Alexis W

I did one of these over the weekend and it was really good fun and also did not take very long. One of the kids asked me if mummies can come back to life. 10/10 experience for any archaeologist I think.

Some day, I am going to win the Ig Nobel just to see what they come up with (apparently this is a thing they do, and it slaps)

2. Map of <some far away country/city> generated with the same prompt.
Try and discuss how accurate it is - this is hard because we're unfamiliar with the (literal) territory. 😶‍🌫️

3. "When you hand in work done with an LLM, imagine when *I* (expert) are that *you* (novice) don't." 🤨

Added 3 slides to my "dear students, don't use LLMs" slidedeck. Here's how it works:

1. Generated map of <our country/city> from prompt "Generate an image: a schematic map of the <X> with major roads, cities, and landmarks."
Discuss how obviously wrong it is. Very fun, many lolz, silly LLM. 🤣

What are people using for calling m6A from pacbio revio data? This is for analysis of fiberseq library. Any suggestions appreciated, we are newbies with m6A analysis!

If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.

GitHub - MilesMcBain/gistfo: Turn your RStudio untitled tabs into gists. You monsters. Turn your RStudio untitled tabs into gists. You monsters. - MilesMcBain/gistfo

:)

I think it’s people like us that prompted @milesmcbain.bsky.social to write github.com/MilesMcBain/...

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...

Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)!
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

📢 Lancement de la campagne ATIP-Avenir 2026

@cnrsbiologie.bsky.social et @inserm.fr ouvre la campagne ATIP-Avenir 2026, destinée à soutenir des projets de recherche innovants portés par de jeunes chercheuses et chercheurs.

📅 Toutes les informations : buff.ly/5DH6mpd

Based on feedback from applicants, reviewers and broader research community, the ERC Scientific Council decided to make changes in the 2026–27 calls for proposal for research funding.

More details from the ERC President 👉 europa.eu/!hP3WWF

What’s your take on this? Tell us! 👇

Changes in ERC eligibilty windows:

"researchers will be eligible to apply for a Starting Grant immediately after defending their PhD, and at any time within the following ten-year period. Consolidator Grant applicants will be eligible to apply between five and fifteen years after defending"

record 17,058 Marie Curie proposals in 2025 vs. 10,360 in 2024!!! the reason is pretty obvious, but wow that is a huge jump marie-sklodowska-curie-actions.ec.europa.eu/news/msca-po...

HuD controls widespread RNA stability to drive neuronal activity-dependent responses Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively...

Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)

Here is some recommended reading 👇 (and enjoy the associated thread for clarity and the beautiful imagery 👍) Lots of different genes, oscillating in different cell types

Thanks for highlighting - thread to follow. Mini-summary: beyond assigning oscillatory genes expression by scRNA-seq to individual cell types, we also show that chromatin opens rhythmically and that we can predict this (and gene expression) with a small set of TFs in a mathematical model.

a bunch of clocks are hanging on a wall including one that says ' 3:00 ' on it ALT: a bunch of clocks are hanging on a wall including one that says ' 3:00 ' on it

New preprint!

How are developmental cycles coordinated across cell types?

It turns out that, like Geppetto's cuckoo clocks in the GIF below, individual cell types are each performing their own little crazy routine, but all in sync with each other.

One like, one stats/data science/polmeth opinion.

#statssky

I just got the notice that all the FlyBase people at Harvard, including me, will be laid off on October 12. I'm devastated.

Carbonara was created in the 1940s, because when the Americans liberated Italy, they brought enormous amounts of bacon with them.

Looking for motivated postdoctoral researcher to join us! Research on neuronal & glial cell mechanisms of circuit formation. Approaches: advanced quantitative imaging, cell, molecular biology, circuit manipulation, cross-species study. Info link in comment, deadline 8th Sept.

a man with a beard is saying `` that burned down , fell over , and then sank into the swamp '' Alt: Holy Grail - "that burned down, fell over, and then sank into the swamp"

In passing, it's wrong to say the submersible design was untested. They built and tested a 1:3 model, which imploded, so they built and tested another one. Which imploded.

So they built a third, which imploded.

But the fourth one -the fourth one - well, no. The fourth one imploded as well.

"Presumably, researchers who work on the hermaphroditic worm C. elegans are out of luck."

Analysis done over days and weeks can be non-reproducible if you ran some steps/skipped steps/ran steps out of order while working interactively. If you have time-intensive chunks, by all means store and re-use these outputs, but use a workflow tool (e.g. targets or make) to ensure reproducibility.

people don't actually want to test point-nulls in NHST, they want to test interval nulls and they rely on the structure of the test to define the "interval null" (*waves hands vaguely*) for them, rather than explicitly defining an interval null and testing it.

This is insane. We've used interferometry to image the face of Betalguese, and yet no one understood this was there. I was staring at this release when @theplanetaryguy.bsky.social 's comment came by, and "This is absurd" is the best way to describe this.

... a new virtual seminar series on apical extracellular matrix #aECM on different #organisms 🪱🪰🐁🌱🦠will start in Fall 2025, with short talks and discussions
If you are interested
👉https://forms.gle/Y6UjbnXPH1pDHAE97
@meera-sundaram.bsky.social @gotworms.bsky.social @heiman.bsky.social

It's mildly interesting to consider that LLMs are perhaps a system for which the Sapir-Whorf hypothesis is most true (i.e., language one speaks influences the way one thinks about reality). What to know: the 'voice' you ask these models to respond in will tend to also affect the content itself.

Cilia in neuron-glia adhesion, Tue PM poster by Leland Wexler

Embryo sense organ morphogenesis, Tue PM poster by Leland Wexler

SAX-7 trafficking and synthetic CAMs, Tue PM poster by Jung Hyun Yoo

Drug screening for Kabuki Syndrome (SET-16/KMT2D), Mon PM poster by Megan Lymburner

It's happening!

Welcome to Issue 1 of RDM Weekly, a weekly roundup of Research Data Management resources!

To kick off this newsletter, I will be doing a drawing for 1 free
@rfortherestofus.com course for anyone who subscribes by Friday!

rdmweekly.substack.com/p/rdm-weekly...