Pai Kusuma
@paikusuma.bsky.social
Wellcome Int'l Training Fellow | MRIN Indonesia | Hunter-gatherer; Genomics; Evolution; Transition
Reposted by 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...
September 5, 2025 at 2:15 AM
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...
Reposted by Pai Kusuma
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution https://www.biorxiv.org/content/10.1101/2025.09.01.673541v1
September 2, 2025 at 8:31 AM
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution https://www.biorxiv.org/content/10.1101/2025.09.01.673541v1
Reposted by Pai Kusuma
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
July 12, 2025 at 1:32 AM
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
Reposted by Pai Kusuma
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/...
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/...
July 10, 2025 at 1:39 PM
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/...
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/...
Reposted by Pai Kusuma
When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1
May 17, 2025 at 8:32 PM
When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1
April 9, 2025 at 12:50 AM
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.
The latest volume in the Terra Australis series explores the human past in West New Guinea.
It describes the environmental and cultural history of the area and the boundary-making that has formed West New Guinea in the recent past.
Available now doi.org/10.22459/TA5...
It describes the environmental and cultural history of the area and the boundary-making that has formed West New Guinea in the recent past.
Available now doi.org/10.22459/TA5...
February 20, 2025 at 4:08 AM
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.
Reposted by Pai Kusuma
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...
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...
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...
doi.org
December 5, 2024 at 9:46 PM
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...
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...
Reposted by Pai Kusuma
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?
Study design and the sampling of deleterious rare variants in biobank-scale datasets https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1
Study design and the sampling of deleterious rare variants in biobank-scale datasets https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1
One key component of study design in population genetics is the "geographic breadth" of a sample (i.
www.biorxiv.org
December 4, 2024 at 5:17 PM
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?
Reposted by Pai Kusuma
Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...
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 ...
www.nature.com
December 4, 2024 at 9:33 PM
Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...
Reposted by Pai Kusuma
🚨 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.
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
github.com
November 28, 2024 at 9:21 AM
🚨 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?
Do we know the selection coefficient of these EPAS1 alleles in the pop?
November 28, 2024 at 2:57 PM
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?
Do we know the selection coefficient of these EPAS1 alleles in the pop?
Oh the landscape block will surely come in handy 👍
Quarto 1.6 is out! 🎉 Download it here: quarto.org/docs/download/
Quarto 1.6 supports unified branding across formats, updates to RevealJS, a new shortcode to reorder content, a landscape page block, and more. Blog post: quarto.org/docs/blog/po...
Quarto 1.6 supports unified branding across formats, updates to RevealJS, a new shortcode to reorder content, a landscape page block, and more. Blog post: quarto.org/docs/blog/po...
Quarto 1.6 – Quarto
Quarto 1.6 supports unified branding across formats, updates to RevealJS, a new shortcode to reorder content, a landscape page block, and more. There are also a couple of breaking changes that will af...
quarto.org
November 25, 2024 at 11:52 PM
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.
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.
Optimist: The cup is half full.
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Optimist: The cup is half full.
Pessimist: The cup is half empty.
Yorkshireman: A cup? Luxury!
Pessimist: The cup is half empty.
Yorkshireman: A cup? Luxury!
November 25, 2024 at 7:13 AM
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.
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.
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.
November 25, 2024 at 12:34 AM
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.
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.