Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current c...

From great collaborations come great things. Excited to share Segger, the solution to segmentation of spatial transcriptomics (ST) data, with the @steglelab.bsky.social and @moritzgerstung.bsky.social labs, spearheaded by the great Andrew Moorman and Elyas Heidari www.biorxiv.org/content/10.1...

Segger logo

Message passing intuition behind the segger’s link-prediction model and the network architecture

1/ New preprint! 🍳

@elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins!

doi.org/10.1101/2025...

Single-cell RNA sequencing of immune cells for over 1,000 people age 18-97 years. A clock of our immune system aging. Tells us about an individual's response to infection, vaccination, Long Covid. Towards an immunome.
www.nature.com/articles/s43...

It is important at this pivotal moment to @standupforscience.bsky.social. Looking forward to sharing my thoughts on why this should be a national priority at tomorrow’s rally in SF:

Looking forward to celebrating 80 years of federally funded science, technology and innovation @standupforscience.bsky.social SF, March 7, Civic Center, 1-3 pm 🧪 🧫 🧬

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...

@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...

Translating Proteomics 2024 Year-End Special: 3 Exciting Examples of Proteomics Research Translating Proteomics hosts Parag Mallick and Andreas Huhmer discuss 3 exciting examples of proteomics research from 2024.

Before we pull out the champagne to ring in the new year, we're celebrating 2024 on the #TranslatingProteomics podcast by highlighting 3 our favorite proteomics publications from the year!

www.nautilus.bio/blog/transla...

#Proteomics #Science #Research #Proteome #Biology #UnleashTheProteome

I just wish this cartoon I drew 10+ years ago wasn't so relevant today...

Here's a fun paper I wrote on how to make and use science comics. Why? Comic/cartoon art is a way of lowering the 'energy barrier' to communicating complex ideas. And comics can be used in many ways to help promote better #scicomm @biodataganache.bsky.social
journals.plos.org/ploscompbiol...

By popular demand, I have updated our starter pack in Stats, ML & Omics. Let me know if you'd like to be added. #ML #AI #singlecell #spatial #omics #statistics
go.bsky.app/73rcuJn

Timescales in Cell Biology #Cell

PDF download:
www.cell.com/cell/pdf/S00...

🎨 In case anyone need…

The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!

Check it out 👇
bioart.niaid.nih.gov

Reposting due to the name!!

If you're interested in trying out LLMs in #rstats but don't know where to begin, I've added a few two vignettes to elmer: elmer.tidyverse.org/articles/elm... and elmer.tidyverse.org/articles/pro...

Would love to get added in this list

Thank science #skeeters for the starter-packs. Do anyone have a proteomics starter pack?