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...

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

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.

🎓 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!

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...

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...

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

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....

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

Nature research paper: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum go.nature.com/45V5IvM

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

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!

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...

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 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...

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...

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

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...

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

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...

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/

🚨 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...

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-/

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!

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...

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 🌾🌱🍃🧫🪴🌿🍄🐝🐞🪲🌎🧬🚜

Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...

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. 🧪🧬🖥️

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/...

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

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?

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!

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.

CpGPT: a Foundation Model for DNA Methylation www.biorxiv.org/content/10.1... MethylGPT: a foundation model for the DNA methylome www.biorxiv.org/content/10.1... Exciting self supervised models trained on massive cross-platform methylation data by @bowang87.bsky.social lab. 1/