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Guillaume Ramstein

@guillramstein.bsky.social
936 followers 376 following 10 posts

Assistant Professor at the Center for Quantitative Genetics and Genomics, Aarhus University. Quantitative genetics, computational biology, and plant breeding.

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Reposted by Guillaume Ramstein
Anne Roulin @anneroulin.bsky.social · 12/08/2026
I missed that one last year but another very great article from Jiang et al! www.nature.com/articles/s41...
nature.com
Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change - Nature Communications
Genetic load is often overlooked in conservation predictions of species response to climate change. This study found that effective population size was the major determinant of genetic load and that g...
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Guillaume Ramstein @guillramstein.bsky.social · 20/05/2026
Very happy to share this exciting opportunity in quantitative genetics applied to organic breeding, in collaboration with Sidsel Schmidt from the Innovation Center for Organic Agriculture, Joanne Russel from James Hutton Institute, and Jan Svenson from NordGen. international.au.dk/about/profil...
international.au.dk
Postdoctoral researcher in quantitative genetics applied to organic oat breeding - Vacancy at Aarhus University
Vacancy at Center for Quantitative Genetics and Genomics, Aarhus University
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Guillaume Ramstein @guillramstein.bsky.social · 18/05/2026
We have a very cool postdoc position in microbial genomics applied to plant-based food production! international.au.dk/about/profil... #PostdocJobs #MicrobialGenomics #MachineLearning #FoodScience #AarhusUniversity #Bioinformatics #SustainableFood
international.au.dk
Postdoctoral researcher in microbial genomics applied to plant-based kefir production - Vacancy at Aarhus University
Vacancy at Center for Quantitative Genetics and Genomics, Aarhus University
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Yeqing Lin @yeqinglin.bsky.social · 08/05/2026
Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8
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Tobias Jores @tobiasjores.bsky.social · 30/04/2026
📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...
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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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IreneJulca @irenejulca.bsky.social · 14/04/2026
(1/2) Interested in plant evolution? We are opening two PhD positions in my lab at QGG - Aarhus University, where you will combine comparative genomics and machine learning to better understand and improve crop traits. #PlantSciJobs #evolution #genomics
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 07/04/2026
Genetic background shapes AI-predicted variant effects www.biorxiv.org/content/10.64898/20…
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 31/03/2026
GxE interactions were documented in 264 ryegrass accessions at Nordic/Baltic distribution limits. Accounting for GxE improved prediction accuracy up to 22% for spring cover. GWAS identified large-effect variants with environment-dependent adaptive effects for persistence traits.
rdcu.be
Genomic prediction of agronomic traits in perennial ryegrass (Lolium perenne L.) and genotype x environment interactions at the limit of the species distribution
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Maud Tenaillon @maudtenaillon.bsky.social · 26/03/2026
🎓 Applications open for Master 2 EvoGEM which provides theoretical and methodological training to interpret evolutionary patterns from genomic data. ✔️ Evolution, Maths, Population and quantitative genetics, Phylogenetics ✔️ Tutored projects ✔️Fully taught in English 📍Paris evogem.fr 📢 Please share!
evogem.fr
Inter-institutional Master in evolutionary genetics
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Anne Roulin @anneroulin.bsky.social · 05/01/2026
Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti... Thanks to those who already shared the link!
sciencedirect.com
Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics
Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…
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Yuval Simons @yuvalsim.bsky.social · 24/10/2025
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/...
journals.plos.org
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...
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
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)
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 20/08/2025
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...
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Guillaume Ramstein @guillramstein.bsky.social · 05/08/2025
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...
link.springer.com
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...
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Doug Fowler @dougfowler.bsky.social · 21/07/2025
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
nature.com
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...
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Peter Koo @pkoo562.bsky.social · 16/07/2025
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
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 ...
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Derek Severi Lundberg @derekseveri.bsky.social · 15/07/2025
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
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...
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Michael Raissig @michaelraissig.bsky.social · 10/07/2025
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
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Nature @nature.com · 10/07/2025
Nature research paper: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum go.nature.com/45V5IvM
go.nature.com
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.
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EvolDir @evoldir.bsky.social · 26/06/2025
Aarhus University seeks a tenure-track assistant professor in population genetics, comparative genomics, or bioinformatics for biodiversity research. More info: www.au.dk/om/stillinger/job/tenure-… #job
au.dk
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
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Žiga Avsec @avsecz.bsky.social · 25/06/2025
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
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 09/03/2025
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.
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Luc Janss @ljanss.bsky.social · 09/03/2025
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...
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Frank Hochholdinger @hochholdingerf.bsky.social · 07/03/2025
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
First slide of the maize meeting.
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Matthias Benoit @mattbnt.bsky.social · 05/03/2025
🚨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!
nature.com
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.
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tibshirani.bsky.social @tibshirani.bsky.social · 24/02/2025
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...
arxiv.org
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. ...
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Guillaume Ramstein @guillramstein.bsky.social · 21/02/2025
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
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
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 18/02/2025
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...
candidate.hr-manager.net
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
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Michelle Stitzer @mcstitzer.bsky.social · 27/01/2025
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...
On top, five Andropogoneae grass species, from left to right Zea mays subsp. mays, Hemarthria uncinata, Miscanthus sinensis, Sorghum bicolor, Andropogon gerardi. On bottom, a map of the world, with collection sites of Andropogoneae grasses in points. A green background shows the distribution of Andropogoneae grasses throughout tropical and temperate latitudesOn left, a phylogeny of Andropogoneae species, with 14 independent polyploidy origins noted. On right, genome size and repeat content of each assembly. Across all assemblies, average assembly size is 1.9 Gb, and average repeat size is 1.5 Gb.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 27/01/2025
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...
mcstitzer.github.io
Panand Genomes
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/01/2025
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...
biorxiv.org
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...
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Anne Roulin @anneroulin.bsky.social · 06/01/2025
with a proper link to the paper... nph.onlinelibrary.wiley.com/doi/full/10....
nph.onlinelibrary.wiley.com
Historic rewiring of grass flowering time pathways and implications for crop improvement under climate change
Grasses are fundamental to human survival, providing a large percentage of our calories, fuel, and fodder for livestock, and an enormous global carbon sink. A particularly important part of the grass...
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@HeredityJournal @heredityjournal.bsky.social · 04/01/2025
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
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Sebastian Soyk @sebastiansoyk.bsky.social · 04/01/2025
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...
nature.com
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...
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Yun S. Song @yun-s-song.bsky.social · 02/01/2025
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
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.
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/12/2024
Announcing a curated collection of long-read genomes for Arabidopsis thaliana: The 1001 Genomes Plus Project. Currently 453 unique accessions/almost 600 assemblies. Interested in contributing? Please contact us! #plantscience www.biorxiv.org/content/10.1...
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Chris Jiggins @chrisjiggins.bsky.social · 18/12/2024
Join us in Cambridge! This evolutionary genomics professorship (lecturer/reader level) has an emphasis on introgression and gene flow. If you study any aspect of evolutionary genomics then please apply! www.jobs.cam.ac.uk/job/49389/
jobs.cam.ac.uk
Associate Professor / Professor of Evolutionary Genomics - Job Opportunities - University of Cambridge
Associate Professor / Professor of Evolutionary Genomics in the Department of Genetics at the University of Cambridge.
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Peter Koo @pkoo562.bsky.social · 17/12/2024
🚨 We’re hiring! 🚨 The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team. If you’re passionate about genomics, AI, and experimental science, we want to hear from you. Help us spread the word! jobrxiv.org/job/cold-spr...
jobrxiv.org
Research Technician - Cold Spring Harbor Laboratory
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
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Michael Raissig @michaelraissig.bsky.social · 11/12/2024
The speaker list is complete for #Brachypodium2025 conference in Monte Verità, Switzerland from July 6-10, 2025! I am thrilled about the line-up www.brachypodium2025.org/speaker2 Registration will open in Feb 2025 | places will be limited Sign up for the #Brachy mailing list at eepurl.com/iSw-H-/
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Iain Johnston @mitomaths.bsky.social · 09/12/2024
Have had some good chats recently about pivoting to non-profit and society journals. A point to share/underline is that such options exist across the "prestige" spectrum. Some examples in the image. All heavily subjective of course; would love to hear thoughts from others!
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Guillaume Ramstein @guillramstein.bsky.social · 03/12/2024
Happy to share this new study in barley breeding! We extended traditional GWAS to account for population-dependent effects and increased statistical power to identify robust QTLs www.nature.com/articles/s41...
nature.com
Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program - Heredity
Heredity - Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program
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J. Chris Pires @jchrispires.bsky.social · 18/11/2024
Great opportunity at #Colorado State University in College of #Agriculture to lead a great Department of Agricultural #Biology as as Professor & Head: jobs.colostate.edu/postings/153... Apply by Jan 15, 2025 #plantscience #weedscience #entomology #plantpathology 🌾🌱🍃🧫🪴🌿🍄🐝🐞🪲🌎🧬🚜
jobs.colostate.edu
Professor & Head, Department of Agricultural Biology
We seek an engaged, innovative, and visionary leader and accomplished scientist to catalyze new initiatives and collaborations, identify strategic priorities, and provide leadership in research, schol...
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Diego Ortega-Del Vecchyo @delvecchyo.bsky.social · 02/12/2024
Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...
meetings.cshl.edu
Probabilistic Modeling in Genomics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 27/11/2024
Welcome back for #CornFax episode 2: mutational madness. This is maybe my favorite corn fact, so you may have seen me post about it previously. 🧪🧬🖥️
A colorful cartoon of a fax machine printing out a piece of paper with an ear of corn on it and the words CORN FAX.
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Anne Roulin @anneroulin.bsky.social · 25/11/2024
Very happy to present our latest study on heat-induced transcription of transposable element in A. thaliana. Using Oxford Nanopore, we tested the extent to which read-through formation is important in the regulation of adjacent genes. More here 👇 academic.oup.com/gbe/article/...
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Jocelyn Poissant @jocelynpoissant.bsky.social · 23/11/2024
I created a starter pack of researchers using quantitative genetics in wild populations. Let me know if you want to be added or have any additional suggestions 👇 go.bsky.app/HTEq79p
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Jonathan Pritchard @jkpritch.bsky.social · 22/11/2024
In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?
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Tatsuya Nobori @tatsuyanobori.bsky.social · 20/11/2024
Exaptation of ancestral cell-identity networks enables C4 photosynthesis www.nature.com/articles/s41... New from the Ecker lab in collaboration with the Hibberd lab. Congrats all!
nature.com
Exaptation of ancestral cell-identity networks enables C4 photosynthesis - Nature
Single-nucleus RNA-sequencing and chromatin-accessibility analyses in rice (a C3 plant) and sorghum (a C4 plant) provide insight into how C4 photosynthesis evolved in bundle-sheath cells, revealing th...
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Graham Coop @gcbias.bsky.social · 19/11/2024
Just posting this to #popgen Here's a link to my notes on population & quantitative genetics: github.com/cooplab/popg... Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
github.com
Releases · cooplab/popgen-notes
Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.
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