Kaur Alasoo
@kauralasoo.bsky.social
Associate Professor of Bioinformatics at University of Tartu, Estonia. Project lead at eQTL Catalogue. https://kauralasoo.github.io/
Reposted by Kaur Alasoo
New pre-print: "Systematic comparison of colocalization methods using protein quantitative trait loci" led by @hwang_seongwon at www.biorxiv.org/content/10.1.... Which method does best? Find out!
Systematic comparison of colocalization methods using protein quantitative trait loci
Colocalization is frequently performed as a step to triage findings from genetic investigations linking molecular and disease data. However, the reliability and consistency of the various colocalizati...
www.biorxiv.org
November 8, 2025 at 3:40 PM
New pre-print: "Systematic comparison of colocalization methods using protein quantitative trait loci" led by @hwang_seongwon at www.biorxiv.org/content/10.1.... Which method does best? Find out!
Reposted by Kaur Alasoo
There are two complementary views of scientific advance: the "heroes" view, individual geniuses driving unique one-of-a-kind advances, and the "multiple discovery" or zeitgeist view, that the time is ripe for a discovery, and the details of who makes it first, where, and how are, well, details.(1/3)
November 8, 2025 at 9:23 AM
There are two complementary views of scientific advance: the "heroes" view, individual geniuses driving unique one-of-a-kind advances, and the "multiple discovery" or zeitgeist view, that the time is ripe for a discovery, and the details of who makes it first, where, and how are, well, details.(1/3)
Reposted by Kaur Alasoo
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Group Leader - Generative Biology and AI
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
tinyurl.com
November 7, 2025 at 9:37 AM
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Reposted by Kaur Alasoo
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Flexibly Modeling Rare Variant Pathogenicity Improves Gene Discovery for Complex Traits
Rare variant burden tests can directly identify genes that influence complex traits, but their power is limited by our ability to separate functional from benign alleles. We introduce FlexRV, an appro...
www.biorxiv.org
November 5, 2025 at 10:29 PM
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Reposted by Kaur Alasoo
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
biorxiv.org
November 5, 2025 at 2:17 PM
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Reposted by Kaur Alasoo
This! Fancy web interfaces let you explore the data, but they are not the same as sharing the data. You can do both!
PSA: it’s all great if you provide an interactive dashboard to browse the data you painstakingly generated. But please do back up the data on persistent archive like zenodo. It’s too bad we can’t access the database when inevitably the server goes down and you moved onto other projects/institutions
October 31, 2025 at 7:16 PM
This! Fancy web interfaces let you explore the data, but they are not the same as sharing the data. You can do both!
Genuine Q - how does blinding work for GLP-1 agonists? I took semaglutide for 5 months earlier this year and had a super obvious effect on apetite in 2-3 hours. I suspect many participants would know quite quickly on which arm of the trial they are?
We've just launched the first large, site-less (home, direct to participant) randomized trial for treatment of #LongCovid, testing tirzepatide (a GLP-1 drug) vs placebo. Please help spread the word
www.scripps.edu/news-and-eve...
www.scripps.edu/news-and-eve...
Scripps Research scientists launch new digital clinical trial to test repurposed drug for long COVID symptom relief
www.scripps.edu
October 31, 2025 at 5:42 PM
Genuine Q - how does blinding work for GLP-1 agonists? I took semaglutide for 5 months earlier this year and had a super obvious effect on apetite in 2-3 hours. I suspect many participants would know quite quickly on which arm of the trial they are?
Reposted by Kaur Alasoo
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature
mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.
www.nature.com
October 30, 2025 at 3:35 PM
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
Reposted by Kaur Alasoo
New: GWAS of serurm antibody levels. Interesting findings include genetically correlated traits with hard-to-find shared causal variants, and apparently genetically uncorrelated traits sharing causal variants that operate in inconsistent directions www.medrxiv.org/content/10.1...
Large-scale GWAS meta-analysis of serum antibody levels reveals distinct genetic architectures
Antibodies are the principal effector proteins of humoral immunity. Dysregulated antibody production is a feature of a number of heritable immune-mediated diseases, such as the antibody deficiencies a...
www.medrxiv.org
October 30, 2025 at 1:30 PM
New: GWAS of serurm antibody levels. Interesting findings include genetically correlated traits with hard-to-find shared causal variants, and apparently genetically uncorrelated traits sharing causal variants that operate in inconsistent directions www.medrxiv.org/content/10.1...
Reposted by Kaur Alasoo
New pre-print "Mendelian randomization in a multi-ancestry world: reflections and practical advice" led by @amymariemason.bsky.social on - arxiv.org/abs/2510.17554
Mendelian randomization in a multi-ancestry world: reflections and practical advice
Many Mendelian randomization (MR) papers have been conducted only in people of European ancestry, limiting transportability of results to the global population. Expanding MR to diverse ancestry groups...
arxiv.org
October 27, 2025 at 8:43 AM
New pre-print "Mendelian randomization in a multi-ancestry world: reflections and practical advice" led by @amymariemason.bsky.social on - arxiv.org/abs/2510.17554
Reposted by Kaur Alasoo
🎉 Come to see @triinuvarvas.bsky.social poster nr W56 at #wcpg2025 today!
Also, we are recruiting in 2026 and if you are interested in PhD or postdoc positions to work with the fantastic Estonian Biobank data then get in touch or fill out the interest form here ➡️ genomics.ut.ee/en/research-...
Also, we are recruiting in 2026 and if you are interested in PhD or postdoc positions to work with the fantastic Estonian Biobank data then get in touch or fill out the interest form here ➡️ genomics.ut.ee/en/research-...
October 22, 2025 at 5:05 PM
🎉 Come to see @triinuvarvas.bsky.social poster nr W56 at #wcpg2025 today!
Also, we are recruiting in 2026 and if you are interested in PhD or postdoc positions to work with the fantastic Estonian Biobank data then get in touch or fill out the interest form here ➡️ genomics.ut.ee/en/research-...
Also, we are recruiting in 2026 and if you are interested in PhD or postdoc positions to work with the fantastic Estonian Biobank data then get in touch or fill out the interest form here ➡️ genomics.ut.ee/en/research-...
Reposted by Kaur Alasoo
Serious questions for the Wellcome Trust and Wellcome Leap to answer here.
Allocating $50m to microbiome pseudoscience is bad enough.
But things get alarmingly murky when you notice that the Program Director is working on commercial microbiomics products.
Allocating $50m to microbiome pseudoscience is bad enough.
But things get alarmingly murky when you notice that the Program Director is working on commercial microbiomics products.
New blogpost on my concerns about Wellcome LEAP new $50m program on autism/microbiome links. deevybee.blogspot.com/2025/10/a-le...
#autism #microbiome #biomarkers #diagnostic
#autism #microbiome #biomarkers #diagnostic
A LEAP into the future, or off a cliff: Wellcome LEAP's new $50M program
A few days ago, I saw this post on LinkedIn: How does the gut microbiome shape early brain development? That’s what FORM, a new $50 million...
deevybee.blogspot.com
October 20, 2025 at 3:59 PM
Serious questions for the Wellcome Trust and Wellcome Leap to answer here.
Allocating $50m to microbiome pseudoscience is bad enough.
But things get alarmingly murky when you notice that the Program Director is working on commercial microbiomics products.
Allocating $50m to microbiome pseudoscience is bad enough.
But things get alarmingly murky when you notice that the Program Director is working on commercial microbiomics products.
Reposted by Kaur Alasoo
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
SAFE-LD: A novel method for the estimation of linkage disequilibrium from summary statistics
Genome-wide association studies (GWAS) have greatly advanced our understanding of the genetic architecture of complex traits. Downstream analyses of GWAS summary statistics require accurate in-sample ...
www.biorxiv.org
October 21, 2025 at 9:47 AM
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
Reposted by Kaur Alasoo
🎉 New preprint out!
"Removing genetic effects on plasma proteins enhances their utility as disease biomarkers"
We show that adjusting plasma proteins for genetic effects can make them stronger predictors of disease
👉 doi.org/10.1101/2025...
"Removing genetic effects on plasma proteins enhances their utility as disease biomarkers"
We show that adjusting plasma proteins for genetic effects can make them stronger predictors of disease
👉 doi.org/10.1101/2025...
October 16, 2025 at 9:16 PM
🎉 New preprint out!
"Removing genetic effects on plasma proteins enhances their utility as disease biomarkers"
We show that adjusting plasma proteins for genetic effects can make them stronger predictors of disease
👉 doi.org/10.1101/2025...
"Removing genetic effects on plasma proteins enhances their utility as disease biomarkers"
We show that adjusting plasma proteins for genetic effects can make them stronger predictors of disease
👉 doi.org/10.1101/2025...
Reposted by Kaur Alasoo
1/7 New BMI GWAS out! Using Estonian Biobank (n=204,747) and replication in FinnGen, we show that even in Europe you can still find region-specific biology if you zoom into population-tailored sumstats. Big thanks to co-author @kanwalbatool.bsky.social :)
October 16, 2025 at 6:54 PM
1/7 New BMI GWAS out! Using Estonian Biobank (n=204,747) and replication in FinnGen, we show that even in Europe you can still find region-specific biology if you zoom into population-tailored sumstats. Big thanks to co-author @kanwalbatool.bsky.social :)
Reposted by Kaur Alasoo
We found a globally rare variant rather common in Estonia that rises BMI by 0.8 units per allele 🤯 @estbiobank.bsky.social
Uuringus, mis põhineb Geenivaramu andmetel, avastati mitmeid olulisi geneetilisi variatsioone, mis mõjutavad kehamassiindeksit (KMI). doi.org/10.1038/s414...
Characterization of prevalent genetic variants in the Estonian Biobank body-mass index GWAS - Nature Communications
Here the authors perform a genome wide association study of 204,747 Estonian Biobank participants revealing 214 BMI loci. Reported signals include ADGRL3, PTPRT, and a protein-truncating POMC variant ...
doi.org
October 14, 2025 at 4:59 PM
We found a globally rare variant rather common in Estonia that rises BMI by 0.8 units per allele 🤯 @estbiobank.bsky.social
Reposted by Kaur Alasoo
I'm very excited to be attending my first #ASHG25 this week! Come find me at poster board 1090F to talk about flexible and efficient eQTL mapping with quasar!
October 13, 2025 at 1:23 PM
I'm very excited to be attending my first #ASHG25 this week! Come find me at poster board 1090F to talk about flexible and efficient eQTL mapping with quasar!
Reposted by Kaur Alasoo
Can DNA sequence models predict mutations affecting human traits?
We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
February 13, 2025 at 8:57 PM
Can DNA sequence models predict mutations affecting human traits?
We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
Reposted by Kaur Alasoo
New pre-print: "PCSK9 and breast cancer survival: a Mendelian Randomization study" www.medrxiv.org/content/10.1... led by Janne Pott. Brief thread:
PCSK9 and breast cancer survival: a Mendelian Randomization study
Background: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is well known for its causal effects on the lipid metabolism. A recent study identified an association between rs562556 within PCSK9 a...
www.medrxiv.org
October 7, 2025 at 8:59 AM
New pre-print: "PCSK9 and breast cancer survival: a Mendelian Randomization study" www.medrxiv.org/content/10.1... led by Janne Pott. Brief thread:
Reposted by Kaur Alasoo
New findings in @natcomms.nature.com demonstrate the impact of allelic variation on monocyte context-specific splicing.
@bpfairfax.bsky.social & colleagues show that many risk polymorphisms lead to differential gene splicing.
➡️Reveals putative mechanisms of diverse disease risk alleles inc. cancer
@bpfairfax.bsky.social & colleagues show that many risk polymorphisms lead to differential gene splicing.
➡️Reveals putative mechanisms of diverse disease risk alleles inc. cancer
Genetic determinants of monocyte splicing are enriched for disease susceptibility loci - Nature Communications
Our understanding of variation in monocyte context-specific splicing and transcript usage is limited. Here, the authors find genetic variants that affect gene splicing in monocytes in specific contexts, including several diseases, and in response to stimulants.
www.nature.com
October 3, 2025 at 11:01 AM
New findings in @natcomms.nature.com demonstrate the impact of allelic variation on monocyte context-specific splicing.
@bpfairfax.bsky.social & colleagues show that many risk polymorphisms lead to differential gene splicing.
➡️Reveals putative mechanisms of diverse disease risk alleles inc. cancer
@bpfairfax.bsky.social & colleagues show that many risk polymorphisms lead to differential gene splicing.
➡️Reveals putative mechanisms of diverse disease risk alleles inc. cancer
Reposted by Kaur Alasoo
Trans-eQTL mapping prioritizes USP18 as a negative regulator of interferon response at a #lupus risk locus
www.nature.com/articles/s41... @natcomms.nature.com @unitartupress.bsky.social @kauralasoo.bsky.social
www.nature.com/articles/s41... @natcomms.nature.com @unitartupress.bsky.social @kauralasoo.bsky.social
October 3, 2025 at 5:27 PM
Trans-eQTL mapping prioritizes USP18 as a negative regulator of interferon response at a #lupus risk locus
www.nature.com/articles/s41... @natcomms.nature.com @unitartupress.bsky.social @kauralasoo.bsky.social
www.nature.com/articles/s41... @natcomms.nature.com @unitartupress.bsky.social @kauralasoo.bsky.social
Reposted by Kaur Alasoo
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency
In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...
www.biorxiv.org
October 3, 2025 at 3:09 PM
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
This is one of the coolest studies that I have seen recently! Thanks for highlighting, @jeffreypullin.bsky.social!
Genes and environment profoundly affect the human virome
Genes and environment profoundly affect the human virome
October 2, 2025 at 4:42 PM
This is one of the coolest studies that I have seen recently! Thanks for highlighting, @jeffreypullin.bsky.social!
Genes and environment profoundly affect the human virome
Genes and environment profoundly affect the human virome
Happy to share that this work together with @opentargets.org is now out at Nature Communications.
Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type!
An Open Targets team led by Krista Freimann and @kauralasoo.bsky.social analysed 3,734 lymphoblastoid cell line samples across nine cohorts, identifying four robust loci
www.nature.com/articles/s41...
An Open Targets team led by Krista Freimann and @kauralasoo.bsky.social analysed 3,734 lymphoblastoid cell line samples across nine cohorts, identifying four robust loci
www.nature.com/articles/s41...
Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus - Nature Communications | Open Targets
Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type!
An Open Targets team led by Krista Freimann and Kaur Alasoo analysed 3,734 lymphoblastoid cell line samples across...
www.linkedin.com
October 2, 2025 at 1:05 PM
Happy to share that this work together with @opentargets.org is now out at Nature Communications.