New method drop:
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...

'Positive review only': Researchers hide AI prompts in papers Instructions in preprints from 14 universities highlight controversy on AI in peer review

This is insane! "'Positive review only': Researchers hide AI prompts in papers"
asia.nikkei.com/Business/Tec...
h/t Ryan Pack

We turn 25 today!

July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser.

Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code.

See our news for more: bit.ly/genomeBrowser...

Franklin Stahl, biologist who helped reveal how DNA replicates, dies at 95 — The Washington Post An early experiment, with colleague Matthew Meselson, helped set the stage for a revolution in genetics.

apple.news/A6s0jhagcSLy...

New paper:
More than 2700 human 3′UTRs are highly conserved. These 3′UTRs are essential components in mRNA templates, as their deletion decreases protein activity without changing protein abundance. Highly conserved 3′UTRs help the folding of proteins with long IDRs.

www.biorxiv.org/content/10.1...

Scientists use bacteria to turn plastic waste into paracetamol Genetically modified E coli used to create painkillers from material produced from plastic bottles

Scientists use bacteria to turn plastic waste into paracetamol www.theguardian.com/science/2025...

Scientists use bacteria to turn plastic waste into paracetamol

Genome-wide mapping of mesoscale neuronal RNA organization and condensation Subcellular RNA organization can affect critical cellular functions. However, our understanding of RNA microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack ...

What drives cytoplasmic mRNA organization? We created unbiased, genome-wide maps of mesoscale RNA-RNA spatial proximity, revealing impact of encoded protein function. Fantastic work from @lindsayabecker.bsky.social @sofiquinodoz.bsky.social @davidaknowles.bsky.social www.biorxiv.org/content/10.1...

New pre-print from the lab with some great collaborators. Julia worked so hard!

Are material phase transitions more than simple regulators of tissue deformability? Check our latest work uncovering that rigidity transitions can trigger cell polarity! Congratulations to @laura-rustarazo.bsky.social , @crisp-c.bsky.social and Adrián for leading this work!

A nearly 9 year effort to design and implement new CLIP-based technologies to define multimeric protein assemblies on RNA.

Enables ‘watching’ of RNP assemblies inside living cells

Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com
www.nature.com/articles/s41...

our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!

key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity

many are "negative regulators" & misexpressed in cancer

www.sciencedirect.com/science/arti...

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis Schärfen et al. develop a method to measure the structure of nascent RNAs during their synthesis by RNA polymerases. Base pairing occurs rapidly in cells, revealing the strong regulatory potential of ...

Here is our paper showing in vivo folding of nascent RNA right after synthesis, published now in @cp-molcell.bsky.social!

With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social

www.cell.com/molecular-ce...

Why AI won’t replace scientists capable of making disruptive conceptual breakthroughs - they pose questions that challenge, rather than align with, the training data set

thomwolf.io/blog/scienti...

Susan Lindquist School on Proteostasis Cells constantly surveil and monitor their proteome to ensure proper function. These processes, spanning multiple steps from protein synthesis to folding and degradation, are collectively known as pr…

Apply now for the Susan Lindquist School on Proteostasis EMBO-FEBS Lecture Course, 16-19 Sept 2025 in Espoo, Finland! Top speakers cover the latest in proteostasis. Open to 60 PhDs & postdocs. Deadline: 15 June 2025. meetings.embo.org/event/25-pro...

Interested in doing a sabbatical at EMBL, at one of its 6 sites in Barcelona, Cambridge, Grenoble, Hamburg, Heidelberg or Rome?

Funding call with deadline 15 June, decisions in July.

www.embl.org/about/info/s...

Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces The localization of biomolecular condensates to intracellular membrane surfaces has emerged as an important feature of sub-cellular organization. In this work,

New paper out! Why do condensates prefer some surfaces and not others? Check it out here: doi.org/10.1063/5.02...

I’m crying, this is so funny

WEAPONIZED MANSPLAINING FOR ESPIONAGE ☠️☠️

NIH cuts are hitting young scientists the hardest. By David Baker. timmermanreport.com/2025/03/davi...

Fantastic @embo.org lecture course in Pune, India! Lots of cool science, great interactions and condensation (pun intended) with RNA enthusiasts from all over the world. With Rick @rickmarsman.bsky.social and Sakshi @sakshigorey.bsky.social presenting posters. #EMBOrnaProtein #RNA

Single-molecule live-cell RNA imaging with CRISPR–Csm - Nature Biotechnology Single-molecule live-cell fluorescence in situ hybridization uses an RNA-targeting CRISPR–Csm complex to image and track endogenous RNAs.

Visualizing RNA in live cells using CRISPR
nature.com/articles/s41...

Sign the Petition Petition to Reverse the NIH Indirect Cost Cap (NOT-OD-25-068)

Petition to Reverse the NIH Indirect Cost Cap initiated by Tom Maniatis. Please amplify
Sign the Petition: chng.it/kK2HMP5pGk
"Share with Leadership & Faculty. Reach out to professional societies, biotech and pharma leaders, and philanthropic organizations to raise awareness and mobilize support."

G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration Boraas et al. identify that mRNAs and the stress granule RNA-binding protein G3BP1 form ribonucleoprotein (RNP) complexes at FAs. These RNPs regulate FA protein mobility and cell migration under norma...

G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration: Cell Reports

www.cell.com/cell-reports...

Amazing work by Liana Boraas, Mengwei Hu, ..., @christinemayr.bsky.social, Siyuan Wang, @nicolilab.bsky.social.

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We stud...

1/ 🚨We’re thrilled to share our latest study:

"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟

www.biorxiv.org/content/10.1...

How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️

The conformational space of RNase P RNA in solution - Nature Using a deep neural network and statistical analyses of atomic force microscopy images of individual RNA molecules enables the mapping of RNA conformational space in solution.

www.nature.com/articles/s41...

Check out the latest Reviews and Perspectives from experts in RNA biology in this joint collection from @CellChemBiol and @MolecularCell http://dlvr.it/TGwFkr

Insightful thread by @erikvannimwegen.bsky.social arguing for nudges in the publishing system instead of blowing it up. What I find curious is how our truly vast publishing ecosystem is stubbornly resistant to any *experimentation*. eLife tries a couple things and gets vilified. What the heck! 1/2

DNA copy number variation is strongly buffered at the protein level.

The buffering is much stronger than at the RNA level.

I do the same! @karlaneugebauer.bsky.social