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)

A deep-time landscape of plant cis-regulatory sequence evolution https://www.biorxiv.org/content/10.1101/2025.09.17.676453v1

Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below! doi.org/10.1126/scie...

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/... ), we find the opposite: animals exchange genes more, and for longer, than plants

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...

Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1

2/2 With ‪@derekseveri.bsky.social‬, Joy Bergelson, Fabrice Roux and Talia Karasov. Illustration: Genetically diverse Arabidopsis grown in the lab | Closely related wild Arabidopsis during the natural growing season | Diversity of Arabidopsis habitats.

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr

So cool!

If you're new to demographic history inference from population genomics, try this webapp I created to illustrate how dadi fits bottleneck models to site frequency spectra: ryangutenkunst-dadi-two-epoch.hf.space . It even outputs files for submitting to the GHIST competition! ghi.st

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana https://www.biorxiv.org/content/10.1101/2025.07.14.664700v1

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Accurate diagram 😂

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

New paper out! 🎉 With an innovative approach of CRISPRing a gene mutation on many backgrounds, we provide a proof of concept for how “pan-genetic” analysis can reveal the true extent of genetic networks in a species. Thanks @plantevolution.bsky.social-lab! Open-access: tinyurl.com/3aw7t6ff

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

Detlef Weigel- Max Planck Inst- Tubingen- honored for his lifetime of excellence in research, mentorship, and support of the Arabidopsis community #ICAR2025

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Long-term flowering-time data on Japanese mountain cherry (recorded since the 9th century!) shows a shift in full-flowering date beginning in the late 19th century. Fascinating new @newphyt.bsky.social paper by @jgpausas.bsky.social onlinelibrary.wiley.com/doi/abs/10.1...

As the world warms, plants in natural ecosystems and agricultural settings find ways to respond to the heat. In a new special issue of Science, researchers examine how heat affects plants at multiple scales, from the molecular level to the biosphere. scim.ag/44cSw3Z

Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...

With the publication of a new preprint (www.biorxiv.org/content/10.1...) with collaborators @labschneeberger.bsky.social @plantevolution.bsky.social and @jurriaanton.bsky.social, I feel it is timely to talk about what will probably be the most successful 'failed' experiment of my career.

Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana https://www.biorxiv.org/content/10.1101/2025.05.28.654549v1

I started tgv to learn Rust and building it has been unbelievably fun! If you wanna pick up a super fast and fun programming language, tgv is open for contribution! There aren't many bioinformatics tools built entirely by the community. If tgv can become one, I'll be so psyched

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...

Check out the beautiful cover to our focus issue on Translational research from Arabidopsis to crop plants and beyond. More articles coming shortly. Congrats Patrice Salome and @jotlovell.bsky.social. @theplantcell.bsky.social academic.oup.com/plcell/issue...

Ancestral sequence reconstruction often assumes unrealistic homogeneous substitution models; however @rmuniztrejo.bsky.social et al. find that reconstruction accuracy is determined by phylogenetic signal, not model choice. 🔗 doi.org/10.1093/molb... #evobio #molbio

A ridiculous amount of very careful work by @jahemker.bsky.social and coauthors gave a clear answer - one needs ultra-long and not just long reads to call SVs correctly in Drosophila. Now we are ready to quantify evolutionary impact of Drosophila SVs. Let us know what you think!

Conventional and organic farms with more intensive management have lower soil functionality | Science www.science.org/doi/10.1126/...

Have you ever wondered how a specialized metabolite enzyme/gene under fluctuating selection goes through speciation? Well the answer is it gets lost a lot. And by a lot we mean a lot. >25 gene copies were empirically tested using a phylo-functional approach. www.biorxiv.org/content/10.1...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search. rdcu.be/eg4OA w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n

With @hybridzones.bsky.social & @jenncoughlan.bsky.social, we have been working on an update to Daven Presgraves' influential 2010 review on hybrid incompatibilities (shorturl.at/cJndf). The preprint is available here (shorturl.at/DTC48) with an updated table of almost 100 incompatibilities!

When you go to wrong hotel, but right plant

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

Deadline was just extended to 30th March! :)

Investigating the topological motifs of inversions in pangenome graphs https://www.biorxiv.org/content/10.1101/2025.03.14.643331v1

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Telomeric transposons are pervasive in linear bacterial genomes | Science www.science.org/doi/10.1126/...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social. www.nature.com/articles/s41...

GrAnnoT, a tool for effecient and reliable annotation transfer through pangenome graph https://www.biorxiv.org/content/10.1101/2025.02.26.640337v1

Thrilled to share our latest preprint, an interdisciplinary look at epistasis between variants in the coding and noncoding genome! #plantscienceresearch www.biorxiv.org/content/10.1...

Want to level up in #pangenomics? Join our workshop, conference & biohackathon in #Memphis, May 11-15, 2025. Connect with leading scientists, embrace genomic diversity, and contribute to cutting-edge software. Register now! pangenome.github.io/MemPanG25/ #Bioinformatics #MemPanG25

Disruption of the mRNA m6A writer complex triggers autoimmunity in Arabidopsis https://www.biorxiv.org/content/10.1101/2025.02.18.638636v1

In @elife.bsky.social: Systems genomics of salinity stress response in rice doi.org/10.7554/eLif... !

Another piece to add in the emerging golden era of centromere research. Our review of centrophilic transposons in plants @annualreviews.bsky.social with @hendersi.bsky.social and Tetsuji Kakutani. www.annualreviews.org/content/jour...