The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...

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

Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.

A useful analogy.

One can say that much of the progress in computer programming is aligned with ever increasing levels abstraction.
LLM-based coding tools are "just" a next level.

The choice of objective, and the measure of success, still remains something external to the tool.

Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?

Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

usethis/R/rcpp.R at f8a7bb7eef0fbb11cc81aa182c0f13ffb3e2695f · r-lib/usethis Set up commonly used 📦 components. Contribute to r-lib/usethis development by creating an account on GitHub.

Maybe this is it: `usethis::use_rcpp_armadillo`

github.com/r-lib/usethi...

Why so many #rstats packages unnecessarily link `$(FLIBS)`? I'd guess 90% packages that do this never need it. Maybe a tutorial everyone follows, i.e., copy-pasta of an example `Makevars`?

Also see linking LAPACK, when only BLAS needed, but a bit more understandable.

New #miRNA paper from Lai lab!! 🧬🔥

some think this field, despite recent Nobel to Ambros and Ruvkun, doesn't have much surprises left. but, do we EVEN KNOW WHAT a miRNA precursor LOOKS LIKE? we found some conserved miRNA hairpins up to 10x longer than suspected. this is mir-12, just bonkers! 1/n

Scalable co-sequencing of RNA and DNA from individual nuclei - PubMed The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution; however, existing tools lack...

"attack-seq" so that DEFND-seq has a counterpart

pubmed.ncbi.nlm.nih.gov/39939719/

Empirical quantiles in the violin plots! That's a nice improvement for scientific publishing. 🎉

So excited that this is finally out. This was among the longest and most uncertain (no)pun intended during my PhD, with different challenges, starting my from evaluation metrics to finding the right datasets, to tweak the method and interpreting the results.
github.com/NPSDC/mehenDi

Rethinking RNA-binding proteins: Riboregulation challenges prevailing views The advent of system-wide proteomic approaches has largely expanded the number of RNA-binding proteins (RBPs). This review discusses how recent discoveries are transforming our understanding of biolog...

Still much to be characterized about mRNAs beyond just templating proteins.

"Rethinking RNA-binding proteins: Riboregulation challenges prevailing views" www.cell.com/cell/fulltex...

Happy 10th Anniversary to @conda-forge.org ! 🍾🥂

conda-forge.org/blog/2025/04...

Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8

Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities

Answering my own question - manuscript shows going down to 50K cells/reaction.

Neat work - congrats!

Curious what the input requirements are. How many cells/sample does one need to start with to run the protocol and how many samples for reasonable statistical power? Does it need a non-specific background run?

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis An RNA′s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and d...

I'm excited to share the preprint for the first chunk of my PhD work! We combined DMS structure probing with nascent RNA enrichment to report high-resolution, dynamic structures of transcripts just after synthesis - inside cells. @karlaneugebauer.bsky.social
www.biorxiv.org/content/10.1...

Stereochemistry in the disorder–order continuum of protein interactions - Nature Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???

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

Check it out! The RNA Society 2025 Meeting Site is now live! Registration will open in January RNASociety Note the fabulous artwork by former EmoryBCDB student Dr. Carly Lancaster- make your plans now to join us in San Diego May 27-June 1, 2025

Single-molecule states link transcription factor binding to gene expression - Nature A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...

Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...

A cell atlas foundation model for scalable search of similar human cells | Nature

Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles.

#Genomics #SingleCell
www.nature.com/articles/s41...

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives | PNAS RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are...

Well, with the new activity here, thought I'd post some threads with some of our recent work -- starting with our paper where we use Bayesian statistical modeling to show bacterial transcripts have subminute half-lives, far shorter than previously thought 🧫🦠🧬💻 #RNAsky www.pnas.org/doi/10.1073/...

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

LARP1 binds ribosomes and TOP mRNAs in repressed complexes | The EMBO Journal imageimageThe LARP1 protein regulates translation and stability of mRNAs characterized by a terminal oligopyrimidine (TOP) motif, which encode most proteins of the translation machinery. This study pr...

LARP1 directly binds non-translating ribosomes and TOP mRNAs

www.embopress.org/doi/full/10....

Let's make a thread of RNA-related conferences in 2025 🧵 (add missing!)

Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...

mfansler - Overview R Team @conda-forge. Postdoc in Cvejic Lab, BRIC, UCPH. PhD from @Mayrlab MSKCC. scUTRquant creator. Reproducible research enthusiast. - mfansler

📣 Heads up for new followers (welcome! 🫶). I work in #RNAbiology (3' UTRs) and now #hematopoiesis #grns. I’m always eager to help make #bioinfo workflows more reproducible, so if you ever need #conda #condaforge #bioconda help please reach out! 🚀

github.com/mfansler

Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution - Nature Structural & Molecular Biology Here, using mathematical modeling and an in vitro deadenylation system, the authors quantitatively demonstrate the effect of non-adenosines in the poly(A) tail and exemplify how tail sequence regulate...

Our collaborative work with Narry Kim on the kinetics of mRNA poly(A) tail shortening. Led by Young-suk Lee, who established his own lab while the work was in progress, and Yevgen Levdansky in my lab. #RNASky #RNABiology www.nature.com/articles/s41...

Excited to share a new paper from my lab, now out in AJHG.
With my postdoc Silva Kasela and others, we analyzed cellular and environmental modifiers of regulatory variants in the TOPMed multi-omics pilot data from the MESA cohort. t.co/taDlhCJZpb