection coefficient of these EPAS1 alleles in the pop?

Oh the landscape block will surely come in handy 👍

Optimist: The cup is half full.
Pessimist: The cup is half empty.
Population geneticist teaching drift: Sample with replacement the atoms of water in this cup until the next cup is full and assume the total number of atoms stays constant.

Noob here. Migrating from Black to Blue.

1st intro post with 0 follower

Hello world! My name is Pai. A Wellcome Int'l Training Fellow at MR Institute Indonesia and an Honorary Research Assoc at McDonald Inst for Archaeological Research, Uni Cambridge.

Looking forward to a more peaceful life here.