Age-dependent Phylodynamics with Application to Single-cell Lineage Trees Abstract. As novel technologies for single-cell lineage tracing emerge, phylogenetic and phylodynamic tools are increasingly being used to study developmen

Mulberry, Pilarski, Dinger, and @tanjastadler.bsky.social present a phylodynamic method that generalizes the traditional birth-death approach to model cellular dynamics to an age-dependent phylodynamic model.

🔗 doi.org/10.1093/molb...

#evobio #molbio

Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...

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...

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

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

Lineage recording in monoclonal gastruloids reveals heritable modes of early development Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...

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...

A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites | Philosophical Transactions of the Royal Society B: Biological Sciences Analysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. Clustered regularly interspaced short palindromic repeats (CRISPR)-based dynamic lineage tracing relies ...

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

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities Author summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...

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...

Mapping cells through time and space with moscot - Nature Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

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

Workshop on Molecular Evolution | Marine Biological Laboratory The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology.

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: www.mbl.edu/education/advanced-resea... #workshop

Developmental timing across species: From mechanisms to evolutionary insights Like choreography, development consists of a highly ordered suite of steps and transitions. Modifying developmental tempo can affect final size and composition of tissues, as well as their plasticity…

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...

Probabilistic Modeling in Genomics Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

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

Bayesian phylodynamic inference of multi-type population trajectories using genomic data Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important tool for understanding both the spread of epidemics as we...

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

Would love to be added too!

Thank you for highlighting our review!

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

A time- and single-cell-resolved model of murine bone marrow hematopoiesis The paradigmatic hematopoietic tree model is increasingly recognized to be limited, as it is based on heterogeneous populations largely defined by non…

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.

Sky Follower Bridge - Chrome Web Store Instantly find and follow the same users from your Twitter follows on Bluesky.

In addition to starter packs, don't forget to import your twitter/X follows!

chromewebstore.google.com/detail/sky-f...