In a new (ish) preprint, we used CRISPR barcodes to label germline stem cell clones in zebrafish, then tracked their contributions to sperm production for 2 years. Instead of staying stable, individual clones rose, fell, and disappeared over time. www.biorxiv.org/content/10.6...

Clonal dynamics deviate from neutral drift in zebrafish spermatogenesis

Spermatogonial stem cells (SSCs) maintain male fertility, but how their clonal dynamics change with age remains poorly understood. Here, we use in vivo CRISPR barcoding in zebrafish to label SSCs and ...

biorxiv.org

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

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

This started in 2019 as daydreamy PhD student musings with Tatsuya Araki. We're as excited as ever about germinal centers as a platform for experimental evolution. Many thanks to PIs @victora.bsky.social @matsen.bsky.social, co-1st authors Ashni Vora and Tatsuya, and many other key collaborators!

Replaying germinal center evolution on a quantified affinity landscape

Antibody affinity maturation results from a somatic evolutionary process that takes place in the germinal center. A “parallel replay” experiment on germinal center B cells reveals the evolutionary for...

cell.com

Happy to announce our new MSc in Earth System Dynamics and Evolution beginning this Oct 2026 at FAU Germany. We provide interdisciplinary training in Earth systems and science diplomacy 🌍🧪📈👩‍💻 📝 Funding provided by the Elite Network of Bavaria. Application deadline: July 15. More info below👇

Do you teach undergrad bioinformatics? If so, I'd love to hear about how (if at all) you're changing your course to reflect advances in generative AI. Please send me a DM!

a cat wearing a blue shirt is sitting on a laptop computer

Alt: a cat wearing a blue shirt is sitting on a laptop computer typing

media.tenor.com

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

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

doi.org

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...

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...

biorxiv.org

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

Institute of Molecular Biotechnology@imbavienna.bsky.social · 6mo ago

Daan de Groot is joining IMBA as group leader, and he is hiring now! https://imba.science/3M9sfxg The de Groot Lab will study how cells make fate decisions during embryonic development, a research area with broad implications for both fundamental biology and biomedical applications. Welcome to

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...

SIB Swiss Institute of Bioinformatics@sib.swiss · last yr.

💡 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...

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...

SIB Swiss Institute of Bioinformatics@sib.swiss · last yr.

💡 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...

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!

EMBO@embo.org · last yr.

This year's EMBO Young Scientists’ Forum (EYSF) will take place in Vilnius, #Lithuania from 24–26 Sep 2025. The EYSF brings together scientists across #Europe for #networking and scientific exchange – Apply now: meetings.embo.org/event/25-eysf 🧪 Abstract submission by 1 Aug Registration by 15 Aug

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)

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...

biorxiv.org

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

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 ...

royalsocietypublishing.org

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...

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...

journals.plos.org

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

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...

tinyurl.com

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

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.

mbl.edu

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...

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…

meetings.embo.org

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...

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.

meetings.cshl.edu