Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵

Glad to see this out at last! Check out Arnau's summary below for all the highlights

Arnau Sebé-Pedrós@arnausebe.bsky.social · 3d ago

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

What drives the variation in mutation rates between seals and walruses, gulls and pelicans? Maybe selection counteracting the burden of deleterious mutations- or maybe it is a spandrel, a neutral byproduct of the diversification of development and life-history academic.oup.com/evolut/advan...

Mutation rate variation as the neutral byproduct of developmental and life history diversification

Abstract. Understanding why species differ in their rates of mutation is central to explaining patterns of molecular and phenotypic evolution. Mutation rat

academic.oup.com

📝 NEW PREPRINT It’s with an immense joy that our preprint is finally out and it’s my first first co-author paper!!! 🧬🍄 What is the diversity of 3D genome architectures in fungi? We reconstructed the 3D genome architecture of public Hi-C data from 55 fungal. Preprint: lnkd.in/enxTh2Cm

Our group is moving from @mpi-bio-fml.bsky.social to the maritime city of Kiel! ⛵️🩵 I will lead the Department of Marine Plant Development and Physiology @uni-kiel.de 🌱🪸🌊 Look out for opportunities to join us in this exciting & growing hub for Plant, Marine & Evolutionary Biology in North Germany 🇩🇪

Our paper is out! Giant viruses lay silent in algal genome across generations, but reactivate in reproductive cell types and under specific environnemental condition to produce virions. Thank you all for your contributions !

Nature Microbiology@natmicrobiol.nature.com · 3mo ago

Out Now! Latent endogenous giant viruses drive active infection and inheritance in a multicellular algal host #MicroSky

Big paper from @hejnol.bsky.social lab. Title says it all. Congrats, Stanislav Kremnyov and the team. www.nature.com/articles/s41...

A blastoporal organizer in a ctenophore - Nature

Experiments using the comb jelly Mnemiopsis leidyi and the sea anemone Nematostella vectensis reveal that the emergence of a core signalling pathway may have been a key innovation enabling the transit...

nature.com

1/10 For decades, cellular aggregation was considered an evolutionary dead end. Cells could come together temporarily. But complex multicellular organisms like animals? Our study, led by JP Gerdt, with Ruibao & @jennahed.bsky.social suggests it may be time to rethink that🧵 #ProtistsOnSKy

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere Work led by the indomitable @sheilaroitman.bsky.social‬ #plantscience #microbiome #holobiont www.biorxiv.org/content/10.6...

New Pre-Print Alert! Evolving initial conditions: an alternative developmental route to morphological diversity with Shannon Taylor and @jamesehammond.bsky.social www.biorxiv.org/content/10.6...

Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬 Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15 www.biorxiv.org/content/10.6...

🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo

Behind the scenes! go.nature.com/4bYY8BM

What brown algae taught me about the importance of jumping genes for genome evolution

go.nature.com

Our work on chromatin evolution in brown algae is now published in @natecoevo.nature.com! We show that developmentally complex brown algae evolved without epigenetic silencing pathways long thought universal, underscoring why non-model lineages are important to study. www.nature.com/articles/s41...

Now that it's official i've got some news! Our group has moved from @mpi-bio-fml.bsky.social to @unihalle.bsky.social where I am now leading the department for phytopathology and plant protection 🍄🌾🧬

Our work on chromatin evolution in brown algae is finally out! This is also my first "co-first author" paper!! I’m excited to share what we found 👇

Nature Ecology & Evolution@natecoevo.nature.com · 4mo ago

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...

Evolution of a distinct chromatin regulatory landscape in brown algae - Nature Ecology & Evolution

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidat...

nature.com

I am very grateful to be featured discussing my work on transcription associated proteins and TAPscan @rensingstefan.bsky.social Many thanks to @theplantjournal.bsky.social for the opportunity and recognition!

The Plant Journal@theplantjournal.bsky.social · 4mo ago

🗣️ 𝐈𝐧 𝐜𝐨𝐧𝐯𝐞𝐫𝐬𝐚𝐭𝐢𝐨𝐧 𝐰𝐢𝐭𝐡 𝐑𝐨𝐦𝐲 𝐏𝐞𝐭𝐫𝐨𝐥𝐥 @petrollromy.bsky.social TPJ Outstanding Resource Article Award 🏆 Romy is a PhD student at the @MPI_Bio Tübingen 🌿 Her work sheds light on the evolution of gene regulation across algae and plants ✍️ @luisdeluna.bsky.social 👉 doi.org/10.1111/tpj.70829

How much protein diversity can Life on Earth actually generate? With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks. 📚Paper: www.nature.com/articles/s41... 💻Code: github.com/bbuchfink/di...

I am thrilled to share our new publication in @natcomms.nature.com showing that the vertebrate developmental hourglass has a cellular basis. We asked whether this embryonic pattern is already evident at the level of cells, the building blocks of complex organisms. rdcu.be/e70XT

A cellular basis for the hourglass pattern in vertebrate embryogenesis

Nature Communications - The developmental hourglass has long been seen at the level of embryos. By zooming in to single cells, this Perspective shows that mid-embryonic conservation arises from...

rdcu.be

After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data! But first, I would like to talk a bit about RNA velocity and normalization. 1/

Nature Methods@natmethods.nature.com · 9mo ago

Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social www.nature.com/articles/s41...

Heya science peeps, my first first-author paper is on Biorxiv! We show how transcriptome-wide expression variability in outbred animals responds massively to an environmental stressor and is underpinned by cryptic variability- (not just mean-) controlling alleles. www.biorxiv.org/content/10.6...

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.

One protein. One pathway. A whole germline fate. New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS: Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...

Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS

ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that play central roles in gene regulation and developmental process...

pnas.org

🧵 Just out in Cell after more than 10 years in the making! 🎓 www.cell.com/cell/fulltex... Plants and animals evolve radically different body plans. Do they also operate under fundamentally different molecular evolutionary constraints during organ formation? @cellpress.bsky.social

Genome editing in brown algae! 🧬🪸🌿 Now out in Cell Reports Methods! Excited to share this highly efficient, transgene-free CRISPR–Cas genome editing protocol for brown algae, requiring no cloning and no specialized equipment. doi.org/10.1016/j.cr... #CRISPR #BrownAlgae @mpi-bio-fml.bsky.social

DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/di...

GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.

Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond

github.com

Can we tune a plant’s epigenetic toolkit to disrupt plant homeostasis in ways that enable phenotypic innovation? 🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social! www.sciencedirect.com/science/arti...

🎉 Our deconstructed, stem-cell–based approach to studying signaling centers and limb-development cell types is out! 🥳 So nice to see it in its final form after the preprint— and huge thanks to the community for all the enthusiasm and interest since then! www.science.org/doi/10.1126/...

Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model

Stem cell–derived mesodermal organoids reveal how signaling centers guide cell fate and tissue organization.

science.org