Does hidden protein biology live in the suboptimal alignment space?
When we align two divergent proteins, we usually trust a single optimal alignment. 🧬
But what if the real structural signal lies in the space of near-optimal solutions?
With EMERALD-UI you can unfold this perspective.
📣 Meet the new ERC Synergy Grant awardees!
Sixty-six research teams have been selected for funding, bringing together 239 scientists. Congratulations to all!
➡️ buff.ly/PSn3bi9
#EUfunded #HorizonEurope #ERCSyG
This Halloween, we have a spooky evolutionary story for you.
The brainchild of @delaconcepcionjc.bsky.social, Nick Irwin and our fantastic collaborators is now out in @natplants.nature.com www.nature.com/articles/s41...
Here’s why I love this work — and why I think you’ll enjoy it too. 👇
#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Excited to introduce Auxenochlorella as a new algal reference organism for fundamental plant science and bioengineering. A paper in two parts: a genetic toolkit for site-specific genomic manipulation, paired with the most unusual genome I’ve ever worked on
academic.oup.com/plcell/artic...
1/9 New in @science.org www.science.org/doi/10.1126/science.ado8005
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.
3/9 The black-or-white throat polymorphism is explained by the interaction of a transposable element (an LTR retrotransposon) upstream ASIP with ASIP coding variation. Mantle and neck side coloration is encoded by additive effects of regulatory variants upstream ASIP.
We discovered an endogenous retrovirus that's still spreading in natural D. melanogaster populations! It was horizontally transferred from D. erecta in Central Africa, so we named it "Kuruka", which means "jump" in Swahili. Read its cool story here: www.biorxiv.org/content/10.1...
Thrilled to share what we learned from re-annotating the mobilome of the brown algae model [Ectocarpus] 🌊🌿🏖️
genomebiology.biomedcentral.com/articles/10....
A wonderful collaboration with @ericadinatale.bsky.social, @cssmartinho.bsky.social, @rorycraig.bsky.social, and Susana Coelho! 🎉
It would be exciting to study whether there are clear "causal" links between TE regulation and body plan formation in brown algae, where 'artificial' mobilisation of young TEs can drive innovation (and overcome constraints) in the formation of multicellular phenotypes.
Thank you!!
Thank you Vangeli!
Huge thanks to Susana Coelho, @hajkdrost.bsky.social, @cssmartinho.bsky.social and @rorycraig.bsky.social for their guidance and support throughout this massive work!
5/5 🔮 Brown algae are a unique lineage in the tree of life, and working on them gave me a new perspective on the diversity of TE landscapes and regulation mechanisms across eukaryotes!
4/5 ✨ And my favourite part: intact TEs are preferentially associated with small RNAs and with the histone modification H3K79me2. Their interplay offers a curious insight into alternative regulatory strategies.
3/5 🧬 Over 80% of genes contain at least one intronic TE insertion. These intronic elements are shorter and more degraded than intergenic TEs, and overall they show minimal impact on gene expression.
2/5 🧜 TEs form discrete, repeat-rich islands that don’t correspond to centromeres. We also found an interesting enrichment in the pseudo-autosomal region of the sex chromosome, likely fueled by local hopping of DNA transposons from the sex-determining region.
1/5 🌊 The Ectocarpus genome harbors a high diversity of evolutionarily young TEs. DNA transposons dominate, but Gypsy elements carrying a Tudor domain caught our eye!
So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH
New research: With ancient origins & surprising flexibility, #BrownAlgae reveal a compelling story of sex chromosome evolution. This could rewrite how we view sex determination. Learn more: s.gwdg.de/YDoZ3L
Congrats to @agalip.bsky.social & Josue Barrera for their work in @natecoevo.nature.com
Genomes of brown algae with different sex determination systems show that U/V sex chromosomes evolved 450–224 million years ago and show remarkable conservation of genes within the sex-determining region, despite independent expansions of the sex locus in each lineage
www.nature.com/articles/s41...
Free online ebook: R and python comparisons side by side
www.anotherbookondatascience.com/chapter1.html
Thank you Toby! Brown algae and TEs make a cool combo 🌊🦘🪅
Delighted to share the peer-reviewed version of our study led by @tomlewin.bsky.social now out in Genome Biology @bmc.springernature.com! We analyzed 64 chromosome-level genomes across 15 animal phyla and found that extensive genome rearrangements are the norm in bilaterians.
doi.org/10.1186/s130...
💥🥳 At long last, our latest paper is out!
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Transposable elements in brown algae? 🌊
Yes, they’re full of surprises ✨
Come meet Ectocarpus at #ESEB2025!
📍Room 113 - S28.03
🗓️ Thursday, 2:30pm
#ESEB2025 check out poster 221!
The amazing work of @petrollromy.bsky.social and @borglab.bsky.social is also here ⤵️
www.cell.com/current-biol...
#TEsky #RNAsky #RNAbiology
