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Reposted by Zhigui Bao 鲍志贵

Yun S. Song @yun-s-song.bsky.social · 19d

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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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 22d

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

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Pierre Baduel @pierrebaduel.bsky.social · 23d

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...

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance

DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...

doi.org

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PLOS Biology @plosbiology.org · 26d

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

Top: Dscam1 gene structure and isoform diversity in pancrustacean species. Top: Schematic diagrams of Drosophila melanogaster Dscam1 gene and protein structure. The variable exons or domains are shown in color, while the constant exons or domains are shown in gray. Middle: Phylogenetic distribution of Dscam1 isoform diversity. A phylogenetic tree of Pancrustacean species is shown in the lower panel. The upper panel shows distribution of the number of exons in variable exon 4, exon 6, or exon 9 clusters in Pancrustacean species, with variable exon clusters shown in different colors. The middle panel shows distribution of the number of potential ectodomains diversity, where species with a special number of diversities are highlighted. Bottom: Reducing the Dscam1 diversity affects adult survival upon Beauveria bassiana infection. Survival curves after Triton or B. bassiana infection for wild-type and exon 4 (left), exon 6 (middle), and exon 9 (right) mutants are shown, respectively. The Triton groups (control) are represented by solid lines, while the B. bassiana groups are represented by dashed lines.

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Camille Roux @crouxevo.bsky.social · 29d

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

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Zhigui Bao 鲍志贵 @zbao.bsky.social · Aug 18

Curious to see what happen if all genome were re-annotated by helixer only.

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Zamin Iqbal @zaminiqbal.bsky.social · Aug 17

"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...

Protein structure alignment significance is often exaggerated

Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

www.biorxiv.org

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Aug 15

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

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PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 14

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.

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K.D. Murray @kdm9.bsky.social · Aug 14

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

Pangenomic context reveals the extent of intraspecific plant NLR evolution

Individual- and population-level diversity is required for pathogen defense by nucleotide-binding site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent A. thaliana gen...

www.cell.com

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Zhigui Bao 鲍志贵 @zbao.bsky.social · Aug 11

So cool!

Nick Desnoyer @nickdesnoyer.bsky.social · Aug 11

To promote the collection, I’ve launched a designer clothing line where synthetic biology meets aesthetics.

I will give out 100 free limited edition shirts to the first who retweet and order with their handle in the name! Available here → nickdesnoyer.com 🧵(6/7)

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Ryan Gutenkunst @ryangutenkunst.bsky.social · Aug 5

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

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · Jul 18

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

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

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...

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Erik Garrison @thinks.lol · Jul 17

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

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Adam Phillippy @aphillippy.bsky.social · Jul 11

Accurate diagram 😂

Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 11

We finished this edition with a delightful keynote by Jean Monlong who guided us through his journey about finding SVs in pangenomes #JOBIM2025 👏🏻

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Heng Li @lh3lh3.bsky.social · Jul 8

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

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Ulrich Lutz @ulrich-lutz.bsky.social · Jul 7

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

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David A Knowles @davidaknowles.bsky.social · Jul 2

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...

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

www.biorxiv.org

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Zhigui Bao 鲍志贵 @zbao.bsky.social · Jun 24

If you are using HapHiC, you could add track from long reads
alignment. It could be false duplication from haplotype or some repeat in the genome.

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North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · Jun 16

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

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Heng Li @lh3lh3.bsky.social · Jun 17

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

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Andrew Hipp @andrewlhipp.bsky.social · Jun 16

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...

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Science Magazine @science.org · Jun 12

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

Infrared imaging shows heat levels in sun-exposed leaves of Alstonia scholaris from the Australian Wet Tropics. As climate change increases temperatures and the severity of heat waves, both natural ecosystems and agricultural plants are increasingly affected by heat. Examining heat responses at cellular, genetic, physiological, and ecosystem scales, this special issue explores how plants sense and respond to high temperatures.

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Vaughn Cooper @vscooper.micropopbio.org · Jun 8

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...

Student-led experimental evolution reveals novel biofilm regulatory networks underlying adaptations to multiple niches

We established a research-education partnership known as EvolvingSTEM that provides secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution....

www.biorxiv.org

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