1⃣Small panels in #CODEX, #Xenium & #CosMx make fine cell typing tough. Our collab with Bokai Zhu , Sizun Jiang & Garry P. Nolan brings #CellLENS! Published today in Nature Immunology: nature.com/articles/s4159….

Check out our recent tool using deep learning to better discover immune cells in tissues! Always a pleasure to work with this great team: Zongming Ma, Sizun Jiang, Garry P. Nolan, Sheng Gao (Sheng Gao), Shuxiao Chen, Shalek Lab and the rest who may or may not be on this platform!

Several mammal species live in cold-water environments thanks to adaptations like blubber and large size. A notable exception is the sea otter—so how does it stay warm? A 2021 Science study found an answer: skeletal muscle thermogenesis. Learn more on #WorldOtterDay:

Excited to share our newest paper, online today nature! We report the discovery of a highly unusual mechanism of antiviral immunity through the synthesis of long, homopolymeric DNA. nature.com/articles/s4158…

Are you looking for homologous sequences but alignments do not seem to work? SHARK-dive is available as a webserver 🦈: compare any sequences or search against precomputed IDR datasets: bio-shark.org Nucleic Acids Res Center for Systems Biology Dresden Physics of Life Dresden MPI-CBG doi.org/10.1093/nar/gk…

Selection gene drives re-engineer tumors to suppress drug resistance go.nature.com/4bLLeFb rdcu.be/em30l

I hope we're finally getting it. The more we gatekeep "quality" science the more we leave it open to political attacks. We get funded to explore our curiosity so let's make sure our discoveries reach curious minds everywhere. Open access should just be FULL ACCESS.

Long-read 🧬sequencing reveals hidden cancer mutations, but existing tools often produce false positives. SAVANA is a machine learning algorithm trained on cancer genomes, built to make analysis faster and clinically reliable. ebi.ac.uk/about/news/res… #CancerResearch

Thrilled to announce that our work on Expansion In Situ Genome Sequencing (ExIGS) is now published in Science Magazine! ExIGS allows us to sequence DNA and image proteins with super-resolution directly within single cells. science.org/doi/10.1126/sc…

Thrilled to share our latest work now out in Nature Methods 🥳 We present SAVANA, a novel machine-learning based algorithm to detect somatic structural variants and copy number aberrations from long-read (Oxford Nanopore & PacBio ) sequencing data with and without matched control!👇

This is so cool and a severely overlooked aspect of the TME and stroma: spatially disordered geometries of the microenvironment promote invasion shifts from collective to single mode. biorxiv.org/content/10.110…

The HCA Archive Resource is now available for users, via the new Archive Discovery Portal. Established as a digital memory bank, the HCA Archive ensures the unique achievements of the HCA consortium are recorded and preserved. Learn more at humancellatlas.org/news/hca-archi…

HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes. #SnakeMake #GeneDuplication #Genomics #Bioinformatics 💻 🧬 academic.oup.com/bioinformatics…

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. #Ontology #BiomedicalOntologies #BioPortal Nucleic Acids Res academic.oup.com/nar/advance-ar…

An atlas of transcription factor-driven gene programs across human cells Teichlab biorxiv.org/content/10.110…

Improving gene isoform quantification with miniQuant nature.com/articles/s4158… #journals #feedly

What controls condensate composition and function beyond binding stoichiometry? We show that condensate microenvironments play a key role, and can be probed by a micropeptide killswitch in live cells. nature.com/articles/s4158… out now in nature with Henri Niskanen Denes Hnisz & team.

The off-target effects of any CRISPR-based genome editor are identified with Tracking-seq go.nature.com/45QH0L5 rdcu.be/em32d

Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations hubs.li/Q03njKxr0 Collection highlight from Cell Genomics

🧵1/ We Tahoe Therapeutics (Formerly Vevo) just published a new post on the Tahoe blog—a story of how we used Tahoe-100M, the world’s largest drug-perturbed single-cell dataset, to find compounds that upregulate MHC-I and make tumors more visible to the immune system. Here’s how 🧬🔍👇