Marco Breinig
@breinigmarco.bsky.social
61 followers 190 following 8 posts
*The necessity and power of random, under-sampled experiments in biology... *🍫-🐭, PERTURB-CAST, RUBIX...
Posts Media Videos Starter Packs
Reposted by Marco Breinig
alleninstitute.org
Introducing CellTransformer, a new AI tool developed with UCSF that makes it easier to explore massive neuroscience datasets and identify important subregions of the brain. 🧵
Reposted by Marco Breinig
molsystbiol.org
generative AI model PerturbNet predicts changes in gene expression and cell state in response to unseen chemical and genetic perturbations ➡️ www.embopress.org/doi/full/10....
Reposted by Marco Breinig
moritzgerstung.bsky.social
A spatial transcriptomics analysis led by my student Zaira reveals the distinct nature (gene expression, tumour cell states and local microenvironments) of radionecrosis and recurrence in glioblastoma. 👏
zaira-sef.bsky.social
🚨 new glioblastoma preprint alert!

we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.

🧵 1/
Reposted by Marco Breinig
genometdcc.org
New highlight video! 🧪🧬💻
RAEFISH from Steven Wang at Yale unlocks whole-transcriptome imaging at single-molecule resolution. See 20,000+ RNAs light up in cells and tissues. Plus get direct gRNA detection in high-content CRISPR screens. Spatial biology just leveled up

www.youtube.com/watch?v=P2j6...
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
YouTube video by GenomeTDCC
www.youtube.com
Reposted by Marco Breinig
addgene.bsky.social
New CRISPR libraries from the @johndoench.bsky.social and Root labs — Jacquere (human) and Julianna (mouse).
A perfect pairing for your next screen. 🍷🧀
https://twp.ai/9PX2kT
https://twp.ai/4irnYP
new at addgene
Reposted by Marco Breinig
rndries.bsky.social
Very proud to finally publish Giotto Suite after many years of hard work. It's a big milestone for our lab and will be a massive stepping stone for our ongoing projects and ideas. Take a look at giottosuite.com and feel free to share feedback and ideas for improvement.
Reposted by Marco Breinig
biorxiv-genomic.bsky.social
X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models https://www.biorxiv.org/content/10.1101/2025.06.11.659105v1
Reposted by Marco Breinig
Reposted by Marco Breinig
andrewcpayne.bsky.social
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.

Read more: e11.bio/blog/prism
Reposted by Marco Breinig
biorxiv-neursci.bsky.social
Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context https://www.biorxiv.org/content/10.1101/2025.09.26.678648v1
Reposted by Marco Breinig
deniswirtz.bsky.social
We have developed a new workflow to map in 3D at single-cell resolution whole human organs.

Prof. Rong Fan (Yale) mapped out immune cell populations in the vicinity of ovarian precancerous lesions in healthy women and found no enrichment.

More here: www.biorxiv.org/content/10.1...
Reposted by Marco Breinig
labwaggoner.bsky.social
Highly multiplexed 3D profiling of cell states and immune niches in human tumors @natmethods.nature.com @harvardmed.bsky.social
www.nature.com/articles/s41...
Reposted by Marco Breinig
aidoq.bsky.social
Big step forward in phenotype-directed drug discovery:

By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping.

Super cool!!

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

#AI #drugdiscovery #cancer
Reposted by Marco Breinig
Reposted by Marco Breinig
arcinstitute.org
For decades, human genome editing has been limited to small, localized modifications.

Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.
Reposted by Marco Breinig
arcinstitute.org
New work from Arc's @pauldatlinger.bsky.social of our Genome Engineering Technology Center. Congrats!
pauldatlinger.bsky.social
CAR T cells showcase the enormous potential of cell therapies, but often fail due to lack of evolutionary optimization. Today in @nature.com , we use #CELLFIE to engineer cell therapies at scale and share the largest resource of CRISPR screens in CAR T cells. www.nature.com/articles/s41...
Systematic discovery of CRISPR-boosted CAR T cell immunotherapies - Nature
CELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.
www.nature.com
Reposted by Marco Breinig
deniswirtz.bsky.social
We have developed a new workflow to map whole human organs at single-cell resolution, while integrating spatial transcriptomics, proteomics, and metabolomics.

We applied this workflow to map precancerous lesions of the fallopian tubes.

More here: www.biorxiv.org/content/10.1...
Reposted by Marco Breinig
mgarnett.bsky.social
The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.

Start mining data now: dataminer.depmap.sanger.ac.uk
depmap miner logo
Reposted by Marco Breinig
mscience.bsky.social
📢 NEW! Visium HD 3’ + Long Reads from @10xgenomics.bsky.social

Explore whole transcriptome spatial analysis at single-cell resolution. Now sequence full-length transcripts to uncover isoforms & SNVs.

👉 Protocols: shorturl.at/E3A4G

#SpatialTranscriptomics #VisiumHD #LongReadSeq #ONT #PacBio