danilexn.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Pavel Tomancak asks everyone who uses FIJI in the crowd to stand ... and dammit, 90% of the crowd stood. What a testament to the power of such tools. #DROS25

submitted 1 day ago • 2 comments

UCSF, like all UC campuses, announced an immediate hiring freeze today. UCSF is the second largest employer in the city. There will be wide ripple effects in the Bay Area and beyond, including the future of biotech and pharma in the area. 🧪

submitted 2 days ago • 2 comments

Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16

submitted 3 days ago • 6 comments

🚨 Paper Alert 🚨 Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!! www.nature.com/articles/s41...

submitted 4 days ago • 11 comments

Using gene–gene covariance structure to represent cellular neighborhoods improves the integration of single-cell RNA sequencing and spatial transcriptomics data go.nature.com/4auQI72 rdcu.be/ebBiU

submitted 8 days ago • 0 comments

Happy Friday youtu.be/CS7MA5osGq0

submitted 15 days ago • 0 comments

When they announce more funding for science, a chunk of the budget magically disappears in the ‘unexecuted funds’ black hole. But when they pledge to increase military spending? Oh, you can bet every cent will be locked, loaded, and spent. Efficiency depends on the target, I guess.

submitted 15 days ago • 1 comment

If you’ve got $20,000 a month to spend on a “PhD level” ai agent, just hire a person.

submitted 16 days ago • 75 comments

Pearson correlation FTW

submitted 16 days ago • 0 comments

geneRNIB: a living benchmark for gene regulatory network inference www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/openproblems...

submitted 16 days ago • 0 comments

☕️Afonso et al. show that, during #anaphase, chromosome movement can be driven by large cytoplasmic flows. These dynein-dependent cytoplasmic flows scale with cell size, slowing in smaller cells, thereby scaling anaphase. bit.ly/41k8XsG

submitted 17 days ago • 1 comment

Review | Decoding cell–cell communication using spatial transcriptomics www.nature.com/articles/s41...

submitted 19 days ago • 0 comments

This is from the Illumina #AGBT25 workshop about their ST tech. But, from our observations, under heavy lateral diffusion (real or simulated), clustering on large sets of genes (i.e. “whole transcriptome”) leads to niche- rather than cell-type clustering. This might be problematic.

submitted 20 days ago • 1 comment

submitted 21 days ago • 48 comments

Cristina Almagro-P\'erez, Andrew H. Song, Luca Weishaupt, Ahrong Kim, Guillaume Jaume, Drew F. K. Williamson, Konstantin Hemker, Ming Y. Lu, Kritika Singh, Bowen Chen, Long Phi Le, Alexander S. Baras, Sizun Jiang, ... AI-driven 3D Spatial Transcriptomics https://arxiv.org/abs/2502.17761

submitted 24 days ago • 0 comments

Open-ST is such a great method.

submitted 25 days ago • 0 comments

That’s it?

submitted 25 days ago • 1 comment

"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models +1 www.cell.com/cell-systems...

submitted 29 days ago • 3 comments

Compare and contrast the emails from McKnight (left) and Chan-Zuckerberg (right). Proud to be part of the McKnight community.

submitted 29 days ago • 3 comments

“but we have put a lot of investment in R&D” aka: reading the seq-scope and Open-ST papers.

submitted 30 days ago • 0 comments

I am so sorry, Mr. Busoni, that my hands are not big enough.

submitted 33 days ago • 0 comments

SpaceBar enables clone tracing in spatial transcriptomic data [new] Enables clone tracing in spatial transcriptomics via combinatorial barcoding, differentiating clonal vs. environmentally-driven gene expression.

submitted 34 days ago • 0 comments

📣📣Genomic data sharing: you don’t know what you’ve got (till it’s gone) www.nature.com/articles/s41... A comment @natrevgenet.bsky.social from @katholt.bsky.social and me

submitted 37 days ago • 3 comments

Irregular timberland killed me

submitted 37 days ago • 0 comments

New #preprint from the lab! Do you want to see the invisible? So did we! When DNA genomes get broken, cells somehow find related sequences to fix the break. But how do they find it? We developed a way to look at sequence search, not just sequence usage. doi.org/10.1101/2025...

submitted 37 days ago • 2 comments

Are protein language models the universal key? doi.org/10.1016/j.sb... Brilliant and thoughtful piece.

submitted 37 days ago • 0 comments

And the same happens with genome-based LLMs. Who’s really, systematically looking at sequence similarity?

submitted 38 days ago • 1 comment

🔬🎤 As pre-announced a few days ago... please let us proudly present to you: 𝑴𝒊𝒄𝒓𝒐𝕊𝒑𝒍𝒊𝒕 - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. 🔬 doi.org/10.1101/2025... Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏

submitted 38 days ago • 2 comments

👋🏻💻🧬

submitted 39 days ago • 0 comments

Title: our new super-cool bioinformatics method solves cancer. Paper: we found that β-Catenin is important in cancer.

submitted 40 days ago • 2 comments

AIR-SPACE: integrative high-res spatial transcriptomics paired w/ high-fidelity long-read sequencing of TCR/BCR reveals adaptive antiviral immune response in lymph nodes doi.org/10.1101/2025...

submitted 43 days ago • 0 comments

Genomic Foundationless Models: Pretraining Does Not Promise Performance I've long believed genomic foundation models are not as useful as claimed. In my mind, there isn't enough training data to justify their size. Interesting to see more work in this direction. www.biorxiv.org/content/10.1...

submitted 47 days ago • 3 comments

🎼Spark #9: SooJin Anjou & Shanshan Yao wowed us with performances of works by Sidney Corbett, A. Dvorák & Amy Beach. Anjou, Yao & Corbett then discussed with @michaelsigal.bsky.social, @danilexn.bsky.social, N. Rajewsky & attendees about ‘Focus: The long and the short of it’ @mdc-berlin.bsky.social

submitted 46 days ago • 0 comments

Connecting gene activity & precise location of protein function by Deterministic Barcoding in Tissue sequencing (DBiTplus) 📷: Archibald Enninful, Zhaojun Zhang et al Mina Xu, Zongming Ma @rongfan8.bsky.social @yale.edu in @biorxivpreprint.bsky.social ➡️: bpod.org.uk/archive/2025... & AntDLewis

submitted 46 days ago • 0 comments

This is beyond everything else youtu.be/R76MEBpldEs

submitted 48 days ago • 1 comment

A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment www.nature.com/articles/s41... @garrypnolan.bsky.social @naturecomms.bsky.social

submitted 49 days ago • 0 comments