Have you ever wondered what increasing environmental stress will do to microbial communities? In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5) www.biorxiv.org/content/10.1...

Big news! At least for me. I'll start building my own research group at the amazing IMBA in Vienna. Starting from single-cell omics data, we will develop computational tools and theoretical models to understand how single cells make decisions, in particular during development. I think that IMBA is

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome. We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated. Funded by a new grant from MIT-HEALS.

The are many anecdotes for #ChatGPT helping patients. But here's one with fallacious A.I. guidance that resulted in serious complications www.acpjournals.org/doi/10.7326/...

Interested in #Bayesian #phylogenetics for analysing #single-cell lineage data? 🧬 To estimate timed trees 🕒, uncertainty and cell dynamic params! I am teaching a BEAST 2 and TiDeTree tutorial during the #BC2 conference. 📍Basel, Sep 8, 2025 📅 Apply by Sep 1 Register here: bc2.ch/registration...

Interested in #Bayesian #phylogenetics for analysing #single-cell lineage data? 🧬 To estimate timed trees 🕒, uncertainty and cell dynamic params! I am teaching a BEAST 2 and TiDeTree tutorial during the #BC2 conference. 📍Basel, Sep 8, 2025 📅 Apply by Sep 1 Register here: bc2.ch/registration...

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

Our lab is helping with the organisation of this year's EMBO YSF. We have a great line up of invited speakers from (mostly) the wider Baltic region & a @nightsciencepod.bsky.social workshop on creativity in science (I did it a couple of years ago, it was awesome). Please share & consider joining us!

POSTDOC ALERT: Applications now open for SeaBridge postdoc fellowship; opportunity to work on leading-edge biotech w/researchers at the Seattle Hub for Synthetic Biology. brotmanbaty.org/news/new-pos... @marionpepper.bsky.social @jshendure.bsky.social @coletrapnell.bsky.social

New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)

Interested in #Bayesian #phylogenetics? 🧬 Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing! 📍Beijing, July 14–18, 2025 📅 Apply by April 25 I'll teach on TiDeTree & cell trees 🔗 taming-the-beast.org/news/Deadlin...

Interested in #Bayesian #phylogenetics? 🧬 Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing! 📍Beijing, July 14–18, 2025 📅 Apply by April 25 I'll teach on TiDeTree & cell trees 🔗 taming-the-beast.org/news/Deadlin...

💡 Learn to analyze genetic lineage tracing data with TiDeTree in BEAST 2! Gain hands-on experience in setting up and running analyses, from preparing data to interpreting results. 🔹 Organized by @seidels.bsky.social & Antoine Zwaans (@ethzurich.bsky.social) 👉 Register: bc2.ch/registration...

Quantification of developmental processes (here early Danio rerio development) with our novel Bayesian phylogenetic methodology - leveraging single cell lineage tracing data based on CRISPR/Cas9 technology royalsocietypublishing.org/doi/10.1098/... Antoine Zwaans @seidels.bsky.social Marc Manceau

Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :) journals.plos.org/ploscompbiol...

Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep

Join the 2025 Workshop on Molecular Evolution at the Marine Biological Laboratory from May 22 to June 1. Apply by January 29, 2025. More info: https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/workshop-molecular-evolution #workshop

Join us in Paris 6-9 May 2025 for the #EvoDevoTempo conference (2nd edition) with a fantastic line up of speakers confirmed!! Organized by @mdiazcuadros.bsky.social @vanderhaeghenp2.bsky.social @bassemh.bsky.social and me. Please RT to spread the word meetings.embo.org/event/25-dev...

We've wondered for a while why #gastruloids are so sensitive to initial cell numbers. Here www.biorxiv.org/content/10.1... led by U, Fiuza, we explore this & observe effects of a number of variables on final structure and think what this tells us @ embryogenesis #IInNumbersWeTrust #NotInTheGenes

Weini Huang, @xiaofu90.bsky.social, Dmitrii Shek and I are excited to be guest editing a BMC Cancer collection on "Spatial tumor heterogeneity". We welcome studies ranging from spatial transcriptomics to math models. For details and submission guidelines see www.biomedcentral.com/collections/... 🧪

Spread the word! Registration for the "Mutations in Time and Space" conference is open. The meeting is all about the origins, patterns, and consequences of mutations across cells, individuals, populations, species. Abstract submission deadline is Jan 17th broadinstitute.swoogo.com/mits2025/597...

Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...

We are excited to share our new preprint „Bayesian phylodynamic inference of multi-type population trajectories using genomic data“ www.biorxiv.org/content/10.1.... Using BEAST2, you can estimate past population sizes and spillover events between populations based on genetic sequencing data. 1/2

Interested in recording cell dynamics? Beautiful review from colleagues around Tanja Stadler and Martin Tran @NatureRevGenet on DNA recording in single cells and lienages. With lots of exciting opportunities for single cell modeling. nature.com/articles/s41576-024-00788-w

Very happy to share our latest paper:”Time and single-cell resolved model of murine bone marrow hematopoiesis”: www.sciencedirect.com/science/arti... With the groups of Kamil Kranc and Donal O’Carroll, we have generated a new hematopoiesis model fit for the single cell genomics era.

In addition to starter packs, don't forget to import your twitter/X follows! chromewebstore.google.com/detail/sky-f...

Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza

How can we understand the lives of cells over time? In this review we discuss **why** DNA recording cellular histories matters, **how** to record and reconstruct them (spoiler alert: there will be phylogenies 😉) and **what** biological insights they reveal...

New synthetic biology / genomic recording lab opening in the New York city! Please reach out via choij10 _at_ mskcc.org if you are interested in joining / collaborating! Mskcc.org/research/ski/labs/junhong-choi

Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5