Did you ever want to sequence that one interesting cell you observed in your microscopy experiment? We have a new pre-print out today that describes a genetic barcoding method, Waldo, to perform live-cell imaging and single-cell sequencing on the same single cells. www.biorxiv.org/content/10.6...

Linking live-cell imaging to single-cell sequencing using genetic barcoding

Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures gen...

biorxiv.org

arxiv.org/abs/2610.10072

Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22

Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right? TLDR: No. #methodsmatter Not even close. On realistic synthetic data MILK performs worse than UMAP.

nf-co.re/tumourevo/1....

Hace 200 años, Darwin y Hooker se preguntaron si era posible cambiar el clima de una isla construyendo un ecosistema de novo. Demostraron que sí. Ahora he viajado a Ascension con @nastassiakn.bsky.social para entender cómo ocurrió y cómo podemos exportarlo. Gracias @pflis.bsky.social por contarlo.

Ascensión, la isla desértica que se hizo selva

Este remoto paraje en medio del Atlántico podría esconder la fórmula para combatir la desertificación en otros lugares del planeta. Un científico español ha decidido investigarlo. Viajamos hasta allí ...

elpais.com

"Written in development and lost in ageing: the grammar of cellular identity". Review in @nature.com www.nature.com/articles/s41...

Written in development and lost in ageing: the grammar of cellular identity - Nature

Ageing reflects progressive decanalization of mammalian cell identity, driven by erosion of a regulatory grammar written during development.

nature.com

📢 The 𝗜𝗥𝗕 𝗕𝗮𝗿𝗰𝗲𝗹𝗼𝗻𝗮 𝗜𝗻𝘁𝗲𝗿𝗻𝗮𝘁𝗶𝗼𝗻𝗮𝗹 #𝗣𝗵𝗗 #𝗙𝗲𝗹𝗹𝗼𝘄𝘀𝗵𝗶𝗽𝘀 – 𝗘𝘅𝘁𝗿𝗮𝗼𝗿𝗱𝗶𝗻𝗮𝗿𝘆 𝗖𝗮𝗹𝗹 𝟮𝟬𝟮𝟲 is now open, offering up to 8 PhD fellowships in #Biomedicine or #OrganicChemistry. Explore the participating groups, check the application requirements and apply 👉 https://shorturl.at/7iSOa 🧪

🧬 Preprint! 🧵 Our goal is to genetically manipulate every embryonic germ layer to enable high throughput in vivo studies. We previously showed mouse ectoderm can be targeted by amniotic injection, enabling cell-specific manipulation, lineage tracing, and knockouts. But how to reach mesoderm?

While the Fields Medal celebrates the under-40s, the mathematician Joan Birman has, at the age of 99, solved a major open problem in representations of the Braid groups, a topic she has worked on for more than 60 years.

A single-cell RNA-seq catalog of ground truth gene coregulation https://www.biorxiv.org/content/10.64898/2026.09.18.752692v1

Would like to heat thoughts of the community on this. Looking forward to the version after peer reviewing!

#SingleCell preprints@prepub-singlecell.bsky.social · last mo.

Confounder-Aware Feature Correction for Single-Cell Batch Integration #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2608.28849

Must be crazy to be David Baker and have your scientific dreams come true in your lifetime in your lab

bioRxiv Biochemistry@biorxiv-biochem.bsky.social · last mo.

De novo design of allosterically controlled enzymes https://www.biorxiv.org/content/10.64898/2026.09.08.750245v1

Already several mentions of uses in bioinformatics like transcriptomics. little doubt that it’s useful but still a universal problem of how many. If you give several analyst the same data I think there could be a 10 fold variation on the # clusters "identified". This paper nicely asks "how many?"

CHOIR improves significance-based detection of cell types and states from single-cell data - Nature Genetics

Cluster hierarchy optimization by iterative random forests (CHOIR) offers a robust and accurate method to identify cell clusters across a variety of single-cell resolution data with statistical suppor...

doi.org

Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native. doi.org/10.64898/202...

It's been preprint week! Joe's great Perturb-seq story "back-to-back" with our single cell AML atlas (led by @simonhaas.bsky.social). 🤒: www.biorxiv.org/content/10.6... 🧬: www.biorxiv.org/content/10.6... These two apparently very different stories were posted back to back because of a surprise 😮🧵:

Joe Bowness@joebowness.bsky.social · last mo.

Very happy to share the first pre-print from my postdoc work with @larsplus.bsky.social (which we also presented at the excellent @isehsociety.bsky.social Annual Meeting last weekend). Here we performed a CRISPRi Perturb-seq screen targeting >500 transcriptional regulators in ex vivo mouse HSPCs.

Big paper alert! This project has been years in the making. A comprehensive description of somatic mutation rates and signatures across 53 tissues or cell types using NanoSeq. A large collective effort led by Mimy Pham, Mike Stratton and @r-rahbari.bsky.social. www.biorxiv.org/content/10.6...

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune syst...

biorxiv.org

Very happy to share the first pre-print from my postdoc work with @larsplus.bsky.social (which we also presented at the excellent @isehsociety.bsky.social Annual Meeting last weekend). Here we performed a CRISPRi Perturb-seq screen targeting >500 transcriptional regulators in ex vivo mouse HSPCs.

Sharing a new preprint about technical variation in (bulk/ #SingleCell ) #ATACseq and motif accessibility analyses, and methods to correct for them www.biorxiv.org/content/10.6...

The paper is here: www.nature.com/articles/s41...

Ultrafast and reference-free sequence discovery in single-cell data - Nature

Malva enables ultrafast, reference-free searching of raw single-cell sequences across millions of cells, transforming static transcriptomic atlases into dynamic resources for understanding the functio...

nature.com

0/ New preprint from the Stark and Grün labs! @reyna-rosales.bsky.social @dominicgrun.bsky.social @alex-stark.bsky.social We developed BARe-seq to ask what in the DNA controls transcriptional bursting - key findings for anyone working on transcription, gene regulation, or cis-regulatory elements 🧵

I've tried Bonsai in various datasets through the web server. It has always added some insights to my understanding of the data. Totally recommended, especially seeing the new additions 🤩

Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo ago

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

Can Bonsai also identify clusters/cell types in the data? Yes, Bonsai has both an unsupervised method for finding clearly distinct clades of cells in the tree, and a supervised method that finds the clades that best match a given reference annotation. 4/n

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

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.

nature.com

Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Latest from our lab: highly multiplexed spatial miRNA profiling, with @agustinrobles.bsky.social, @augjensen.bsky.social, @nilssonlab.org and others! www.biorxiv.org/content/10.6...

Spatial microRNA profiling at single-cell resolution by in situ barcoded extension

The spatial organization of post-transcriptional regulation is a fundamental yet difficult to access layer of tissue biology. MicroRNAs (miRNAs) are small RNAs with a key role in post-transcriptional ...

biorxiv.org

Mathematics in the age of AI by Terence Tao An essay on how the mathematical community might respond to the arrival of AI tools that are capable of performing research-level mathematical tasks. arxiv.org/abs/2608.16753

Mathematics in the age of AI

An essay, based on a public lecture delivered at the 2026 International Congress of Mathematicians, on how the mathematical community might respond to the arrival of artificial intelligence tools that...

arxiv.org

@nature.com Matters Arising @caleblareau.bsky.social @leifludwig.bsky.social Artefacts in single-cell mtDNA analyses misinform phylogenies www.nature.com/articles/s41... on www.nature.com/articles/s41... response @bloodgenes.bsky.social www.nature.com/articles/s41...

Get your calendars, because the new 2027 EMBL Annual Poster has arrived: s.embl.org/2027-poster Whether you'd like to enhance your skills in a practical course or engage with the latest research at one of our conferences, we've got you covered. See you at EMBL in 2027! 🙌 #LifeSciences #EMBL

New preprint alert!!! Super proud to finally share an authentic 'tour-de-force' from the amazing PhD students Shivani Gunnan @shivanigunnan.bsky.social, Max Kotz and Lucas Ribas, in collaboration with @friedrich-group.bsky.social 👇a small thread www.biorxiv.org/content/10.6...

Developmental growth rates adapt to enable self-correction of organ morphology after injury.

Proportional organ growth requires tissue-level control of cell behavior. Yet the cues that adapt growth rates, especially after organ injury, remain unclear. Here, we uncover that developing organs a...

biorxiv.org

Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming - @institutcurie.bsky.social www.nature.com/articles/s41...

Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming - Nature Biotechnology

OneCell CUT&Tag enables multiomic analysis of a single cell without computation.

nature.com