I missed that one last year but another very great article from Jiang et al! www.nature.com/articles/s41...

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...

nature.com

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...

Postdoctoral researcher in quantitative genetics applied to organic oat breeding - Vacancy at Aarhus University

Vacancy at Center for Quantitative Genetics and Genomics, Aarhus University

international.au.dk

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

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

international.au.dk

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

📢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...

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

(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

Genetic background shapes AI-predicted variant effects https://www.biorxiv.org/content/10.64898/2026.04.04.715328v1

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.

Genomic prediction of agronomic traits in perennial ryegrass (Lolium perenne L.) and genotype x environment interactions at the limit of the species distribution

rdcu.be

🎓 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!

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!

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…

sciencedirect.com

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/...

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

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)

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...

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

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...

nature.com

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....

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

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/...

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

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

Nature research paper: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum 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

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

au.dk

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

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.

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...

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

🚨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

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...

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

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...

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

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...

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

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...