RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques https://www.biorxiv.org/content/10.1101/2025.10.04.680405v1

BREAKING: Our client Mario Guevara, an Emmy-winning journalist detained by ICE in retaliation for livestreaming law enforcement activity, will be deported tomorrow to El Salvador.

Mario and his family are being punished for his reporting. This cruelty is meant to stifle our free press.

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

Some personal news:

I've been fired from the Washington Post in the aftermath of the Charlie Kirk shooting.

Thread incoming.

substack.com/@karenattiah...

🚨 New paper alert 🚨 Using LLMs as data annotators, you can produce any scientific result you want. We call this **LLM Hacking**.

Paper: arxiv.org/pdf/2509.08825

White text on white background instructing LLMs to give positive reviews is apparently now common enough to show up in searches for boilerplate text.

For many of those who were asking on BLOW5 vs POD5 for nanopore signal data, here is a finally detailed benchmark we did:
biorxiv.org/content/10.1...
Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.

"LMCompress shatters all previous lossless compression records on four media types: text, images, video and audio."

www.nature.com/articles/s42...

Analysis by altmetric shows increasing posting of research content on Bluesky but more sharing (reposting) on X.

We need to increase Bluesky connectivity and share more.

Toward single-molecule protein sequencing using nanopores
www.nature.com/articles/s41...

Roche SBX preprint out

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

Roche Xpounds on New Sequencing Technology

My deep dive on this exciting new entrant

omicsomics.blogspot.com/2025/02/roch...

🧬🖥️

Verena Rukes telling us about: Charge-based fingerprinting of unlabeled full-length proteins using an
aerolysin nanopore

Timescales in Cell Biology

I took biochem in 2001, and for nearly 20 years read amino acid sequences daily… and I never knew Dayhoff named them or even the logic behind things like Q until last Friday (h/t Mike Janech). Also, this is another big Dayhoff moment for me. She was incredible!

#proteomics #bioinformatics

This worked like a charm to import accounts following on Twitter chromewebstore.google.com/detail/sky-f...