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Arnau Sebé-Pedrós

@arnausebe.bsky.social
1.8K followers 950 following 121 posts

Group leader CRG; Associate Faculty ToL Sanger Institute. Genome regulation, chromatin, cell types, and evolution. www.sebepedroslab.org

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Reposted by Arnau Sebé-Pedrós
Michael Hiller @hillermich.bsky.social · 23/09/2026
Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...
nature.com
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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Maya Voichek @mayavoichek.bsky.social · 24/09/2026
Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)
AI-generated illustration of the soma-to-germline transmission of retrotransposons described in our work
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Centre de Regulació Genòmica (CRG) @crg.eu · 21/09/2026
The CRG's 2027 PhD call is now open! We have multiple, fully-funded positions across fifteen different research groups. Successful candidates will spend four years pursuing cutting-edge questions at our labs in Barcelona. Deadline is 22 November. www.crg.eu/en/content/t...
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 21/09/2026
Must admit, ever since I was a kid, I’ve dreamt of seeing microscopy images of #protists in @lemonde.fr Today, protists are everywhere, and several images were taken by the team. And seeing #ichthyosporeans there too?! 🥹 One step closer to showcasing the beauty of the invisible microbial world. 🔬✨
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Jake Harris @c-jake-harris.bsky.social · 18/09/2026
Very excited to share the new preprint from our lab on transcriptional memory and immune priming! Herculean effort from first authors Linhao and Jenia. Epigenome-engineering experiments provide evidence that H3K4me3 plays a causal role!  doi.org/10.64898/202...
doi.org
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paveltomancak.bsky.social @paveltomancak.bsky.social · 20/09/2026
21627 applications. Nothing to celebrate here. Impossible to evaluate fairly & safely. Neither the science (too diverse & possibly LLM generated) nor the soft criteria (likely LLM generated). Without an interview stage - a security risk! marie-sklodowska-curie-actions.ec.europa.eu/whats-new/ne...
marie-sklodowska-curie-actions.ec.europa.eu
MSCA Postdoctoral Fellowships 2026 receives record number of applications
The 2026 call has attracted considerable interest from the research community with 21,627 applications submitted.
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Reposted by Arnau Sebé-Pedrós
Pawel Burkhardt @pawelburkhardt.bsky.social · 16/09/2026
Lovely to see several pieces of our ctenophore work featured in this beautiful new story from @quantamagazine.org 🪼 Great piece by @mstarling.bsky.social, also featuring work by @stevehaddock.bsky.social, @arnausebe.bsky.social & @hejnol.bsky.social. www.quantamagazine.org/ctenophores-...
quantamagazine.org
Ctenophores Aren’t Just Beautiful. They’re Biological Wonders. | Quanta Magazine
Comb jellies are helping answer fundamental questions in biology, from how the earliest nervous systems evolved to how bioluminescence works.
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Arnaud Krebs @arnaudkr.bsky.social · 14/09/2026
your starter pack for Single Molecule Genomics! Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 11/09/2026
Very proud of the team, led by @baukjeje.bsky.social & @fmikus.bsky.social To all of you doing #Expansion #Microscopy #UExM Try Concanavalin A. Its cheap, easy to use & labels the #nuclear #Envelope @moorefound.bsky.social @embl.org @sciencesunige.bsky.social @erc.europa.eu @snsf.ch
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Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️
biorxiv.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...
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Peter Andersen @germline.bsky.social · 29/08/2026
We watched piRNAs and transposons across development, saw them dance tightly and wrote a paper about it. It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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Darrin T. Schultz @dts.bsky.social · 19/08/2026
Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...
Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.
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Darrin T. Schultz @dts.bsky.social · 19/08/2026
I'm thrilled to share that I've started as an Assistant Professor in Biological Sciences and the Oceans Research Center at Lehigh University! I'm building a group in evolutionary genomics to study the origin of animals, and to use those concepts to better understand human disease. More: evogeno.me
Darrin Schultz, a man with curly dark hair and tortoiseshell glasses, smiling at the camera in a brown blazer over a blue patterned shirt with sunglasses hooked on the collar, standing in front of a stone wall.
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Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
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Gulnara Tagirdzhanova @metalichen.bsky.social · 11/08/2026
Our study on giant transposons Starship 🚀🧬 in the genome of the lichen fungus Xanthoria is now out in @pnas.org! What did we find out about Starships in #lichen fungi? 👇Updated thread below 🖥️ 🧪 🦠 🧫 #SymbioSky 1/6 www.pnas.org/doi/10.1073/...
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mara lawniczak @marakat.bsky.social · 10/08/2026
new preprint from our group led by Talleh Almelli -- important for folks doing single cell on malaria parasites or other organisms with hyperdiverse gene families. www.biorxiv.org/content/10.6...
biorxiv.org
Evaluating the impact of a sample-matched reference genome on single-cell transcriptomic inferences in Plasmodium falciparum
Background Plasmodium falciparum field isolates exhibit genomic variation, including copy number variation and sequence divergence. In contrast, the P. falciparum 3D7 reference genome (Pf3D7) was deri...
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Marc A. Marti-Renom @mamartirenom.bsky.social · 08/08/2026
🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...
science.org
3D genome organization in tissue regeneration involves long-range chromatin loops
Chromosome conformation analysis in Drosophila wing discs reveals the requirement of specific meta-loops during regeneration.
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Isabel Almudi @isabelalmudi.bsky.social · 07/08/2026
What happens when evolution adds an extra pair of eyes? Male mayflies evolve an extra pair of dorsal compound eyes, the Turbanate eyes, thought to help males detect females during mating swarms. we have investigate how this remarkable evolutionary novelty develops. www.biorxiv.org/content/10.6...
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Robin Andersson @randersson.bsky.social · 05/08/2026
Thrilled to share that our scE2G paper is now published in Nature Genetics! www.nature.com/articles/s41... scE2G predicts enhancer-gene regulatory interactions from single-cell data with state-of-the-art performance. Amazing work led by @mayayayas.bsky.social and @613weilin.bsky.social!
nature.com
Mapping enhancer–gene regulatory interactions from single-cell data - Nature Genetics
scE2G is a family of models that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues.
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Alex de Mendoza @alexdemendoza.bsky.social · 03/08/2026
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. 🧵
the indo-pacific bluebottle (Physalia utriculus)
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
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
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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RobertoFeuda @robertofeuda.bsky.social · 30/07/2026
We're hiring 4 postdocs at @unibo.it to study nervous system evolution. Seeking expertise in single-cell genomics, molecular or developmental biology in ctenophores, cnidarians, echinoderms, flies or human stem cells. 2+2 yrs contract. Deadline: 26 Aug. Please share! bandi.unibo.it/s/apos7/proc...
bandi.unibo.it
Procedura di valutazione comparativa per titoli e colloquio per il conferimento di n. 4 contratti di ricerca presso il Dipartimento di Scienze Biologiche, Geologiche e Ambientali - SSD BIOS-04/A - GSD...
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sandraduharcourt.bsky.social @sandraduharcourt.bsky.social · 30/07/2026
Open position in our lab for a research engineer. The applicant must hold a PhD in life sciences and have demonstrable experience in molecular biology and biochemistry. For more info: emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Job offer - Research Engineer (M/F), genome stability, Institut Jacques Monod, Paris, France
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Varsha Mathur @varshamathur.bsky.social · 21/07/2026
So happy to share our new paper out now in @natmicrobiol.nature.com! We establish Pirsonia-Coscinodiscus as a model pathosystem and uncover how this tiny parasite infects and kills bloom-forming marine diatoms 🌊🦠 rdcu.be/fuQyF
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Darío Lupiáñez @dariloops.bsky.social · 21/07/2026
🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 20/07/2026
The third chapter in our coral single-cell trilogy is here. After mapping cell type diversity in Stylophora (Levy 2021) and exploring facultative symbiosis in Oculina (Levy 2025), we now uncover cell type-specific responses to heat stress. Find out more in @xgrau.bsky.social's thread below.
biorxiv.org
Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery
Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are dis...
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Emília Santos @emiliapsantos.bsky.social · 14/07/2026
🎨 job alert 🐠 Come join us! We have two positions open! These are part of our @erc.europa.eu funded project on the mechanisms underpinning convergence of colour patterns in cichlid fishes! Closing date: 16th August. Postdoc: www.cam.ac.uk/jobs/researc... Technician: www.cam.ac.uk/jobs/researc...
static.klipy.com
Callipterus Cichlid Collecting Shell
ALT: Callipterus Cichlid Collecting Shell
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Pawel Burkhardt @pawelburkhardt.bsky.social · 10/07/2026
Our News & Views article “Body-plan organizer in comb jellies hints at animal ancestry” now published in @nature.com 🎉 We discuss fascinating work revealing organizer activity in comb jellies & the evolution of animal development. rdcu.be/fsLWq @ruthstyfhals.bsky.social @msarscentre.bsky.social
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Maxim Greenberg @maxvcg.bsky.social · 06/07/2026
I had an (honestly) really fun time writing up an "In Preprints" piece on the two fantastic studies from @grandlab.bsky.social and @schubelerlab.bsky.social. Check it out here. I have also put the original threads from the authors below. journals.biologists.com/dev/article/...
journals.biologists.com
In preprints – housekeeping the housekeeping genes
The term ‘housekeeping gene’ evokes a sense of banality. These are the boring genes that hum in the background, impervious to cell state or stress. For a developmental biologist captivated by the impa...
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Thibaut Brunet @thibautbrunet.bsky.social · 07/07/2026
Discovery of an adhesion GPCR regulating mating in choanoflagellates, by Alain Garcia de las Bayonas & Nicole King. Absolutely stunning work - choano cell biology is going next level www.biorxiv.org/content/10.6...
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Michael Borg @borglab.bsky.social · 07/07/2026
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 🇩🇪
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Chung Hyun Cho @chc-evobio.bsky.social · 04/07/2026
Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
biorxiv.org
Emergence of histone-based chromatin complexity in Asgard archaea
The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...
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Hanh Vu @hanhtkvu.bsky.social · 01/07/2026
Super excited that the first preprint from the lab is out! Led by an amazing student, Gaurav @gvaidya.bsky.social, jointly supervised with @mwdorr.bsky.social.
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Phil Abitua @ohnolog.bsky.social · 30/06/2026
Annual killifish continue to surprise us: they make neutrophils before almost every other cell type, even before gastrulation. Neutrophils usually arise from the lateral plate mesoderm (forming in cyan), but in killifish they are already patrolling around the embryo in gold. tinyurl.com/killiphil
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Marcin J. Suskiewicz @msuskiewicz.eurosky.social · 25/06/2026
I'm old enough to remember QED's authors said it's just providing an author with internal feedback, and emphatically isn't trying to mimic human review. Now it's compared to human review or journal selectivity and used to rank (other people's) work. The authors seem to ignore the black box aspect1/3
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Mike Dorrity @mwdorr.bsky.social · 19/06/2026
First pre-print from the lab, a collaborative effort led by Jess Bourn @bournsupremacy.bsky.social, a fantastic PhD in my group. We resolve a key problem in development + evolution: how do we quantify heterochrony and link temporal variation to phenotype? www.biorxiv.org/content/10.6...
biorxiv.org
Quantitative mapping of heterochrony to species-specific phenotypes
The genetic program of animal development is conserved, but its rate of execution varies across species. Heterochrony, shifts in the relative timing of developmental events, generates phenotypic varia...
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Philip Ball @philipcball.bsky.social · 19/06/2026
If the genome is not a blueprint, what is it? My attempt to unravel this particularly knotty question, in @quantamagazine.bsky.social www.quantamagazine.org/why-the-huma...
quantamagazine.org
Why the Human Genome’s Tangled Physicality May Confound AI | Quanta Magazine
Our genetic heritage is not a blueprint or an algorithm, as many biologists have imagined, but something else entirely.
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Xavier Grau-Bové 🌾 @xgrau.bsky.social · 19/06/2026
Do you work with scRNAseq data in non-model organisms that have less-than-stellar gene annotations? ✨ 🧬 You might be interested in GeneExt, a nifty little tool by @zolotarg.bsky.social in @arnausebe.bsky.social's lab, published in #Bioinformatics earlier this year. #singlecell #transcriptomics
academic.oup.com
GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis
AbstractMotivation. Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species whe
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genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
Congratulations to @kremnyovs.bsky.social, @tclebedeva.bsky.social and @hejnol.bsky.social - this is a fantastic paper. www.nature.com/articles/s41... Very happy to have been part of this collaboration.
nature.com
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...
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
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...
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Camille Berthelot @camilleberthelot.bsky.social · 10/06/2026
sPYce is now published in Nature Ecology and Evolution! sPYce is a method to integrate single-cell regulatory data across species, without requiring whole-genome alignments between species. More below ⬇️ www.nature.com/articles/s41...
nature.com
Alignment-free integration of single-nucleus ATAC-seq across species with sPYce - Nature Ecology & Evolution
This paper presents sPYce, a method that integrates single-nucleus ATAC-seq data across species, allowing for comparison of gene regulatory evolution across species.
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 10/06/2026
Long-term aggregation induced by bacteria in the filasteran Ministeria, with increased mating frequency inside aggregates. Truly remarkable observations by JP Gerdt, @multicellgenome.bsky.social and team! www.nature.com/articles/s41...
nature.com
A unicellular relative links aggregative multicellularity to animal origins - Nature
Nature - A unicellular relative links aggregative multicellularity to animal origins
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 09/06/2026
"Humbled to receive this recognition. This belongs as much to my team, my family, & to my home, Palestine: the people, the place, the joyful stubbornness to enjoy life." Cheers buddy @gautamdey.bsky.social Thx to my mentors @sophiemartinlab.bsky.social, @paveltomancak.bsky.social, & Pierre Gönczy.
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 05/06/2026
A big preprint from my group! Muller Elements are considered to be conserved in flies. We tested it by reconstructing the ancestral dipteran karyotype using 340 chromosomal genomes and suprise suprise, they're not... Led by @juliagries.bsky.social and Sam Ebdon. www.biorxiv.org/content/10.6... 🧵👇
Schema of three major chromosomal rearrangements leading to Muller Elements of Drosophila melanogaster since the common ancestor of Diptera.
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James Gahan @jgahan.bsky.social · 20/05/2026
We are looking for a new colleague to join us in Galway. The position is in Biochemistry and if research focus lines up we hope the successful person will join us in the Centre for Chromosome biology (chromosome.ie). Reach out if you are interested in applying! tinyurl.com/2jy4rj3r
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