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 www.biorxiv.org/content/10.64898/2026.04...

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

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.

🎓 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!

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…

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!

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...

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/...

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...

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...

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...

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...

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

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 ...

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....

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...

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/...

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

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.

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

go.nature.com/45V5IvM

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

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

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...

First slide of the maize meeting.

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

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.

🚨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!

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. ...

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...

Please feel free to reach out to Torben Asp or DM me if you have any questions regarding the offer.

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

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...

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

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...

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 latitudes

On 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.

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...

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...

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...

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...

with a proper link to the paper...
nph.onlinelibrary.wiley.com/doi/full/10....

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