Gregor Gorjanc
@gregorgorjanc.bsky.social
Managing and improving populations using data science, genetics and breeding: @HighlanderLab, @RoslinInstitute, & @TheDickVet.
https://www.ed.ac.uk/roslin/highlanderlab
https://www.ed.ac.uk/roslin/highlanderlab
Reposted by Gregor Gorjanc
Did anyone try telling an AI agent to format your ms according to the journal requirements?
January 15, 2026 at 3:24 PM
Did anyone try telling an AI agent to format your ms according to the journal requirements?
Reposted by Gregor Gorjanc
A very lazy Q: Is Levy process considered commonly in phylo comparative methods?
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
January 8, 2026 at 9:55 AM
A very lazy Q: Is Levy process considered commonly in phylo comparative methods?
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Gregor Gorjanc
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/.
December 22, 2025 at 3:55 AM
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/.
Reposted by Gregor Gorjanc
December 21, 2025 at 3:22 PM
Reposted by Gregor Gorjanc
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.
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 10:43 PM
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.
Reposted by Gregor Gorjanc
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"
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
December 14, 2025 at 11:36 AM
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"
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
Reposted by Gregor Gorjanc
A whole Advent Calendar of Nigel Farage repeating Vladimir Putin's talking points. Brilliant. bylinetimes.com/2025/12/10/n...
Nigel Farage's Russian Influence Advent Calendar
Byline Times has compiled a festive offering of the prize moments when the Reform leader has gifted the political agenda to Vladimir Putin and Russia
bylinetimes.com
December 10, 2025 at 6:10 PM
A whole Advent Calendar of Nigel Farage repeating Vladimir Putin's talking points. Brilliant. bylinetimes.com/2025/12/10/n...
Reposted by Gregor Gorjanc
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.
December 2, 2025 at 12:18 AM
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!
www.biorxiv.org/content/10.1...
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
Genetic prediction with ARG-powered linear algebra
Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...
www.biorxiv.org
November 30, 2025 at 7:30 PM
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!
Reposted by Gregor Gorjanc
Am I the only person to read teaspoon as teasposons 😂😂
70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute
Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute ...
pmc.ncbi.nlm.nih.gov
November 20, 2025 at 2:26 PM
Am I the only person to read teaspoon as teasposons 😂😂
Reposted by Gregor Gorjanc
In deeper pedigrees, the estimand pertains to the founders of the population. In SNP LMMs, do you know who these are?
November 24, 2025 at 3:16 PM
In deeper pedigrees, the estimand pertains to the founders of the population. In SNP LMMs, do you know who these are?
Reposted by Gregor Gorjanc
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.
November 24, 2025 at 3:04 PM
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.
Reposted by Gregor Gorjanc
@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...
www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
www.nature.com
November 19, 2025 at 6:43 PM
@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...
www.nature.com/articles/d41...
Reposted by Gregor Gorjanc
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
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
November 17, 2025 at 3:48 PM
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
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
Reposted by Gregor Gorjanc
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.
November 10, 2025 at 11:01 PM
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.
Reposted by Gregor Gorjanc
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.
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.
November 7, 2025 at 2:08 PM
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.
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.
Reposted by Gregor Gorjanc
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...
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...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
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...
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...
Reposted by Gregor Gorjanc
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).
(8/8).
November 5, 2025 at 10:58 PM
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).
(8/8).
Reposted by Gregor Gorjanc
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)
(7/n)
November 5, 2025 at 10:56 PM
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)
(7/n)
Reposted by Gregor Gorjanc
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...
(1/n)
academic.oup.com/genetics/adv...
Kinship estimation bias carries over to heritability estimation bias using variance components
Abstract. Heritability is a fundamental parameter of diseases and other traits, quantifying the contribution of genetics to that trait. Kinship matrices ar
academic.oup.com
November 5, 2025 at 10:43 PM
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...
(1/n)
academic.oup.com/genetics/adv...
Reposted by Gregor Gorjanc
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.
False equivalence in the media is killing us.
November 5, 2025 at 3:39 PM
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.
False equivalence in the media is killing us.
Reposted by Gregor Gorjanc
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. :)
October 18, 2025 at 4:43 PM
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. :)
Reposted by Gregor Gorjanc
Is it possible to download the whole tree from the math genealogy project?
October 19, 2025 at 1:12 AM
Is it possible to download the whole tree from the math genealogy project?
Reposted by Gregor Gorjanc
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
December 5, 2024 at 5:09 PM
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
Reposted by Gregor Gorjanc
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...
IGD: A simple, efficient genotype data format
Motivation While there are a variety of file formats for storing reference-sequence-aligned genotype data, many are complex or inefficient. Programming language support for such formats is often limit...
www.biorxiv.org
February 12, 2025 at 1:03 AM
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...