Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).
A brief 🧵 (carried over from the old place)
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/
🎮 pokemon tree of life
for pokémon's 30th anniversary, explore a visualization and field guide to 1,000+ pokémon. what inspired them, where they came from, and how they connect.
포켓몬 30주년, 1,000개 이상의 포켓몬을 시각화했습니다!
➡️ str.sg/viz-poke30
Just discovered the wonderful covers of 'Genes to Cells', the journal of the Molecular Biology Society of Japan @mbsj-official.bsky.social – absolutely beautiful!
here some examples inspired by mitosis, CRISPR, the DNA helix, and plant pigments
POV of the sea from the PRBB in Barcelona
Hello from Barcelona!
Thrilled to announce my recent joining of the @arnausebe.bsky.social Lab at CRG with the support of a Beatriu de Pinós fellowship. Glad to be back in the city that saw me grow as a scientist.
More more single cell omics, more evo-devo, more weird organisms... coming soon!
Thrilled to share that I’ve been awarded a FIS-3 Advanced Grant (ERC-inspired) to study the evolution of neurogenic GRNs.
Recruiting soon: 4 postdocs + 3 PhDs
Press release in Italian — to decolonise scientific language 😄
magazine.unibo.it/it/articoli/...
Email me if interested in joining the lab
🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...
Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.
www.nature.com/articles/s41...
Lovely Xmas gift 🎄—our paper is out today in @natecoevo.nature.com www.nature.com/articles/s41...! Huge thanks to everyone who made it possible, especially @aelek.bsky.social and @arnausebe.bsky.social
Exciting news to start the new year! We’re thrilled to see this work finally out in @natecoevo.nature.com, the result of a major collaboration between my lab and the labs of Veronica Hinman and Nacho Maeso, began many years ago with the dear José Luis Gómez-Skarmeta.
www.nature.com/articles/s41...
(Cont. ; I'm very used to long posts from Mastodon): Thanks to @gacthel.bsky.social, Elena Emili, Anna Guixeras, Virginia Vanni, @drsalamander.bsky.social, @cireniasketches.bsky.social, Siebren Frölich, Simon Van Heeringen, Francesc Cebrià, @spiralcleavage.bsky.social & @jordisolana.bsky.social
We hope this work proves a valuable resource for the community (lots of classic functional experiments re-mapped to recent versions of the planarian genome), and helps paving the way into new hypotheses about which genes and regulatory elements mediate stem cell differentiation.
Once again thanks!
I learned so, so much in this project. Not only in terms of tools and analyses, but especially from the rest of the team, friends & peers at @jordisolana.bsky.social . Including critical thinking, how to coordinate a whole project -it's massive-, and how to communicate this research.
Very happy to announce that our article in multimodal single cell analyses in planaria is out in Nature Communications @natcomms.nature.com ! Thank you very much to everyone that made this work possible. I am very happy to see it out (: www.nature.com/articles/s41...
Just uploaded our new preprint to @ecoevorxiv.bsky.social
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Happy to share Jialin's first publication. She did a great job exploring the transition to land in animals. Co-supervised by the great Jordi Paps and me and in collaboration with Davide Pisani and @phil-donoghue.bsky.social
Just gonna put this here for now
www.science.org/doi/10.1126/...
bsky.app/profile/jlst...
Picture of #LifelongDevSI Guest Editor Mansi Srivastava taken in an office with a whiteboard and sunny window. Mansi is wearing a white shirt and a flower pendant necklace with colourful petals
Mansi Srivastava is a Guest Editor for our Special Issue on Lifelong Development #LifelongDevSI. In this interview, Mansi talks about her research path, the links between regeneration and development and the exciting questions her lab is trying to answer.
journals.biologists.com/dev/article/...
congratulations @xgrau.bsky.social @arnausebe.bsky.social and the rest of the authors!
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Really grateful to see our work featured by @quantamagazine.bsky.social in this piece on the evolution of genome regulation. Huge thanks to @philipcball.bsky.social for such a beautifully written article.
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
Congratulations, amazing work! I remember when you explained to me the TF/motif strategy in the Sevilla meeting. I'm happy it worked well!
I am very happy to have posted my first bioRxiv preprint. A long time in the making - and still adding a few final touches to it - but we're excited to finally have it out there in the wild:
www.biorxiv.org/content/10.1...
Read below for a few highlights...
A single-cell ATACseq atlas of our favourite sea anemone, Nematostella vectensis! By @aelek.bsky.social @martaig.bsky.social
Congratulations to the new PhD at #CABD: Marta Moreno Oñate!
Dr. Moreno did an amazing job explaining the projects of her PhD work! Marta's thesis was done with @pablodeolavide.upo.es’s PhD program and was co-supervised by @martinfranke.bsky.social and Juan Tena!
I am very proud of you, Marta. You did outstanding work in the lab, and your defence was spotless. I am also very happy to now know an expert in gene compensation between paralogous genes!
Decoding cnidarian cell type gene regulation https://www.biorxiv.org/content/10.1101/2025.07.01.662323v1
