Guillaume Ramstein
@guillramstein.bsky.social
Assistant Professor at the Center for Quantitative Genetics and Genomics, Aarhus University. Quantitative genetics, computational biology, and plant breeding.
Reposted by Guillaume Ramstein
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
journals.plos.org
October 24, 2025 at 1:51 AM
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Reposted by Guillaume Ramstein
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Guillaume Ramstein
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy to share this review led by Janek Sendrowski, and written with Thomas Bataillon. We provided an overview of sequence-based AI models: what they can (and cannot) do, and what differentiates them from traditional techniques based on statistical associations link.springer.com/article/10.1...
In silico prediction of variant effects: promises and limitations for precision plant breeding - Theoretical and Applied Genetics
Key message Sequence-based AI models show great potential for prediction of variant effects at high resolution, but their practical value in plant breeding remains to be confirmed through rigorous val...
link.springer.com
August 5, 2025 at 1:40 PM
Happy to share this review led by Janek Sendrowski, and written with Thomas Bataillon. We provided an overview of sequence-based AI models: what they can (and cannot) do, and what differentiates them from traditional techniques based on statistical associations link.springer.com/article/10.1...
Reposted by Guillaume Ramstein
Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
Multiplexed assays of variant effect for clinical variant interpretation
Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...
www.nature.com
July 21, 2025 at 7:34 PM
Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
Reposted by Guillaume Ramstein
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Evaluating the representational power of pre-trained DNA language models for regulatory genomics - Genome Biology
Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of ...
genomebiology.biomedcentral.com
July 16, 2025 at 12:12 PM
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Guillaume Ramstein
This work started nearly 10 years ago and was once my main postdoctoral project at @plantevolution.bsky.social before I slowed work on it to a trickle because it became confusing. But it always remained extremely interesting.
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions
In controlled greenhouse conditions, Arabidopsis thaliana plants with a hyperactive allele of the ACD6 gene have stronger pathogen defenses but are smaller and make fewer seeds, in a classic fitness t...
journals.plos.org
July 15, 2025 at 10:10 AM
This work started nearly 10 years ago and was once my main postdoctoral project at @plantevolution.bsky.social before I slowed work on it to a trickle because it became confusing. But it always remained extremely interesting.
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Guillaume Ramstein
What a community, what a welcoming and inclusive atmosphere, what a location! Thank you @snsf.ch, CSF @ethz.ch, @newphyt.bsky.social, @biologists.bsky.social and @cerealcell.bsky.social for supporting us.
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
July 10, 2025 at 1:27 PM
What a community, what a welcoming and inclusive atmosphere, what a location! Thank you @snsf.ch, CSF @ethz.ch, @newphyt.bsky.social, @biologists.bsky.social and @cerealcell.bsky.social for supporting us.
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
Reposted by Guillaume Ramstein
Nature research paper: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
go.nature.com/45V5IvM
go.nature.com/45V5IvM
A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum - Nature
A study describes the assembly and analysis of a haplotype-resolved pangenome of bulbous barley with the potential to improve domesticated barley and illustrates its use in evolutionary research and trait mapping.
go.nature.com
July 10, 2025 at 8:13 AM
Nature research paper: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
go.nature.com/45V5IvM
go.nature.com/45V5IvM
Reposted by Guillaume Ramstein
Aarhus University seeks a tenure-track assistant professor in population genetics, comparative genomics, or bioinformatics for biodiversity research. More info: https://www.au.dk/om/stillinger/job/tenure-track-assistant-professor-in-biodiversity-research-using-genetics #job
Tenure-Track Assistant Professor in Biodiversity Research Using Genetics - Ledig stilling på Aarhus Universitet
Ledig stilling ved Center for Kvantitativ Genetik og Genomforskning, Aarhus, Aarhus Universitet
www.au.dk
June 26, 2025 at 2:46 PM
Aarhus University seeks a tenure-track assistant professor in population genetics, comparative genomics, or bioinformatics for biodiversity research. More info: https://www.au.dk/om/stillinger/job/tenure-track-assistant-professor-in-biodiversity-research-using-genetics #job
Reposted by Guillaume Ramstein
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 2:29 PM
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
Reposted by Guillaume Ramstein
Nearing 400 members on our Zeavolution slack! Want to interact with other members of the maize genetics community? We have a weekly webinar on maize diversity/evolution as well. DM me and I'll share a link to join the slack.
March 9, 2025 at 12:05 AM
Nearing 400 members on our Zeavolution slack! Want to interact with other members of the maize genetics community? We have a weekly webinar on maize diversity/evolution as well. DM me and I'll share a link to join the slack.
Reposted by Guillaume Ramstein
Our summer course on #genomicPrediction with me and @guillramstein.bsky.social is running this year 4-8 August, application deadline 18 March. Info and registration see: international.au.dk/education/ad...
March 9, 2025 at 1:00 PM
Our summer course on #genomicPrediction with me and @guillramstein.bsky.social is running this year 4-8 August, application deadline 18 March. Info and registration see: international.au.dk/education/ad...
Reposted by Guillaume Ramstein
Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting:
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
March 7, 2025 at 2:39 AM
Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting:
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
Reposted by Guillaume Ramstein
🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!
Solanum pan-genetics reveals paralogues as contingencies in crop engineering - Nature
Gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability.
nature.com
March 5, 2025 at 4:43 PM
🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!
Reposted by Guillaume Ramstein
I am happy to announce our new paper "Univariate-guided sparse regression". It's a new lasso that leverages the signs and magnitude of univariate coefficients .
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Univariate-Guided Sparse Regression
In this paper, we introduce ``UniLasso'' -- a novel statistical method for sparse regression. This two-stage approach preserves the signs of the univariate coefficients and leverages their magnitude. ...
arxiv.org
February 24, 2025 at 4:57 AM
I am happy to announce our new paper "Univariate-guided sparse regression". It's a new lasso that leverages the signs and magnitude of univariate coefficients .
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
The Center for Quantitative Genetics and Genomics (QGG) in Denmark is looking for talented candidates who have interests in quantitative genetics or related fields. The working environment at QGG is great, and Denmark has very good opportunities for research funding.
tech.au.dk/en/about-the...
tech.au.dk/en/about-the...
Tenure Track Assistant Professor in Plant Quantitative Genetics - Vacancy at Aarhus University
Vacancy at Center for Quantitative Genetics and Genomics - Quantitative Gen. and Genomics, Flakkeberg, Aarhus University
tech.au.dk
February 21, 2025 at 12:01 PM
The Center for Quantitative Genetics and Genomics (QGG) in Denmark is looking for talented candidates who have interests in quantitative genetics or related fields. The working environment at QGG is great, and Denmark has very good opportunities for research funding.
tech.au.dk/en/about-the...
tech.au.dk/en/about-the...
Reposted by Guillaume Ramstein
PhD position on the domestication of common beans and its coevolution with rhizobia through studying ancient and modern genomes. At U. Copenhagen with
Jazmín Ramos Madrigal.
candidate.hr-manager.net/ApplicationI...
Jazmín Ramos Madrigal.
candidate.hr-manager.net/ApplicationI...
PhD fellowship in Evolutionary Biology at the Globe Institute
A PhD fellowship in Evolutionary Biology is being posted in the research team lead by Assistant Prof Jazmín Ramos Madrigal commencing 1 July 2025 or as soon as
candidate.hr-manager.net
February 18, 2025 at 2:12 PM
PhD position on the domestication of common beans and its coevolution with rhizobia through studying ancient and modern genomes. At U. Copenhagen with
Jazmín Ramos Madrigal.
candidate.hr-manager.net/ApplicationI...
Jazmín Ramos Madrigal.
candidate.hr-manager.net/ApplicationI...
Reposted by Guillaume Ramstein
New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...
January 27, 2025 at 9:33 PM
New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...
Reposted by Guillaume Ramstein
I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...
January 27, 2025 at 5:58 AM
I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...
Reposted by Guillaume Ramstein
The consequences of polyploidy are... well, complicated. A deep dive into polyploidy in a massively successful tribe of grasses. A masterpiece led by Michelle Stitzer, representing the work of a lot of folks on the PanAnd project over last 7 years. www.biorxiv.org/content/10.1...
Extensive genome evolution distinguishes maize within a stable tribe of grasses
Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most product...
www.biorxiv.org
January 26, 2025 at 9:16 PM
The consequences of polyploidy are... well, complicated. A deep dive into polyploidy in a massively successful tribe of grasses. A masterpiece led by Michelle Stitzer, representing the work of a lot of folks on the PanAnd project over last 7 years. www.biorxiv.org/content/10.1...
Reposted by Guillaume Ramstein
with a proper link to the paper...
nph.onlinelibrary.wiley.com/doi/full/10....
nph.onlinelibrary.wiley.com/doi/full/10....
January 6, 2025 at 1:13 PM
with a proper link to the paper...
nph.onlinelibrary.wiley.com/doi/full/10....
nph.onlinelibrary.wiley.com/doi/full/10....
Reposted by Guillaume Ramstein
New podcast!
Meet Heredity editor Bastiaan Star (University of Oslo), we talk about his work with ancient fish DNA and why he enjoys working with the journal
@gensocuk.bsky.social @biovitenskap.bsky.social
Meet Heredity editor Bastiaan Star (University of Oslo), we talk about his work with ancient fish DNA and why he enjoys working with the journal
@gensocuk.bsky.social @biovitenskap.bsky.social
January 4, 2025 at 12:22 PM
New podcast!
Meet Heredity editor Bastiaan Star (University of Oslo), we talk about his work with ancient fish DNA and why he enjoys working with the journal
@gensocuk.bsky.social @biovitenskap.bsky.social
Meet Heredity editor Bastiaan Star (University of Oslo), we talk about his work with ancient fish DNA and why he enjoys working with the journal
@gensocuk.bsky.social @biovitenskap.bsky.social
Reposted by Guillaume Ramstein
Very happy to see our work on deleterious mutations in #tomato published in @naturegenet.bsky.social 🧬🌱🍅! We identify deleterious mutations that were enriched during #domestication and apply #CRISPR to repair a mutation in cultivated tomato. #genetics #plantscience
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing - Nature Genetics
A deleterious mutation in the tomato transcription factor SSP2 was enriched during domestication. Repairing the deleterious mutation in cultivated tomato by base editing leads to compact growth and ea...
www.nature.com
January 4, 2025 at 11:29 AM
Very happy to see our work on deleterious mutations in #tomato published in @naturegenet.bsky.social 🧬🌱🍅! We identify deleterious mutations that were enriched during #domestication and apply #CRISPR to repair a mutation in cultivated tomato. #genetics #plantscience
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Guillaume Ramstein
Happy New Year! Our GPN-MSA paper is finally published, under a slightly different title from the preprint. Please check it out and share it with your colleagues:
doi.org/10.1038/s415...
1/4
doi.org/10.1038/s415...
1/4
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - Nature Biotechnology
A language model predicts the effects of genetic variants in the human genome.
doi.org
January 2, 2025 at 8:24 PM
Happy New Year! Our GPN-MSA paper is finally published, under a slightly different title from the preprint. Please check it out and share it with your colleagues:
doi.org/10.1038/s415...
1/4
doi.org/10.1038/s415...
1/4